Merge branch 'master' into replace-supplies-drains

obophenotype · Dec 10, 2024 · feb9493 · feb9493
2 parents 51a5ce1 + 99ecf28
commit feb9493
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diff --git a/.github/workflows/diff.yml b/.github/workflows/diff.yml
@@ -10,7 +10,7 @@ env:
 # A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
   branch_status:
-    if: ${{ github.event.issue.pull_request }}
+    if: ${{ github.event.issue.pull_request && github.event.issue.state == 'open' }}
     runs-on: ubuntu-latest
     permissions:
       contents: read

diff --git a/.gitignore b/.gitignore
@@ -113,6 +113,7 @@ src/ontology/ed_definitions_merged.owl
 src/ontology/imports/*.obo
 imports/*.obo
 uberon-lastbuild.owl
+uberon-lastbuild.obo
 src/mappings/uberon-local.sssom.tsv
 src/mappings/uberon.sssom.tsv
 src/ontology/imports/*_terms_combined.txt

diff --git a/src/ontology/diffs/uberon-diff.md b/src/ontology/diffs/uberon-diff.md
diff --git a/src/ontology/reports/uberon-edit.obo-obo-report.tsv b/src/ontology/reports/uberon-edit.obo-obo-report.tsv
@@ -1327,7 +1327,7 @@ WARN	duplicate_scoped_synonym	UBERON:0004717	oboInOwl:hasBroadSynonym	B09-29
 WARN	duplicate_scoped_synonym	UBERON:0004717	oboInOwl:hasExactSynonym	B09-29
 WARN	duplicate_scoped_synonym	UBERON:0004718	oboInOwl:hasBroadSynonym	B09-26
 WARN	duplicate_scoped_synonym	UBERON:0004718	oboInOwl:hasExactSynonym	B09-26
-WARN	duplicate_scoped_synonym	UBERON:0004726	oboInOwl:hasExactSynonym	arteriolae rectae renis
+WARN	duplicate_scoped_synonym	UBERON:0004726	oboInOwl:hasNarrowSynonym	arteriolae rectae renis
 WARN	duplicate_scoped_synonym	UBERON:0004726	oboInOwl:hasRelatedSynonym	arteriolae rectae renis
 WARN	duplicate_scoped_synonym	UBERON:0004918	oboInOwl:hasExactSynonym	musculus sphincter urethrae internus
 WARN	duplicate_scoped_synonym	UBERON:0004918	oboInOwl:hasRelatedSynonym	musculus sphincter urethrae internus
@@ -1954,7 +1954,6 @@ WARN	missing_definition	IAO:0000115	IAO:0000115
 WARN	missing_definition	IAO:0000116	IAO:0000115	
 WARN	missing_definition	IAO:0000232	IAO:0000115	
 WARN	missing_definition	IAO:0000233	IAO:0000115	
-WARN	missing_definition	IAO:0000425	IAO:0000115	
 WARN	missing_definition	IAO:0000700	IAO:0000115	
 WARN	missing_definition	IAO:0006012	IAO:0000115	
 WARN	missing_definition	IAO:0100001	IAO:0000115	
@@ -1978,9 +1977,13 @@ WARN	missing_definition	RO:0002134	IAO:0000115
 WARN	missing_definition	RO:0002150	IAO:0000115	
 WARN	missing_definition	RO:0002158	IAO:0000115	
 WARN	missing_definition	RO:0002159	IAO:0000115	
+WARN	missing_definition	RO:0002161	IAO:0000115	
 WARN	missing_definition	RO:0002162	IAO:0000115	
 WARN	missing_definition	RO:0002170	IAO:0000115	
 WARN	missing_definition	RO:0002171	IAO:0000115	
+WARN	missing_definition	RO:0002173	IAO:0000115	
+WARN	missing_definition	RO:0002174	IAO:0000115	
+WARN	missing_definition	RO:0002175	IAO:0000115	
 WARN	missing_definition	RO:0002176	IAO:0000115	
 WARN	missing_definition	RO:0002177	IAO:0000115	
 WARN	missing_definition	RO:0002178	IAO:0000115	
@@ -2019,9 +2022,11 @@ WARN	missing_definition	RO:0002385	IAO:0000115
 WARN	missing_definition	RO:0002387	IAO:0000115	
 WARN	missing_definition	RO:0002433	IAO:0000115	
 WARN	missing_definition	RO:0002473	IAO:0000115	
+WARN	missing_definition	RO:0002475	IAO:0000115	
 WARN	missing_definition	RO:0002488	IAO:0000115	
 WARN	missing_definition	RO:0002489	IAO:0000115	
 WARN	missing_definition	RO:0002491	IAO:0000115	
+WARN	missing_definition	RO:0002492	IAO:0000115	
 WARN	missing_definition	RO:0002493	IAO:0000115	
 WARN	missing_definition	RO:0002494	IAO:0000115	
 WARN	missing_definition	RO:0002495	IAO:0000115	
@@ -7645,6 +7650,7 @@ INFO	missing_superclass	UBERON:8410080	rdfs:subClassOf
 INFO	missing_superclass	UBERON:8420000	rdfs:subClassOf	
 INFO	missing_superclass	UBERON:8440011	rdfs:subClassOf	
 INFO	missing_superclass	UBERON:8450002	rdfs:subClassOf	
+INFO	missing_superclass	UBERON:8450003	rdfs:subClassOf	
 INFO	missing_superclass	UBERON:8470000	rdfs:subClassOf	
 INFO	missing_superclass	UBERON:8480000	rdfs:subClassOf	
 INFO	missing_superclass	UBERON:8480001	rdfs:subClassOf	

diff --git a/src/ontology/uberon.Makefile b/src/ontology/uberon.Makefile
@@ -1249,8 +1249,8 @@ EXTERNAL_SSSOM_PROVIDERS = fbbt cl biomappings
 # All the sets coming from the above ontologies.
 EXTERNAL_SSSOM_SETS = $(foreach provider, $(EXTERNAL_SSSOM_PROVIDERS), $(MAPPINGDIR)/$(provider).sssom.tsv)
 
-# We only refresh external resources under IMP=true
-ifeq ($(strip $(IMP)),true)
+# We only refresh external resources under MIR=true
+ifeq ($(strip $(MIR)),true)
 
 # FBbt mapping set. We filter it to only keep UBERON-related mappings
 # (CL-related mappings are already bundled with the CL set).
@@ -1296,7 +1296,7 @@ endif
 ifeq ($(BRI),true)
 
 # Those bridges are generated separately (see below).
-CUSTOM_BRIDGES = $(BRIDGEDIR)/uberon-bridge-to-mba.owl \
+EXTERN_BRIDGES = $(BRIDGEDIR)/uberon-bridge-to-mba.owl \
 		 $(BRIDGEDIR)/uberon-bridge-to-dmba.owl
 
 # 1. Prepare the ruleset file.
@@ -1312,7 +1312,7 @@ $(TMPDIR)/bridges.rules: $(SCRIPTSDIR)/sssomt.m4 $(BRIDGEDIR)/bridges.rules.m4
 $(TMPDIR)/bridges: $(SRC) $(IMPORTDIR)/local-cl.owl \
 		   $(MAPPINGDIR)/uberon.sssom.tsv $(MAPPINGDIR)/cl.sssom.tsv \
 		   $(TMPDIR)/bridges.rules $(BRIDGEDIR)/bridges.dispatch \
-		   $(CUSTOM_BRIDGES) | all_robot_plugins
+		   $(EXTERN_BRIDGES) | all_robot_plugins
 	$(ROBOT) merge -i $(SRC) -i $(IMPORTDIR)/local-cl.owl \
 		 sssom:inject --sssom $(MAPPINGDIR)/uberon.sssom.tsv \
 		              --sssom $(MAPPINGDIR)/cl.sssom.tsv \
@@ -1342,8 +1342,8 @@ UBERON_BRIDGE_MBA = "https://raw.githubusercontent.com/brain-bican/mouse_brain_a
 UBERON_BRIDGE_DMBA = "https://raw.githubusercontent.com/brain-bican/developing_mouse_brain_atlas_ontology/main/src/ontology/new-bridges/new-uberon-bridge-to-dmba.owl"
 
 # Only refresh those bridges when we explicitly allow refreshing
-# external resources (IMP=true).
-ifeq ($(strip $(IMP)),true)
+# external resources (MIR=true).
+ifeq ($(strip $(MIR)),true)
 $(BRIDGEDIR)/uberon-bridge-to-mba.owl: $(SRC)
 	$(ROBOT) annotate -I $(UBERON_BRIDGE_MBA) --ontology-iri $(ONTBASE)/$@ -o $@
 
@@ -1408,7 +1408,7 @@ DEPLOY_GH=true
 
 .PHONY: uberon
 uberon:
-	$(MAKE) prepare_release IMP=false PAT=false BRI=true CLEANFILES=tmp/merged-uberon-edit.obo
+	$(MAKE) prepare_release MIR=false IMP=false PAT=false BRI=true CLEANFILES=tmp/merged-uberon-edit.obo
 	$(MAKE) release-diff
 	if [ $(DEPLOY_GH) = true ]; then $(MAKE) deploy_release GHVERSION="v$(TODAY)"; fi
 
@@ -1489,15 +1489,15 @@ clean: clean_uberon
 
 .PHONY: refresh-mappings
 refresh-mappings:
-	$(MAKE) MIR=true IMP=true $(EXTERNAL_SSSOM_SETS)
+	$(MAKE) MIR=true $(EXTERNAL_SSSOM_SETS)
 
 .PHONY: refresh-bridges
 refresh-bridges:
-	$(MAKE) MIR=true IMP=true BRI=true tmp/bridges
+	$(MAKE) MIR=true BRI=true tmp/bridges
 
 .PHONY: refresh-external-resources
 refresh-external-resources:
-	$(MAKE) MIR=true IMP=true BRI=true PAT=false IMP_LARGE=true all_imports all_local_imports tmp/bridges
+	$(MAKE) MIR=true IMP=true BRI=true PAT=false IMP_LARGE=true all_imports all_local_imports $(EXTERNAL_SSSOM_SETS) $(EXTERN_BRIDGES)
 
 
 # ----------------------------------------

diff --git a/src/scripts/sssomt.m4 b/src/scripts/sssomt.m4
@@ -9,7 +9,7 @@ ifelse($2, , `dnl
     predicate==skos:exactMatch               -> create_axiom("%subject_id EquivalentTo: %object_id");
     predicate==skos:broadMatch               -> create_axiom("%subject_id SubClassOf: %object_id");
     predicate==skos:narrowMatch              -> create_axiom("%object_id SubClassOf: %subject_id");',`dnl
-    predicate==semapv:crossSpeciesExactMatch -> create_axiom("%subject_id EquivalentTo: %object_id and (<%TAXREL> some $2)");')')
+    predicate==semapv:crossSpeciesExactMatch -> create_axiom("%subject_id EquivalentTo: %object_id and (%TAXREL some $2)");')')
 
 dnl Expand to instructions to create all possible bridging axioms
 dnl both for Uberon and for CL