Merge pull request #3102 from obophenotype/new-taxon-constraint-check

Enforce taxon constraints
obophenotype · Nov 10, 2023 · 177c7af · 177c7af
2 parents 3f3d303 + c1ca725
commit 177c7af
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Showing 12 changed files with 367 additions and 95 deletions.
diff --git a/.github/workflows/qc.yml b/.github/workflows/qc.yml
@@ -27,10 +27,35 @@ jobs:
       - uses: actions/checkout@v2
 
       - name: Run ontology QC checks
+        id: check
+        continue-on-error: true
         env:
           DEFAULT_BRANCH: master
           ROBOT_JAVA_ARGS: -Xmx6G
         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: Reason over taxon constraints
+        id: explaintc
+        continue-on-error: true
+        if: steps.check.outcome == 'failure'
+        run: |
+          if [ -s src/ontology/reports/taxon-constraint-check.txt ]; then
+            robot explain -i src/ontology/tmp/uberon-edit-plus-tax-equivs.owl -M unsatisfiability -u all -r ELK -e taxon-unsats.md
+            echo "<details>\n<summary>This PR violates some taxon constraints. Here is what the reasoner has to say:</summary>\n" > comment.md
+            cat taxon-unsats.md >> comment.md
+            echo "</details>" >> comment.md
+            exit 1
+          fi
+      - name: Post explanation for taxon constraint violations
+        if: steps.explaintc.outcome == 'failure'
+        uses: NejcZdovc/comment-pr@v2
+        with:
+          github_token: ${{secrets.GITHUB_TOKEN}}
+          file: "../../comment.md"
+          identifier: "TAXON_CONSTRAINTS_REASONING"
+
       - name: Last rows of QC report
-        if: ${{ failure() }}
-        run: tail -20 src/ontology/TESTLOG.log
+        if: steps.check.outcome == 'failure'
+        run: |
+          tail -20 src/ontology/TESTLOG.log
+          exit 1
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 omo
+IMPORTS =  pr cl go envo ro bspo chebi pato bfo ncbitaxon ncbitaxondisjoints nbo orcidio omo
 
 IMPORT_ROOTS =  $(IMPORTDIR)/merged_import
 IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl)
@@ -496,6 +496,14 @@ mirror-ncbitaxon: | $(TMPDIR)
 		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
 
 
+## ONTOLOGY: ncbitaxondisjoints
+.PHONY: mirror-ncbitaxondisjoints
+.PRECIOUS: $(MIRRORDIR)/ncbitaxondisjoints.owl
+mirror-ncbitaxondisjoints: | $(TMPDIR)
+	if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim-disjoint-over-in-taxon.owl -o $@.tmp.owl &&\
+		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
+
+
 ## ONTOLOGY: nbo
 .PHONY: mirror-nbo
 .PRECIOUS: $(MIRRORDIR)/nbo.owl

diff --git a/src/ontology/bridge/uberon-bridge-to-aeo.obo b/src/ontology/bridge/uberon-bridge-to-aeo.obo
@@ -1,5 +1,5 @@
 ontology: uberon/bridge/uberon-bridge-to-aeo
-data-version: 2023-10-27
+data-version: 2023-10-30
 property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/references/reference_0000026" xsd:anyURI
 
 [Term]
@@ -697,11 +697,6 @@ id: AEO:0001010 !
 property_value: IAO:0000589 "differentiating neuroepithelium (AEO)" xsd:string
 equivalent_to: UBERON:0034707 ! differentiating neuroepithelium
 
-[Term]
-id: AEO:0000154 ! 
-property_value: IAO:0000589 "anatomical surface region (AEO)" xsd:string
-equivalent_to: UBERON:0036215 ! anatomical surface region
-
 [Typedef]
 id: part_of
 xref: BFO:0000050

diff --git a/src/ontology/bridge/uberon-bridge-to-aeo.owl b/src/ontology/bridge/uberon-bridge-to-aeo.owl
@@ -13,7 +13,7 @@
      xmlns:terms="http://purl.org/dc/terms/"
      xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-aeo.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-aeo/2023-10-27/uberon/bridge/uberon-bridge-to-aeo.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-aeo/2023-10-30/uberon/bridge/uberon-bridge-to-aeo.owl"/>
         <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://purl.obolibrary.org/obo/uberon/references/reference_0000026</rdfs:seeAlso>
     </owl:Ontology>
 
@@ -1118,8 +1118,6 @@
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/AEO_0000154">
         <owl:equivalentClass rdf:resource="http://purl.obolibrary.org/obo/UBERON_0002416"/>
-        <owl:equivalentClass rdf:resource="http://purl.obolibrary.org/obo/UBERON_0036215"/>
-        <obo:IAO_0000589 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">anatomical surface region (AEO)</obo:IAO_0000589>
         <obo:IAO_0000589 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">integumental system (AEO)</obo:IAO_0000589>
         <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">AEO:0000154</oboInOwl:id>
     </owl:Class>
@@ -2531,12 +2529,6 @@
     <!-- http://purl.obolibrary.org/obo/UBERON_0034707 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0034707"/>
-
-
-
-    <!-- http://purl.obolibrary.org/obo/UBERON_0036215 -->
-
-    <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0036215"/>
 </rdf:RDF>
 
 

diff --git a/src/ontology/bridge/uberon-bridge-to-dmba.obo b/src/ontology/bridge/uberon-bridge-to-dmba.obo
@@ -1319,13 +1319,6 @@ intersection_of: BFO:0000050 NCBITaxon:10090 {name="anterior nucleus of hypothal
 property_value: IAO:0000589 "posterior part of anterior hypothalamic nucleus" xsd:string
 property_value: status "Verified" xsd:string {source="https://ror.org/03cpe7c52"}
 
-[Term]
-id: DMBA:16271
-intersection_of: UBERON:0000435 {name="lateral tuberal nucleus"}
-intersection_of: BFO:0000050 NCBITaxon:10090 {name="lateral tuberal nucleus"}
-property_value: IAO:0000589 "lateral tuberal nucleus" xsd:string
-property_value: status "Verified" xsd:string {source="https://ror.org/03cpe7c52"}
-
 [Term]
 id: DMBA:16308
 intersection_of: UBERON:0001894 {name="diencephalon"}

diff --git a/src/ontology/bridge/uberon-bridge-to-dmba.owl b/src/ontology/bridge/uberon-bridge-to-dmba.owl
@@ -5723,37 +5723,6 @@
 
 
 
-    <!-- http://purl.obolibrary.org/obo/DMBA_16271 -->
-
-    <owl:Class rdf:about="http://purl.obolibrary.org/obo/DMBA_16271">
-        <owl:equivalentClass rdf:nodeID="genid1129"/>
-        <obo:IAO_0000589>lateral tuberal nucleus</obo:IAO_0000589>
-        <oboInOwl:status>Verified</oboInOwl:status>
-    </owl:Class>
-    <owl:Class rdf:nodeID="genid1129">
-        <owl:intersectionOf rdf:parseType="Collection">
-            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/UBERON_0000435"/>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
-                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_10090"/>
-            </owl:Restriction>
-        </owl:intersectionOf>
-    </owl:Class>
-    <owl:Axiom>
-        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/DMBA_16271"/>
-        <owl:annotatedProperty rdf:resource="http://www.w3.org/2002/07/owl#equivalentClass"/>
-        <owl:annotatedTarget rdf:nodeID="genid1129"/>
-        <rdfs:label>lateral tuberal nucleus</rdfs:label>
-    </owl:Axiom>
-    <owl:Axiom>
-        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/DMBA_16271"/>
-        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#status"/>
-        <owl:annotatedTarget>Verified</owl:annotatedTarget>
-        <oboInOwl:source>https://ror.org/03cpe7c52</oboInOwl:source>
-    </owl:Axiom>
-
-
-
     <!-- http://purl.obolibrary.org/obo/DMBA_16308 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/DMBA_16308">

diff --git a/src/ontology/components/hra_subset.owl b/src/ontology/components/hra_subset.owl
@@ -14131,15 +14131,6 @@
 
 
 
-    <!-- http://purl.obolibrary.org/obo/UBERON_8440041 -->
-
-    <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_8440041">
-        <obo:RO_0002175 rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_9606"/>
-        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas"/>
-    </owl:Class>
-
-
-
     <!-- http://purl.obolibrary.org/obo/UBERON_8450002 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_8450002">
@@ -14209,6 +14200,33 @@
         <obo:RO_0002175 rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_9606"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas"/>
     </owl:Class>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/UBERON_8600019 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_8600019">
+        <obo:RO_0002175 rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_9606"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas"/>
+    </owl:Class>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/UBERON_8600020 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_8600020">
+        <obo:RO_0002175 rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_9606"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas"/>
+    </owl:Class>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/UBERON_8600021 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_8600021">
+        <obo:RO_0002175 rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_9606"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas"/>
+    </owl:Class>
 </rdf:RDF>