Merge pull request #1223 from ontodev/fix-repair-merge-axiom-annotations

Fix repair merge axiom annotations
ontodev · Nov 12, 2024 · 82daac6 · 82daac6
2 parents 4eb86f5 + 1d3a6ba
commit 82daac6
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Fixed
 - Output inferred object property assertions using Whelk reasoner, by updating to Whelk 1.1.3. [#1121]
+- Bug was fixed that caused logical axioms with axiom annotations not to be processed correctly when merging axiom annotations [#1223]
 
 ### Changed
 - Update Whelk to 1.2.1 [#1221]

diff --git a/docs/examples/uberon_axiom_annotation_merged.owl b/docs/examples/uberon_axiom_annotation_merged.owl
@@ -247,9 +247,16 @@
 
 
 
+    <!-- http://purl.obolibrary.org/obo/ROBOT_SuperClass -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/ROBOT_SuperClass"/>
+
+
+
     <!-- http://purl.obolibrary.org/obo/UBERON_0000062 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000062">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/ROBOT_SuperClass"/>
         <rdfs:subClassOf>
             <owl:Restriction>
                 <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
@@ -268,6 +275,13 @@
         <oboInOwl:id>UBERON:0000062</oboInOwl:id>
         <rdfs:label>organ</rdfs:label>
     </owl:Class>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000062"/>
+        <owl:annotatedProperty rdf:resource="http://www.w3.org/2000/01/rdf-schema#subClassOf"/>
+        <owl:annotatedTarget rdf:resource="http://purl.obolibrary.org/obo/ROBOT_SuperClass"/>
+        <rdfs:comment>Comment A</rdfs:comment>
+        <rdfs:comment>Comment B</rdfs:comment>
+    </owl:Axiom>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000062"/>
         <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
@@ -293,5 +307,5 @@
 
 
 
-<!-- Generated by the OWL API (version 4.5.26) https://github.com/owlcs/owlapi -->
+<!-- Generated by the OWL API (version 4.5.29) https://github.com/owlcs/owlapi -->
 
diff --git a/docs/examples/uberon_axiom_annotation_merging.owl b/docs/examples/uberon_axiom_annotation_merging.owl
@@ -1,14 +1,14 @@
 <?xml version="1.0"?>
 <rdf:RDF xmlns="http://purl.obolibrary.org/obo/uberon.owl#"
      xml:base="http://purl.obolibrary.org/obo/uberon.owl"
-     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+     xmlns:obo="http://purl.obolibrary.org/obo/"
      xmlns:owl="http://www.w3.org/2002/07/owl#"
-     xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"
+     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
      xmlns:xml="http://www.w3.org/XML/1998/namespace"
      xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
+     xmlns:foaf="http://xmlns.com/foaf/0.1/"
      xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
-     xmlns:obo="http://purl.obolibrary.org/obo/"
-     xmlns:foaf="http://xmlns.com/foaf/0.1/">
+     xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/uberon.owl"/>
 
 
@@ -214,11 +214,11 @@
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000050">
         <owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
         <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
-        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BFO:0000050</oboInOwl:hasDbXref>
-        <oboInOwl:hasOBONamespace rdf:datatype="http://www.w3.org/2001/XMLSchema#string">uberon</oboInOwl:hasOBONamespace>
-        <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">part_of</oboInOwl:id>
-        <oboInOwl:shorthand rdf:datatype="http://www.w3.org/2001/XMLSchema#string">part_of</oboInOwl:shorthand>
-        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">part_of</rdfs:label>
+        <oboInOwl:hasDbXref>BFO:0000050</oboInOwl:hasDbXref>
+        <oboInOwl:hasOBONamespace>uberon</oboInOwl:hasOBONamespace>
+        <oboInOwl:id>part_of</oboInOwl:id>
+        <oboInOwl:shorthand>part_of</oboInOwl:shorthand>
+        <rdfs:label>part_of</rdfs:label>
     </owl:ObjectProperty>
 
 
@@ -227,11 +227,11 @@
 
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000051">
         <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
-        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BFO:0000051</oboInOwl:hasDbXref>
-        <oboInOwl:hasOBONamespace rdf:datatype="http://www.w3.org/2001/XMLSchema#string">uberon</oboInOwl:hasOBONamespace>
-        <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">has_part</oboInOwl:id>
-        <oboInOwl:shorthand rdf:datatype="http://www.w3.org/2001/XMLSchema#string">has_part</oboInOwl:shorthand>
-        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">has_part</rdfs:label>
+        <oboInOwl:hasDbXref>BFO:0000051</oboInOwl:hasDbXref>
+        <oboInOwl:hasOBONamespace>uberon</oboInOwl:hasOBONamespace>
+        <oboInOwl:id>has_part</oboInOwl:id>
+        <oboInOwl:shorthand>has_part</oboInOwl:shorthand>
+        <rdfs:label>has_part</rdfs:label>
     </owl:ObjectProperty>
 
 
@@ -247,62 +247,85 @@
 
 
 
+    <!-- http://purl.obolibrary.org/obo/ROBOT_SuperClass -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/ROBOT_SuperClass"/>
+
+
+
     <!-- http://purl.obolibrary.org/obo/UBERON_0000062 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000062">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/ROBOT_SuperClass"/>
         <rdfs:subClassOf>
             <owl:Restriction>
                 <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
                 <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000467"/>
             </owl:Restriction>
         </rdfs:subClassOf>
-        <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Anatomical structure that performs a specific function or group of functions [WP].</obo:IAO_0000115>
+        <obo:IAO_0000115>Anatomical structure that performs a specific function or group of functions [WP].</obo:IAO_0000115>
         <oboInOwl:hasDbXref rdf:resource="http://en.wikipedia.org/wiki/page1"/>
         <oboInOwl:hasDbXref rdf:resource="http://en.wikipedia.org/wiki/page2"/>
         <oboInOwl:hasDbXref rdf:resource="http://linkedlifedata.com/resource/umls/id/C0178784"/>
         <oboInOwl:hasDbXref rdf:resource="http://ncicb.nci.nih.gov/xml/owl/EVS/Organ"/>
-        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">WBbt:0003760</oboInOwl:hasDbXref>
-        <oboInOwl:hasRelatedSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">anatomical unit</oboInOwl:hasRelatedSynonym>
-        <oboInOwl:hasRelatedSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">body organ</oboInOwl:hasRelatedSynonym>
-        <oboInOwl:hasRelatedSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">element</oboInOwl:hasRelatedSynonym>
-        <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UBERON:0000062</oboInOwl:id>
-        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">organ</rdfs:label>
+        <oboInOwl:hasDbXref>WBbt:0003760</oboInOwl:hasDbXref>
+        <oboInOwl:hasRelatedSynonym>anatomical unit</oboInOwl:hasRelatedSynonym>
+        <oboInOwl:hasRelatedSynonym>body organ</oboInOwl:hasRelatedSynonym>
+        <oboInOwl:hasRelatedSynonym>element</oboInOwl:hasRelatedSynonym>
+        <oboInOwl:id>UBERON:0000062</oboInOwl:id>
+        <rdfs:label>organ</rdfs:label>
     </owl:Class>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000062"/>
-        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym"/>
-        <owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">body organ</owl:annotatedTarget>
-        <oboInOwl:source rdf:resource="http://en.wikipedia.org/wiki/page1"/>
+        <owl:annotatedProperty rdf:resource="http://www.w3.org/2000/01/rdf-schema#subClassOf"/>
+        <owl:annotatedTarget rdf:resource="http://purl.obolibrary.org/obo/ROBOT_SuperClass"/>
+        <rdfs:comment>Comment A</rdfs:comment>
     </owl:Axiom>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000062"/>
-        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym"/>
-        <owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">body organ</owl:annotatedTarget>
-        <oboInOwl:source rdf:resource="http://en.wikipedia.org/wiki/page2"/>
+        <owl:annotatedProperty rdf:resource="http://www.w3.org/2000/01/rdf-schema#subClassOf"/>
+        <owl:annotatedTarget rdf:resource="http://purl.obolibrary.org/obo/ROBOT_SuperClass"/>
+        <rdfs:comment>Comment B</rdfs:comment>
+    </owl:Axiom>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000062"/>
+        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
+        <owl:annotatedTarget>Anatomical structure that performs a specific function or group of functions [WP].</owl:annotatedTarget>
+        <oboInOwl:hasDbXref rdf:resource="http://en.wikipedia.org/wiki/page1"/>
+    </owl:Axiom>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000062"/>
+        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
+        <owl:annotatedTarget>Anatomical structure that performs a specific function or group of functions [WP].</owl:annotatedTarget>
+        <oboInOwl:hasDbXref rdf:resource="http://en.wikipedia.org/wiki/page2"/>
     </owl:Axiom>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000062"/>
         <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym"/>
-        <owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">body organ</owl:annotatedTarget>
+        <owl:annotatedTarget>body organ</owl:annotatedTarget>
         <oboInOwl:hasDbXref rdf:resource="UBERON:123"/>
     </owl:Axiom>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000062"/>
-        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
-        <owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Anatomical structure that performs a specific function or group of functions [WP].</owl:annotatedTarget>
-        <oboInOwl:hasDbXref rdf:resource="http://en.wikipedia.org/wiki/page1"/>
+        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym"/>
+        <owl:annotatedTarget>body organ</owl:annotatedTarget>
+        <oboInOwl:source rdf:resource="http://en.wikipedia.org/wiki/page1"/>
     </owl:Axiom>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000062"/>
-        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
-        <owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Anatomical structure that performs a specific function or group of functions [WP].</owl:annotatedTarget>
-        <oboInOwl:hasDbXref rdf:resource="http://en.wikipedia.org/wiki/page2"/>
+        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym"/>
+        <owl:annotatedTarget>body organ</owl:annotatedTarget>
+        <oboInOwl:source rdf:resource="http://en.wikipedia.org/wiki/page2"/>
     </owl:Axiom>
 
-
+
+
+    <!-- http://purl.obolibrary.org/obo/UBERON_0000467 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000467"/>
 </rdf:RDF>
 
 
 
-<!-- Generated by the OWL API (version 0.0.1-SNAPSHOT) https://github.com/owlcs/owlapi -->
+<!-- Generated by the OWL API (version 4.5.26.2023-07-17T20:34:13Z) https://github.com/owlcs/owlapi -->
 
diff --git a/robot-core/src/main/java/org/obolibrary/robot/RepairOperation.java b/robot-core/src/main/java/org/obolibrary/robot/RepairOperation.java
@@ -152,10 +152,8 @@ public static void mergeAxiomAnnotations(OWLOntology ontology) {
     Set<OWLAxiom> newAxioms = new HashSet<>();
     for (Map.Entry<OWLAxiom, Set<OWLAnnotation>> mergedAxiom : mergedAxioms.entrySet()) {
       OWLAxiom axiom = mergedAxiom.getKey();
-      if (axiom.isAnnotationAxiom()) {
-        OWLAxiom newAxiom = axiom.getAnnotatedAxiom(mergedAxiom.getValue());
-        newAxioms.add(newAxiom);
-      }
+      OWLAxiom newAxiom = axiom.getAnnotatedAxiom(mergedAxiom.getValue());
+      newAxioms.add(newAxiom);
     }
     manager.addAxioms(ontology, newAxioms);
   }