Remove restriction on ROBOT repair to work only on annotation axioms

For some reason, ROBOT repair --merge-axiom-annotations not only was restricted to annotation axioms (which is wrong), it also drops logical axioms with annotations as they are (1) first added to the heap of axioms that need to be processed, (2) dropped from the ontology because they are in that heap and finally (3) because of the wrong conditional we are fixing here, not added back. Adding and example for axiom annotation merging on subclass axioms to our test case
ontodev · Nov 11, 2024 · c4e9708 · c4e9708
1 parent 0acc87e
commit c4e9708
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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
@@ -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 +275,18 @@
         <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>
+    </owl:Axiom>
+    <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 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"/>

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);
   }