Merge pull request #1171 from hkir-dev/issue_1163

annotate-defined-by parameter excludes datatypes
ontodev · Dec 4, 2023 · 977bf65 · 977bf65
2 parents 182046b + 04a0052
commit 977bf65
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Fixed
 - '--annotate-with-source true' does not work with extract --method subset [#1160]
 - Fix how Template adds entities to the QuotedEntityChecker [#1104]
+- [`merge`] and 'annotate' operations '--annotate-defined-by' excludes reserved OWL 2 vocabularies [#1171]
 - Handle IRIs that are not entities in export [#1168]
 
 ## [1.9.5] - 2023-09-20
@@ -381,6 +382,7 @@ First official release of ROBOT!
 [`template`]: http://robot.obolibrary.org/template
 [`validate`]: http://robot.obolibrary.org/validate
 
+[#1171]: https://github.com/ontodev/robot/pull/1171
 [#1168]: https://github.com/ontodev/robot/pull/1168
 [#1160]: https://github.com/ontodev/robot/pull/1160
 [#1148]: https://github.com/ontodev/robot/pull/1148

diff --git a/docs/examples/example2_defined_by.owl b/docs/examples/example2_defined_by.owl
@@ -78,62 +78,12 @@
 
 
 
-    <!-- http://www.w3.org/2000/01/rdf-schema#comment -->
-
-    <rdf:Description rdf:about="http://www.w3.org/2000/01/rdf-schema#comment">
-        <rdfs:isDefinedBy rdf:resource="https://github.com/ontodev/robot/examples/edit.owl"/>
-    </rdf:Description>
-
-
-
-    <!-- http://www.w3.org/2000/01/rdf-schema#isDefinedBy -->
-
-    <rdf:Description rdf:about="http://www.w3.org/2000/01/rdf-schema#isDefinedBy">
-        <rdfs:isDefinedBy rdf:resource="https://github.com/ontodev/robot/examples/edit.owl"/>
-    </rdf:Description>
-
-
-
-    <!-- http://www.w3.org/2000/01/rdf-schema#label -->
-
-    <rdf:Description rdf:about="http://www.w3.org/2000/01/rdf-schema#label">
-        <rdfs:isDefinedBy rdf:resource="https://github.com/ontodev/robot/examples/edit.owl"/>
-    </rdf:Description>
-
-
-
     <!-- http://www.w3.org/ns/prov#wasDerivedFrom -->
 
     <owl:AnnotationProperty rdf:about="http://www.w3.org/ns/prov#wasDerivedFrom">
         <rdfs:isDefinedBy rdf:resource="https://github.com/ontodev/robot/examples/edit.owl"/>
     </owl:AnnotationProperty>
-
-
-
-    <!-- 
-    ///////////////////////////////////////////////////////////////////////////////////////
-    //
-    // Datatypes
-    //
-    ///////////////////////////////////////////////////////////////////////////////////////
-     -->
-
-
-
-
-    <!-- http://www.w3.org/1999/02/22-rdf-syntax-ns#PlainLiteral -->
-
-    <rdf:Description rdf:about="http://www.w3.org/1999/02/22-rdf-syntax-ns#PlainLiteral">
-        <rdfs:isDefinedBy rdf:resource="https://github.com/ontodev/robot/examples/edit.owl"/>
-    </rdf:Description>
-
-
-
-    <!-- http://www.w3.org/2001/XMLSchema#string -->
 
-    <rdf:Description rdf:about="http://www.w3.org/2001/XMLSchema#string">
-        <rdfs:isDefinedBy rdf:resource="https://github.com/ontodev/robot/examples/edit.owl"/>
-    </rdf:Description>
 
 
 
@@ -284,18 +234,6 @@
         <rdfs:isDefinedBy rdf:resource="https://github.com/ontodev/robot/examples/edit.owl"/>
         <rdfs:label>dummy individal 5</rdfs:label>
     </owl:NamedIndividual>
-
-
-
-    <!-- 
-    ///////////////////////////////////////////////////////////////////////////////////////
-    //
-    // Annotations
-    //
-    ///////////////////////////////////////////////////////////////////////////////////////
-     -->
-
-    <rdf:Description rdf:about="http://www.w3.org/1999/02/22-rdf-syntax-ns#PlainLiteral"/>
 </rdf:RDF>
 
 

diff --git a/docs/examples/merged_defined_by.owl b/docs/examples/merged_defined_by.owl
@@ -78,54 +78,12 @@
 
 
 
-    <!-- http://www.w3.org/2000/01/rdf-schema#comment -->
-
-    <rdf:Description rdf:about="http://www.w3.org/2000/01/rdf-schema#comment">
-        <rdfs:isDefinedBy rdf:resource="https://github.com/ontodev/robot/examples/edit.owl"/>
-    </rdf:Description>
-
-
-
-    <!-- http://www.w3.org/2000/01/rdf-schema#isDefinedBy -->
-
-    <rdf:Description rdf:about="http://www.w3.org/2000/01/rdf-schema#isDefinedBy">
-        <rdfs:isDefinedBy rdf:resource="https://github.com/ontodev/robot/examples/edit.owl"/>
-    </rdf:Description>
-
-
-
-    <!-- http://www.w3.org/2000/01/rdf-schema#label -->
-
-    <rdf:Description rdf:about="http://www.w3.org/2000/01/rdf-schema#label">
-        <rdfs:isDefinedBy rdf:resource="https://github.com/ontodev/robot/examples/edit.owl"/>
-    </rdf:Description>
-
-
-
     <!-- http://www.w3.org/ns/prov#wasDerivedFrom -->
 
     <owl:AnnotationProperty rdf:about="http://www.w3.org/ns/prov#wasDerivedFrom">
         <rdfs:isDefinedBy rdf:resource="https://github.com/ontodev/robot/examples/edit.owl"/>
     </owl:AnnotationProperty>
-
-
-
-    <!-- 
-    ///////////////////////////////////////////////////////////////////////////////////////
-    //
-    // Datatypes
-    //
-    ///////////////////////////////////////////////////////////////////////////////////////
-     -->
-
-
 
-
-    <!-- http://www.w3.org/2001/XMLSchema#string -->
-
-    <rdf:Description rdf:about="http://www.w3.org/2001/XMLSchema#string">
-        <rdfs:isDefinedBy rdf:resource="https://github.com/ontodev/robot/examples/edit.owl"/>
-    </rdf:Description>
 
 
 

diff --git a/docs/merge.md b/docs/merge.md
@@ -46,3 +46,5 @@ It’s also possible to annotate the imported or merged ontology axioms with the
     robot merge --input example2.owl --input merge.owl \
       --annotate-defined-by true \
       --output results/merged_defined_by.owl
+
+`--annotate-defined-by` excludes entities from the reserved OWL 2 vocabularies (RDF, RDFS, XSD and OWL).
diff --git a/robot-command/src/main/java/org/obolibrary/robot/AnnotateCommand.java b/robot-command/src/main/java/org/obolibrary/robot/AnnotateCommand.java
@@ -318,7 +318,9 @@ public CommandState execute(CommandState state, String[] args) throws Exception
         OWLAnnotationProperty rdfsIsDefinedBy =
             ontology.getOWLOntologyManager().getOWLDataFactory().getRDFSIsDefinedBy();
         for (OWLEntity owlEntity : ontology.getSignature()) {
-          OntologyHelper.addEntityAnnotation(ontology, owlEntity, rdfsIsDefinedBy, ontIRI, false);
+          if (!owlEntity.getIRI().isReservedVocabulary()) {
+            OntologyHelper.addEntityAnnotation(ontology, owlEntity, rdfsIsDefinedBy, ontIRI, false);
+          }
         }
       }
     }

diff --git a/robot-core/src/main/java/org/obolibrary/robot/MergeOperation.java b/robot-core/src/main/java/org/obolibrary/robot/MergeOperation.java
@@ -363,8 +363,10 @@ private static void annotateWithOntologyIRI(
       OWLAnnotationProperty rdfsIsDefinedBy =
           targetOntology.getOWLOntologyManager().getOWLDataFactory().getRDFSIsDefinedBy();
       for (OWLEntity owlEntity : sourceOntology.getSignature(includeImportsClosure)) {
-        OntologyHelper.addEntityAnnotation(
-            targetOntology, owlEntity, rdfsIsDefinedBy, ontIRI, false);
+        if (!owlEntity.getIRI().isReservedVocabulary()) {
+          OntologyHelper.addEntityAnnotation(
+              targetOntology, owlEntity, rdfsIsDefinedBy, ontIRI, false);
+        }
       }
     }
   }

diff --git a/robot-core/src/test/java/org/obolibrary/robot/MergeOperationTest.java b/robot-core/src/test/java/org/obolibrary/robot/MergeOperationTest.java
@@ -101,9 +101,9 @@ public void testMergeDefinedBy() throws IOException {
     assertEquals(5, simple.getAxiomCount());
     OWLOntology merged = MergeOperation.merge(ontologies, false, false, true, false);
 
-    assertEquals(9, merged.getAxiomCount());
+    assertEquals(7, merged.getAxiomCount());
     OWLOntology expected = loadOntology("/simple_defined_by.owl");
-    assertEquals(9, expected.getAxiomCount());
+    assertEquals(7, expected.getAxiomCount());
     assertIdentical(expected, merged);
   }
 }
diff --git a/robot-core/src/test/resources/simple_defined_by.owl b/robot-core/src/test/resources/simple_defined_by.owl
@@ -8,43 +8,6 @@
      xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
     <owl:Ontology rdf:about="https://github.com/ontodev/robot/robot-core/src/test/resources/simple.owl"/>
 
-
-
-    <!-- 
-    ///////////////////////////////////////////////////////////////////////////////////////
-    //
-    // Annotation properties
-    //
-    ///////////////////////////////////////////////////////////////////////////////////////
-     -->
-
-
-
-
-    <!-- http://www.w3.org/2000/01/rdf-schema#label -->
-
-    <rdf:Description rdf:about="http://www.w3.org/2000/01/rdf-schema#label">
-        <rdfs:isDefinedBy rdf:resource="https://github.com/ontodev/robot/robot-core/src/test/resources/simple.owl"/>
-    </rdf:Description>
-
-
-
-    <!-- 
-    ///////////////////////////////////////////////////////////////////////////////////////
-    //
-    // Datatypes
-    //
-    ///////////////////////////////////////////////////////////////////////////////////////
-     -->
-
-
-
-
-    <!-- http://www.w3.org/1999/02/22-rdf-syntax-ns#PlainLiteral -->
-
-    <rdf:Description rdf:about="http://www.w3.org/1999/02/22-rdf-syntax-ns#PlainLiteral">
-        <rdfs:isDefinedBy rdf:resource="https://github.com/ontodev/robot/robot-core/src/test/resources/simple.owl"/>
-    </rdf:Description>