resolves issue #1163

ontodev · Dec 1, 2023 · 6408553 · 6408553
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Showing 7 changed files with 13 additions and 67 deletions.
diff --git a/docs/examples/example2_defined_by.owl b/docs/examples/example2_defined_by.owl
@@ -107,33 +107,7 @@
     <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>
 
 
 

diff --git a/docs/examples/merged_defined_by.owl b/docs/examples/merged_defined_by.owl
@@ -107,25 +107,7 @@
     <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
@@ -36,13 +36,17 @@ It’s also possible to annotate the imported or merged ontology axioms with the
 
   * `--annotate-derived-from true`: annotates all axioms with the source's version IRI if it exists, else with the ontology IRI, using `prov:wasDerivedFrom`. If the axiom already has an annotation using this property (`prov:wasDerivedFrom`), the existing annotation will be kept and no new annotation will be added.
 
+```
     robot merge --catalog catalog.xml \
       --input imports-nucleus.owl \
       --annotate-derived-from true \
       --output results/merged_derived_from.owl
+```
       
   * `--annotate-defined-by true`: annotates all entities (class, data, annotation, object property and named individual declaration axioms) with the source's IRI using `rdfs:isDefinedBy`. If the term already has an annotation using this property (`rdfs:isDefinedBy`), the existing annotation will be kept and no new annotation will be added.
 
+```
     robot merge --input example2.owl --input merge.owl \
       --annotate-defined-by true \
       --output results/merged_defined_by.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.isOWLDatatype() && owlEntity.asOWLDatatype().isBuiltIn())) {
+            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.isOWLDatatype() && owlEntity.asOWLDatatype().isBuiltIn())) {
+          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(8, merged.getAxiomCount());
     OWLOntology expected = loadOntology("/simple_defined_by.owl");
-    assertEquals(9, expected.getAxiomCount());
+    assertEquals(8, 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
@@ -27,24 +27,6 @@
         <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>