Changing behavior for reduce, fixes #321

Previously the procedure included axioms such as Domain in its test for redundant axioms.
This mean it was too vigorous in throwing out SubClassOf axioms.

Now an axiom is only reduced if it can be inferred purely from SubClassOf plus
OPCharacteristic axioms (e.g. transitivity)

Author: cmungall

robot-core/src/main/java/org/obolibrary/robot/ReduceOperation.java

@@ -16,10 +16,12 @@
 import org.semanticweb.owlapi.model.OWLClassExpression;
 import org.semanticweb.owlapi.model.OWLDataFactory;
 import org.semanticweb.owlapi.model.OWLEquivalentClassesAxiom;
+import org.semanticweb.owlapi.model.OWLObjectPropertyCharacteristicAxiom;
 import org.semanticweb.owlapi.model.OWLOntology;
 import org.semanticweb.owlapi.model.OWLOntologyCreationException;
 import org.semanticweb.owlapi.model.OWLOntologyManager;
 import org.semanticweb.owlapi.model.OWLSubClassOfAxiom;
+import org.semanticweb.owlapi.model.OWLTransitiveObjectPropertyAxiom;
 import org.semanticweb.owlapi.model.parameters.Imports;
 import org.semanticweb.owlapi.reasoner.Node;
 import org.semanticweb.owlapi.reasoner.OWLReasoner;
@@ -99,10 +101,10 @@ public static void reduce(
     OWLDataFactory dataFactory = manager.getOWLDataFactory();
 
     // we treat an axiom as redundant if its is redundant within the
-    // subClassOf graph, excluding equivalence axioms
+    // subClassOf graph, including OP characteristic axioms (e.g. transitivity)
     OWLOntology subOntology = manager.createOntology();
     for (OWLAxiom a : ontology.getAxioms(Imports.INCLUDED)) {
-      if (!(a instanceof OWLEquivalentClassesAxiom)) {
+      if (a instanceof OWLSubClassOfAxiom || a instanceof OWLObjectPropertyCharacteristicAxiom) {
         manager.addAxiom(subOntology, a);
       }
     }

robot-core/src/test/java/org/obolibrary/robot/ReduceOperationTest.java

@@ -120,7 +120,7 @@ public void testReduceWithEquiv() throws IOException, OWLOntologyCreationExcepti
     assertIdentical("/equiv_reduce_test_reduced.obo", reasoned);
   }
 
-  /**
+ /**
    * Edge case, taken from GO
    *
    * <p>See: 'central nervous system development' in the test file
@@ -135,8 +135,26 @@ public void testReduceEdgeCase() throws IOException, OWLOntologyCreationExceptio
 
     Map<String, String> options = new HashMap<String, String>();
     options.put("remove-redundant-subclass-axioms", "true");
-
+ 
     ReduceOperation.reduce(reasoned, reasonerFactory, options);
     assertIdentical("/reduce-edgecase-cnd-reduced.obo", reasoned);
   }
+  
+  /**
+   * Domain case, see https://github.com/ontodev/robot/issues/321
+   *
+   * 
+   * @throws IOException
+   * @throws OWLOntologyCreationException
+   */
+  @Test
+  public void testReduceDomainCase() throws IOException, OWLOntologyCreationException {
+    OWLOntology reasoned = loadOntology("/reduce-domain-test.owl");
+    OWLReasonerFactory reasonerFactory = new org.semanticweb.elk.owlapi.ElkReasonerFactory();
+
+    Map<String, String> options = new HashMap<String, String>();
+ 
+    ReduceOperation.reduce(reasoned, reasonerFactory, options);
+    assertIdentical("/reduce-domain-test.owl", reasoned);
+  }
 }

robot-core/src/test/resources/reduce-domain-test.owl

@@ -0,0 +1,12 @@
+Prefix: : <http://x.org/>
+Ontology: <http://x.org/>
+
+ObjectProperty: supplies Domain: artery
+        
+Class: brain_artery
+    EquivalentTo: artery and supplies some brain
+    SubClassOf: artery
+    SubClassOf: supplies some brain
+
+Class: artery
+Class: brain