create skeleton for adding indirect existentials in materialize

docs/examples/hubcap.owl

@@ -0,0 +1,85 @@
+<?xml version="1.0"?>
+<rdf:RDF xmlns="http://www.semanticweb.org/vinicius/ontologies/2024/7/untitled-ontology-2/"
+     xml:base="http://www.semanticweb.org/vinicius/ontologies/2024/7/untitled-ontology-2/"
+     xmlns:owl="http://www.w3.org/2002/07/owl#"
+     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:rdfs="http://www.w3.org/2000/01/rdf-schema#">
+    <owl:Ontology rdf:about="http://www.semanticweb.org/vinicius/ontologies/2024/7/untitled-ontology-2"/>
+
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Object Properties
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+
+
+
+    <!-- http://www.semanticweb.org/vinicius/ontologies/2024/7/untitled-ontology-2#has_part -->
+
+    <owl:ObjectProperty rdf:about="http://www.semanticweb.org/vinicius/ontologies/2024/7/untitled-ontology-2#has_part">
+        <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
+    </owl:ObjectProperty>
+
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Classes
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+
+
+
+    <!-- http://www.semanticweb.org/vinicius/ontologies/2024/7/untitled-ontology-2#car -->
+
+    <owl:Class rdf:about="http://www.semanticweb.org/vinicius/ontologies/2024/7/untitled-ontology-2#car">
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://www.semanticweb.org/vinicius/ontologies/2024/7/untitled-ontology-2#has_part"/>
+                <owl:someValuesFrom rdf:resource="http://www.semanticweb.org/vinicius/ontologies/2024/7/untitled-ontology-2#wheel"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
+    </owl:Class>
+
+
+
+    <!-- http://www.semanticweb.org/vinicius/ontologies/2024/7/untitled-ontology-2#convertible -->
+
+    <owl:Class rdf:about="http://www.semanticweb.org/vinicius/ontologies/2024/7/untitled-ontology-2#convertible">
+        <rdfs:subClassOf rdf:resource="http://www.semanticweb.org/vinicius/ontologies/2024/7/untitled-ontology-2#car"/>
+    </owl:Class>
+
+
+
+    <!-- http://www.semanticweb.org/vinicius/ontologies/2024/7/untitled-ontology-2#hubcap -->
+
+    <owl:Class rdf:about="http://www.semanticweb.org/vinicius/ontologies/2024/7/untitled-ontology-2#hubcap"/>
+
+
+
+    <!-- http://www.semanticweb.org/vinicius/ontologies/2024/7/untitled-ontology-2#wheel -->
+
+    <owl:Class rdf:about="http://www.semanticweb.org/vinicius/ontologies/2024/7/untitled-ontology-2#wheel">
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://www.semanticweb.org/vinicius/ontologies/2024/7/untitled-ontology-2#has_part"/>
+                <owl:someValuesFrom rdf:resource="http://www.semanticweb.org/vinicius/ontologies/2024/7/untitled-ontology-2#hubcap"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
+    </owl:Class>
+</rdf:RDF>
+
+
+
+<!-- Generated by the OWL API (version 4.5.29.2024-05-13T12:11:03Z) https://github.com/owlcs/owlapi -->
+

robot-command/src/main/java/org/obolibrary/robot/MaterializeCommand.java

@@ -44,6 +44,8 @@ public MaterializeCommand() {
     o.addOption("o", "output", true, "save reasoned ontology to a file");
     o.addOption("t", "term", true, "a property to materialize");
     o.addOption("T", "term-file", true, "load properties from a file");
+    o.addOption(
+        "c", "include-indirect", true, "if true include redundant existential restrictions");
     options = o;
   }
 
@@ -131,6 +133,8 @@ public CommandState execute(CommandState state, String[] args) throws Exception
       }
     }
 
+    boolean includeIndirect = CommandLineHelper.getBooleanValue(line, "include-indirect", false);
+
     Set<IRI> terms = CommandLineHelper.getTerms(ioHelper, line, true);
     Set<OWLObjectProperty> properties = new HashSet<>();
     for (IRI term : terms) {

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

@@ -77,6 +77,7 @@ public static void materialize(
    * @param options A map of options for the operation
    * @param reasonOverImportsClosure if true will first perform materialization over all ontologies
    *     in the import closure
+   * @param includeIndirect if true include redundant existential restrictions
    * @throws OWLOntologyCreationException on ontology problem
    * @throws OntologyLogicException on logic problem
    */
@@ -87,12 +88,37 @@ public static void materialize(
       Map<String, String> options,
       boolean reasonOverImportsClosure)
       throws OntologyLogicException, OWLOntologyCreationException {
+    materialize(ontology, reasonerFactory, properties, options, reasonOverImportsClosure, false);
+  }
+
+  /**
+   * Replace EquivalentClass axioms with weaker SubClassOf axioms.
+   *
+   * @param ontology The OWLOntology to relax
+   * @param reasonerFactory reasoner factory for the reasoner that is to be wrapped
+   * @param properties object properties whose existentials are to be materialized (null
+   *     materializes all)
+   * @param options A map of options for the operation
+   * @param reasonOverImportsClosure if true will first perform materialization over all ontologies
+   *     in the import closure
+   * @throws OWLOntologyCreationException on ontology problem
+   * @throws OntologyLogicException on logic problem
+   */
+  public static void materialize(
+      OWLOntology ontology,
+      OWLReasonerFactory reasonerFactory,
+      Set<OWLObjectProperty> properties,
+      Map<String, String> options,
+      boolean reasonOverImportsClosure,
+      boolean includeIndirect)
+      throws OntologyLogicException, OWLOntologyCreationException {
 
     if (reasonOverImportsClosure) {
       logger.info("Materializing imported ontologies...");
       for (OWLOntology importedOntology : ontology.getImportsClosure()) {
         if (!importedOntology.equals(ontology)) {
-          materialize(importedOntology, reasonerFactory, properties, options, false);
+          materialize(
+              importedOntology, reasonerFactory, properties, options, false, includeIndirect);
         }
       }
     }
@@ -143,7 +169,7 @@ public static void materialize(
         logger.debug("Excluding classes not in main ontology: " + c);
         continue;
       }
-      Set<OWLClassExpression> sces = emr.getSuperClassExpressions(c, true);
+      Set<OWLClassExpression> sces = emr.getSuperClassExpressions(c, !includeIndirect);
       if (!emr.isSatisfiable(c)) {
         logger.error("Ontology is not coherent! Unsatisfiable: " + c);
         throw new IncoherentTBoxException(Collections.singleton(c));