Problems querying OWL ontology through OWL API

Question

I have the ontology used in the OWL API examples.

private static final String KOALA = "<?xml version=\"1.0\"?>\n"
    + "<rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:rdfs=\"http://www.w3.org/2000/01/rdf-schema#\" xmlns:owl=\"http://www.w3.org/2002/07/owl#\" xmlns=\"http://protege.stanford.edu/plugins/owl/owl-library/koala.owl#\" xml:base=\"http://protege.stanford.edu/plugins/owl/owl-library/koala.owl\">\n"
    + "  <owl:Ontology rdf:about=\"\"/>\n"
    + "  <owl:Class rdf:ID=\"Female\"><owl:equivalentClass><owl:Restriction><owl:onProperty><owl:FunctionalProperty rdf:about=\"#hasGender\"/></owl:onProperty><owl:hasValue><Gender rdf:ID=\"female\"/></owl:hasValue></owl:Restriction></owl:equivalentClass></owl:Class>\n"
    + "  <owl:Class rdf:ID=\"Marsupials\"><owl:disjointWith><owl:Class rdf:about=\"#Person\"/></owl:disjointWith><rdfs:subClassOf><owl:Class rdf:about=\"#Animal\"/></rdfs:subClassOf></owl:Class>\n"
    + "  <owl:Class rdf:ID=\"Student\"><owl:equivalentClass><owl:Class><owl:intersectionOf rdf:parseType=\"Collection\"><owl:Class rdf:about=\"#Person\"/><owl:Restriction><owl:onProperty><owl:FunctionalProperty rdf:about=\"#isHardWorking\"/></owl:onProperty><owl:hasValue rdf:datatype=\"http://www.w3.org/2001/XMLSchema#boolean\">true</owl:hasValue></owl:Restriction><owl:Restriction><owl:someValuesFrom><owl:Class rdf:about=\"#University\"/></owl:someValuesFrom><owl:onProperty><owl:ObjectProperty rdf:about=\"#hasHabitat\"/></owl:onProperty></owl:Restriction></owl:intersectionOf></owl:Class></owl:equivalentClass></owl:Class>\n"
    + "  <owl:Class rdf:ID=\"KoalaWithPhD\"><owl:versionInfo>1.2</owl:versionInfo><owl:equivalentClass><owl:Class><owl:intersectionOf rdf:parseType=\"Collection\"><owl:Restriction><owl:hasValue><Degree rdf:ID=\"PhD\"/></owl:hasValue><owl:onProperty><owl:ObjectProperty rdf:about=\"#hasDegree\"/></owl:onProperty></owl:Restriction><owl:Class rdf:about=\"#Koala\"/></owl:intersectionOf></owl:Class></owl:equivalentClass></owl:Class>\n"
    + "  <owl:Class rdf:ID=\"University\"><rdfs:subClassOf><owl:Class rdf:ID=\"Habitat\"/></rdfs:subClassOf></owl:Class>\n"
    + "  <owl:Class rdf:ID=\"Koala\"><rdfs:subClassOf><owl:Restriction><owl:hasValue rdf:datatype=\"http://www.w3.org/2001/XMLSchema#boolean\">false</owl:hasValue><owl:onProperty><owl:FunctionalProperty rdf:about=\"#isHardWorking\"/></owl:onProperty></owl:Restriction></rdfs:subClassOf><rdfs:subClassOf><owl:Restriction><owl:someValuesFrom><owl:Class rdf:about=\"#DryEucalyptForest\"/></owl:someValuesFrom><owl:onProperty><owl:ObjectProperty rdf:about=\"#hasHabitat\"/></owl:onProperty></owl:Restriction></rdfs:subClassOf><rdfs:subClassOf rdf:resource=\"#Marsupials\"/></owl:Class>\n"
    + "  <owl:Class rdf:ID=\"Animal\"><rdfs:seeAlso>Male</rdfs:seeAlso><rdfs:subClassOf><owl:Restriction><owl:onProperty><owl:ObjectProperty rdf:about=\"#hasHabitat\"/></owl:onProperty><owl:minCardinality rdf:datatype=\"http://www.w3.org/2001/XMLSchema#int\">1</owl:minCardinality></owl:Restriction></rdfs:subClassOf><rdfs:subClassOf><owl:Restriction><owl:cardinality rdf:datatype=\"http://www.w3.org/2001/XMLSchema#int\">1</owl:cardinality><owl:onProperty><owl:FunctionalProperty rdf:about=\"#hasGender\"/></owl:onProperty></owl:Restriction></rdfs:subClassOf><owl:versionInfo>1.1</owl:versionInfo></owl:Class>\n"
    + "  <owl:Class rdf:ID=\"Forest\"><rdfs:subClassOf rdf:resource=\"#Habitat\"/></owl:Class>\n"
    + "  <owl:Class rdf:ID=\"Rainforest\"><rdfs:subClassOf rdf:resource=\"#Forest\"/></owl:Class>\n"
    + "  <owl:Class rdf:ID=\"GraduateStudent\"><rdfs:subClassOf><owl:Restriction><owl:onProperty><owl:ObjectProperty rdf:about=\"#hasDegree\"/></owl:onProperty><owl:someValuesFrom><owl:Class><owl:oneOf rdf:parseType=\"Collection\"><Degree rdf:ID=\"BA\"/><Degree rdf:ID=\"BS\"/></owl:oneOf></owl:Class></owl:someValuesFrom></owl:Restriction></rdfs:subClassOf><rdfs:subClassOf rdf:resource=\"#Student\"/></owl:Class>\n"
    + "  <owl:Class rdf:ID=\"Parent\"><owl:equivalentClass><owl:Class><owl:intersectionOf rdf:parseType=\"Collection\"><owl:Class rdf:about=\"#Animal\"/><owl:Restriction><owl:onProperty><owl:ObjectProperty rdf:about=\"#hasChildren\"/></owl:onProperty><owl:minCardinality rdf:datatype=\"http://www.w3.org/2001/XMLSchema#int\">1</owl:minCardinality></owl:Restriction></owl:intersectionOf></owl:Class></owl:equivalentClass><rdfs:subClassOf rdf:resource=\"#Animal\"/></owl:Class>\n"
    + "  <owl:Class rdf:ID=\"DryEucalyptForest\"><rdfs:subClassOf rdf:resource=\"#Forest\"/></owl:Class>\n"
    + "  <owl:Class rdf:ID=\"Quokka\"><rdfs:subClassOf><owl:Restriction><owl:hasValue rdf:datatype=\"http://www.w3.org/2001/XMLSchema#boolean\">true</owl:hasValue><owl:onProperty><owl:FunctionalProperty rdf:about=\"#isHardWorking\"/></owl:onProperty></owl:Restriction></rdfs:subClassOf><rdfs:subClassOf rdf:resource=\"#Marsupials\"/></owl:Class>\n"
    + "  <owl:Class rdf:ID=\"TasmanianDevil\"><rdfs:subClassOf rdf:resource=\"#Marsupials\"/></owl:Class>\n"
    + "  <owl:Class rdf:ID=\"MaleStudentWith3Daughters\"><owl:equivalentClass><owl:Class><owl:intersectionOf rdf:parseType=\"Collection\"><owl:Class rdf:about=\"#Student\"/><owl:Restriction><owl:onProperty><owl:FunctionalProperty rdf:about=\"#hasGender\"/></owl:onProperty><owl:hasValue><Gender rdf:ID=\"male\"/></owl:hasValue></owl:Restriction><owl:Restriction><owl:onProperty><owl:ObjectProperty rdf:about=\"#hasChildren\"/></owl:onProperty><owl:cardinality rdf:datatype=\"http://www.w3.org/2001/XMLSchema#int\">3</owl:cardinality></owl:Restriction><owl:Restriction><owl:allValuesFrom rdf:resource=\"#Female\"/><owl:onProperty><owl:ObjectProperty rdf:about=\"#hasChildren\"/></owl:onProperty></owl:Restriction></owl:intersectionOf></owl:Class></owl:equivalentClass></owl:Class>\n"
    + "  <owl:Class rdf:ID=\"Degree\"/>\n  <owl:Class rdf:ID=\"Gender\"/>\n"
    + "  <owl:Class rdf:ID=\"Male\"><owl:equivalentClass><owl:Restriction><owl:hasValue rdf:resource=\"#male\"/><owl:onProperty><owl:FunctionalProperty rdf:about=\"#hasGender\"/></owl:onProperty></owl:Restriction></owl:equivalentClass></owl:Class>\n"
    + "  <owl:Class rdf:ID=\"Person\"><rdfs:subClassOf rdf:resource=\"#Animal\"/><owl:disjointWith rdf:resource=\"#Marsupials\"/></owl:Class>\n"
    + "  <owl:ObjectProperty rdf:ID=\"hasHabitat\"><rdfs:range rdf:resource=\"#Habitat\"/><rdfs:domain rdf:resource=\"#Animal\"/></owl:ObjectProperty>\n"
    + "  <owl:ObjectProperty rdf:ID=\"hasDegree\"><rdfs:domain rdf:resource=\"#Person\"/><rdfs:range rdf:resource=\"#Degree\"/></owl:ObjectProperty>\n"
    + "  <owl:ObjectProperty rdf:ID=\"hasChildren\"><rdfs:range rdf:resource=\"#Animal\"/><rdfs:domain rdf:resource=\"#Animal\"/></owl:ObjectProperty>\n"
    + "  <owl:FunctionalProperty rdf:ID=\"hasGender\"><rdfs:range rdf:resource=\"#Gender\"/><rdf:type rdf:resource=\"http://www.w3.org/2002/07/owl#ObjectProperty\"/><rdfs:domain rdf:resource=\"#Animal\"/></owl:FunctionalProperty>\n"
    + "  <owl:FunctionalProperty rdf:ID=\"isHardWorking\"><rdfs:range rdf:resource=\"http://www.w3.org/2001/XMLSchema#boolean\"/><rdfs:domain rdf:resource=\"#Person\"/><rdf:type rdf:resource=\"http://www.w3.org/2002/07/owl#DatatypeProperty\"/></owl:FunctionalProperty>\n"
    + "  <Degree rdf:ID=\"MA\"/>\n</rdf:RDF>";

I used this code (https://neo4j.com/blog/using-owl-with-neo4j/) to query the owl ontology:

OWLReasoner reasoner = reasonerFactory.createNonBufferingReasoner(ontology);
    if (!reasoner.isConsistent()) {

        logger.log(Level.INFO, "Ontology is inconsistent");
        //throw your exception of choice here
        throw new Exception("Ontology is inconsistent");
    }

    try{

        // Node thingNode = getOrCreateNodeWithUniqueFactory("owl:Thing");  

        for (OWLClass c :ontology.getClassesInSignature(true)) {
            String classString = c.toString();
            if (classString.contains("#")) {
                classString = classString.substring(
                classString.indexOf("#")+1,classString.lastIndexOf(">"));
            }
            System.out.println("classString: "+classString);

            // Node classNode = getOrCreateNodeWithUniqueFactory(classString); 

            NodeSet<OWLClass> superclasses = reasoner.getSuperClasses(c, true);

            if (superclasses.isEmpty()) {
                //classNode.createRelationshipTo(thingNode,DynamicRelationshipType.withName("isA")); 
                } else {
                for (org.semanticweb.owlapi.reasoner.Node<OWLClass>
                parentOWLNode: superclasses) {
                     OWLClassExpression parent = parentOWLNode.getRepresentativeElement();
                     String parentString = parent.toString();
                     if (parentString.contains("#")) {
                          parentString = parentString.substring(
                          parentString.indexOf("#")+1,
                          parentString.lastIndexOf(">"));
                     }

                     System.out.println("parentString: "+parentString);
                 //    Node parentNode = getOrCreateNodeWithUniqueFactory(parentString);   
                 //    classNode.createRelationshipTo(parentNode, DynamicRelationshipType.withName("isA"));  
                }
            }

            for (org.semanticweb.owlapi.reasoner.Node<OWLNamedIndividual> in
                    : reasoner.getInstances(c, true)) { 
                    OWLNamedIndividual i = in.getRepresentativeElement();
                    String indString = i.toString();
                    if (indString.contains("#")) {
                         indString = indString.substring(
                              indString.indexOf("#")+1,indString.lastIndexOf(">"));
                    }

                    System.out.println("indString: "+indString);

                //    Node individualNode = getOrCreateNodeWithUniqueFactory(indString);  
                //    individualNode.createRelationshipTo(classNode, DynamicRelationshipType.withName("isA"));  


                    for (OWLObjectPropertyExpression objectProperty:
                        ontology.getObjectPropertiesInSignature()) { System.out.println("objectProperty: "+objectProperty); 
                             for
                             (org.semanticweb.owlapi.reasoner.Node<OWLNamedIndividual>
                             object: reasoner.getObjectPropertyValues(i,
                             objectProperty)) { 
                                  String reltype = objectProperty.toString();
                                  reltype = reltype.substring(reltype.indexOf("#")+1,
                                  reltype.lastIndexOf(">"));
                                  String s =
                                  object.getRepresentativeElement().toString();
                                  s = s.substring(s.indexOf("#")+1,
                                  s.lastIndexOf(">"));

                                  System.out.println("reltype: "+reltype+" s: "+s);
                            //      Node objectNode = getOrCreateNodeWithUniqueFactory(s);
                            //      individualNode.createRelationshipTo(objectNode, DynamicRelationshipType.withName(reltype));
                             }
                       }
                       for (OWLDataPropertyExpression dataProperty:
                       ontology.getDataPropertiesInSignature()) { System.out.println("dataProperty: "+dataProperty.asOWLDataProperty()); 
                             for (OWLLiteral object: reasoner.getDataPropertyValues(
                             i, dataProperty.asOWLDataProperty())) {
                                  String reltype =
                                  dataProperty.asOWLDataProperty().toString();
                                  reltype = reltype.substring(reltype.indexOf("#")+1, 
                                  reltype.lastIndexOf(">"));
                                  String s = object.toString();

                                  System.out.println("reltype: "+reltype+" s: "+s);

                             //     individualNode.setProperty(reltype, s);
                             }
                        }

            }
        }

but I observed that it doesn't return object property values for the specified individual and object property expression.

reasoner.getObjectPropertyValues(i, objectProperty)

returns no items. Why?

I tried even with others Reasoner (HermiT, Pellet) as I read in other post, but the outcome does not change. How can I solve it?

Answer 1

There is no objectProperties asserted in the ontology you are using; So the reasoner find nothing, because there is nothing to find.

Add the following code after loading your ontology, so you can test your code.

final OWLDataFactory factory = manager.getOWLDataFactory();
ontology.add(factory.getOWLObjectPropertyAssertionAxiom(factory.getOWLObjectProperty("#HelloWorldProperty"), factory.getOWLNamedIndividual("#FirstIndividual"), factory.getOWLNamedIndividual("#SecondIndividual")));
reasoner.flush();

Your code look good but a bit complicated. You could get shorter code with 'getFlattened()'

for (final OWLNamedIndividual i : reasoner.getInstances(c, true).getFlattened())

Answer 2

I could not detect the objectProperties declaration and dataProperties directly from a specific instance, in this block code:

for (org.semanticweb.owlapi.reasoner.Node<OWLNamedIndividual> in
                : reasoner.getInstances(c, true)) { 
                OWLNamedIndividual i = in.getRepresentativeElement();
                String indString = i.toString();
                if (indString.contains("#")) {
                     indString = indString.substring(
                          indString.indexOf("#")+1,indString.lastIndexOf(">"));
                }

                ......

That is, I couldn't find a way to extract these information directly from i. So, I identified all them from ontology in this way:

        System.out.println("\n-> ObjectProperties: ");
        for (OWLObjectPropertyExpression objectProperty:
            ontology.getObjectPropertiesInSignature()) { 
            String object = objectProperty.toString();
            if (object.contains("#")) {
                object = object.substring(
                        object.indexOf("#")+1,object.lastIndexOf(">"));
            }
            String domain = reasoner.getObjectPropertyDomains(objectProperty, true).toString();
            if (domain.contains("#")) {
                domain = domain.substring(
                        domain.indexOf("#")+1,domain.lastIndexOf(">"));
            }
            String range =  reasoner.getObjectPropertyRanges(objectProperty, true).toString();
            if (range.contains("#")) {
                range = range.substring(
                        range.indexOf("#")+1,range.lastIndexOf(">"));
            }
            System.out.println(domain+" "+object+" "+range);
        }

        System.out.println("\n-> DataProperties: ");
        for (OWLDataProperty dataProperty:
            ontology.getDataPropertiesInSignature()) { 
            String data = dataProperty.toString();
            if (data.contains("#")) {
                data = data.substring(
                        data.indexOf("#")+1,data.lastIndexOf(">"));
            }
            String domain = reasoner.getDataPropertyDomains(dataProperty, true).toString();
            if (domain.contains("#")) {
                domain = domain.substring(
                        domain.indexOf("#")+1,domain.lastIndexOf(">"));
            }
            System.out.println(domain+" "+data);
        }

I thought to add an edge like domain->(objectProperty)->range for all objectProperties found, in order to not lose this information.