OWL API: Traverse imported ontology

Question

I'm trying to import an ontology to the primary ontology, and traverse over all classes:

     manager = OWLManager.createOWLOntologyManager();
            ontology = manager.loadOntologyFromOntologyDocument(new File("data/prim.owl"));
            factory = manager.getOWLDataFactory();
            OWLImportsDeclaration im = factory.getOWLImportsDeclaration(IRI.create("https://protege.stanford.edu/ontologies/pizza/pizza.owl"));
            manager.applyChange(new AddImport(ontology,im));
            reasoner = OpenlletReasonerFactory.getInstance().createReasoner(ontology);

I’m running this code to get all classes:

      //*********************
            Set<OWLClass> allCls = ontology.getClassesInSignature();
            allCls.forEach(System.out::println);

Classes belonging to prim.owl are returned, but classes in the imported ontology (pizza.owl) are not returned.

As usual, the Javadoc is your friend ... as you can see if you click the link, there is the option to provide an argument: Set<OWLClass> getClassesInSignature(boolean includeImportsClosure) with the description "includeImportsClosure - if true, include imports closure." — UninformedUser
Incidentally, to traverse all classes you don't need a reasoner. — Ignazio

ssz ssz · Accepted Answer · 2019-05-06T11:57:03

The code in the question contains a mistake: it does not load the desired imported ontology (pizza) into the manager.

OWLImportsDeclaration im = factory.getOWLImportsDeclaration(IRI.create("https://protege.stanford.edu/ontologies/pizza/pizza.owl"));
manager.applyChange(new AddImport(ontology,im));

These lines just add the owl:imports declaration into the ontology header (_:x a owl:Ontology) for the pizza-iri.

To make the code work, you need to load the pizza-ontology separately:

OWLOntology pizza = manager.loadOntology(IRI.create("https://protege.stanford.edu/ontologies/pizza/pizza.owl"));
OWLImportsDeclaration im = factory.getOWLImportsDeclaration(pizza.getOntologyID().getOntologyIRI().orElseThrow(AssertionError::new));
manager.applyChange(new AddImport(ontology, im));

Now you can check that all imports and references are really present and correct, and, therefore, your ontology has a reference to the pizza ontology:

Assert.assertEquals(1, ontology.importsDeclarations().count());
Assert.assertEquals(1, ontology.imports().count());
Assert.assertEquals(2, manager.ontologies().count());

Then you can get all OWL-classes from both ontologies as a single collection or java-Stream:

ontology.classesInSignature(Imports.INCLUDED).forEach(System.err::println);

Also please note: the method Set<OWLClass> getClassesInSignature(boolean includeImportsClosure) is deprecated (in OWL-API v5).

OWL API: Traverse imported ontology

1 Answers