OWL, Jena, Protege, Semantic Web

If we have an OWL model in source.owl, we can use Protege to extend instances of classes in this model like so:

  1. extended:ExtendedClass <– source:Class

To achieve this in Protege 4.0:

  1. Load source.owl in Protege 4.0.
  2. Create a new ontology file, and open it in the current window.
  3. Make sure this ontology file is saved in the same directory as source.owl: Protege expects it to be in the same folder.
  4. Once loaded, go into Ontology Imports and select New for a Direct Import
  5. Select “Import an ontology that has already been loaded/created”.
  6. If the import is “Not Loaded”, make sure it is saved in the same directory, or try reloading the ontologies.

We can now define an ExtendedClass:

  1. Select the Classes tab
  2. Create a new Class called “ExtendedClass”
  3. In Equivalent Classes, select “Class” from the source model

In order to import this into Jena and select instances of this extended model, you can use code similar to the following (this code is using the Pellet reasoner):

IFile rdf = ...;
OntModelSpec ontModelSpec = PelletReasonerFactory.THE_SPEC; // or OntModelSpec.OWL_MEM
Reasoner reasoner = new PelletReasoner(); // or ReasonerRegistry.getOWLReasoner();

PrintUtil.registerPrefix("source", "http://openiaml.org/source#"); // sets up source: prefix
OntModel schema = ModelFactory.createOntologyModel( ontModelSpec );
// load source.owl
schema.read(getSourceOWL(), null /* for resolving relative URIs */);

// enable debug messages?
// reasoner.setParameter(ReasonerVocabulary.PROPtraceOn, true);

// load extension.owl
schema.read(getValidationOWL(), null /* for resolving relative URIs */);
reasoner = reasoner.bindSchema(schema);

// load an RDF instance
Model model = FileManager.get().loadModel("file:" + rdf.getLocation().toString());

// and validate that it conforms to the OWL model
InfModel inf = ModelFactory.createInfModel(reasoner, model);
ValidityReport valid = inf.validate();

if (!valid.isValid()) {
  throw new RuntimeException("Model '" + rdf.getName() + "' was not valid to OWL schema");
}

String uri = "http://openiaml.org/validation/owl/Ontology1255477538318.owl#ExtendedClass";
Resource problem = inf.getResource(uri);
Iterator<Statement> it = inf.listStatements(null, RDF.type, problem);
while (it.hasNext()) {
  // will select all instances of ExtendedClass <-- Class
  throw new RuntimeException(PrintUtil.print(it.next()));
}