CODEWITHSUNDEEP
jenaowlowl-api
PCoder
PCoder

Reputation: 2185

Merging ontologies in OWLAPI with same IRI's

I generally keep my ontologies in two different files.

  1. First ontology file contains the classes, subclasses, data properties and object properties.

  2. The second file containing all the individuals and relationships between the individuals.

So, I need to merge these two files in order to have a complete model. I wonder how this could be achieved using owlapi?

In Jena, I do this as follows:

OntModel model = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM,
                null);
try {
        model.read(new FileInputStream(MyOntologyFile), "...");
        model.read(new FileInputStream(MyOntologyWithIndividualsFile), "...");
} catch (Exception e) { 
        log.error("Loading Model failed:" + e);
}

In the similar fashion when I tried to load my ontology files using owlapi, I get error:

OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
OWLObjectRenderer renderer = new DLSyntaxObjectRenderer();

File file = new File(MyOntologyFile);
File fileIndividuals = new File(MyOntologyWithIndividualsFile);

OWLOntology localOntology = null;
// Now load the local copy
try {
    localOntology = manager.loadOntologyFromOntologyDocument(file);
    localOntology = manager
            .loadOntologyFromOntologyDocument(fileIndividuals);
} catch (OWLOntologyCreationException ex) {
    ex.printStackTrace();
}

Error:

org.semanticweb.owlapi.model.OWLOntologyAlreadyExistsException: Ontology already exists. OntologyID(OntologyIRI(<http://www.semanticweb.org/lp4220/ontologies/2014/4/untitled-ontology-35>))
    at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:880)
    at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:806)
    at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:821)

Update:

As it turns out, merging of ontologies is only possible with those having different IRI's, and hence I presume it is not acceptable to divide an ontology into two with the same IRI. A solution for this (as commented by Joshua) may be to read all individuals and axioms from one ontology and then add them to an already loaded ontology.

For ontologies with distinct IRI's merging can be done as follows (example courtesy Ignazio's OWLED 2011 slides - slide no. 27): 

OWLOntologyManager m = create();
OWLOntology o1 = m.loadOntology(pizza_iri);
OWLOntology o2 = m.loadOntology(example_iri);
// Create our ontology merger
OWLOntologyMerger merger = new OWLOntologyMerger(m);
// Merge all of the loaded ontologies, specifying an IRI for the
new ontology
IRI mergedOntologyIRI =
IRI.create(
"http://www.semanticweb.com/mymergedont"
);
OWLOntology merged = merger.createMergedOntology(m,
mergedOntologyIRI);
assertTrue(merged.getAxiomCount() > o1.getAxiomCount());
assertTrue(merged.getAxiomCount() > o2.getAxiomCount());

Upvotes: 2

Views: 1296

Answers (2)

Alex J.
Alex J.

Reputation: 337

In general, you do not make "Individuals and Relationships" an Ontology, unless they require for classifications - say to define Class "American Company" you need an Individual "US". Otherwise, that other part is should be your RDF triples that refer to the Ontology.

Upvotes: 0

Ignazio
Ignazio

Reputation: 10659

Your problem is not having the same iri in the data but ontologies with the same iris loaded in the same manager. Load the ontologies in separate managers and add all the axioms from one to the other, that will give you a merged ontology.

Upvotes: 2

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