Examples of OWLOntology

edu.stanford.smi.protegex.owl.model.OWLOntology
org.semanticweb.owl.model.OWLOntology
Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group Date: 24-Oct-2006
An OWLOntology contains a set of axioms. Ontologies do not specifically contain entities such as classes, properties or individuals - these entities are merely referenced by the axioms that the ontology contains. They form the signature of the ontology. Unlike some APIs it is therefore not possible to directly add or remove entities to or from an ontology.
An ontology cannot be modified directly. Changes must be applied using an OWLOntologyManager.
org.semanticweb.owlapi.model.OWLOntology
3.org/TR/owl2-syntax/#Ontologies">Ontology in the OWL 2 specification.
An {@code OWLOntology} consists of a possibly empty set of{@link org.semanticweb.owlapi.model.OWLAxiom}s and a possibly empty set of {@link OWLAnnotation}s. An ontology can have an ontology IRI which can be used to identify the ontology. If it has an ontology IRI then it may also have an ontology version IRI. Since OWL 2, an ontology need not have an ontology IRI. (See the OWL 2 Structural Specification An ontology cannot be modified directly. Changes must be applied via its {@code OWLOntologyManager}. @author Matthew Horridge, The University Of Manchester, Bio-HealthInformatics Group @since 2.0.0

Examples of org.semanticweb.owlapi.model.OWLOntology

            @Nonnull IRI iri, int superClassLevel, int subClassLevel,
            OWLReasoner reasoner, boolean verbose)
            throws OWLOntologyCreationException {
        Set<OWLAxiom> axs = extract(signature, superClassLevel, subClassLevel,
                reasoner, verbose);
        OWLOntology newOnt = manager.createOntology(iri);
        LinkedList<AddAxiom> addaxs = new LinkedList<>();
        for (OWLAxiom ax : axs) {
            assert ax != null;
            addaxs.add(new AddAxiom(newOnt, ax));
        }

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Examples of org.semanticweb.owlapi.model.OWLOntology

    }


    @Nonnull
    protected OWLOntology getOntologyWithPunnedInvalidDeclarations()
            throws OWLOntologyCreationException {
        OWLOntology o = m.createOntology(IRI
                .create("urn:forbiddenPunningNotRedeclared"));
        OWLObjectProperty op = df.getOWLObjectProperty(iri("testProperty"));
        OWLAnnotationProperty ap = df
                .getOWLAnnotationProperty(iri("testProperty"));
        m.addAxiom(o, df.getOWLDeclarationAxiom(op));

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Examples of org.semanticweb.owlapi.model.OWLOntology

    }


    @Nonnull
    protected OWLOntology getOntologyWithMissingDeclarations()
            throws OWLOntologyCreationException {
        OWLOntology o = m.createOntology(IRI.create("urn:missingDeclarations"));
        OWLObjectProperty op = df
                .getOWLObjectProperty(iri("testObjectProperty"));
        OWLAnnotationProperty ap = df
                .getOWLAnnotationProperty(iri("testAnnotationProperty"));
        m.addAxiom(o, df.getOWLTransitiveObjectPropertyAxiom(op));

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Examples of org.semanticweb.owlapi.model.OWLOntology

    }


    @Test
    public void shouldNotAddDeclarationsForIllegalPunnings()
            throws OWLOntologyCreationException, OWLOntologyStorageException {
        OWLOntology o = getOntologyWithPunnedInvalidDeclarations();
        OWLOntology reloaded = roundTrip(o, format);
        OWLAnnotationProperty ap = df
                .getOWLAnnotationProperty(iri("testProperty"));
        OWLDeclarationAxiom ax = df.getOWLDeclarationAxiom(ap);
        assertFalse("ap testProperty should not have been declared",
                reloaded.containsAxiom(ax));
    }

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Examples of org.semanticweb.owlapi.model.OWLOntology

    }


    @Test
    public void shouldDeclareMissingEntities()
            throws OWLOntologyCreationException, OWLOntologyStorageException {
        OWLOntology o = getOntologyWithMissingDeclarations();
        OWLOntology reloaded = roundTrip(o, format);
        OWLObjectProperty op = df
                .getOWLObjectProperty(iri("testObjectProperty"));
        OWLAnnotationProperty ap = df
                .getOWLAnnotationProperty(iri("testAnnotationProperty"));
        assertTrue(reloaded.containsAxiom(df.getOWLDeclarationAxiom(ap)));
        assertTrue(reloaded.containsAxiom(df.getOWLDeclarationAxiom(op)));
    }

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Examples of org.semanticweb.owlapi.model.OWLOntology

        // create minimal ontology
        OBODoc oboDocSource = parseOBOFile("roundtrip_cardinality.obo");
        // convert to OWL and retrieve def
        OWLAPIObo2Owl bridge = new OWLAPIObo2Owl(
                OWLManager.createOWLOntologyManager());
        OWLOntology owlOntology = bridge.convert(oboDocSource);
        OWLDataFactory factory = owlOntology.getOWLOntologyManager()
                .getOWLDataFactory();
        OWLClass c = factory.getOWLClass(bridge.oboIdToIRI("PR:000027136"));
        // Relations
        boolean foundRel1 = false;
        boolean foundRel2 = false;
        Set<OWLSubClassOfAxiom> axioms = owlOntology
                .getSubClassAxiomsForSubClass(c);
        assertEquals(3, axioms.size());
        for (OWLSubClassOfAxiom axiom : axioms) {
            OWLClassExpression superClass = axiom.getSuperClass();
            if (superClass instanceof OWLObjectExactCardinality) {

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Examples of org.semanticweb.owlapi.model.OWLOntology

@SuppressWarnings({ "javadoc", "null" })
public class DanglingRoundTripTest extends OboFormatTestBasics {


    @Test
    public void testConvertXPs() throws Exception {
        OWLOntology owlOnt = convertOBOFile("dangling_roundtrip_test.obo");
        OWLAPIOwl2Obo revbridge = new OWLAPIOwl2Obo(
                OWLManager.createOWLOntologyManager());
        OBODoc d2 = revbridge.convert(owlOnt);
        Frame f = d2.getTermFrame("UBERON:0000020");
        Clause rc = f.getClause(OboFormatTag.TAG_NAME);

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Examples of org.semanticweb.owlapi.model.OWLOntology

        roundTripOBOFile("multiple_def_xref_test.obo", true);
    }


    @Test
    public void testDefinitions() {
        OWLOntology owlOnt = convertOBOFile("multiple_def_xref_test.obo");
        int n = 0;
        for (OWLAxiom ax : owlOnt.getAxioms()) {
            // System.out.println(ax);
            for (OWLAnnotation ann : ax.getAnnotations()) {
                OWLAnnotationProperty p = ann.getProperty();
                if (p.getIRI()
                        .equals(IRI

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Examples of org.semanticweb.owlapi.model.OWLOntology

@SuppressWarnings("javadoc")
public class XrefIRITest extends OboFormatTestBasics {


    @Test
    public void testConversion() throws Exception {
        OWLOntology ontology = parseOWLFile("xrefIRItest.owl");
        OBODoc doc = convert(ontology);
        doc.getTermFrame("FOO:1");
        writeOBO(doc);
    }

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Examples of org.semanticweb.owlapi.model.OWLOntology

        roundTripOBOFile("version_iri_test.obo", true);
    }


    @Test
    public void testConvert() {
        OWLOntology owlOnt = convertOBOFile("version_iri_test.obo");
        assertNotNull(owlOnt);
        IRI v = owlOnt.getOntologyID().getVersionIRI().get();
        assertEquals("http://purl.obolibrary.org/obo/go/2012-01-01/go.owl",
                v.toString());
    }

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