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

public class RelationShorthandTest extends OboFormatTestBasics {


    @Test
    public void testConvert() {
        // PARSE TEST FILE, CONVERT TO OWL, AND WRITE TO OWL FILE
        OWLOntology ontology = convert(parseOBOFile("relation_shorthand_test.obo"));
        // TEST CONTENTS OF OWL ONTOLOGY
        Set<OWLSubClassOfAxiom> scas = ontology
                .getAxioms(AxiomType.SUBCLASS_OF);
        boolean ok = false;
        for (OWLSubClassOfAxiom sca : scas) {
            OWLClassExpression sup = sca.getSuperClass();
            if (sup instanceof OWLObjectSomeValuesFrom) {
                OWLObjectProperty p = (OWLObjectProperty) ((OWLObjectSomeValuesFrom) sup)
                        .getProperty();
                OWLClass v = (OWLClass) ((OWLObjectSomeValuesFrom) sup)
                        .getFiller();
                if (p.getIRI().toString()
                        .equals("http://purl.obolibrary.org/obo/BFO_0000051")
                        && v.getIRI()
                                .toString()
                                .equals("http://purl.obolibrary.org/obo/GO_0004055")) {
                    ok = true;
                }
            }
        }
        assertTrue(ok);
        scas = ontology.getAxioms(AxiomType.SUBCLASS_OF);
        ok = false;
        for (OWLSubClassOfAxiom sca : scas) {
            OWLClassExpression sup = sca.getSuperClass();
            if (sup instanceof OWLObjectSomeValuesFrom) {
                OWLObjectProperty p = (OWLObjectProperty) ((OWLObjectSomeValuesFrom) sup)

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Examples of org.semanticweb.owlapi.model.OWLOntology

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


    @Test
    public void testConvertXPs() {
        OWLOntology owlOnt = convertOBOFile("xptest.obo");
        assertNotNull(owlOnt);
    }

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Examples of org.semanticweb.owlapi.model.OWLOntology

        return roundTripOBODoc(obodoc, isExpectRoundtrip);
    }


    public List<Diff> roundTripOBODoc(@Nonnull OBODoc obodoc,
            boolean isExpectRoundtrip) throws Exception {
        OWLOntology oo = convert(obodoc);
        OBODoc obodoc2 = convert(oo);
        obodoc2.check();
        writeOBO(obodoc2);
        List<Diff> diffs = OBODocDiffer.getDiffs(obodoc, obodoc2);
        if (isExpectRoundtrip) {

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Examples of org.semanticweb.owlapi.model.OWLOntology

        return diffs;
    }


    public boolean roundTripOWLFile(String fn, boolean isExpectRoundtrip)
            throws IOException, OWLOntologyCreationException {
        OWLOntology oo = parseOWLFile(fn);
        return roundTripOWLOOntology(oo, isExpectRoundtrip);
    }

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Examples of org.semanticweb.owlapi.model.OWLOntology

        OWLAPIOwl2Obo bridge = new OWLAPIOwl2Obo(
                OWLManager.createOWLOntologyManager());
        OBODoc obodoc = bridge.convert(oo);
        writeOBO(obodoc);
        obodoc.check();
        OWLOntology oo2 = convert(obodoc);
        writeOWL(oo2);
        boolean ok = compareOWLOntologiesPartial(oo, oo2, isExpectRoundtrip,
                bridge.getUntranslatableAxioms());
        return ok || !isExpectRoundtrip;
    }

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Examples of org.semanticweb.owlapi.model.OWLOntology

    }


    @Test
    public void shouldContainExpectedAnnotation() {
        OBODoc oboFile = parseOBOFile(file);
        OWLOntology o = convert(oboFile);
        IRI expected = IRI
                .create("http://purl.obolibrary.org/obo/GO_0042062%3A");
        assertEquals(18, o.getAnnotationAssertionAxioms(expected).size());
    }

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Examples of org.semanticweb.owlapi.model.OWLOntology


    @Test(expected = OWLOntologyRenameException.class)
    public void testRenameToExistingOntology()
            throws OWLOntologyCreationException {
        IRI ontologyAIRI = IRI("http://www.semanticweb.org/ontologies/ontologyA");
        OWLOntology onto = m.createOntology(ontologyAIRI);
        m.addAxiom(onto,
                df.getOWLDeclarationAxiom(Class(IRI("urn:test:testclass"))));
        IRI ontologyBIRI = IRI("http://www.semanticweb.org/ontologies/ontologyB");
        OWLOntology ontologyB = m.createOntology(ontologyBIRI);
        m.applyChange(new SetOntologyID(ontologyB, new OWLOntologyID(
                of(ontologyAIRI), absent())));
    }

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Examples of org.semanticweb.owlapi.model.OWLOntology

        // it is expected that only one implementation of
        // OWLOntologyManagerFactory will be available, but if there is more
        // than one, no harm done
        try {
            for (OWLOntologyManagerFactory f : ontologyManagerFactories) {
                OWLOntology ontology = f.get()
                        .loadOntologyFromOntologyDocument(source);
                new RioRenderer(ontology, getRDFHandler(), getRDFFormat()
                        .getOWLFormat()).render();
                return;
            }

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Examples of org.semanticweb.owlapi.model.OWLOntology


    @Test
    public void testrun() throws Exception {
        OWLOntologyManager m = OWLManager.createOWLOntologyManager();
        m.getIRIMappers().add(new AutoIRIMapper(new File("."), false));
        OWLOntology o = m.loadOntologyFromOntologyDocument(getClass()
                .getResourceAsStream("/pizza.owl"));
        m.addAxiom(o, DF.getOWLDeclarationAxiom(DF.getOWLClass(iri)));
        m.addAxiom(
                o,
                DF.getOWLSubClassOfAxiom(c,
                        DF.getOWLClass(string, prefixmanager)));
        m.addAxiom(o, DF.getOWLEquivalentClassesAxiom(DF.getOWLClass(iri), c));
        m.addAxiom(o, DF.getOWLDisjointClassesAxiom(DF.getOWLClass(iri), c));
        m.addAxiom(o, DF.getOWLSubObjectPropertyOfAxiom(op, op));
        m.addAxiom(o, DF.getOWLSubPropertyChainOfAxiom(
                listowlobjectpropertyexpression, op));
        m.addAxiom(o, DF.getOWLEquivalentObjectPropertiesAxiom(setop));
        m.addAxiom(o, DF.getOWLDisjointObjectPropertiesAxiom(setop));
        m.addAxiom(o, DF.getOWLInverseObjectPropertiesAxiom(op, op));
        m.addAxiom(o, DF.getOWLObjectPropertyDomainAxiom(op, c));
        m.addAxiom(o, DF.getOWLObjectPropertyRangeAxiom(op, c));
        m.addAxiom(o, DF.getOWLFunctionalObjectPropertyAxiom(op));
        m.addAxiom(o,
                DF.getOWLAnnotationAssertionAxiom(ap, as, owlannotationvalue));
        m.applyChange(new AddImport(o, DF.getOWLImportsDeclaration(iri)));
        m.addAxiom(o, DF.getOWLAnnotationPropertyDomainAxiom(ap, iri));
        m.addAxiom(o, DF.getOWLAnnotationPropertyRangeAxiom(ap, iri));
        m.addAxiom(o, DF.getOWLSubAnnotationPropertyOfAxiom(ap, ap));
        m.addAxiom(o, DF.getOWLInverseFunctionalObjectPropertyAxiom(op));
        m.addAxiom(o, DF.getOWLReflexiveObjectPropertyAxiom(op));
        m.addAxiom(o, DF.getOWLIrreflexiveObjectPropertyAxiom(op));
        m.addAxiom(o, DF.getOWLSymmetricObjectPropertyAxiom(op));
        m.addAxiom(o, DF.getOWLAsymmetricObjectPropertyAxiom(op));
        m.addAxiom(o, DF.getOWLTransitiveObjectPropertyAxiom(op));
        m.addAxiom(o, DF.getOWLSubDataPropertyOfAxiom(dp, dp));
        m.addAxiom(o, DF.getOWLEquivalentDataPropertiesAxiom(setdp));
        m.addAxiom(o, DF.getOWLDisjointDataPropertiesAxiom(setdp));
        m.addAxiom(o, DF.getOWLDataPropertyDomainAxiom(dp, c));
        m.addAxiom(o, DF.getOWLDataPropertyRangeAxiom(dp, dr));
        m.addAxiom(o, DF.getOWLFunctionalDataPropertyAxiom(dp));
        m.addAxiom(o, DF.getOWLHasKeyAxiom(c, setowlpropertyexpression));
        m.addAxiom(o, DF.getOWLDatatypeDefinitionAxiom(owldatatype, dr));
        m.addAxiom(o, DF.getOWLSameIndividualAxiom(setowlindividual));
        m.addAxiom(o, DF.getOWLDifferentIndividualsAxiom(setowlindividual));
        m.addAxiom(o, DF.getOWLClassAssertionAxiom(c, ai));
        m.addAxiom(o, DF.getOWLObjectPropertyAssertionAxiom(op, ai, ai));
        m.addAxiom(o, DF.getOWLNegativeObjectPropertyAssertionAxiom(op, ai, ai));
        m.addAxiom(o, DF.getOWLDataPropertyAssertionAxiom(dp, ai, owlliteral));
        m.addAxiom(o,
                DF.getOWLNegativeDataPropertyAssertionAxiom(dp, ai, owlliteral));
        m.addAxiom(
                o,
                DF.getOWLInverseObjectPropertiesAxiom(op,
                        DF.getOWLObjectInverseOf(op)));
        m.addAxiom(
                o,
                DF.getOWLSubClassOfAxiom(c,
                        DF.getOWLDataExactCardinality(1, dp)));
        m.addAxiom(o,
                DF.getOWLSubClassOfAxiom(c, DF.getOWLDataMaxCardinality(1, dp)));
        m.addAxiom(o,
                DF.getOWLSubClassOfAxiom(c, DF.getOWLDataMinCardinality(1, dp)));
        m.addAxiom(
                o,
                DF.getOWLSubClassOfAxiom(c,
                        DF.getOWLObjectExactCardinality(1, op)));
        m.addAxiom(
                o,
                DF.getOWLSubClassOfAxiom(c,
                        DF.getOWLObjectMaxCardinality(1, op)));
        m.addAxiom(
                o,
                DF.getOWLSubClassOfAxiom(c,
                        DF.getOWLObjectMinCardinality(1, op)));
        m.addAxiom(
                o,
                DF.getOWLDataPropertyRangeAxiom(dp,
                        DF.getOWLDatatype(string, prefixmanager)));
        m.addAxiom(
                o,
                DF.getOWLDataPropertyAssertionAxiom(dp, ai,
                        DF.getOWLLiteral(string, owldatatype)));
        m.addAxiom(
                o,
                DF.getOWLDataPropertyRangeAxiom(dp,
                        DF.getOWLDataOneOf(owlliteral)));
        m.addAxiom(o,
                DF.getOWLDataPropertyRangeAxiom(dp, DF.getOWLDataUnionOf(dr)));
        m.addAxiom(
                o,
                DF.getOWLDataPropertyRangeAxiom(dp,
                        DF.getOWLDataIntersectionOf(dr)));
        m.addAxiom(o,
                DF.getOWLDataPropertyRangeAxiom(dp, DF
                        .getOWLDatatypeRestriction(owldatatype, owlfacet,
                                owlliteral)));
        m.addAxiom(
                o,
                DF.getOWLDataPropertyRangeAxiom(
                        dp,
                        DF.getOWLDatatypeRestriction(owldatatype,
                                DF.getOWLFacetRestriction(owlfacet, 1))));
        m.addAxiom(
                o,
                DF.getOWLSubClassOfAxiom(
                        c,
                        DF.getOWLObjectIntersectionOf(c,
                                DF.getOWLClass(string, prefixmanager))));
        m.addAxiom(o, DF.getOWLSubClassOfAxiom(c,
                DF.getOWLDataSomeValuesFrom(dp, dr)));
        m.addAxiom(o,
                DF.getOWLSubClassOfAxiom(c, DF.getOWLDataAllValuesFrom(dp, dr)));
        m.addAxiom(
                o,
                DF.getOWLSubClassOfAxiom(c,
                        DF.getOWLDataHasValue(dp, owlliteral)));
        m.addAxiom(
                o,
                DF.getOWLSubClassOfAxiom(c,
                        DF.getOWLObjectComplementOf(DF.getOWLClass(iri))));
        m.addAxiom(
                o,
                DF.getOWLSubClassOfAxiom(c,
                        DF.getOWLObjectOneOf(DF.getOWLNamedIndividual(iri))));
        m.addAxiom(o, DF.getOWLSubClassOfAxiom(c,
                DF.getOWLObjectAllValuesFrom(op, c)));
        m.addAxiom(
                o,
                DF.getOWLSubClassOfAxiom(c,
                        DF.getOWLObjectSomeValuesFrom(op, c)));
        m.addAxiom(o,
                DF.getOWLSubClassOfAxiom(c, DF.getOWLObjectHasValue(op, ai)));
        m.addAxiom(
                o,
                DF.getOWLSubClassOfAxiom(c,
                        DF.getOWLObjectUnionOf(DF.getOWLClass(iri))));
        m.addAxiom(
                o,
                DF.getOWLAnnotationAssertionAxiom(iri,
                        DF.getOWLAnnotation(ap, owlannotationvalue)));
        m.addAxiom(o, DF.getOWLAnnotationAssertionAxiom(DF
                .getOWLNamedIndividual(iri).getIRI(), DF.getOWLAnnotation(ap,
                owlannotationvalue)));
        ByteArrayOutputStream out = new ByteArrayOutputStream();
        ObjectOutputStream stream = new ObjectOutputStream(out);
        stream.writeObject(m);
        stream.flush();
        // System.out.println(out.toString());
        ByteArrayInputStream in = new ByteArrayInputStream(out.toByteArray());
        ObjectInputStream inStream = new ObjectInputStream(in);
        OWLOntologyManager copy = (OWLOntologyManager) inStream.readObject();
        for (OWLOntology onto : copy.getOntologies()) {
            OWLOntology original = m.getOntology(onto.getOntologyID()
                    .getOntologyIRI().get());
            assertEquals("Troubles with ontology " + onto.getOntologyID(),
                    original.getAxioms(), onto.getAxioms());
        }
    }

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Examples of org.semanticweb.owlapi.model.OWLOntology

    }


    /** @return current ontology from walker */
    @Nonnull
    public OWLOntology getCurrentOntology() {
        OWLOntology ontology = walker.getOntology();
        if (ontology == null) {
            throw new OWLRuntimeException(
                    "No current ontology; is the walker being used outside of an ontology visit?");
        }
        return ontology;

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