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

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


    @Test
    public void testUntranslatableAxioms() throws Exception {
        OWLOntology original = parseOWLFile("untranslatable_axioms.owl");
        OWLAPIOwl2Obo owl2Obo = new OWLAPIOwl2Obo(
                OWLManager.createOWLOntologyManager());
        OBODoc obo = owl2Obo.convert(original);
        renderOboToString(obo);
        Frame headerFrame = obo.getHeaderFrame();
        String owlAxiomString = headerFrame.getTagValue(
                OboFormatTag.TAG_OWL_AXIOMS, String.class);
        assertNotNull(owlAxiomString);
        OWLAPIObo2Owl obo2Owl = new OWLAPIObo2Owl(
                OWLManager.createOWLOntologyManager());
        OWLOntology converted = obo2Owl.convert(obo);
        Set<OWLEquivalentClassesAxiom> originalEqAxioms = original
                .getAxioms(AxiomType.EQUIVALENT_CLASSES);
        Set<OWLEquivalentClassesAxiom> convertedEqAxioms = converted
                .getAxioms(AxiomType.EQUIVALENT_CLASSES);
        assertEquals(originalEqAxioms.size(), convertedEqAxioms.size());
        assertTrue(originalEqAxioms.containsAll(convertedEqAxioms));
        assertTrue(convertedEqAxioms.containsAll(originalEqAxioms));
    }

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Examples of org.semanticweb.owlapi.model.OWLOntology

        assertTrue(convertedEqAxioms.containsAll(originalEqAxioms));
    }


    @Test
    public void testUntranslatableAxioms2() throws Exception {
        OWLOntology original = parseOWLFile("untranslatable_axioms2.owl");
        OWLAPIOwl2Obo owl2Obo = new OWLAPIOwl2Obo(
                OWLManager.createOWLOntologyManager());
        OBODoc obo = owl2Obo.convert(original);
        renderOboToString(obo);
        Frame headerFrame = obo.getHeaderFrame();
        String owlAxiomString = headerFrame.getTagValue(
                OboFormatTag.TAG_OWL_AXIOMS, String.class);
        assertNotNull(owlAxiomString);
        OWLAPIObo2Owl obo2Owl = new OWLAPIObo2Owl(
                OWLManager.createOWLOntologyManager());
        OWLOntology converted = obo2Owl.convert(obo);
        Set<OWLEquivalentClassesAxiom> originalEqAxioms = original
                .getAxioms(AxiomType.EQUIVALENT_CLASSES);
        Set<OWLEquivalentClassesAxiom> convertedEqAxioms = converted
                .getAxioms(AxiomType.EQUIVALENT_CLASSES);
        assertEquals(originalEqAxioms.size(), convertedEqAxioms.size());
        assertTrue(originalEqAxioms.containsAll(convertedEqAxioms));
        assertTrue(convertedEqAxioms.containsAll(originalEqAxioms));
    }

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Examples of org.semanticweb.owlapi.model.OWLOntology

public class RoundTripOboAnnotations extends RoundTripTest {


    @Test
    public void testIsInferredAnnotation() throws Exception {
        OBODoc input = parseOBOFile("is_inferred_annotation.obo");
        OWLOntology owl = convert(input);
        // check round trip
        OBODoc output = convert(owl);
        String outObo = renderOboToString(output);
        assertEquals(readResource("is_inferred_annotation.obo"), outObo);
        // check owl
        IRI t1 = IRI.create("http://purl.obolibrary.org/obo/TEST_0001");
        IRI t3 = IRI.create("http://purl.obolibrary.org/obo/TEST_0003");
        IRI isInferredIRI = IRI.create(Obo2OWLConstants.OIOVOCAB_IRI_PREFIX,
                "is_inferred");
        boolean hasAnnotation = false;
        Set<OWLSubClassOfAxiom> axioms = owl.getAxioms(AxiomType.SUBCLASS_OF);
        for (OWLSubClassOfAxiom axiom : axioms) {
            OWLClassExpression superClassCE = axiom.getSuperClass();
            OWLClassExpression subClassCE = axiom.getSubClass();
            if (!superClassCE.isAnonymous() && !subClassCE.isAnonymous()) {
                OWLClass superClass = (OWLClass) superClassCE;

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Examples of org.semanticweb.owlapi.model.OWLOntology

@SuppressWarnings("javadoc")
public class Obo2OwlTest extends OboFormatTestBasics {


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

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Examples of org.semanticweb.owlapi.model.OWLOntology

        assertNotNull(owlOnt);
    }


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

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Examples of org.semanticweb.owlapi.model.OWLOntology

    }


    @Test
    public void testWriteReadConvertedOWL() throws Exception {
        OBODoc oboDoc = parseOBOFile("namespace-id-rule.obo");
        OWLOntology owlOntology = convert(oboDoc);
        OWLOntologyManager manager = owlOntology.getOWLOntologyManager();
        StringDocumentTarget documentTarget = new StringDocumentTarget();
        manager.saveOntology(owlOntology, new OWLXMLDocumentFormat(),
                documentTarget);
        String owlString = documentTarget.toString();
        OWLOntologyDocumentSource documentSource = new StringDocumentSource(
                owlString);
        OWLOntology reloadedOwl = OWLManager.createOWLOntologyManager()
                .loadOntologyFromOntologyDocument(documentSource);
        assertEquals(owlOntology.getAxiomCount(), reloadedOwl.getAxiomCount());
    }

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Examples of org.semanticweb.owlapi.model.OWLOntology

public class TransitiveOverTest extends RoundTripTest {


    @Test
    public void testConvert() {
        // PARSE TEST FILE, CONVERT TO OWL
        OWLOntology ontology = convert(parseOBOFile("relation_shorthand_test.obo"));
        // TEST CONTENTS OF OWL ONTOLOGY
        IRI regulatesIRI = getIriByLabel(ontology, "regulates");
        assertNotNull(regulatesIRI);
        boolean ok = false;
        // test that transitive over is translated to a property chain
        Set<OWLSubPropertyChainOfAxiom> axioms = ontology
                .getAxioms(AxiomType.SUB_PROPERTY_CHAIN_OF);
        for (OWLSubPropertyChainOfAxiom axiom : axioms) {
            OWLObjectProperty p = (OWLObjectProperty) axiom.getSuperProperty();
            if (regulatesIRI.equals(p.getIRI())) {
                List<OWLObjectPropertyExpression> chain = axiom

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Examples of org.semanticweb.owlapi.model.OWLOntology

    @Test
    public void testConvert() throws Exception {
        OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
        String input = "Prefix(:=<http://www.example.org/#>)\nOntology(<http://example.org/>\nSubClassOf(:a :b) )";
        StringDocumentSource source = new StringDocumentSource(input);
        OWLOntology origOnt = manager.loadOntologyFromOntologyDocument(source);
        assertNotNull(origOnt);
        assertEquals(1, manager.getOntologies().size());
        assertFalse(origOnt.getOntologyID().getVersionIRI().isPresent());
        assertTrue(origOnt.getAxiomCount() > 0);
        Optional<IRI> ontologyIRI = origOnt.getOntologyID().getOntologyIRI();
        assertTrue(ontologyIRI.isPresent());
        OWLOntology newOnt = manager.getOntology(ontologyIRI.get());
        assertNotNull(newOnt);
    }

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Examples of org.semanticweb.owlapi.model.OWLOntology

                        "Sequential hermaphroditic organism that produces\ngametes first of the male sex, and then later of the\nfemale sex."));
        oboDocSource.addTermFrame(sourceFrame);
        // convert to OWL and retrieve def
        OWLAPIObo2Owl bridge = new OWLAPIObo2Owl(
                OWLManager.createOWLOntologyManager());
        OWLOntology owlOntology = bridge.convert(oboDocSource);
        OWLDataFactory factory = owlOntology.getOWLOntologyManager()
                .getOWLDataFactory();
        // IRI
        IRI iri = bridge.oboIdToIRI("CARO:0000049");
        OWLClass c = factory.getOWLClass(iri);
        // Def
        OWLAnnotationProperty defProperty = factory
                .getOWLAnnotationProperty(Obo2OWLVocabulary.IRI_IAO_0000115
                        .getIRI());
        int counter = 0;
        for (OWLAnnotationAssertionAxiom ax : owlOntology
                .getAnnotationAssertionAxioms(c.getIRI())) {
            if (ax.getProperty().equals(defProperty)) {
                counter++;
                assertTrue(ax.getValue() instanceof OWLLiteral);
                String owlDef = ((OWLLiteral) ax.getValue()).getLiteral();

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Examples of org.semanticweb.owlapi.model.OWLOntology

public class GCIQualifierTest extends OboFormatTestBasics {


    @Test
    public void testConvert() {
        // PARSE TEST FILE, CONVERT TO OWL, AND WRITE TO OWL FILE
        OWLOntology ontology = convert(parseOBOFile("gci_qualifier_test.obo"));
        Set<OWLSubClassOfAxiom> scas = ontology
                .getAxioms(AxiomType.SUBCLASS_OF);
        boolean ok = !scas.isEmpty();
        assertTrue(ok);
        // CONVERT BACK TO OBO
        OBODoc obodoc = convert(ontology);

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