Examples of OWLAxiom

org.semanticweb.owl.model.OWLAxiom
Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group Date: 24-Oct-2006 An OWL ontology contains a set of axioms. These axioms can be annotation axioms, declaration axioms, imports axioms or logical axioms
org.semanticweb.owlapi.model.OWLAxiom
3.org/TR/owl2-syntax/#Axioms">Axioms in the OWL 2 Specification.
An OWL ontology contains a set of axioms. These axioms can be annotation axioms, declaration axioms, imports axioms or logical axioms @author Matthew Horridge, The University Of Manchester, Bio-HealthInformatics Group @since 2.0.0

Examples of org.semanticweb.owl.model.OWLAxiom

        URI objectTripleObject = getConsumer().getResourceObject(subject, OWLRDFVocabulary.OWL_OBJECT.getURI(), true);
        if(objectTripleObject == null) {
            // Perhaps a legacy mapping
            objectTripleObject = getConsumer().getResourceObject(subject, OWLRDFVocabulary.RDF_OBJECT.getURI(), true);
        }
        OWLAxiom ax = null;
        if (objectTripleObject != null) {
            ax = handleAxiomTriples(subjectTripleObject, predicateTripleObject, objectTripleObject);
        }
        else {
            OWLConstant con = getConsumer().getLiteralObject(subject, OWLRDFVocabulary.RDF_OBJECT.getURI(), true);

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Examples of org.semanticweb.owlapi.model.OWLAxiom

            OWLAnnotationProperty p = trAnnotationProp(id);
            add(fac.getOWLDeclarationAxiom(p));
            // handle xrefs also for meta data tags
            String xid = translateShorthandIdToExpandedId(id);
            if (!id.equals(xid)) {
                OWLAxiom ax = fac.getOWLAnnotationAssertionAxiom(
                        trTagToAnnotationProp("shorthand"), p.getIRI(),
                        trLiteral(id), new HashSet<OWLAnnotation>());
                add(ax);
            }
            typedefToAnnotationProperty.put(p.getIRI().toString(), p);

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Examples of org.semanticweb.owlapi.model.OWLAxiom

            String id = typedefFrame.getId();
            OWLObjectProperty p = trObjectProp(id);
            add(fac.getOWLDeclarationAxiom(p));
            String xid = translateShorthandIdToExpandedId(id);
            if (!xid.equals(id)) {
                OWLAxiom ax = fac.getOWLAnnotationAssertionAxiom(
                        trTagToAnnotationProp("shorthand"), p.getIRI(),
                        trLiteral(id), new HashSet<OWLAnnotation>());
                add(ax);
            }
            /*
             * // See 5.9.3 Special Rules for Relations Collection<Xref> xrefs =
             * typedefFrame.getTagValues(OboFormatTag.TAG_XREF, Xref.class);
             * String xrefStr = null; for (Xref xref: xrefs) { if (xref != null)
             * { String xid = xref.getIdref(); if ((xid.startsWith("RO") ||
             * xid.startsWith("BFO")) && !xid.equals(id)) { // RO and BFO have
             * special status. // avoid cycles (in case of self-xref) //
             * fac.getOWLAnnotationAssertionAxiom(prop, p.getIRI(),
             * trLiteral(id), new HashSet<>()); OWLAxiom ax =
             * fac.getOWLAnnotationAssertionAxiom(
             * trTagToAnnotationProp("shorthand"), p.getIRI(), trLiteral(id),
             * new HashSet<>()); add(ax); // return
             * oboIdToIRI(xid); } } }
             */
            for (String tag : typedefFrame.getTags()) {
                Collection<Clause> clauses = typedefFrame.getClauses(tag);
                OboFormatTag tagConstant = OBOFormatConstants.getTag(tag);
                if (tagConstant == OboFormatTag.TAG_INTERSECTION_OF) {
                    OWLAxiom axiom = trRelationIntersectionOf(id, p, clauses);
                    if (axiom != null) {
                        add(axiom);
                    }
                } else if (tagConstant == OboFormatTag.TAG_UNION_OF) {
                    OWLAxiom axiom = trRelationUnionOf(id, p, clauses);
                    if (axiom != null) {
                        add(axiom);
                    }
                } else {
                    for (Clause clause : clauses) {

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Examples of org.semanticweb.owlapi.model.OWLAxiom

            String gciFiller = getQVString("gci_filler", qvs);
            OWLClassExpression r = trRel(gciRel, gciFiller,
                    new HashSet<QualifierValue>());
            clsx = fac.getOWLObjectIntersectionOf(cls, r);
        }
        OWLAxiom ax;
        if (tagConstant == OboFormatTag.TAG_IS_A) {
            ax = fac.getOWLSubClassOfAxiom(clsx,
                    trClass((String) clause.getValue()), annotations);
        } else if (tagConstant == OboFormatTag.TAG_RELATIONSHIP) {
            // TODO

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Examples of org.semanticweb.owlapi.model.OWLAxiom

     */
    @SuppressWarnings("null")
    @Nullable
    protected OWLAxiom trTypedefClause(@Nonnull OWLObjectProperty p,
            String tag, @Nonnull Clause clause) {
        OWLAxiom ax = null;
        Object v = clause.getValue();
        Set<OWLAnnotation> annotations = trAnnotations(clause);
        OboFormatTag tagConstant = OBOFormatConstants.getTag(tag);
        if (tagConstant == OboFormatTag.TAG_IS_A) {
            ax = fac.getOWLSubObjectPropertyOfAxiom(p,

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Examples of org.semanticweb.owlapi.model.OWLAxiom

            @Nonnull String tag, @Nonnull Clause clause) {
        Set<OWLAnnotation> annotations = trAnnotations(clause);
        if (clause.getValue() == null) {
            LOG.error("Problem: {}", clause);
        }
        OWLAxiom ax = null;
        OboFormatTag tagConstant = OBOFormatConstants.getTag(tag);
        // System.out.println("CLAUSE: "+clause+" // TAG="+_tag);
        if (tagConstant == OboFormatTag.TAG_NAME) {
            ax = fac.getOWLAnnotationAssertionAxiom(trTagToAnnotationProp(tag),
                    sub, trLiteral(clause.getValue()), annotations);

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Examples of org.semanticweb.owlapi.model.OWLAxiom

        }
        return iri;
    }


    void parse() {
        OWLAxiom ax;
        label_1: while (true) {
            if (jj_2_1(2)) {} else {
                break label_1;
            }
            ax = TBoxStatement();

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Examples of org.semanticweb.owlapi.model.OWLAxiom

        }
        jj_consume_token(0);
    }


    private OWLAxiom TBoxStatement() {
        OWLAxiom ax;
        if (jj_2_5(2)) {
            ax = DefinePrimitiveConcept();
        } else if (jj_2_6(2)) {
            ax = DefineConcept();
        } else if (jj_2_7(2)) {

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Examples of org.semanticweb.owlapi.model.OWLAxiom

        iri = Name();
        return dataFactory.getOWLObjectProperty(iri);
    }


    private OWLAxiom ABoxStatement() {
        OWLAxiom ax;
        if (jj_2_21(2)) {
            ax = Instance();
        } else if (jj_2_22(2)) {
            ax = Related();
        } else if (jj_2_23(2)) {

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Examples of org.semanticweb.owlapi.model.OWLAxiom

                    .build();
        }
        Set<OWLOntology> ontologies = getOntologies();
        Set<OWLAnnotation> annotations = parseAnnotations();
        Set<OWLPropertyExpression> properties = parsePropertyList();
        OWLAxiom propertyAxiom;
        if (properties.iterator().next().isObjectPropertyExpression()) {
            Set<OWLObjectPropertyExpression> ope = new HashSet<>();
            for (OWLPropertyExpression pe : properties) {
                ope.add((OWLObjectPropertyExpression) pe);
            }

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