Examples with OWLAnnotationAssertionAxiom org.semanticweb.owlapi.model.OWLAnnotationAssertionAxiom used on opensource projects

Example 1 with OWLAnnotationAssertionAxiom

use of org.semanticweb.owlapi.model.OWLAnnotationAssertionAxiom in project goci by EBISPOT.

the class DefaultGWASOWLConverter method convertAssociation.

protected void convertAssociation(Association association, OWLOntology ontology, Set<String> issuedWarnings) {
    // get the trait association class
    OWLClass taClass = getDataFactory().getOWLClass(IRI.create(OntologyConstants.TRAIT_ASSOCIATION_CLASS_IRI));
    IRI taIndIRI = getMinter().mint(OntologyConstants.GWAS_ONTOLOGY_BASE_IRI, association);
    // create a new trait association instance
    OWLNamedIndividual taIndiv = getDataFactory().getOWLNamedIndividual(taIndIRI);
    // assert class membership
    OWLClassAssertionAxiom classAssertion = getDataFactory().getOWLClassAssertionAxiom(taClass, taIndiv);
    getManager().addAxiom(ontology, classAssertion);
    // get datatype relations
    OWLDataProperty has_p_value = getDataFactory().getOWLDataProperty(IRI.create(OntologyConstants.HAS_P_VALUE_PROPERTY_IRI));
    // get annotation relations
    OWLAnnotationProperty rdfsLabel = getDataFactory().getOWLAnnotationProperty(OWLRDFVocabulary.RDFS_LABEL.getIRI());
    // pvalue but says it was less then 10-6. So if we have no pvalue we just don't add it.
    if (association.getPvalueMantissa() != null && association.getPvalueExponent() != null) {
        double pval = association.getPvalueMantissa() * Math.pow(10, association.getPvalueExponent());
        OWLLiteral pValue = getDataFactory().getOWLLiteral(pval);
        // OWLLiteral pValue = getDataFactory().getOWLLiteral(association.getPvalueMantissa()+"e"+association.getPvalueExponent());
        OWLDataPropertyAssertionAxiom p_value_relation = getDataFactory().getOWLDataPropertyAssertionAxiom(has_p_value, taIndiv, pValue);
        AddAxiom add_p_value = new AddAxiom(ontology, p_value_relation);
        getManager().applyChange(add_p_value);
    }
    // get the snp instance for this association
    OWLNamedIndividual snpIndiv;
    String rsId = null;
    for (Locus locus : association.getLoci()) {
        for (RiskAllele riskAllele : locus.getStrongestRiskAlleles()) {
            SingleNucleotidePolymorphism snp = riskAllele.getSnp();
            rsId = snp.getRsId();
            snpIndiv = getDataFactory().getOWLNamedIndividual(getMinter().mint(OntologyConstants.GWAS_ONTOLOGY_BASE_IRI, snp));
            if (snpIndiv == null) {
                String warning = "A new SNP with the given RSID only will be created";
                if (!issuedWarnings.contains(warning)) {
                    getLog().warn(warning);
                    issuedWarnings.add(warning);
                }
                snpIndiv = getDataFactory().getOWLNamedIndividual(getMinter().mint(OntologyConstants.GWAS_ONTOLOGY_BASE_IRI, "SingleNucleotidePolymorphism", snp.getRsId(), true));
                // assert class membership
                OWLClass snpClass = getDataFactory().getOWLClass(IRI.create(OntologyConstants.SNP_CLASS_IRI));
                OWLClassAssertionAxiom snpClassAssertion = getDataFactory().getOWLClassAssertionAxiom(snpClass, snpIndiv);
                getManager().addAxiom(ontology, snpClassAssertion);
                // assert rsid relation
                OWLDataProperty has_snp_rsid = getDataFactory().getOWLDataProperty(IRI.create(OntologyConstants.HAS_SNP_REFERENCE_ID_PROPERTY_IRI));
                OWLLiteral rsid = getDataFactory().getOWLLiteral(snp.getRsId());
                OWLDataPropertyAssertionAxiom rsid_relation = getDataFactory().getOWLDataPropertyAssertionAxiom(has_snp_rsid, snpIndiv, rsid);
                AddAxiom add_rsid = new AddAxiom(ontology, rsid_relation);
                getManager().applyChange(add_rsid);
                // assert label
                OWLAnnotationAssertionAxiom snp_label_annotation = getDataFactory().getOWLAnnotationAssertionAxiom(rdfsLabel, snpIndiv.getIRI(), rsid);
                AddAxiom add_snp_label = new AddAxiom(ontology, snp_label_annotation);
                getManager().applyChange(add_snp_label);
            }
            // get object properties
            OWLObjectProperty has_subject = getDataFactory().getOWLObjectProperty(IRI.create(OntologyConstants.HAS_SUBJECT_IRI));
            OWLObjectProperty is_subject_of = getDataFactory().getOWLObjectProperty(IRI.create(OntologyConstants.IS_SUBJECT_OF_IRI));
            // assert relations
            OWLObjectPropertyAssertionAxiom has_subject_snp_relation = getDataFactory().getOWLObjectPropertyAssertionAxiom(has_subject, taIndiv, snpIndiv);
            AddAxiom add_has_subject_snp = new AddAxiom(ontology, has_subject_snp_relation);
            getManager().applyChange(add_has_subject_snp);
            OWLObjectPropertyAssertionAxiom is_subject_of_snp_relation = getDataFactory().getOWLObjectPropertyAssertionAxiom(is_subject_of, snpIndiv, taIndiv);
            AddAxiom add_is_subject_of_snp = new AddAxiom(ontology, is_subject_of_snp_relation);
            getManager().applyChange(add_is_subject_of_snp);
        }
        // get the EFO class for the trait
        for (EfoTrait efoTrait : association.getEfoTraits()) {
            OWLClass traitClass;
            traitClass = getDataFactory().getOWLClass(IRI.create(efoTrait.getUri()));
            if (traitClass == null) {
                String warning = "This trait will be mapped to Experimental Factor";
                if (!issuedWarnings.contains(warning)) {
                    getLog().warn(warning);
                    issuedWarnings.add(warning);
                }
                traitClass = getDataFactory().getOWLClass(IRI.create(OntologyConstants.EXPERIMENTAL_FACTOR_CLASS_IRI));
            }
            // create a new trait instance (puns the class)
            IRI traitIRI = traitClass.getIRI();
            OWLNamedIndividual traitIndiv = getDataFactory().getOWLNamedIndividual(traitIRI);
            if (ontology.containsIndividualInSignature(traitIRI)) {
                getLog().trace("Trait individual '" + traitIRI.toString() + "' (type: " + traitClass + ") already exists");
            } else {
                getLog().trace("Creating trait individual '" + traitIRI.toString() + "' (type: " + traitClass + ")");
            }
            // and also add the gwas label to the individual so we don't lose curated data
            OWLDataProperty has_gwas_trait_name = getDataFactory().getOWLDataProperty(IRI.create(OntologyConstants.HAS_GWAS_TRAIT_NAME_PROPERTY_IRI));
            OWLLiteral gwasTrait = getDataFactory().getOWLLiteral(association.getStudy().getDiseaseTrait().getTrait());
            OWLDataPropertyAssertionAxiom gwas_trait_relation = getDataFactory().getOWLDataPropertyAssertionAxiom(has_gwas_trait_name, taIndiv, gwasTrait);
            AddAxiom add_gwas_trait_name = new AddAxiom(ontology, gwas_trait_relation);
            getManager().applyChange(add_gwas_trait_name);
            // assert class membership
            OWLClassAssertionAxiom traitClassAssertion = getDataFactory().getOWLClassAssertionAxiom(traitClass, traitIndiv);
            getManager().addAxiom(ontology, traitClassAssertion);
            // get object properties
            OWLObjectProperty has_object = getDataFactory().getOWLObjectProperty(IRI.create(OntologyConstants.HAS_OBJECT_IRI));
            OWLObjectProperty is_object_of = getDataFactory().getOWLObjectProperty(IRI.create(OntologyConstants.IS_OBJECT_OF_IRI));
            // assert relations
            OWLObjectPropertyAssertionAxiom has_object_trait_relation = getDataFactory().getOWLObjectPropertyAssertionAxiom(has_object, taIndiv, traitIndiv);
            AddAxiom add_has_object_trait = new AddAxiom(ontology, has_object_trait_relation);
            getManager().applyChange(add_has_object_trait);
            OWLObjectPropertyAssertionAxiom is_object_of_trait_relation = getDataFactory().getOWLObjectPropertyAssertionAxiom(is_object_of, traitIndiv, taIndiv);
            AddAxiom add_is_object_of_trait = new AddAxiom(ontology, is_object_of_trait_relation);
            getManager().applyChange(add_is_object_of_trait);
        }
        // finally, assert label for this association
        OWLLiteral label = getDataFactory().getOWLLiteral("Association between " + rsId + " and " + association.getStudy().getDiseaseTrait().getTrait());
        OWLAnnotationAssertionAxiom label_annotation = getDataFactory().getOWLAnnotationAssertionAxiom(rdfsLabel, taIndiv.getIRI(), label);
        AddAxiom add_band_label = new AddAxiom(ontology, label_annotation);
        getManager().applyChange(add_band_label);
    }
}

Example 2 with OWLAnnotationAssertionAxiom

use of org.semanticweb.owlapi.model.OWLAnnotationAssertionAxiom in project goci by EBISPOT.

the class DefaultGWASOWLConverter method convertSNP.

protected void convertSNP(SingleNucleotidePolymorphism snp, OWLOntology ontology) {
    log.debug("converting snp: " + snp.getId() + ", rsid: " + snp.getRsId());
    // get the snp class
    OWLClass snpClass = getDataFactory().getOWLClass(IRI.create(OntologyConstants.SNP_CLASS_IRI));
    // create a new snp instance
    OWLNamedIndividual snpIndiv = getDataFactory().getOWLNamedIndividual(getMinter().mint(OntologyConstants.GWAS_ONTOLOGY_BASE_IRI, snp));
    // assert class membership
    OWLClassAssertionAxiom classAssertion = getDataFactory().getOWLClassAssertionAxiom(snpClass, snpIndiv);
    getManager().addAxiom(ontology, classAssertion);
    // add datatype properties...
    // get datatype relations
    OWLDataProperty has_snp_rsid = getDataFactory().getOWLDataProperty(IRI.create(OntologyConstants.HAS_SNP_REFERENCE_ID_PROPERTY_IRI));
    OWLDataProperty has_bp_pos = getDataFactory().getOWLDataProperty(IRI.create(OntologyConstants.HAS_BP_POSITION_PROPERTY_IRI));
    // get annotation relations
    OWLAnnotationProperty rdfsLabel = getDataFactory().getOWLAnnotationProperty(OWLRDFVocabulary.RDFS_LABEL.getIRI());
    // assert rsid relation
    OWLLiteral rsid = getDataFactory().getOWLLiteral(snp.getRsId());
    OWLDataPropertyAssertionAxiom rsid_relation = getDataFactory().getOWLDataPropertyAssertionAxiom(has_snp_rsid, snpIndiv, rsid);
    AddAxiom add_rsid = new AddAxiom(ontology, rsid_relation);
    getManager().applyChange(add_rsid);
    // assert bp_pos relation
    if (snp.getLocations() != null) {
        for (Location snpLocation : snp.getLocations()) {
            if (snpLocation.getChromosomePosition() != null) {
                OWLLiteral bp_pos = // getDataFactory().getOWLLiteral(snpLocation.getChromosomePosition(), OWL2Datatype.XSD_INT);
                getDataFactory().getOWLLiteral(snpLocation.getChromosomePosition());
                OWLDataPropertyAssertionAxiom bp_pos_relation = getDataFactory().getOWLDataPropertyAssertionAxiom(has_bp_pos, snpIndiv, bp_pos);
                AddAxiom add_bp_pos = new AddAxiom(ontology, bp_pos_relation);
                getManager().applyChange(add_bp_pos);
            }
        }
    } else {
        getLog().debug("No SNP location available for SNP " + rsid);
    }
    // assert label
    OWLAnnotationAssertionAxiom snp_label_annotation = getDataFactory().getOWLAnnotationAssertionAxiom(rdfsLabel, snpIndiv.getIRI(), rsid);
    AddAxiom add_snp_label = new AddAxiom(ontology, snp_label_annotation);
    getManager().applyChange(add_snp_label);
    // get the band class
    OWLClass bandClass = getDataFactory().getOWLClass(IRI.create(OntologyConstants.CYTOGENIC_REGION_CLASS_IRI));
    // get datatype relations
    OWLDataProperty has_name = getDataFactory().getOWLDataProperty(IRI.create(OntologyConstants.HAS_NAME_PROPERTY_IRI));
    // get object relations
    OWLObjectProperty located_in = getDataFactory().getOWLObjectProperty(IRI.create(OntologyConstants.LOCATED_IN_PROPERTY_IRI));
    OWLObjectProperty location_of = getDataFactory().getOWLObjectProperty(IRI.create(OntologyConstants.LOCATION_OF_PROPERTY_IRI));
    // get datatype relations
    OWLDataProperty has_chr_name = getDataFactory().getOWLDataProperty(IRI.create(OntologyConstants.HAS_NAME_PROPERTY_IRI));
    // get object properties
    OWLObjectProperty has_part = getDataFactory().getOWLObjectProperty(IRI.create(OntologyConstants.HAS_PART_PROPERTY_IRI));
    OWLObjectProperty part_of = getDataFactory().getOWLObjectProperty(IRI.create(OntologyConstants.PART_OF_PROPERTY_IRI));
    for (Location location : snp.getLocations()) {
        Region region = location.getRegion();
        if (region.getName() != null) {
            // create a new band individual
            OWLNamedIndividual bandIndiv = getDataFactory().getOWLNamedIndividual(getMinter().mint(OntologyConstants.GWAS_ONTOLOGY_BASE_IRI, "CytogeneticRegion", region.getName()));
            // assert class membership
            OWLClassAssertionAxiom bandClassAssertion = getDataFactory().getOWLClassAssertionAxiom(bandClass, bandIndiv);
            getManager().addAxiom(ontology, bandClassAssertion);
            // assert name relation
            OWLLiteral name = getDataFactory().getOWLLiteral(region.getName());
            OWLDataPropertyAssertionAxiom name_relation = getDataFactory().getOWLDataPropertyAssertionAxiom(has_name, bandIndiv, name);
            AddAxiom add_name = new AddAxiom(ontology, name_relation);
            getManager().applyChange(add_name);
            // assert label
            OWLAnnotationAssertionAxiom band_label_annotation = getDataFactory().getOWLAnnotationAssertionAxiom(rdfsLabel, bandIndiv.getIRI(), name);
            AddAxiom add_band_label = new AddAxiom(ontology, band_label_annotation);
            getManager().applyChange(add_band_label);
            // assert located_in relation
            OWLObjectPropertyAssertionAxiom located_in_relation = getDataFactory().getOWLObjectPropertyAssertionAxiom(located_in, snpIndiv, bandIndiv);
            AddAxiom add_located_in = new AddAxiom(ontology, located_in_relation);
            getManager().applyChange(add_located_in);
            // assert location_of relation
            OWLObjectPropertyAssertionAxiom location_of_relation = getDataFactory().getOWLObjectPropertyAssertionAxiom(location_of, bandIndiv, snpIndiv);
            AddAxiom add_location_of = new AddAxiom(ontology, location_of_relation);
            getManager().applyChange(add_location_of);
            // get the appropriate chromosome class given the chromosome name
            OWLClass chrClass = getDataFactory().getOWLClass(IRI.create(OntologyConstants.CHROMOSOME_CLASS_IRI));
            // create a new chromosome individual
            // If a snp has a chromosome name, create the chromosome individual if it doesn't have one (ex : the snp is
            // no mapped any more) then just don't create it.
            String chromName = location.getChromosomeName();
            if (chromName != null) {
                OWLNamedIndividual chrIndiv = getDataFactory().getOWLNamedIndividual(getMinter().mint(OntologyConstants.GWAS_ONTOLOGY_BASE_IRI, "Chromosome", chromName));
                OWLClassAssertionAxiom chrClassAssertion = getDataFactory().getOWLClassAssertionAxiom(chrClass, chrIndiv);
                getManager().addAxiom(ontology, chrClassAssertion);
                // assert chr_name relation
                OWLLiteral chr_name = getDataFactory().getOWLLiteral(chromName);
                OWLDataPropertyAssertionAxiom chr_name_relation = getDataFactory().getOWLDataPropertyAssertionAxiom(has_chr_name, chrIndiv, chr_name);
                AddAxiom add_chr_name = new AddAxiom(ontology, chr_name_relation);
                getManager().applyChange(add_chr_name);
                // assert label
                OWLLiteral chr_label = getDataFactory().getOWLLiteral("Chromosome " + chromName);
                OWLAnnotationAssertionAxiom chr_label_annotation = getDataFactory().getOWLAnnotationAssertionAxiom(rdfsLabel, chrIndiv.getIRI(), chr_label);
                AddAxiom add_chr_label = new AddAxiom(ontology, chr_label_annotation);
                getManager().applyChange(add_chr_label);
                // assert has_part relation
                OWLObjectPropertyAssertionAxiom has_part_relation = getDataFactory().getOWLObjectPropertyAssertionAxiom(has_part, chrIndiv, bandIndiv);
                AddAxiom add_has_part = new AddAxiom(ontology, has_part_relation);
                getManager().applyChange(add_has_part);
                // assert part_of relation
                OWLObjectPropertyAssertionAxiom part_of_relation = getDataFactory().getOWLObjectPropertyAssertionAxiom(part_of, bandIndiv, chrIndiv);
                AddAxiom add_part_of = new AddAxiom(ontology, part_of_relation);
                getManager().applyChange(add_part_of);
            }
        } else {
            getLog().trace("No known region for location on chromosomse " + location.getChromosomeName());
        }
    }
}

Example 3 with OWLAnnotationAssertionAxiom

use of org.semanticweb.owlapi.model.OWLAnnotationAssertionAxiom in project stanbol by apache.

the class RegistryManagerImpl method createModel.

@Override
public Set<Registry> createModel(Set<OWLOntology> registryOntologies) {
    Set<Registry> results = new HashSet<Registry>();
    // Reset population
    population.clear();
    // Build the transitive imports closure of the union.
    Set<OWLOntology> closure = new HashSet<OWLOntology>();
    for (OWLOntology rego : registryOntologies) closure.addAll(rego.getOWLOntologyManager().getImportsClosure(rego));
    /*
         * For each value in this map, index 0 is the score of the library class, while 1 is the score of the
         * ontology class.
         */
    final Map<IRI, int[]> candidateTypes = new HashMap<IRI, int[]>();
    /*
         * Scans class assertions and object property values and tries to determine the type of each
         * individual it finds.
         */
    OWLAxiomVisitor scanner = new OWLAxiomVisitorAdapter() {

        /*
             * For a given identifier, returns the array of integers whose value determine the likelihood if
             * the corresponding entity being a library or an ontology. If no such array exists, it is
             * created.
             */
        private int[] checkScores(IRI key) {
            int[] scores;
            if (candidateTypes.containsKey(key))
                scores = candidateTypes.get(key);
            else {
                scores = new int[] { 0, 0 };
                candidateTypes.put(key, scores);
            }
            return scores;
        }

        @Override
        public void visit(OWLAnnotationAssertionAxiom axiom) {
            /*
                 * Works like object property assertions, in case hasOntology and isOntologyOf are not
                 * detected to be object properties (e.g. due to a failure to load codolight or the registry
                 * metamodel).
                 */
            OWLAnnotationProperty prop = axiom.getProperty();
            if (hasOntologyAnn.equals(prop)) {
                IRI iri;
                // The axiom subject gets a +1 in its library score.
                OWLObject ind = axiom.getSubject();
                if (ind instanceof IRI) {
                    iri = (IRI) ind;
                    checkScores(iri)[0]++;
                }
                // The axiom object gets a +1 in its ontology score.
                ind = axiom.getValue();
                if (ind instanceof IRI) {
                    iri = (IRI) ind;
                    checkScores(iri)[1]++;
                }
            } else if (isOntologyOfAnn.equals(prop)) {
                IRI iri;
                // The axiom subject gets a +1 in its ontology score.
                OWLObject ind = axiom.getSubject();
                if (ind instanceof IRI) {
                    iri = (IRI) ind;
                    checkScores(iri)[1]++;
                }
                // The axiom object gets a +1 in its library score.
                ind = axiom.getValue();
                if (ind instanceof IRI) {
                    iri = (IRI) ind;
                    checkScores(iri)[0]++;
                }
            }
        }

        @Override
        public void visit(OWLClassAssertionAxiom axiom) {
            OWLIndividual ind = axiom.getIndividual();
            // Do not accept anonymous registry items.
            if (ind.isAnonymous())
                return;
            IRI iri = ind.asOWLNamedIndividual().getIRI();
            int[] scores = checkScores(iri);
            OWLClassExpression type = axiom.getClassExpression();
            // If the type is stated to be a library, increase its library score.
            if (cRegistryLibrary.equals(type)) {
                scores[0]++;
            } else // If the type is stated to be an ontology, increase its ontology score.
            if (cOntology.equals(type)) {
                scores[1]++;
            }
        }

        @Override
        public void visit(OWLObjectPropertyAssertionAxiom axiom) {
            OWLObjectPropertyExpression prop = axiom.getProperty();
            if (hasOntology.equals(prop)) {
                IRI iri;
                // The axiom subject gets a +1 in its library score.
                OWLIndividual ind = axiom.getSubject();
                if (!ind.isAnonymous()) {
                    iri = ind.asOWLNamedIndividual().getIRI();
                    checkScores(iri)[0]++;
                }
                // The axiom object gets a +1 in its ontology score.
                ind = axiom.getObject();
                if (!ind.isAnonymous()) {
                    iri = ind.asOWLNamedIndividual().getIRI();
                    checkScores(iri)[1]++;
                }
            } else if (isOntologyOf.equals(prop)) {
                IRI iri;
                // The axiom subject gets a +1 in its ontology score.
                OWLIndividual ind = axiom.getSubject();
                if (!ind.isAnonymous()) {
                    iri = ind.asOWLNamedIndividual().getIRI();
                    checkScores(iri)[1]++;
                }
                // The axiom object gets a +1 in its library score.
                ind = axiom.getObject();
                if (!ind.isAnonymous()) {
                    iri = ind.asOWLNamedIndividual().getIRI();
                    checkScores(iri)[0]++;
                }
            }
        }
    };
    // First pass to determine the types.
    for (OWLOntology o : closure) for (OWLAxiom ax : o.getAxioms()) ax.accept(scanner);
    // Then populate on the registry
    OWLDataFactory df = OWLManager.getOWLDataFactory();
    for (IRI iri : candidateTypes.keySet()) {
        int[] scores = candidateTypes.get(iri);
        if (scores != null && (scores[0] > 0 || scores[1] > 0)) {
            if (scores[0] > 0 && scores[1] == 0)
                population.put(iri, riFactory.createLibrary(df.getOWLNamedIndividual(iri)));
            else if (scores[0] == 0 && scores[1] > 0)
                population.put(iri, riFactory.createRegistryOntology(df.getOWLNamedIndividual(iri)));
        }
    // else log.warn("Unable to determine type for registry item {}", iri);
    }
    for (OWLOntology oReg : registryOntologies) {
        try {
            results.add(populateRegistry(oReg));
        } catch (RegistryContentException e) {
            log.error("An error occurred while populating an ontology registry.", e);
        }
    }
    return results;
}

Example 4 with OWLAnnotationAssertionAxiom

use of org.semanticweb.owlapi.model.OWLAnnotationAssertionAxiom in project stanbol by apache.

the class RegistryManagerImpl method populateOntology.

protected RegistryOntology populateOntology(OWLNamedObject ind, Set<OWLOntology> registries) throws RegistryContentException {
    IRI ontId = ind.getIRI();
    RegistryItem ront = null;
    if (population.containsKey(ontId)) {
        // We are not allowing multityping either.
        ront = population.get(ontId);
        if (!(ront instanceof RegistryOntology))
            throw new RegistryContentException("Inconsistent multityping: for item " + ontId + " : {" + RegistryOntology.class + ", " + ront.getClass() + "}");
    } else {
        ront = riFactory.createRegistryOntology(ind);
        try {
            population.put(ront.getIRI(), ront);
        } catch (Exception e) {
            log.error("Invalid identifier for library item " + ront, e);
            return null;
        }
    }
    // EXIT nodes.
    Set<OWLNamedObject> libs = new HashSet<OWLNamedObject>();
    OWLDataFactory df = OWLManager.getOWLDataFactory();
    for (OWLOntology o : registries) {
        if (ind instanceof OWLIndividual) {
            // Get usages of isOntologyOf as an object property
            for (OWLIndividual value : ((OWLIndividual) ind).getObjectPropertyValues(isOntologyOf, o)) if (value.isNamed())
                libs.add(value.asOWLNamedIndividual());
            // Get usages of isOntologyOf as an annotation property
            for (OWLAnnotationAssertionAxiom ann : o.getAnnotationAssertionAxioms(ind.getIRI())) if (isOntologyOfAnn.equals(ann.getProperty())) {
                OWLAnnotationValue value = ann.getValue();
                if (value instanceof OWLNamedObject)
                    libs.add((OWLNamedObject) value);
                else if (value instanceof IRI)
                    libs.add(df.getOWLNamedIndividual((IRI) value));
            }
        }
    }
    for (OWLNamedObject ilib : libs) {
        IRI parentId = ilib.getIRI();
        // If some populate*() method has created it, it will be there.
        RegistryItem rlib = population.get(parentId);
        // Otherwise populating it will also put it in population.
        if (rlib == null)
            rlib = populateLibrary(ilib, registries);
        ront.addParent(rlib);
        if (ontologyIndex.get(ontId) == null)
            ontologyIndex.put(ontId, new HashSet<IRI>());
        ontologyIndex.get(ontId).add(parentId);
    }
    return (RegistryOntology) ront;
}

Example 5 with OWLAnnotationAssertionAxiom

use of org.semanticweb.owlapi.model.OWLAnnotationAssertionAxiom in project stanbol by apache.

the class ConversionTester method testAxiomOwlToJenaResource.

public void testAxiomOwlToJenaResource() {
    JenaToOwlConvert j2o = new JenaToOwlConvert();
    OWLOntologyManager mgr = OWLManager.createOWLOntologyManager();
    OWLOntology ont = null;
    try {
        ont = mgr.createOntology();
    } catch (OWLOntologyCreationException e) {
        e.printStackTrace();
        fail("Can not create ontology");
    }
    OWLDataFactory factory = mgr.getOWLDataFactory();
    StmtIterator resource = null;
    OWLClass cls = factory.getOWLClass(IRI.create(CLAZZ));
    OWLDataProperty dp = factory.getOWLDataProperty(IRI.create(DP));
    OWLObjectProperty op = factory.getOWLObjectProperty(IRI.create(OP));
    OWLAnnotationProperty oa = factory.getOWLAnnotationProperty(IRI.create(label));
    OWLAnnotation oav = factory.getOWLAnnotation(oa, factory.getOWLStringLiteral(clazzlabel, "en"));
    OWLDatatype dt = factory.getOWLDatatype(IRI.create(DATATYPE));
    OWLNamedIndividual sub = factory.getOWLNamedIndividual(IRI.create(SUBJECT));
    OWLNamedIndividual obj = factory.getOWLNamedIndividual(IRI.create(OBJECT));
    OWLLiteral literal1 = factory.getOWLTypedLiteral(VALUE, dt);
    // Classe
    OWLDeclarationAxiom daxiomcls = factory.getOWLDeclarationAxiom(cls);
    // obj prop
    OWLDeclarationAxiom daxiomop = factory.getOWLDeclarationAxiom(op);
    // data prop
    OWLDeclarationAxiom daxiomdp = factory.getOWLDeclarationAxiom(dp);
    // subject
    OWLDeclarationAxiom daxiomsub = factory.getOWLDeclarationAxiom(sub);
    // object
    OWLDeclarationAxiom daxiomobj = factory.getOWLDeclarationAxiom(obj);
    // Istanza
    OWLClassAssertionAxiom axiomsub = factory.getOWLClassAssertionAxiom(cls, sub);
    // Istanza
    OWLClassAssertionAxiom axiomobj = factory.getOWLClassAssertionAxiom(cls, obj);
    // Obj
    OWLObjectPropertyAssertionAxiom axiomop = factory.getOWLObjectPropertyAssertionAxiom(op, sub, obj);
    // prop
    // tra
    // individui
    OWLDataPropertyAssertionAxiom axiomvalue = factory.getOWLDataPropertyAssertionAxiom(dp, obj, // Dataprop all'istanza;
    literal1);
    // Annotazione
    OWLAnnotationAssertionAxiom axioman = factory.getOWLAnnotationAssertionAxiom(cls.getIRI(), oav);
    mgr.addAxiom(ont, daxiomcls);
    mgr.addAxiom(ont, daxiomop);
    mgr.addAxiom(ont, daxiomdp);
    mgr.addAxiom(ont, daxiomsub);
    mgr.addAxiom(ont, daxiomobj);
    mgr.addAxiom(ont, axiomsub);
    mgr.addAxiom(ont, axiomobj);
    mgr.addAxiom(ont, axiomop);
    mgr.addAxiom(ont, axiomvalue);
    mgr.addAxiom(ont, axioman);
    Set<OWLAxiom> setaxiom = ont.getAxioms();
    try {
        resource = j2o.AxiomOwlToJenaResource(setaxiom, RDFXML);
        if (resource == null) {
            fail("Some errors occur");
        } else {
            String statment = "[http://www.w3.org/2000/01/rdf-schema#label, http://www.w3.org/2000/01/rdf-schema#range, http://www.w3.org/2000/01/rdf-schema#Literal] " + "[http://example.org/dummy#hasAge, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://www.w3.org/2002/07/owl#DatatypeProperty] " + "[http://example.org/dummy#Linus, http://example.org/dummy#hasAge, \"8\"^^http://www.w3.org/2001/XMLSchema#int] " + "[http://example.org/dummy#Linus, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://example.org/dummy#Peanut] " + "[http://example.org/dummy#hasSibling, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://www.w3.org/2002/07/owl#ObjectProperty] " + "[http://example.org/dummy#Lucy, http://example.org/dummy#hasSibling, http://example.org/dummy#Linus] " + "[http://example.org/dummy#Lucy, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://example.org/dummy#Peanut] " + "[http://www.w3.org/2000/01/rdf-schema#label, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://www.w3.org/2002/07/owl#AnnotationProperty] " + "[http://example.org/dummy#Peanut, http://www.w3.org/2000/01/rdf-schema#label, \"Peanut\"@en] " + "[http://example.org/dummy#Peanut, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://www.w3.org/2002/07/owl#Class]";
            int size = setaxiom.size();
            int count = 0;
            while (resource.hasNext()) {
                Statement stm = resource.nextStatement();
                Resource jsubj = stm.getSubject();
                if (jsubj.getURI().equals(OP.toString()) || jsubj.getURI().equals(DP.toString()) || jsubj.getURI().equals(CLAZZ.toString()) || jsubj.getURI().equals(OBJECT.toString()) || jsubj.getURI().equals(SUBJECT.toString()) || jsubj.getURI().equals(label.toString()))
                    if (statment.contains(stm.toString()))
                        count++;
            }
            assertEquals(size, count);
        }
    } catch (Exception e) {
        e.printStackTrace();
        fail("Exception caugth");
    } finally {
        assertNotNull(resource);
    }
}