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

Example 1 with OWLNamedIndividual

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

the class KBLoader method quantifyKnowledgeBase.

public Map<IRI, Integer> quantifyKnowledgeBase(URL efoLocation, URL gwasSchemaLocation, URL kbLocation) throws OWLOntologyCreationException, URISyntaxException {
    Map<IRI, Integer> results = new HashMap<IRI, Integer>();
    OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
    // do iri mapping
    URI efoURI = efoLocation.toURI();
    URI gwasSchemaURI = gwasSchemaLocation.toURI();
    URI kbURI = kbLocation.toURI();
    getLog().info("Mapping EFO to " + efoURI);
    manager.addIRIMapper(new SimpleIRIMapper(IRI.create(OntologyConstants.EFO_ONTOLOGY_SCHEMA_IRI), IRI.create(efoURI)));
    getLog().info("Mapping GWAS schema to " + gwasSchemaURI);
    manager.addIRIMapper(new SimpleIRIMapper(IRI.create(OntologyConstants.GWAS_ONTOLOGY_SCHEMA_IRI), IRI.create(gwasSchemaURI)));
    System.out.println("Loading knowledge base " + kbURI);
    getLog().info("Loading knowledge base " + kbURI);
    // load the knowledgebase
    OWLOntology kb = manager.loadOntology(IRI.create(kbURI));
    System.out.println("Processing knowledge base");
    getLog().info("Processing knowledge base");
    // retrieve all individuals
    Set<OWLNamedIndividual> inds = kb.getIndividualsInSignature();
    System.out.println("The knowledge base contains " + inds.size() + " individuals");
    getLog().info("The knowledge base contains " + inds.size() + " individuals");
    for (OWLNamedIndividual ind : inds) {
        // for each individual, check if it is an association
        boolean isAssociation = false;
        Set<OWLClassExpression> types = ind.getTypes(kb);
        for (OWLClassExpression type : types) {
            if (type.asOWLClass().getIRI().toString().equals(OntologyConstants.TRAIT_ASSOCIATION_CLASS_IRI)) {
                isAssociation = true;
                break;
            }
        }
        if (isAssociation) {
            // get the IRI of the trait class (from EFO) this individual is associated with
            Set<IRI> traitClasses = getTraitClass(kb, ind);
            for (IRI traitClass : traitClasses) {
                // skip SNPs
                if (traitClass.toString().equals(OntologyConstants.SNP_CLASS_IRI)) {
                    continue;
                }
                // increment count
                if (results.containsKey(traitClass)) {
                    int count = results.get(traitClass) + 1;
                    results.put(traitClass, count);
                } else {
                    results.put(traitClass, 1);
                }
            }
        }
    }
    return results;
}

Example 2 with OWLNamedIndividual

use of org.semanticweb.owlapi.model.OWLNamedIndividual 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 3 with OWLNamedIndividual

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

the class DefaultGWASOWLConverter method convertSNP.

protected void convertSNP(SingleNucleotidePolymorphism snp, OWLOntology ontology) {
    // 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 4 with OWLNamedIndividual

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

the class SessionManagerResource method listSessions.

@GET
@Produces(value = { RDF_XML, OWL_XML, TURTLE, X_TURTLE, FUNCTIONAL_OWL, MANCHESTER_OWL, RDF_JSON, N3, N_TRIPLE, TEXT_PLAIN })
public Response listSessions(@Context UriInfo uriInfo, @Context HttpHeaders headers) {
    OWLOntologyManager ontMgr = OWLManager.createOWLOntologyManager();
    OWLDataFactory df = ontMgr.getOWLDataFactory();
    OWLClass cSession = df.getOWLClass(IRI.create("http://stanbol.apache.org/ontologies/meta/Session"));
    OWLOntology o;
    try {
        o = ontMgr.createOntology(IRI.create(uriInfo.getRequestUri()));
        List<OWLOntologyChange> changes = new ArrayList<OWLOntologyChange>();
        for (String id : sessionManager.getRegisteredSessionIDs()) {
            IRI sessionid = IRI.create(sessionManager.getDefaultNamespace() + sessionManager.getID() + "/" + id);
            OWLNamedIndividual ind = df.getOWLNamedIndividual(sessionid);
            changes.add(new AddAxiom(o, df.getOWLClassAssertionAxiom(cSession, ind)));
        }
        ontMgr.applyChanges(changes);
    } catch (OWLOntologyCreationException e) {
        throw new WebApplicationException(e, INTERNAL_SERVER_ERROR);
    }
    ResponseBuilder rb = Response.ok(o);
    MediaType mediaType = MediaTypeUtil.getAcceptableMediaType(headers, null);
    if (mediaType != null)
        rb.header(HttpHeaders.CONTENT_TYPE, mediaType);
    //        addCORSOrigin(servletContext, rb, headers);
    return rb.build();
}

Example 5 with OWLNamedIndividual

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

the class TestOWLAPIInputSources method testOfflineImport.

/**
     * Uses a {@link ParentPathInputSource} to load an ontology importing a modified FOAF, both located in the
     * same resource directory.
     * 
     * @throws Exception
     */
@Test
public void testOfflineImport() throws Exception {
    URL url = getClass().getResource("/ontologies/maincharacters.owl");
    assertNotNull(url);
    File f = new File(url.toURI());
    assertNotNull(f);
    OntologyInputSource<OWLOntology> coreSource = new ParentPathInputSource(f);
    // // Check that all the imports closure is made of local files
    // Set<OWLOntology> closure = coreSource.getImports(true);
    // for (OWLOntology o : closure)
    // assertEquals("file", o.getOWLOntologyManager().getOntologyDocumentIRI(o).getScheme());
    assertEquals(coreSource.getRootOntology().getOntologyID().getOntologyIRI(), IRI.create(Constants.PEANUTS_MAIN_BASE));
    // Linus is stated to be a foaf:Person
    OWLNamedIndividual iLinus = df.getOWLNamedIndividual(IRI.create(Constants.PEANUTS_MAIN_BASE + "#Linus"));
    // Lucy is stated to be a foaf:Perzon
    OWLNamedIndividual iLucy = df.getOWLNamedIndividual(IRI.create(Constants.PEANUTS_MAIN_BASE + "#Lucy"));
    OWLClass cPerzon = df.getOWLClass(IRI.create("http://xmlns.com/foaf/0.1/Perzon"));
    Set<OWLIndividual> instances = cPerzon.getIndividuals(coreSource.getRootOntology());
    assertTrue(!instances.contains(iLinus) && instances.contains(iLucy));
}