Examples with SimpleIRIMapper org.semanticweb.owlapi.util.SimpleIRIMapper used on opensource projects

Example 1 with SimpleIRIMapper

use of org.semanticweb.owlapi.util.SimpleIRIMapper in project goci by EBISPOT.

the class AbstractOntologyLoader method doInitialization.

@Override
protected void doInitialization() throws Exception {
    // init owl fields
    this.manager = OWLManager.createOWLOntologyManager();
    if (getOntologyResource() != null) {
        getLog().info("Mapping ontology IRI from " + getOntologyURI() + " to " + getOntologyResource().getURI());
        this.manager.addIRIMapper(new SimpleIRIMapper(IRI.create(getOntologyURI()), IRI.create(getOntologyResource().getURI())));
    }
    if (getOntologyImportMappings() != null) {
        for (IRI from : getOntologyImportMappings().keySet()) {
            IRI to = getOntologyImportMappings().get(from);
            getLog().info("Mapping imported ontology IRI from " + from + " to " + to);
            this.manager.addIRIMapper(new SimpleIRIMapper(from, to));
        }
    }
    this.factory = manager.getOWLDataFactory();
    // init cache fields
    this.ontologyAccessions = new HashMap<>();
    this.ontologyLabels = new HashMap<>();
    this.ontologyParentLabels = new HashMap<>();
    this.ontologyChildLabels = new HashMap<>();
    this.ontologySynonyms = new HashMap<>();
    this.ontologyRelationships = new HashMap<>();
    // init other fields (label, synonym annotation properties)
    this.rdfsLabelAnnotationProperty = getFactory().getOWLAnnotationProperty(OWLRDFVocabulary.RDFS_LABEL.getIRI());
    this.synonymAnnotationProperties = getSynonymURIs().stream().map(ap -> getFactory().getOWLAnnotationProperty(IRI.create(ap))).collect(Collectors.toSet());
    // load the ontology
    this.ontology = loadOntology();
}

Example 2 with SimpleIRIMapper

use of org.semanticweb.owlapi.util.SimpleIRIMapper 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 3 with SimpleIRIMapper

use of org.semanticweb.owlapi.util.SimpleIRIMapper in project webprotege by protegeproject.

the class ProjectDocumentStore method createFreshProjectOntology.

private OWLOntology createFreshProjectOntology(OWLOntologyManager manager) throws OWLOntologyCreationException, OWLOntologyStorageException {
    logger.info("Creating a fresh project with an Id of {}", projectId);
    File parentDirectory = rootOntologyDocument.getParentFile();
    parentDirectory.mkdirs();
    IRI ontologyIRI = createUniqueOntologyIRI();
    IRI documentIRI = IRI.create(rootOntologyDocument);
    SimpleIRIMapper mapper = new SimpleIRIMapper(ontologyIRI, documentIRI);
    manager.addIRIMapper(mapper);
    OWLOntology ontology = manager.createOntology(ontologyIRI);
    manager.removeIRIMapper(mapper);
    writeNewProject(manager, ontology);
    return ontology;
}