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

Example 56 with OWLOntology

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

the class GOCIDataPublisherDriver method publishAndSave.

public void publishAndSave(File assertedOntologyFile, File inferredOntologyFile) throws RuntimeException {
    try {
        // publishAndSave the data
        System.out.println("Attempting to convert and publish GWAS data as OWL...");
        OWLOntology ontology = getGwasOwlPublisher().publishGWASData();
        // and save the result
        System.out.print("Ontology converted, saving asserted results...");
        getGwasOwlPublisher().saveGWASData(ontology, assertedOntologyFile);
        System.out.println("..done!");
        if (inferredOntologyFile != null) {
            // now get the inferred view
            System.out.println("Evaluating inferred view...");
            OWLReasoner reasoner = getGwasOwlPublisher().publishGWASDataInferredView(ontology);
            // now save inferred view
            System.out.print("Ontology fully classified, saving inferred results...");
            getGwasOwlPublisher().saveGWASDataInferredView(reasoner, inferredOntologyFile);
            System.out.println("..done!");
        }
    } catch (OWLConversionException e) {
        System.err.println("Failed to publish data to OWL: " + e.getMessage());
        getLog().error("Failed to publish data to OWL: ", e);
        throw new RuntimeException(e);
    } catch (Exception e) {
        System.err.println("Failed to publish data to OWL (an unexpected exception occurred): " + e.getMessage());
        getLog().error("Failed to publish data to OWL (an unexpected exception occurred): ", e);
        throw new RuntimeException(e);
    }
}

Example 57 with OWLOntology

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

the class ReasonedOntologyLoader method indexOntology.

protected OWLOntology indexOntology(OWLOntology ontology) throws OWLOntologyCreationException {
    getLog().debug("Trying to create a reasoner over ontology '" + getOntologyURI() + "'");
    OWLReasonerFactory factory = new Reasoner.ReasonerFactory();
    ReasonerProgressMonitor progressMonitor = new LoggingReasonerProgressMonitor(getLog());
    OWLReasonerConfiguration config = new SimpleConfiguration(progressMonitor);
    this.reasoner = factory.createReasoner(ontology, config);
    getLog().debug("Precomputing inferences...");
    reasoner.precomputeInferences();
    getLog().debug("Checking ontology consistency...");
    reasoner.isConsistent();
    getLog().debug("Checking for unsatisfiable classes...");
    if (reasoner.getUnsatisfiableClasses().getEntitiesMinusBottom().size() > 0) {
        throw new OWLOntologyCreationException("Once classified, unsatisfiable classes were detected in '" + getOntologyIRI() + "'");
    } else {
        getLog().debug("Reasoning complete! ");
    }
    Set<OWLClass> allClasses = ontology.getClassesInSignature();
    removeExcludedClasses(ontology, allClasses, superclass -> reasoner.getSubClasses(superclass, false).getFlattened());
    int labelCount = 0;
    int labelledClassCount = 0;
    int synonymCount = 0;
    int synonymedClassCount = 0;
    getLog().debug("Loading " + allClasses.size() + " classes...");
    for (OWLClass ontologyClass : allClasses) {
        IRI clsIri = ontologyClass.getIRI();
        // get IRI fragment/path
        Optional<String> accession = evaluateAccessionValue(ontology, ontologyClass);
        if (accession.isPresent()) {
            addClassAccession(clsIri, accession.get());
        }
        // get label annotations
        Optional<String> label = evaluateLabelAnnotationValue(ontology, ontologyClass);
        if (label.isPresent()) {
            addClassLabel(clsIri, label.get());
            labelledClassCount++;
            labelCount++;
        }
        // get all synonym annotations
        getLog().trace("Loading synonyms of " + clsIri.toString() + "...");
        Set<String> synonyms = evaluateSynonymAnnotationValues(ontology, ontologyClass);
        if (!synonyms.isEmpty()) {
            addSynonyms(clsIri, synonyms);
            synonymCount += synonyms.size();
            synonymedClassCount++;
        }
        // get parent labels
        getLog().trace("Loading parents of " + clsIri.toString() + "...");
        Set<OWLClass> parents = reasoner.getSuperClasses(ontologyClass, false).getFlattened();
        // only add type if the parent isn't excluded
        Set<String> parentLabelSet = parents.stream().filter(allClasses::contains).peek(parent -> getLog().trace("Next parent of " + label + ": " + parent)).map(parent -> evaluateLabelAnnotationValue(ontology, parent)).filter(Optional::isPresent).map(Optional::get).collect(Collectors.toSet());
        // always also add current class to the parents
        label.ifPresent(parentLabelSet::add);
        addClassParentLabels(clsIri, parentLabelSet);
        // get child labels
        getLog().trace("Loading children of " + clsIri.toString() + "...");
        Set<OWLClass> children = reasoner.getSubClasses(ontologyClass, false).getFlattened();
        // only add type if the child isn't excluded
        Set<String> childLabelSet = children.stream().filter(allClasses::contains).peek(child -> getLog().trace("Next child of " + label + ": " + child)).map(child -> evaluateLabelAnnotationValue(ontology, child)).filter(Optional::isPresent).map(Optional::get).collect(Collectors.toSet());
        // always also add current class to the parents
        label.ifPresent(childLabelSet::add);
        addClassChildLabels(clsIri, childLabelSet);
    }
    getLog().debug("Successfully indexed " + labelCount + " labels on " + labelledClassCount + " classes and " + synonymCount + " synonyms on " + synonymedClassCount + " classes!");
    return ontology;
}

Example 58 with OWLOntology

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

the class OntologyService method populateClassMaps.

private void populateClassMaps() {
    OWLOntology ontology = ontologyLoader.getOntology();
    for (OWLClass owlClass : ontology.getClassesInSignature()) {
        // check this isn't an obsolete class
        if (!isObsolete(ontology, obsoleteClass, owlClass)) {
            // get class names, and enter them in the maps
            List<String> classNames = getClassNames(owlClass);
            classToLabelMap.put(owlClass, classNames);
            for (String name : getClassNames(owlClass)) {
                if (name != null) {
                    name = normalizeSearchString(name);
                    if (!labelToClassMap.containsKey(name)) {
                        labelToClassMap.put(name, new HashSet<OWLClass>());
                    }
                    labelToClassMap.get(name).add(owlClass);
                }
            }
            // get IRI, and enter it into the map
            iriToClassMap.put(owlClass.getIRI(), owlClass);
        }
    }
}

Example 59 with OWLOntology

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

the class ScopeSetRenderer method getScopes.

public static OWLOntology getScopes(Set<Scope> scopes) {
    OWLOntologyManager mgr = OWLManager.createOWLOntologyManager();
    OWLOntology ont = null;
    try {
        ont = mgr.createOntology();
    } catch (OWLOntologyCreationException e) {
        LoggerFactory.getLogger(ScopeSetRenderer.class).error("KReS :: could not create empty ontology for rendering scopes.", e);
        return null;
    }
    List<OWLOntologyChange> additions = new LinkedList<OWLOntologyChange>();
    // The ODP metadata vocabulary is always imported.
    // TODO : also import the ONM meta when it goes online.
    additions.add(new AddImport(ont, __factory.getOWLImportsDeclaration(IRI.create("http://www.ontologydesignpatterns.org/schemas/meta.owl"))));
    for (Scope scope : scopes) {
        OWLNamedIndividual iScope = __factory.getOWLNamedIndividual(IRI.create(scope.getDefaultNamespace() + scope.getID()));
        OWLAxiom ax = __factory.getOWLClassAssertionAxiom(cScope, iScope);
        additions.add(new AddAxiom(ont, ax));
    }
    mgr.applyChanges(additions);
    return ont;
}

Example 60 with OWLOntology

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

the class CustomSpaceImpl method getOntologyAsOWLOntology.

@Override
protected OWLOntology getOntologyAsOWLOntology(OWLOntologyID ontologyId, boolean merge, org.semanticweb.owlapi.model.IRI universalPrefix) {
    OWLOntology o = super.getOntologyAsOWLOntology(ontologyId, merge, universalPrefix);
    switch(getConnectivityPolicy()) {
        case LOOSE:
            break;
        case TIGHT:
            String s = getID();
            // strip "custom"
            s = s.substring(0, s.indexOf(SUFFIX));
            // concatenate "core"
            s += SpaceType.CORE.getIRISuffix();
            org.semanticweb.owlapi.model.IRI target = org.semanticweb.owlapi.model.IRI.create(universalPrefix + s);
            o.getOWLOntologyManager().applyChange(new AddImport(o, OWLManager.getOWLDataFactory().getOWLImportsDeclaration(target)));
            break;
        default:
            break;
    }
    return o;
}