public static OWLOntology createOWLThingTypeDeclForIndividuals(OWLOntology ont) throws OWLOntologyCreationException, IOException { OWLOntology ret = ont.getOntologyID()!=null && ont.getOntologyID().getOntologyIRI()!=null? ont.getOWLOntologyManager().createOntology(ont.getOntologyID().getOntologyIRI()): ont.getOWLOntologyManager().createOntology(); OWLDataFactory fac = ret.getOWLOntologyManager().getOWLDataFactory(); OWLClass owlThing = ret.getOWLOntologyManager().getOWLDataFactory().getOWLThing(); for (OWLNamedIndividual ind: ont.getIndividualsInSignature()) { OWLNamedIndividual ni = fac.getOWLNamedIndividual(ind.getIRI()); OWLAxiom ax = fac.getOWLClassAssertionAxiom(owlThing, ni); ret.getOWLOntologyManager().addAxiom(ret, ax); } return ret; }
public static OWLOntology load(File... inputFiles) throws OWLOntologyCreationException { OWLOntologyManager manager= OWLManager.createOWLOntologyManager(); OWLOntology ont = manager.createOntology(); for (File f:inputFiles) { manager= OWLManager.createOWLOntologyManager(); manager.setSilentMissingImportsHandling(false); IRI documentIRI = IRI.create(f); OWLOntology ontology = manager.loadOntologyFromOntologyDocument(documentIRI); ont.getOWLOntologyManager().addAxioms(ont, ontology.getAxioms()); } return ont; }
private static synchronized void cacheOntology(URI physicalRemoteUri, File file, OWLOntology ont) throws UnknownOWLOntologyException, OWLOntologyStorageException { uris.put(physicalRemoteUri, file); oiri.put(physicalRemoteUri, ont.getOntologyID().getOntologyIRI()); manager.setOntologyDocumentIRI(ont, IRI.create(file)); manager.saveOntology(ont, new RDFXMLOntologyFormat(), IRI.create(file)); }
private void createDebuggingOntology() throws OWLException { if (debuggingOntology != null) { man.removeOntology(verifyNotNull(debuggingOntology)); } debuggingOntology = man.createOntology(debuggingAxioms); }
/** * Asserts that the individual has a particular OWL type. */ public void assertOwlType(OWLClassExpression type) { OWLOntologyManager manager = owlOntology.getOWLOntologyManager(); OWLDataFactory factory = manager.getOWLDataFactory(); manager.addAxiom(owlOntology, factory.getOWLClassAssertionAxiom(type, owlIndividual)); }
private void writeDeclarations(OWLEntity entity, Set<OWLAxiom> alreadyWrittenAxioms, Collection<IRI> illegals) { Collection<OWLDeclarationAxiom> axioms = asList(ont.declarationAxioms(entity).sorted()); axioms.stream().filter(alreadyWrittenAxioms::add).forEach(this::acceptAndReturn); // if multiple illegal declarations already exist, they have already // been outputted the renderer cannot take responsibility for removing // them. It should not add declarations for illegally punned entities // here, though if (addMissingDeclarations && axioms.isEmpty() && !entity.isBuiltIn() && !illegals.contains(entity.getIRI()) && !ont.isDeclared(entity, Imports.INCLUDED)) { OWLDeclarationAxiom declaration = ont.getOWLOntologyManager().getOWLDataFactory().getOWLDeclarationAxiom(entity); acceptAndReturn(declaration); } }
protected OWLReasonerBase(OWLOntology rootOntology, OWLReasonerConfiguration configuration, BufferingMode bufferingMode) { this.rootOntology = checkNotNull(rootOntology, "rootOntology cannot be null"); this.bufferingMode = checkNotNull(bufferingMode, "bufferingMode cannot be null"); this.configuration = checkNotNull(configuration, "configuration cannot be null"); timeOut = configuration.getTimeOut(); manager = rootOntology.getOWLOntologyManager(); manager.addOntologyChangeListener(this::handleRawOntologyChanges); reasonerAxioms = asUnorderedSet( rootOntology.importsClosure().flatMap(o -> Stream.concat(o.logicalAxioms(), o .axioms(AxiomType.DECLARATION))) .map(ax -> OWLAxiom.getAxiomWithoutAnnotations(ax))); }
public IncrementalClassifier(final OpenlletReasoner reasoner, final ModuleExtractor extractor) { _reasoner = reasoner; _extractor = extractor; final OWLOntology ontology = reasoner.getRootOntology(); ontology.importsClosure().map(OWLOntology::axioms).forEach(extractor::addAxioms); reasoner.getManager().addOntologyChangeListener(this); }
@Override public void visit(OWLObjectProperty property) { add(axioms, ontology.axioms(property).filter(this::threewayDisjointObject)); add(axioms, ontology.axioms(SUB_PROPERTY_CHAIN_OF) .filter(ax -> ax.getSuperProperty().equals(property))); OWLObjectInverseOf inverse = ontology.getOWLOntologyManager().getOWLDataFactory() .getOWLObjectInverseOf(property); add(axioms, ontology.axioms(inverse)); }
/** * Instantiates a new definition tracker. * * @param ontology ontology to track */ public DefinitionTracker(OWLOntology ontology) { this.ontology = checkNotNull(ontology, "ontology cannot be null"); ontology.importsClosure().flatMap(OWLOntology::axioms).forEach(this::addAxiom); ontology.getOWLOntologyManager().addOntologyChangeListener(this); }
private void modularityTest(final String file) { final OWLOntology ontology = OntologyUtils.loadOntology(_manager, "file:" + file, false); final Set<OWLEntity> signature = new HashSet<>(); signature.addAll(TestUtils.selectRandomElements(ontology.classesInSignature().collect(Collectors.toList()), 5)); modularityTest(ontology, signature); _manager.removeOntology(ontology); }
@SuppressWarnings("null") protected AbstractMacroExpansionVisitor(OWLOntology o) { df = o.getOWLOntologyManager().getOWLDataFactory(); expandExpressionMap = new HashMap<>(); expandAssertionToMap = new HashMap<>(); OWLAnnotationProperty ap424 = df.getOWLAnnotationProperty(IRI_IAO_0000424.getIRI()); o.objectPropertiesInSignature() .forEach(p -> getAnnotationObjects(p, o.importsClosure(), ap424).forEach( a -> mapToExpand(p, a))); o.annotationPropertiesInSignature().forEach(p -> expandAssertions(o, p)); OIO_ISEXPANSION = df.getOWLAnnotationProperty( IRI.create(Obo2OWLConstants.OIOVOCAB_IRI_PREFIX, "is_expansion")); expansionMarkerAnnotation = df.getOWLAnnotation(OIO_ISEXPANSION, df.getOWLLiteral(true)); }
private OWLOntologyManager mergeOntologiesInNewManager(final OWLOntologyManager manager) throws OWLOntologyCreationException { final OWLOntologyManager newManager = OWLManager.createOWLOntologyManager(); final OWLOntology merged = newManager.createOntology(); final List<OWLOntologyChange> changes = new ArrayList<>(); manager.ontologies().forEach(ontology -> ontology.axioms().forEach(ax -> changes.add(new AddAxiom(merged, ax)))); newManager.applyChanges(changes); return newManager; }
public void addImport(IOntology ontology) { if (!this.ontology.getImports().contains(((Ontology) ontology).ontology)) { OWLDataFactory factory = this.ontology.getOWLOntologyManager() .getOWLDataFactory(); OWLImportsDeclaration imp = factory.getOWLImportsDeclaration(IRI .create(((Ontology) ontology).ontology.getOntologyID() .getOntologyIRI().toString())); this.ontology.getOWLOntologyManager() .applyChange(new AddImport(this.ontology, imp)); this.imported.add(ontology.getConceptSpace()); } }
public OWLOntologyID getOntologyId() { OWLOntologyManager manager = OWLManager.createOWLOntologyManager(); try { OWLOntology ontology = manager.loadOntologyFromOntologyDocument(IRI.create(location)); return ontology.getOntologyID(); } catch (Throwable t) { log.info("Exception caught trying to get ontology id for " + location, t); return null; } }
public OntologyLoader(String ontologyName, File ontologyFile) throws OWLOntologyCreationException { this.ontologyFile = ontologyFile; this.manager = OWLManager.createOWLOntologyManager(); this.factory = manager.getOWLDataFactory(); this.ontologyName = ontologyName; this.ontology = manager.loadOntologyFromOntologyDocument(ontologyFile); this.ontologyIRI = ontology.getOntologyID().getOntologyIRI().toString(); }
private static void addVersion(OWLOntology ontology, String version, OWLOntologyManager manager){ OWLDataFactory fac = manager.getOWLDataFactory(); OWLAnnotationProperty ap = fac.getOWLAnnotationProperty( Obo2Owl.trTagToIRI(OboFormatTag.TAG_REMARK.getTag())); OWLAnnotation ann = fac.getOWLAnnotation(ap, fac.getOWLLiteral(version)); OWLAxiom ax = fac.getOWLAnnotationAssertionAxiom(ontology.getOntologyID().getOntologyIRI(), ann); manager.applyChange(new AddAxiom(ontology, ax)); } }
@Override public boolean addIndividual(Individual indvdl) { OWLIndividual oi; if(indvdl instanceof OWLAPIIndividual) { oi = ((OWLAPIIndividual)indvdl).indiv; } else { oi = dataFactory.getOWLNamedIndividual(IRI.create(indvdl.getURI())); } final List<OWLOntologyChange> changes = manager.addAxiom(onto, dataFactory.getOWLClassAssertionAxiom(dataFactory.getOWLClass(IRI.create(OWL+"Thing")),oi)); return !changes.isEmpty(); }
/*Load the ontology from a local file and do the initialisations*/ File inputfile = new File("ontologyPath"); OWLOntologyManager manager = OWLManager.createOWLOntologyManager(); ; OWLDataFactory dataFactory = manager.getOWLDataFactory(); OWLOntology yourOntology = manager.loadOntologyFromOntologyDocument(inputfile); IRI ontologyIRI = yourOntology.getOntologyID().getOntologyIRI(); /*Get an object property and its ranges*/ OWLObjectProperty o_p_about = dataFactory.getOWLObjectProperty(IRI.create(ontologyIRI + "#"+"about")); Set<OWLClassExpression> ranges_of_about = about.getRanges(LUCADAOntology);
public static void main(String[] args) throws Exception { String solrServerURL = "http://solr.aksw.org/en_dbpedia_resources/"; String searchField = "comment"; OWLOntology ontology = OWLManager.createOWLOntologyManager().loadOntologyFromOntologyDocument(new File("src/test/resources/org/dllearner/algorithms/isle/dbpedia_3.9.owl")); SolrSyntacticIndex index = new SolrSyntacticIndex(ontology, solrServerURL, searchField); index.loadCache(new File("entity_frequencies.obj")); OWLDataFactory df = new OWLDataFactoryImpl(); long n = index.getNumberOfDocumentsFor(df.getOWLClass(IRI.create("http://dbpedia.org/ontology/Comics"))); System.out.println(n); n = index.getNumberOfDocumentsFor(df.getOWLClass(IRI.create("http://dbpedia.org/ontology/Comics")), df.getOWLObjectProperty(IRI.create("http://dbpedia.org/ontology/largestCity"))); System.out.println(n); }