OntModel autoOntology = ModelFactory.createOntologyModel( OntModelSpec.OWL_MEM ); String ns = Namespaces.KARMA; autoOntology.setNsPrefix("karma", ns); OntClass topClass = autoOntology.createClass( ns + worksheet.getTitle().replaceAll(" ", "_")); // replace blank spaces with undrscore for (HNode hNode : sortedLeafHNodes){
public void convert(EntrySet entrySet, String format, Writer writer) { if (format.startsWith("BioPAX")) { BioPAXLevel biopaxLevel; if (format.equals(RdfFormat.BIOPAX_L2.getName())) { biopaxLevel = BioPAXLevel.L2; } else { biopaxLevel = BioPAXLevel.L3; } try { convertToBioPAXAndFixURIs(entrySet, biopaxLevel, writer); } catch (IOException e) { throw new RuntimeException("Problem converting EntrySet to BioPAX", e); } } else { final String baseUri = "http://org.hupo.psi.mi"; OntModel jenaModel = convertToJena(entrySet); final RDFWriter rdfWriter = jenaModel.getWriter(format); rdfWriter.setProperty("xmlbase", baseUri); jenaModel.setNsPrefix("", baseUri); rdfWriter.write(jenaModel, writer, baseUri); } try { writer.flush(); } catch (IOException e) { throw new RuntimeException("Problem flushing writer", e); } }
public static Model toNIF(ComplexProof proof, Evidence evidence, Triple triple) { OntModel model = ModelFactory.createOntologyModel(); model.setNsPrefix("nif", "http://persistence.uni-leipzig.org/nlp2rdf/ontologies/nif-core#"); model.setNsPrefix("prov", PROV_NAMESPACE); WebSite webSite = proof.getWebSite(); String contextString = proof.getProofPhrase(); String text = webSite.getText(); // nif int start = webSite.getText().indexOf(contextString); int end = start + contextString.length(); Individual contextIndividual = nifConverter.createContextIndividual(DEFACTO_NAMESPACE, text, new ContextHashBasedString(), model); Individual cStringIndividual = nifConverter.createCStringIndividual(DEFACTO_NAMESPACE, contextIndividual, new Span(start, end), new ContextHashBasedString(), model); ObjectProperty sourceURL = NIFObjectProperties.sourceUrl.getObjectProperty(model); contextIndividual.addProperty(sourceURL, webSite.getUrl()); // prov model.add(ProvenanceInformationGenerator.generateProvenanceInformation(webSite, triple.getSubject().toString(), triple.getPredicate().toString(), triple.getObject().toString())); return model; }