Java RDFXMLDocumentFormat类代码示例

import org.semanticweb.owlapi.formats.RDFXMLDocumentFormat; //导入依赖的package包/类
@UITopiaVariant(
  author = "onprom team",
  affiliation = "Free University of Bozen-Bolzano",
  email = "[email protected]",
  website = "http://onprom.inf.unibz.it"
)
@PluginVariant(requiredParameterLabels = {0, 1})
public void export(PluginContext context, OWLOntology ontology, File file) {
  try {
    //default format is RDF/XML format for the ontology
    RDFDocumentFormat format = new RDFXMLDocumentFormat();
    //save the given ontology using the format to the file
    OWLManager.createOWLOntologyManager().saveOntology(ontology, format, new FileOutputStream(file));
    context.log("Exported ontology to the file: " + file.getName());
  } catch (Exception e) {
    context.log("Couldn't export ontology to the file: " + file.getName() + " ->" + e.getMessage());
  }
}
 

import org.semanticweb.owlapi.formats.RDFXMLDocumentFormat; //导入依赖的package包/类
public void headerOWL() {
	if (isOWLOntologyFormat()) {
		LOG.info("using OWL ontology header");
		OWLDocumentFormat ofmt = this.getOWLOntologyFormat();
		if (ofmt instanceof RDFXMLDocumentFormat) {
			response.setContentType("application/rdf+xml;charset-utf-8");
		}
		else if (ofmt instanceof OWLXMLDocumentFormat) {
			response.setContentType("application/xml;charset-utf-8");
		}
		else {
			response.setContentType("text/plain;charset-utf-8");
		}
	}
	else {
		response.setContentType("text/plain;charset-utf-8");
	}
	response.setStatus(HttpServletResponse.SC_OK);
}
 

import org.semanticweb.owlapi.formats.RDFXMLDocumentFormat; //导入依赖的package包/类
@Ignore
@Test
public void testConversion() throws Exception {
	ParserWrapper pw = new ParserWrapper();
	OWLOntology ont = pw.parse("http://purl.obolibrary.org/obo/go.owl");
	OWLGraphWrapper g = new OWLGraphWrapper(ont);

	GafObjectsBuilder builder = new GafObjectsBuilder();

	GafDocument gafdoc = builder.buildDocument("http://geneontology.org/gene-associations/gene_association.GeneDB_Spombe.gz");

	GAFOWLBridge bridge = new GAFOWLBridge(g);
	OWLOntology gafOnt = g.getManager().createOntology();
	bridge.setTargetOntology(gafOnt);
	bridge.translate(gafdoc);
	
	OWLDocumentFormat owlFormat = new RDFXMLDocumentFormat();
	g.getManager().saveOntology(gafOnt, owlFormat, IRI.create(new File("/tmp/gaf.owl")));
	
	for (OWLAxiom ax : gafOnt.getAxioms()) {
		//LOG.info("AX:"+ax);
	}

}
 

import org.semanticweb.owlapi.formats.RDFXMLDocumentFormat; //导入依赖的package包/类
@Test
public void testConversion() throws Exception{
	ParserWrapper pw = new ParserWrapper();
	OWLOntology ont = pw.parse(getResourceIRIString("go_xp_predictor_test_subset.obo"));
	OWLGraphWrapper g = new OWLGraphWrapper(ont);
	g.addSupportOntology(pw.parse(getResourceIRIString("gorel.owl")));

	GafObjectsBuilder builder = new GafObjectsBuilder();

	GafDocument gafdoc = builder.buildDocument(getResource("xp_inference_test.gaf"));

	GAFOWLBridge bridge = new GAFOWLBridge(g);
	OWLOntology gafOnt = g.getManager().createOntology();
	bridge.setTargetOntology(gafOnt);
	bridge.translate(gafdoc);
	
	OWLDocumentFormat owlFormat = new RDFXMLDocumentFormat();
	g.getManager().saveOntology(gafOnt, owlFormat, IRI.create(new File("/tmp/gaf.owl")));
	
	for (OWLAxiom ax : gafOnt.getAxioms()) {
		LOG.info("AX:"+ax);
	}

}
 

import org.semanticweb.owlapi.formats.RDFXMLDocumentFormat; //导入依赖的package包/类
@Test
public void testConversion() throws Exception{
	ParserWrapper pw = new ParserWrapper();
	OWLOntology ont = pw.parse(getResourceIRIString("go_xp_predictor_test_subset.obo"));
	OWLGraphWrapper g = new OWLGraphWrapper(ont);
	g.addSupportOntology(pw.parse(getResourceIRIString("gorel.owl")));

	GafObjectsBuilder builder = new GafObjectsBuilder();

	GafDocument gafdoc = builder.buildDocument(getResource("xp_inference_test.gaf"));

	BasicABox bridge = new BasicABox(g);
	OWLOntology gafOnt = g.getManager().createOntology();
	bridge.setTargetOntology(gafOnt);
	bridge.translate(gafdoc);
	
	OWLDocumentFormat owlFormat = new RDFXMLDocumentFormat();
	g.getManager().saveOntology(gafOnt, owlFormat, IRI.create(new File("target/foo.owl")));
	
	for (OWLAxiom ax : gafOnt.getAxioms()) {
		LOG.info("AX:"+ax);
	}

}
 

import org.semanticweb.owlapi.formats.RDFXMLDocumentFormat; //导入依赖的package包/类
@Test
public void testConversion() throws Exception{
	ParserWrapper pw = new ParserWrapper();
	OWLOntology ont = pw.parse(getResourceIRIString("go_xp_predictor_test_subset.obo"));
	OWLGraphWrapper g = new OWLGraphWrapper(ont);
	g.addSupportOntology(pw.parse(getResourceIRIString("gorel.owl")));

	GafObjectsBuilder builder = new GafObjectsBuilder();

	GafDocument gafdoc = builder.buildDocument(getResource("mgi-exttest.gaf"));

	GAFOWLBridge bridge = new GAFOWLBridge(g);
	bridge.setGenerateIndividuals(false);
	OWLOntology gafOnt = g.getManager().createOntology();
	bridge.setTargetOntology(gafOnt);
	bridge.translate(gafdoc);
	
	OWLDocumentFormat owlFormat = new RDFXMLDocumentFormat();
	g.getManager().saveOntology(gafOnt, owlFormat, IRI.create(new File("target/gaf.owl")));
	
	for (OWLAxiom ax : gafOnt.getAxioms()) {
		//LOG.info("AX:"+ax);
	}

}
 

import org.semanticweb.owlapi.formats.RDFXMLDocumentFormat; //导入依赖的package包/类
@Test
public void testConversionToIndividuals() throws Exception{
	ParserWrapper pw = new ParserWrapper();
	OWLOntology ont = pw.parse(getResourceIRIString("go_xp_predictor_test_subset.obo"));
	OWLGraphWrapper g = new OWLGraphWrapper(ont);
	g.addSupportOntology(pw.parse(getResourceIRIString("gorel.owl")));

	GafObjectsBuilder builder = new GafObjectsBuilder();

	GafDocument gafdoc = builder.buildDocument(getResource("mgi-exttest.gaf"));

	GAFOWLBridge bridge = new GAFOWLBridge(g);
	bridge.setGenerateIndividuals(false);
	OWLOntology gafOnt = g.getManager().createOntology();
	bridge.setTargetOntology(gafOnt);
	bridge.setBasicAboxMapping(true);
	bridge.translate(gafdoc);
	
	OWLDocumentFormat owlFormat = new RDFXMLDocumentFormat();
	g.getManager().saveOntology(gafOnt, owlFormat, IRI.create(new File("target/gaf-abox.owl")));
	
	for (OWLAxiom ax : gafOnt.getAxioms()) {
		//LOG.info("AX:"+ax);
	}

}
 

import org.semanticweb.owlapi.formats.RDFXMLDocumentFormat; //导入依赖的package包/类
private String getSuffix(OWLDocumentFormat format) {
	if (format instanceof RDFXMLDocumentFormat) {
		return "owl";
	}
	if (format instanceof FunctionalSyntaxDocumentFormat) {
		return "ofn";
	}
	if (format instanceof OWLXMLDocumentFormat) {
		return "owx";
	}
	if (format instanceof ManchesterSyntaxDocumentFormat) {
		return "omn";
	}

	return "owl";
}
 

import org.semanticweb.owlapi.formats.RDFXMLDocumentFormat; //导入依赖的package包/类
/**
         * Method that uses the loaded ontology and parses it in case there are imports that have not been considered
         * @param considerImportedOntologies
         * @param manager
         * @param ontology
         * @return
         * @throws OWLOntologyCreationException
         * @throws OWLOntologyStorageException
         * @throws URISyntaxException 
         */
	private static String parseImports(
                        boolean considerImportedOntologies, 
                        OWLOntologyManager manager,
                        OWLOntology ontology) 
	throws OWLOntologyCreationException, OWLOntologyStorageException, URISyntaxException {
            String result = "";
            if (considerImportedOntologies) {
                //considerImportedClosure || //<- removed for the moment
                Set<OWLOntology> setOfImportedOntologies = new HashSet<OWLOntology>();
                setOfImportedOntologies.addAll(ontology.getDirectImports());
//                else {
//                        setOfImportedOntologies.addAll(ontology.getImportsClosure());
//                }
                for (OWLOntology importedOntology : setOfImportedOntologies) {
                        manager.addAxioms(ontology, importedOntology.getAxioms());
                }
            }
            OWLOntologyDocumentTarget parsedOntology = new StringDocumentTarget();
            manager.saveOntology(ontology,new RDFXMLDocumentFormat(), parsedOntology);
            result = parsedOntology.toString();
//		}

            return result;
	}
 

import org.semanticweb.owlapi.formats.RDFXMLDocumentFormat; //导入依赖的package包/类
static void saveOntology(OWLOntology ontology, File file) throws Exception {
    if (file.getName().endsWith(".ttl")) {
        manager.saveOntology(ontology, new TurtleDocumentFormat(), new FileOutputStream(file));
    } else if (file.getName().endsWith(".xml")) {
        manager.saveOntology(ontology, new OWLXMLDocumentFormat(), new FileOutputStream(file));
    } else {
        manager.saveOntology(ontology, new RDFXMLDocumentFormat(), new FileOutputStream(file));
    }
}
 

import org.semanticweb.owlapi.formats.RDFXMLDocumentFormat; //导入依赖的package包/类
/**
 * Initialize the format with standard default prefixes
 * (rdf, rdfs, xsd, owl) and with the prefixes we will use
 * (obo, oio, iao).
 *
 * @return The format with the prefixes set.
 */
protected static RDFXMLDocumentFormat initializeFormat() {
	RDFXMLDocumentFormat format = new RDFXMLDocumentFormat();
	format.copyPrefixesFrom(new DefaultPrefixManager());
	format.setPrefix("obo", OBO);
	format.setPrefix("oio", OIO);
	format.setPrefix("iao", IAO);
	format.setPrefix("ncbi", NCBI);
	format.setPrefix("ncbitaxon", OBO + "ncbitaxon#");
	return format;
}
 

import org.semanticweb.owlapi.formats.RDFXMLDocumentFormat; //导入依赖的package包/类
private String expandLabel(String subject, String property,
		String value) {
	RDFXMLDocumentFormat format = OWLConverter.format;
	// TODO: Why is "Annotation" always doubled?
	return "AnnotationAssertion(" +
		property + " <" +
		format.getIRI(subject) + "> \"" +
		value +"\"^^xsd:string)";
}
 

import org.semanticweb.owlapi.formats.RDFXMLDocumentFormat; //导入依赖的package包/类
private String expandAnnotation(String subject, String property,
		String value) {
	RDFXMLDocumentFormat format = OWLConverter.format;
	// TODO: Why is "Annotation" always doubled?
	return "AnnotationAssertion(<" +
		format.getIRI(property) + "> <" +
		format.getIRI(subject) + "> \"" +
		value +"\"^^xsd:string)";
}
 

import org.semanticweb.owlapi.formats.RDFXMLDocumentFormat; //导入依赖的package包/类
private String expandSynonym(String subject, String type, 
		String property, String value) {
	RDFXMLDocumentFormat format = OWLConverter.format;
	return "AnnotationAssertion(Annotation(<" +
		format.getIRI("oio:hasSynonymType").toString() + "> <" +
		format.getIRI(type).toString() + ">) <" +
		format.getIRI(property) + "> <" +
		format.getIRI(subject) + "> \"" +
		value +"\"^^xsd:string)";
}
 

import org.semanticweb.owlapi.formats.RDFXMLDocumentFormat; //导入依赖的package包/类
public void saveOntology(String fn) throws FileNotFoundException, OWLOntologyStorageException {
	FileOutputStream os = new FileOutputStream(new File(fn));
	OWLDocumentFormat owlFormat = new RDFXMLDocumentFormat();

	owlOntologyManager.saveOntology(sourceOntology, owlFormat, os);
}