Java OWLReasoner.flush方法代码示例

import org.semanticweb.owlapi.reasoner.OWLReasoner; //导入方法依赖的package包/类
public boolean isEdgeEntailed(OWLEdge e, OWLOntology currentOntology, OWLReasoner reasoner) {
	OWLOntologyManager m = getManager();

	Set<OWLSubClassOfAxiom> scas = currentOntology.getSubClassAxiomsForSubClass(e.c);
	Set<OWLSubClassOfAxiom> rmAxioms = new HashSet<OWLSubClassOfAxiom>();
	for (OWLSubClassOfAxiom sca : scas) {
		if (sca.getSuperClass().equals(e.p)) {
			LOG.info("REMOVING: "+sca);
			rmAxioms.add(sca);
		}
	}
	boolean isEdgeAsserted = rmAxioms.size() > 0;
	if (isEdgeAsserted) {
		m.removeAxioms(currentOntology, rmAxioms);
		reasoner.flush();
	}
	boolean isEntailed;
	isEntailed = reasoner.getSuperClasses(e.c, false).containsEntity(e.p);
	if (isEdgeAsserted) {
		m.addAxioms(currentOntology, rmAxioms);
		reasoner.flush();
	}

	return isEntailed;
}
 

import org.semanticweb.owlapi.reasoner.OWLReasoner; //导入方法依赖的package包/类
public static void main(String[] args) throws OWLOntologyStorageException,
		OWLOntologyCreationException {
	OWLOntologyManager manager = OWLManager.createOWLOntologyManager();

	// Load your ontology
	OWLOntology ont = manager.loadOntologyFromOntologyDocument(new File("path-to-ontology"));

	// Create an ELK reasoner.
	OWLReasonerFactory reasonerFactory = new ElkReasonerFactory();
	OWLReasoner reasoner = reasonerFactory.createReasoner(ont);

	// Classify the ontology.
	reasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY);

	OWLDataFactory factory = manager.getOWLDataFactory();
	OWLClass subClass = factory.getOWLClass(IRI.create("http://www.co-ode.org/ontologies/galen#AbsoluteShapeState"));
	OWLAxiom removed = factory.getOWLSubClassOfAxiom(subClass, factory.getOWLClass(IRI.create("http://www.co-ode.org/ontologies/galen#ShapeState")));
	
	OWLAxiom added = factory.getOWLSubClassOfAxiom(subClass, factory.getOWLClass(IRI.create("http://www.co-ode.org/ontologies/galen#GeneralisedStructure")));
	// Remove an existing axiom, add a new axiom
	manager.addAxiom(ont, added);
	manager.removeAxiom(ont, removed);
	// This is a buffering reasoner, so you need to flush the changes
	reasoner.flush();
	
	// Re-classify the ontology, the changes should be accommodated
	// incrementally (i.e. without re-inferring all subclass relationships)
	// You should be able to see it from the log output
	reasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY);		
	
	// Terminate the worker threads used by the reasoner.
	reasoner.dispose();
}
 

import org.semanticweb.owlapi.reasoner.OWLReasoner; //导入方法依赖的package包/类
@Test
public void testPValue() throws Exception {
	ParserWrapper pw = new ParserWrapper();
	sourceOntol = pw.parseOBO(getResource("sim/mp-subset-1.obo").getAbsolutePath());
	g =  new OWLGraphWrapper(sourceOntol);
	parseAssociations(getResource("sim/mgi-gene2mp-subset-1.tbl"), g);

	LOG.info("Initialize OwlSim ..");

	OWLReasoner reasoner = new ElkReasonerFactory().createReasoner(sourceOntol);
	reasoner.flush();
	
	try {
		owlsim = owlSimFactory.createOwlSim(sourceOntol);
		owlsim.createElementAttributeMapFromOntology();
		owlsim.computeSystemStats();
	} catch (UnknownOWLClassException e) {
		e.printStackTrace();
	} finally {
		reasoner.dispose();
	}

	// Source sourceOntol and g are used as background knowledge ... 
	OWLSimReferenceBasedStatistics refBasedStats = new OWLSimReferenceBasedStatistics(owlsim, sourceOntol, g);
	
	IRI iri = IRI.create("http://purl.obolibrary.org/obo/MGI_101761");
	
	String[] testClasses = new String[] {"MP:0002758", "MP:0002772", "MP:0005448", "MP:0003660"};
	Set<OWLClass> testClassesSet = new HashSet<OWLClass>();
	for (String testClass : testClasses) {
		testClassesSet.add(this.getOBOClass(testClass));
	}

	PValue pValue = refBasedStats.getPValue(testClassesSet, iri);
	LOG.info(pValue.getSimplePValue());

}
 

import org.semanticweb.owlapi.reasoner.OWLReasoner; //导入方法依赖的package包/类
@Test
public void testFindCoAnnotationList() throws Exception {
	ParserWrapper pw = new ParserWrapper();
	sourceOntol = pw.parseOWL(getResourceIRIString("sim/mp-subset-1.obo"));
	g =  new OWLGraphWrapper(sourceOntol);
	parseAssociations(getResource("sim/mgi-gene2mp-subset-1.tbl"), g);

	owlpp = new OWLPrettyPrinter(g);
	
	// assume buffering
	OWLReasoner reasoner = new ElkReasonerFactory().createReasoner(sourceOntol);
	try {

		createOwlSim();
			//sos.setReasoner(reasoner);
		LOG.info("Reasoner="+owlsim.getReasoner());
		reasoner.flush();
		owlsim.createElementAttributeMapFromOntology();

		owlsim.populateFullCoannotationMatrix();


		SimJSONEngine sj = new SimJSONEngine(g, owlsim);


		List<OWLClass> allClasses = new ArrayList<OWLClass>();
		allClasses.addAll(g.getAllOWLClasses());
		Collections.shuffle(allClasses);

		int limit = 5;
		String jsonStr = sj.getCoAnnotationListForAttribute(g.getOWLClassByIdentifier("MP:0002082"),limit);
		LOG.info("Dumping coannotations and scores for all annotated classes");
		
		LOG.info("EXAMPLE:"+jsonStr);
	
	}
	finally {
		reasoner.dispose();
	}
}
 

import org.semanticweb.owlapi.reasoner.OWLReasoner; //导入方法依赖的package包/类
@Test 
public void testGetEntropy() throws OWLOntologyCreationException, IOException, OBOFormatParserException, UnknownOWLClassException {
	ParserWrapper pw = new ParserWrapper();
	sourceOntol = pw.parseOBO(getResourceIRIString("sim/mp-subset-1.obo"));
	g =  new OWLGraphWrapper(sourceOntol);
	parseAssociations(getResource("sim/mgi-gene2mp-subset-1.tbl"), g);

	owlpp = new OWLPrettyPrinter(g);

	// assume buffering
	OWLReasoner reasoner = new ElkReasonerFactory().createReasoner(sourceOntol);
	try {

		owlsim = new SimpleOwlSim(sourceOntol);
		((SimpleOwlSim) owlsim).setReasoner(reasoner);

		reasoner.flush();
		Double e = owlsim.getEntropy();
		LOG.info("ENTROPY OF ONTOLOGY = "+e);

		for (String subset : g.getAllUsedSubsets()) {
			LOG.info("SUBSET:"+subset);
			e = owlsim.getEntropy(g.getOWLClassesInSubset(subset));
			LOG.info(" ENTROPY OF "+subset+" = "+e);
		}
	}
	finally {
		reasoner.dispose();
	}		
}
 

import org.semanticweb.owlapi.reasoner.OWLReasoner; //导入方法依赖的package包/类
/**
 * Test fetching commonly co-annotated classes in a set of individuals 
 * vs the background (entire) corpus using the TF-IDF method.
 * @throws Exception
 * @throws MathException
 */
@Test
public void coAnnotatedTest() throws Exception, MathException {
	ParserWrapper pw = new ParserWrapper();
	sourceOntol = pw.parseOWL(getResourceIRIString("sim/mp-subset-1.obo"));
	g =  new OWLGraphWrapper(sourceOntol);
	parseAssociations(getResource("sim/mgi-gene2mp-subset-1.tbl"), g);

	owlpp = new OWLPrettyPrinter(g);

	// assume buffering
	OWLReasoner reasoner = new ElkReasonerFactory().createReasoner(sourceOntol);
	try {

		this.createOwlSim();
		owlsim.createElementAttributeMapFromOntology();

		reasoner.flush();
		owlsim.populateFullCoannotationMatrix();
		Set<OWLNamedIndividual> inds = sourceOntol.getIndividualsInSignature();
		for (OWLNamedIndividual i : inds) {
			//get a random set of other individuals to do the subset
			List<ClassCount> coaClasses = owlsim.getCoAnnotatedClassesForIndividual(i);
			LOG.info("Found "+coaClasses.size()+" coannotated classes for "+g.getIdentifier(i));
			for (ClassCount cc : coaClasses) {
				LOG.info(owlpp.render(cc.c)+cc.score);
			}
		}
	}
	finally {
		reasoner.dispose();
	}
	

}
 

import org.semanticweb.owlapi.reasoner.OWLReasoner; //导入方法依赖的package包/类
/**
 * Test fetching commonly co-annotated classes in the entire corpus, which
 * uses the TF-IDF method.
 * @throws Exception
 */
@Test
public void testGetCoannotatedClassesForAttribute() throws Exception {
	ParserWrapper pw = new ParserWrapper();
	sourceOntol = pw.parseOWL(getResourceIRIString("sim/mp-subset-1.obo"));
	g =  new OWLGraphWrapper(sourceOntol);
	parseAssociations(getResource("sim/mgi-gene2mp-subset-1.tbl"), g);

	owlpp = new OWLPrettyPrinter(g);

	// assume buffering
	OWLReasoner reasoner = new ElkReasonerFactory().createReasoner(sourceOntol);
	try {

		this.createOwlSim();
		owlsim.createElementAttributeMapFromOntology();

		reasoner.flush();
		owlsim.populateFullCoannotationMatrix();
		Set<OWLNamedIndividual> inds = sourceOntol.getIndividualsInSignature();
		Set<OWLClass> cs = owlsim.getAllAttributeClasses();
		LOG.info("Dumping coannotations and scores for all annotated classes");
		for (OWLClass c : cs) {
			List<ClassCount> lcc = owlsim.getCoannotatedClassesForAttribute(c,inds.size());
			for (ClassCount cc : lcc) {
				LOG.info(owlpp.render(c)+owlpp.render(cc.c)+cc.score);
			}
		}
	}
	finally {
		reasoner.dispose();
	}
}
 

import org.semanticweb.owlapi.reasoner.OWLReasoner; //导入方法依赖的package包/类
@Test
public void testScores() throws OWLOntologyCreationException, IOException, UnknownOWLClassException, OBOFormatParserException {
	ParserWrapper pw = new ParserWrapper();
	sourceOntol = pw.parseOBO(getResource("sim/mp-subset-1.obo").getAbsolutePath());
	g =  new OWLGraphWrapper(sourceOntol);
	parseAssociations(getResource("sim/mgi-gene2mp-subset-1.tbl"), g);

	owlpp = new OWLPrettyPrinter(g);
	final int truncLen = 200;
	
	// assume buffering
	OWLReasoner reasoner = new ElkReasonerFactory().createReasoner(sourceOntol);
	try {

		createOwlSim();
			//sos.setReasoner(reasoner);
		LOG.info("Reasoner="+owlsim.getReasoner());

		SimJSONEngine sj = new SimJSONEngine(g, owlsim);

		//sos.saveOntology("/tmp/z.owl");

		reasoner.flush();
		
		owlsim.createElementAttributeMapFromOntology();
		//owlsim.computeSystemStats();
		
		for (OWLNamedIndividual i : sourceOntol.getIndividualsInSignature()) {
			String jsonStr = sj.getAnnotationSufficiencyScore(i);
			LOG.info("ANNOTSUFFICIENCY:"+jsonStr);
		}
	}
	finally {
		reasoner.dispose();
	}
}
 

import org.semanticweb.owlapi.reasoner.OWLReasoner; //导入方法依赖的package包/类
@Test
public void testPhenoSimMouse() throws IOException, OWLOntologyCreationException, OWLOntologyStorageException, MathException {
	ParserWrapper pw = new ParserWrapper();
	sourceOntol = pw.parseOWL(getResourceIRIString("test_phenotype.owl"));
	g =  new OWLGraphWrapper(sourceOntol);
	 owlpp = new OWLPrettyPrinter(g);
	
	// assume buffering
	OWLReasoner reasoner = new ElkReasonerFactory().createReasoner(sourceOntol);
	try {
		pproc = new PhenoSimHQEPreProcessor();
		pproc.setInputOntology(sourceOntol);
		pproc.setOutputOntology(sourceOntol);
		pproc.setReasoner(reasoner);
		pproc.setOWLPrettyPrinter(owlpp);
		((PhenoSimHQEPreProcessor)pproc).defaultLCSElementFrequencyThreshold = 0.7;

		//sos.setSimPreProcessor(pproc);
		//sos.preprocess();
		pproc.preprocess();
		reasoner.flush();

		sos = new SimpleOwlSim(sourceOntol);
		sos.setSimPreProcessor(pproc);
		sos.createElementAttributeMapFromOntology();

		//sos.saveOntology("/tmp/z.owl");

		reasoner.flush();
		for (OWLNamedIndividual i : sourceOntol.getIndividualsInSignature()) {
			for (OWLNamedIndividual j : sourceOntol.getIndividualsInSignature()) {
				showSim(i,j);
			}
		}
	}
	finally {
		reasoner.dispose();
	}
}
 

import org.semanticweb.owlapi.reasoner.OWLReasoner; //导入方法依赖的package包/类
@Test
public void testBasicSim() throws IOException, OWLOntologyCreationException, OWLOntologyStorageException, MathException, UnknownOWLClassException {
	ParserWrapper pw = new ParserWrapper();
	sourceOntol = pw.parseOWL(getResourceIRIString("sim/mp-subset-1.obo"));
	g =  new OWLGraphWrapper(sourceOntol);
	parseAssociations(getResource("sim/mgi-gene2mp-subset-1.tbl"), g);

	owlpp = new OWLPrettyPrinter(g);

	// assume buffering
	OWLReasoner reasoner = new ElkReasonerFactory().createReasoner(sourceOntol);
	try {

		owlsim = new SimpleOwlSim(sourceOntol);
		((SimpleOwlSim) owlsim).setReasoner(reasoner);
		LOG.info("Reasoner="+owlsim.getReasoner());

		//sos.saveOntology("/tmp/z.owl");

		reasoner.flush();
		for (OWLNamedIndividual i : sourceOntol.getIndividualsInSignature()) {
			//System.out.println("COMPARING: "+i);
			for (OWLNamedIndividual j : sourceOntol.getIndividualsInSignature()) {
				showSimOld(i,j);
			}
		}
	}
	finally {
		reasoner.dispose();
	}
}
 

import org.semanticweb.owlapi.reasoner.OWLReasoner; //导入方法依赖的package包/类
@Test
	public void testStats() throws IOException, OWLOntologyCreationException, MathException, UnknownOWLClassException, OBOFormatParserException {
		ParserWrapper pw = new ParserWrapper();
		sourceOntol = pw.parseOBO(getResource("sim/mp-subset-1.obo").getAbsolutePath());
		g =  new OWLGraphWrapper(sourceOntol);
		parseAssociations(getResource("sim/mgi-gene2mp-subset-1.tbl"), g);
		setOutput("target/basic-owlsim-test.out");

		// assume buffering
		OWLReasoner reasoner = new ElkReasonerFactory().createReasoner(sourceOntol);
		try {
			this.createOwlSim();
			owlsim.createElementAttributeMapFromOntology();
			
			reasoner.flush();
			owlsim.computeSystemStats();
			LOG.info("Overall statistical summary for Test:");
			LOG.info(owlsim.getSystemStats().toString());
			LOG.info("Averaged statistical summary for Individuals in Test:");
//			LOG.info(owlsim.getSummaryStatistics(Stat.MEAN).toString());
			LOG.info("individuals: "+owlsim.getSummaryStatistics().n.getN());
			LOG.info("mean(n/indiv): "+String.format("%1$.5f", owlsim.getSummaryStatistics().n.getMean()));
			LOG.info("mean(meanIC): "+String.format("%1$.5f", owlsim.getSummaryStatistics().mean.getMean()));
			LOG.info("mean(maxIC): "+String.format("%1$.5f", owlsim.getSummaryStatistics().max.getMean()));
			LOG.info("max(maxIC): "+String.format("%1$.5f", owlsim.getSummaryStatistics().max.getMax()));
			LOG.info("mean(sumIC): "+String.format("%1$.5f", owlsim.getSummaryStatistics().max.getMean()));
		}
		finally {
			reasoner.dispose();
		}
	}
 

import org.semanticweb.owlapi.reasoner.OWLReasoner; //导入方法依赖的package包/类
@Test
public void testIxI() throws Exception {
	ParserWrapper pw = new ParserWrapper();
	sourceOntol = pw.parseOBO(getResource("sim/mp-subset-1.obo").getAbsolutePath());
	g =  new OWLGraphWrapper(sourceOntol);
	parseAssociations(getResource("sim/mgi-gene2mp-subset-1.tbl"), g);
	setOutput("target/basic-owlsim-test.out");

	// assume buffering
	OWLReasoner reasoner = new ElkReasonerFactory().createReasoner(sourceOntol);
	try {
		this.createOwlSim();
		owlsim.createElementAttributeMapFromOntology();
		
		reasoner.flush();
		owlsim.computeSystemStats();
		owlsim.calculateMetricStats(owlsim.getAllElements(),owlsim.getAllElements());

		String[] metrics = {"bmaAsymIC","bmaSymIC","bmaInverseAsymIC", "combinedScore", "simJ", "simGIC","maxIC"};
		for (String m : metrics) {
			LOG.info("Test Summary(mean) for "+m+": "+owlsim.getMetricStats(Stat.MEAN).get(m).getSummary());
			LOG.info("Test Summary(min) for "+m+": "+owlsim.getMetricStats(Stat.MIN).get(m).getSummary());
			LOG.info("Test Summary(max) for "+m+": "+owlsim.getMetricStats(Stat.MAX).get(m).getSummary());
		}
	} finally {
		reasoner.dispose();
	}
	
}
 

import org.semanticweb.owlapi.reasoner.OWLReasoner; //导入方法依赖的package包/类
@Test
public void testInfoProfile() throws OWLOntologyCreationException, IOException, UnknownOWLClassException, OBOFormatParserException {

	ParserWrapper pw = new ParserWrapper();
	sourceOntol = pw.parseOBO(getResource("sim/mp-subset-1.obo").getAbsolutePath());
	g =  new OWLGraphWrapper(sourceOntol);
	parseAssociations(getResource("sim/mgi-gene2mp-subset-1.tbl"), g);

	owlpp = new OWLPrettyPrinter(g);
	final int truncLen = 200;
	
	// assume buffering
	OWLReasoner reasoner = new ElkReasonerFactory().createReasoner(sourceOntol);
	try {

		createOwlSim();
			//sos.setReasoner(reasoner);
		LOG.info("Reasoner="+owlsim.getReasoner());

		SimJSONEngine sj = new SimJSONEngine(g, owlsim);

		//sos.saveOntology("/tmp/z.owl");

		reasoner.flush();
		
		owlsim.createElementAttributeMapFromOntology();
		owlsim.computeSystemStats();
		
		for (OWLNamedIndividual i : sourceOntol.getIndividualsInSignature()) {
			String jsonStr = sj.getAttributeInformationProfile(owlsim.getAttributesForElement(i));
			LOG.info("InformationInfo:"+jsonStr);
		}
	}
	finally {
		reasoner.dispose();
	}
}
 

import org.semanticweb.owlapi.reasoner.OWLReasoner; //导入方法依赖的package包/类
@Test
public void testBasicSim() throws Exception {
	ParserWrapper pw = new ParserWrapper();
	sourceOntol = pw.parseOWL(getResourceIRIString("sim/mp-subset-1.obo"));
	g =  new OWLGraphWrapper(sourceOntol);
	parseAssociations(getResource("sim/mgi-gene2mp-subset-1.tbl"), g);
	setOutput("target/find-matches-test.out");

	owlpp = new OWLPrettyPrinter(g);

	// assume buffering
	OWLReasoner reasoner = new ElkReasonerFactory().createReasoner(sourceOntol);
	try {

		this.createOwlSim();
		owlsim.createElementAttributeMapFromOntology();

		//sos.saveOntology("/tmp/z.owl");

		reasoner.flush();
		for (OWLNamedIndividual i : sourceOntol.getIndividualsInSignature()) {

			renderer.getResultOutStream().println("\nI = "+i);
			
			List<ElementPairScores> scoreSets = owlsim.findMatches(i, "MGI");
			int rank = 1;
			for (ElementPairScores s : scoreSets) {
				renderer.getResultOutStream().println("\n  RANK = "+rank);
				renderer.printPairScores(s);
				rank++;
			}
		}
	}
	finally {
		reasoner.dispose();
	}
}
 

import org.semanticweb.owlapi.reasoner.OWLReasoner; //导入方法依赖的package包/类
@Test
public void testSearch() throws Exception {
	ParserWrapper pw = new ParserWrapper();
	sourceOntol = pw.parseOBO(getResource("sim/mp-subset-1.obo").getAbsolutePath());
	g =  new OWLGraphWrapper(sourceOntol);
	parseAssociations(getResource("sim/mgi-gene2mp-subset-1.tbl"), g);

	owlpp = new OWLPrettyPrinter(g);
	final int truncLen = 200;
	
	// assume buffering
	OWLReasoner reasoner = new ElkReasonerFactory().createReasoner(sourceOntol);
	try {

		createOwlSim();
			//sos.setReasoner(reasoner);
		LOG.info("Reasoner="+owlsim.getReasoner());

		SimJSONEngine sj = new SimJSONEngine(g, owlsim);

		//sos.saveOntology("/tmp/z.owl");

		reasoner.flush();
		
		owlsim.createElementAttributeMapFromOntology();
		owlsim.computeSystemStats();
		

		for (OWLNamedIndividual i : sourceOntol.getIndividualsInSignature()) {
			Set<OWLClass> atts = owlsim.getAttributesForElement(i);
			String jsonStr = sj.search(atts, "MGI", true, false);
			
			LOG.info(jsonStr);
		}
		
	}
	finally {
		reasoner.dispose();
	}
}