org.semanticweb.owlapi.vocab.OWLRDFVocabulary Java Examples

/**
 * adds additional axioms specific to this method.
 * Creates a named LCS class equivalent to the generated expression
 * 
 * @param id
 * @param result
 * @param axioms
 */
@Override
protected void translateResultsToOWLAxioms(String id, OWLNamedIndividual result, Set<OWLAxiom> axioms) {
	OWLDataFactory df = graph.getDataFactory();
	
	// declare a named class for the LCS and make this equivalent to the anonymous expression
	OWLClass namedLCS = df.getOWLClass(IRI.create(id+"_LCS"));
	axioms.add(df.getOWLAnnotationAssertionAxiom(df.getOWLAnnotationProperty(OWLRDFVocabulary.RDFS_LABEL.getIRI()),
			namedLCS.getIRI(), 
			df.getOWLLiteral("LCS of "+simEngine.label(a)+" and "+simEngine.label(b))));
	axioms.add(df.getOWLEquivalentClassesAxiom(namedLCS, lcs));

	// link the similarity object to the named LCS
	OWLAnnotationProperty lcsp = df.getOWLAnnotationProperty(annotationIRI("has_least_common_subsumer"));
	axioms.add(df.getOWLAnnotationAssertionAxiom(lcsp, result.getIRI(), namedLCS.getIRI()));
}
 

private void addCommentToOntology(OWLOntology ont, String cmt) {
	OWLDataFactory df = getDataFactory();
	OWLAnnotationProperty p = 
			df.getOWLAnnotationProperty(OWLRDFVocabulary.RDFS_COMMENT.getIRI());
	OWLLiteral v = df.getOWLLiteral(cmt);
	OWLAnnotation ann = df.getOWLAnnotation(p, v);
	AddOntologyAnnotation addAnn = 
			new AddOntologyAnnotation(ont, ann);
	getManager().applyChange(addAnn);
}
 

public String getOntologyLabel() {
  OWLAnnotationProperty labelProperty =
      factory.getOWLAnnotationProperty(OWLRDFVocabulary.RDFS_LABEL.getIRI());
  String ontologyLabel = StringUtils.EMPTY;
  for (OWLAnnotation annotation : ontology.getAnnotations()) {
    if (annotation.getProperty().equals(labelProperty)
        && annotation.getValue() instanceof OWLLiteral) {
      OWLLiteral val = (OWLLiteral) annotation.getValue();
      ontologyLabel = val.getLiteral();
    }
  }
  return ontologyLabel;
}
 

public String getLabel(OWLEntity entity) {
  Set<String> annotation = getAnnotation(entity, OWLRDFVocabulary.RDFS_LABEL.toString());
  if (!annotation.isEmpty()) {
    return annotation.iterator().next();
  } else {
    return extractOWLClassId(entity);
  }
}
 

static boolean isDeprecated(Node n) {
  if (!n.hasProperty(OWLRDFVocabulary.OWL_DEPRECATED.toString())) {
    return false;
  }
  if (n.getProperty(OWLRDFVocabulary.OWL_DEPRECATED.toString()) instanceof Boolean) {
    return (Boolean) n.getProperty(OWLRDFVocabulary.OWL_DEPRECATED.toString());
  } else {
    return Boolean.valueOf((String)n.getProperty(OWLRDFVocabulary.OWL_DEPRECATED.toString(), "false"));
  }
}
 

private void renderControlledAnnotations(OWLNamedObject c) {
	Set<OWLAnnotationAssertionAxiom> annotationAxioms = 
			ontology.getAnnotationAssertionAxioms(c.getIRI());
	renderAnnotationAxiom("Label", OWLRDFVocabulary.RDFS_LABEL.getIRI(), annotationAxioms);
	renderAnnotationAxiom("Definition", Obo2OWLVocabulary.IRI_IAO_0000115.getIRI(), annotationAxioms);
	renderAnnotationAxiom("Comment", OWLRDFVocabulary.RDFS_COMMENT.getIRI(), annotationAxioms);

	renderSection("Synonyms");

	renderAnnotationAxioms("", 
			Obo2OWLVocabulary.IRI_OIO_hasExactSynonym.getIRI(), 
			annotationAxioms);
	renderAnnotationAxioms("", 
			Obo2OWLVocabulary.IRI_OIO_hasBroadSynonym.getIRI(), 
			annotationAxioms);
	renderAnnotationAxioms("", 
			Obo2OWLVocabulary.IRI_OIO_hasNarrowSynonym.getIRI(), 
			annotationAxioms);
	renderAnnotationAxioms("", 
			Obo2OWLVocabulary.IRI_OIO_hasRelatedSynonym.getIRI(), 
			annotationAxioms);

	renderSection("Cross-references");

	renderAnnotationAxioms("", 
			Obo2OWLVocabulary.IRI_OIO_hasDbXref.getIRI(), 
			annotationAxioms);

	renderSection("Subsets");

	renderAnnotationAxioms("", 
			Obo2OWLVocabulary.IRI_OIO_inSubset.getIRI(), 
			annotationAxioms);		
}
 

@Test
public void testMerge() throws OWLOntologyCreationException, IOException, IncoherentOntologyException, OWLOntologyStorageException {
    ParserWrapper pw = new ParserWrapper();
    OWLGraphWrapper g =
            pw.parseToOWLGraph(getResourceIRIString("equivalence-set-merge-util-test.obo"));
    OWLOntology ont1 = g.getSourceOntology();
    ElkReasonerFactory rf = new ElkReasonerFactory();
    OWLReasoner reasoner = rf.createReasoner(ont1);
    EquivalenceSetMergeUtil esmu = new EquivalenceSetMergeUtil(g, reasoner);
    esmu.setPrefixScore("A", 8.0);
    esmu.setPrefixScore("B", 6.0);
    esmu.setPrefixScore("C", 4.0);
    OWLAnnotationProperty lp = g.getDataFactory().getOWLAnnotationProperty( OWLRDFVocabulary.RDFS_LABEL.getIRI() );
    esmu.setPropertyPrefixScore( lp, "C", 5.0);
    esmu.setPropertyPrefixScore( lp, "B", 4.0);
    esmu.setPropertyPrefixScore( lp, "A", 3.0);
    
    OWLAnnotationProperty dp = g.getDataFactory().getOWLAnnotationProperty( Obo2OWLVocabulary.IRI_IAO_0000115.getIRI() );
    esmu.setPropertyPrefixScore( dp, "B", 5.0);
    esmu.setPropertyPrefixScore( dp, "A", 4.0);
    esmu.setPropertyPrefixScore( dp, "C", 3.0);
    
    esmu.setRemoveAxiomatizedXRefs(true);

    esmu.merge();
    OWLDocumentFormat fmt = new OBODocumentFormat();
    pw.saveOWL(g.getSourceOntology(), "target/esmu.owl");
    //pw.setCheckOboDoc(false);
    pw.saveOWL(g.getSourceOntology(), fmt, "target/esmu.obo");
    
    OWLOntology ont2 = pw.parseOWL(getResourceIRIString("equivalence-set-merge-util-expected.obo"));
    assertEquals(0, compare(ont1, ont2));
}
 

public static void addLabel(OWLNamedIndividual i, OWLGraphWrapper g, OWLReasoner reasoner) {
	OWLOntology ontology = g.getSourceOntology();
	Set<OWLClass> types = new HashSet<>();
	if (reasoner == null) {
		for (OWLClassExpression x : OwlHelper.getTypes(i, ontology)) {
			if (!x.isAnonymous()) {
				types.add((OWLClass) x);
			}
		}
	}
	else {
		 types = reasoner.getTypes(i, true).getFlattened();
	}
	StringBuffer iLabel = null;
	for (OWLClass type : types) {
		String label = g.getLabel(type);
		if (iLabel == null)
			iLabel = new StringBuffer("a");
		else
			iLabel.append(" & ");
		iLabel.append(" "+label);
	}
	OWLDataFactory df = g.getDataFactory();
	OWLAxiom ax =
			df.getOWLAnnotationAssertionAxiom(df.getOWLAnnotationProperty(OWLRDFVocabulary.RDFS_LABEL.getIRI()),
			i.getIRI(), 
			df.getOWLLiteral(iLabel.toString()));
	g.getManager().addAxiom(ontology,
			ax);
}
 

@Override
protected void translateResultsToOWLAxioms(String id, OWLNamedIndividual result, Set<OWLAxiom> axioms) {
	OWLDataFactory df = simEngine.getGraph().getDataFactory();
	
	// declare a named class for the LCS and make this equivalent to the anonymous expression
	OWLClass namedLCS = df.getOWLClass(IRI.create(id+"_LCS"));
	axioms.add(df.getOWLAnnotationAssertionAxiom(df.getOWLAnnotationProperty(OWLRDFVocabulary.RDFS_LABEL.getIRI()),
			namedLCS.getIRI(), 
			df.getOWLLiteral("LCS of "+simEngine.label(a)+" and "+simEngine.label(b))));
	axioms.add(df.getOWLEquivalentClassesAxiom(namedLCS, getLCS()));

	// link the similarity object to the named LCS
	OWLAnnotationProperty lcsp = df.getOWLAnnotationProperty(annotationIRI("has_least_common_subsumer"));
	axioms.add(df.getOWLAnnotationAssertionAxiom(lcsp, result.getIRI(), namedLCS.getIRI()));
}
 

/**
 * @return
 */
private OWLProperty getSubClassAsObjectProperty() {
	if (is_a != null)
		return is_a;
	OWLDataFactory df = graph.getDataFactory();
	is_a = df.getOWLObjectProperty(IRI.create("http://foo.org#is_a"));
	OWLAnnotationAssertionAxiom ax = df.getOWLAnnotationAssertionAxiom(
			df.getOWLAnnotationProperty(OWLRDFVocabulary.RDFS_LABEL.getIRI()), 
			is_a.getIRI(),
			df.getOWLLiteral("is_a"));
	graph.getManager().addAxiom(graph.getSourceOntology(), ax);
	return is_a;
}
 

/**
 * Cognate of "is_a" relation as defined in RO-2005
 * @return
 */
private OWLObjectProperty getSubClassOfAsTLR() {
	//return  getOWLDataFactory().getOWLObjectProperty(IRI.create("http:x.org/is_a"));
	return (OWLObjectProperty) trTypeLevel(OWLRDFVocabulary.RDFS_SUBCLASS_OF.getIRI());
}
 

@CLIMethod("--lcsx-all")
public void lcsxAll(Opts opts) throws Exception {
	opts.info("LABEL", "ont 1");
	String ont1 = opts.nextOpt();

	opts.info("LABEL", "ont 2");
	String ont2 = opts.nextOpt();

	if (simOnt == null) {
		simOnt = g.getManager().createOntology();
	}

	SimEngine se = new SimEngine(g);

	Set <OWLObject> objs1 = new HashSet<OWLObject>();
	Set <OWLObject> objs2 = new HashSet<OWLObject>();

	System.out.println(ont1+" -vs- "+ont2);
	for (OWLObject x : g.getAllOWLObjects()) {
		if (! (x instanceof OWLClass))
			continue;
		String id = g.getIdentifier(x);
		if (id.startsWith(ont1)) {
			objs1.add(x);
		}
		if (id.startsWith(ont2)) {
			objs2.add(x);
		}
	}
	Set<OWLClassExpression> lcsh = new HashSet<OWLClassExpression>();
	OWLObjectRenderer r = new ManchesterOWLSyntaxOWLObjectRendererImpl();
	OWLPrettyPrinter owlpp = new OWLPrettyPrinter(g, r);
	owlpp.hideIds();
	for (OWLObject a : objs1) {
		for (OWLObject b : objs2) {
			OWLClassExpression lcs = se.getLeastCommonSubsumerSimpleClassExpression(a, b);
			if (lcs instanceof OWLAnonymousClassExpression) {
				if (lcsh.contains(lcs)) {
					// already seen
					continue;
				}
				lcsh.add(lcs);
				String label = owlpp.render(lcs);
				IRI iri = IRI.create(Obo2OWLConstants.DEFAULT_IRI_PREFIX+"U_"+
						g.getIdentifier(a).replaceAll(":", "_")+"_" 
						+"_"+g.getIdentifier(b).replaceAll(":", "_"));
				OWLClass namedClass = g.getDataFactory().getOWLClass(iri);
				// TODO - use java obol to generate meaningful names
				OWLEquivalentClassesAxiom ax = g.getDataFactory().getOWLEquivalentClassesAxiom(namedClass , lcs);
				g.getManager().addAxiom(simOnt, ax);
				g.getManager().addAxiom(simOnt,
						g.getDataFactory().getOWLAnnotationAssertionAxiom(
								g.getDataFactory().getOWLAnnotationProperty(OWLRDFVocabulary.RDFS_LABEL.getIRI()),
								iri,
								g.getDataFactory().getOWLLiteral(label)));
				System.out.println("LCSX:"+owlpp.render(a)+" -vs- "+owlpp.render(b)+" = \n "+label);
				//LOG.info("  Adding:"+owlpp.render(ax));
				LOG.info("  Adding:"+ax);

			}
		}					
	}
}
 

public void setPropertyToLabel() {
	property = OWLRDFVocabulary.RDFS_LABEL.getIRI();
}
 

public void setPropertyToComment() {
	property = OWLRDFVocabulary.RDFS_COMMENT.getIRI();
}
 

private void addLabel(IRI subj, String value) {
	if (value == null) return;
	addFact(subj, OWLRDFVocabulary.RDFS_LABEL.getIRI(), value);
}
 

public Set<OWLAxiom> translateResultsToOWLAxioms() {

		System.out.println("TRANSLATING TO OWL AXIOM:"+this);
		OWLGraphWrapper graph = simEngine.getGraph();
		Set<OWLAxiom> axioms = new HashSet<OWLAxiom>();

		OWLDataFactory df = graph.getDataFactory();
		if (!(a instanceof OWLNamedObject)) {
			System.err.println(a+ "not named - cant write OWL results");
			return axioms;
		}
		if (!(b instanceof OWLNamedObject)) {
			System.err.println(b+ "not named - cant write OWL results");
			return axioms;
		}
		IRI ia = ((OWLNamedObject) a).getIRI();
		IRI ib = ((OWLNamedObject) b).getIRI();
		String[] toksA = splitIRI(ia);
		String[] toksB = splitIRI(ib);
		String id = toksA[0]+toksA[1]+"-vs-"+toksB[1];

		persistentIRI = IRI.create(id);

		// each similarity is stored as an individual of class similarity_relationship
		OWLNamedIndividual result = df.getOWLNamedIndividual(persistentIRI);
		OWLClass ac = df.getOWLClass(annotationIRI("similarity_relationship"));
		axioms.add(df.getOWLClassAssertionAxiom(ac, result));
		axioms.add(df.getOWLAnnotationAssertionAxiom(df.getOWLAnnotationProperty(OWLRDFVocabulary.RDFS_LABEL.getIRI()),
				result.getIRI(), 
				df.getOWLLiteral("Similarity relationship between "+simEngine.label(a)+" and "+simEngine.label(b))));

		// each object in the pair is connected to the similarity
		OWLAnnotationProperty p = df.getOWLAnnotationProperty(annotationIRI("has_similarity_relationship"));
		axioms.add(df.getOWLAnnotationAssertionAxiom(p, ((OWLNamedObject) a).getIRI(), result.getIRI()));
		axioms.add(df.getOWLAnnotationAssertionAxiom(p, ((OWLNamedObject) b).getIRI(), result.getIRI()));

		// every similarity has a score
		OWLAnnotationProperty sp = df.getOWLAnnotationProperty(annotationIRI("has_score"));
		axioms.add(df.getOWLAnnotationAssertionAxiom(sp, result.getIRI(), df.getOWLLiteral(score)));

		translateResultsToOWLAxioms(id, result, axioms);

		return axioms;
	}
 

static String getNeo4jName(OWLRDFVocabulary vocab) {
  return XMLUtils.getNCNameSuffix(vocab.getIRI());
}
 

@Before
public void setupGraph() throws IOException {
  try (Transaction tx = graphDb.beginTx()) {
    hippocampalFormation = buildConcept("http://example.org/#birnlex5", "Hippocampal formation");
    hippocampus = buildConcept("http://example.org/#hippocampus", "Hippocampus", "foo", "fizz");
    GraphUtil.addProperty(graphDb.getNodeById(hippocampus.getId()), Concept.SYNONYM,
        "cornu ammonis");
    GraphUtil.addProperty(graphDb.getNodeById(hippocampus.getId()), Concept.SYNONYM
        + LuceneUtils.EXACT_SUFFIX, "cornu ammonis");
    GraphUtil.addProperty(graphDb.getNodeById(hippocampus.getId()), Concept.ABREVIATION, "hpcs");
    GraphUtil.addProperty(graphDb.getNodeById(hippocampus.getId()), Concept.ABREVIATION
        + LuceneUtils.EXACT_SUFFIX, "hpcs");
    hippocampusStructure =
        buildConcept("http://example.org/#hippocampusStructure", "Hippocampus structure", "baz");
    structureOfHippocampus =
        buildConcept("http://example.org/#structureOfHippocampus", "Structure of hippocampus",
            "baz");
    cerebellum = buildConcept("http://example.org/#cerebellum", "Cerebellum", "baz", "foo");
    specialChars =
        buildConcept("http://example.org/#specialChars", "(-)-protein alpha", "baz", "foo bar");
    parkinsons = buildConcept("http://example.org/#parkinsons", "Parkinson's Disease", "baz");
    GraphUtil.addProperty(graphDb.getNodeById(parkinsons.getId()), Concept.SYNONYM, "the");
    GraphUtil.addProperty(graphDb.getNodeById(parkinsons.getId()), Concept.ACRONYM, "PD");
    GraphUtil.addProperty(graphDb.getNodeById(parkinsons.getId()), Concept.ACRONYM
        + LuceneUtils.EXACT_SUFFIX, "PD");
    als = buildConcept("http://example.org/#als", "amyotrophic lateral sclerosis");
    GraphUtil.addProperty(graphDb.getNodeById(als.getId()), Concept.SYNONYM, "Lou Gehrig's");
    GraphUtil.addProperty(graphDb.getNodeById(als.getId()), Concept.SYNONYM
        + LuceneUtils.EXACT_SUFFIX, "Lou Gehrig's");
    GraphUtil.addProperty(graphDb.getNodeById(als.getId()), Concept.SYNONYM,
        "motor neuron disease, bulbar");
    GraphUtil.addProperty(graphDb.getNodeById(als.getId()), Concept.SYNONYM
        + LuceneUtils.EXACT_SUFFIX, "motor neuron disease, bulbar");
    GraphUtil.addProperty(graphDb.getNodeById(als.getId()), Concept.ACRONYM, "ALS");
    GraphUtil.addProperty(graphDb.getNodeById(als.getId()), Concept.ACRONYM
        + LuceneUtils.EXACT_SUFFIX, "ALS");
    deprecated = buildConcept("http://example.org/#cerebellum2", "Cerebellum", "baz", "foo");
    GraphUtil.addProperty(graphDb.getNodeById(deprecated.getId()),
        OWLRDFVocabulary.OWL_DEPRECATED.toString(), "true");
    tx.success();
  }

  CurieUtil curieUtil = mock(CurieUtil.class);
  when(curieUtil.getPrefixes()).thenReturn(newHashSet("H", "S"));
  when(curieUtil.getExpansion("H")).thenReturn("http://example.org/#h");
  when(curieUtil.getExpansion("S")).thenReturn("http://example.org/#s");
  when(curieUtil.getIri(anyString())).thenReturn(Optional.<String>empty());
  when(curieUtil.getIri("HP:0008")).thenReturn(Optional.of("http://example.org/#hippocampus"));
  vocabulary = new VocabularyNeo4jImpl(graphDb, null, curieUtil, new NodeTransformer());
}
 

/**
 * gets the value of rdfs:comment for an OWLObject
 * 
 * @param c
 * @return comment of null
 */
public String getComment(OWLObject c) {
	OWLAnnotationProperty lap = getDataFactory().getOWLAnnotationProperty(OWLRDFVocabulary.RDFS_COMMENT.getIRI()); 

	return getAnnotationValue(c, lap);
}
 

/**
 * gets the value of rdfs:comment for an OWLObject
 * <p>
 * This is a curried FlexLoader s-expression version of {@link #getComment(OWLObject)}.
 * 
 * @param c
 * @param sargs
 * @return comment of null
 * @see #getComment(OWLObject)
 */
public String getComment(OWLObject c, List<String> sargs) {
	OWLAnnotationProperty lap = getDataFactory().getOWLAnnotationProperty(OWLRDFVocabulary.RDFS_COMMENT.getIRI()); 

	return getAnnotationValue(c, lap);
}