Java Code Examples for org.semanticweb.owlapi.model.OWLClassAssertionAxiom#getClassExpression()
The following examples show how to use
org.semanticweb.owlapi.model.OWLClassAssertionAxiom#getClassExpression() .
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Example 1
Source File: Sim2CommandRunner.java From owltools with BSD 3-Clause "New" or "Revised" License | 6 votes |
@CLIMethod("--remove-dangling-annotations") public void removeDangningAnnotations(Opts opts) throws Exception { OWLOntology ont = g.getSourceOntology(); int n = 0; Set<OWLAxiom> rmAxioms = new HashSet<OWLAxiom>(); for (OWLNamedIndividual i : ont.getIndividualsInSignature()) { for (OWLClassAssertionAxiom ca : ont.getClassAssertionAxioms(i)) { OWLClassExpression cx = ca.getClassExpression(); if (cx instanceof OWLClass) { OWLClass c = (OWLClass) cx; String label = g.getLabel(c); if (label == null) rmAxioms.add(ca); else n++; } } } LOG.info("Removing " + rmAxioms.size() + " axioms"); ont.getOWLOntologyManager().removeAxioms(ont, rmAxioms); LOG.info("Remaining: " + n + " axioms"); }
Example 2
Source File: PhenoSimHQEPreProcessor.java From owltools with BSD 3-Clause "New" or "Revised" License | 6 votes |
protected void makeHasPhenotypeInstancesDirect() { // x Type has_phenotype some C ==> x Type C LOG.info("x Type has_phenotype some C ==> x Type C"); OWLObjectProperty hasPhenotype = getOWLObjectPropertyViaOBOSuffix(HAS_PHENOTYPE); Set<OWLAxiom> rmAxioms = new HashSet<OWLAxiom>(); Set<OWLAxiom> newAxioms = new HashSet<OWLAxiom>(); for (OWLClassAssertionAxiom caa : outputOntology.getAxioms(AxiomType.CLASS_ASSERTION)) { OWLClassExpression ex = caa.getClassExpression(); OWLIndividual i = caa.getIndividual(); if (ex instanceof OWLObjectSomeValuesFrom) { OWLObjectSomeValuesFrom svf = (OWLObjectSomeValuesFrom)ex; if (svf.getProperty().equals(hasPhenotype)) { rmAxioms.add(caa); newAxioms.add(getOWLDataFactory().getOWLClassAssertionAxiom(svf.getFiller(), i)); } } } LOG.info("making instances direct: +"+newAxioms.size()+ " -"+rmAxioms.size()); addAxiomsToOutput(newAxioms, false); removeAxiomsFromOutput(rmAxioms, false); }
Example 3
Source File: ModelAnnotationSolrDocumentLoader.java From owltools with BSD 3-Clause "New" or "Revised" License | 5 votes |
private OWLClass findFirstType(OWLNamedIndividual relevant) { Set<OWLClassAssertionAxiom> axioms = model.getClassAssertionAxioms(relevant); for (OWLClassAssertionAxiom axiom : axioms) { OWLClassExpression ce = axiom.getClassExpression(); if (ce.isAnonymous() == false) { return ce.asOWLClass(); } } return null; }
Example 4
Source File: ABoxUtils.java From owltools with BSD 3-Clause "New" or "Revised" License | 4 votes |
public static void mapClassAssertionsUp(OWLOntology ont, OWLReasoner reasoner, Set<OWLClass> targetClasses, Set<OWLClass> inputClasses) { Set<OWLAxiom> rmAxioms = new HashSet<OWLAxiom>(); Set<OWLAxiom> newAxioms = new HashSet<OWLAxiom>(); Map<OWLClass, Set<OWLClass>> cmap = new HashMap<OWLClass, Set<OWLClass>>(); LOG.info("Target classes: "+targetClasses.size()); int n=0; for (OWLClassAssertionAxiom ca : ont.getAxioms(AxiomType.CLASS_ASSERTION)) { if (ca.getClassExpression().isAnonymous()) continue; OWLClass c = (OWLClass) ca.getClassExpression(); n++; if (inputClasses == null || inputClasses.contains(c)) { if (targetClasses.contains(c)) continue; Set<OWLClass> supers; if (cmap.containsKey(c)) { supers = cmap.get(c); } else { supers = reasoner.getSuperClasses(c, false).getFlattened(); supers.addAll(reasoner.getEquivalentClasses(c).getEntities()); LOG.info(c+" has #supers: "+supers.size()); LOG.info(c + " ===> "+supers); supers.retainAll(targetClasses); LOG.info(c+" has #supersInTargetSet: "+supers.size()); supers = getNonRedundant(supers, reasoner); //LOG.info(c+" has #NRsupers: "+supers.size()); //LOG.info(c + " ===> "+supers); cmap.put(c, supers); if (supers.size() > 0) { LOG.info(c + " ===> "+supers); } } rmAxioms.add(ca); OWLIndividual individual = ca.getIndividual(); for (OWLClass sc : supers) { newAxioms.add(ont.getOWLOntologyManager().getOWLDataFactory().getOWLClassAssertionAxiom(sc, individual)); } } } LOG.info("named class assertions (start): "+n); LOG.info("rm:"+rmAxioms.size()); LOG.info("new:"+newAxioms.size()); ont.getOWLOntologyManager().removeAxioms(ont, rmAxioms); ont.getOWLOntologyManager().addAxioms(ont, newAxioms); }