public boolean isClass(String uri) { OntClass c = ontModel.getOntClass(uri); if (c != null) return true; return false; }
@Override Collection<OntClass> getRootClasses(@Nonnull final OntModel ontModel) { this.hierarchyRoots = ImmutableSet.<OntClass>builder() .add(ontModel.getOntClass(PHENOME_LABEL)) .add(ontModel.getOntClass(GENETIC_MATERIAL_LABEL)) .build(); final ImmutableSet.Builder<OntClass> selectedRoots = ImmutableSet.builder(); for (final OntClass hierarchyRoot : this.hierarchyRoots) { selectedRoots.addAll(hierarchyRoot.listSubClasses(DIRECT)); } return selectedRoots.build(); }
@Override Collection<OntClass> getRootClasses(@Nonnull final OntModel ontModel) { this.hierarchyRoots = ImmutableSet.<OntClass>builder() .add(ontModel.getOntClass(PHENOME_LABEL)) .add(ontModel.getOntClass(GENETIC_MATERIAL_LABEL)) .build(); final ImmutableSet.Builder<OntClass> selectedRoots = ImmutableSet.builder(); for (final OntClass hierarchyRoot : this.hierarchyRoots) { selectedRoots.addAll(hierarchyRoot.listSubClasses(DIRECT)); } return selectedRoots.build(); }
/** * returns URIs of all subclasses of @param classUri (also considers indirect subclasses if second parameter is true). * @param classUri * @param recursive * @return */ public HashMap<String, Label> getSubClasses(String classUri, boolean recursive) { HashSet<OntResource> resources = new HashSet<>(); OntResource r = ontModel.getOntClass(classUri); if (r == null) return new HashMap<>(); getChildren(r, resources, recursive); return getResourcesLabels(resources); }
/** * returns URIs of all superclasses of @param classUri (also considers indirect superclasses if second parameter is true). * @param classUri * @param recursive * @return */ public HashMap<String, Label> getSuperClasses(String classUri, boolean recursive) { HashSet<OntResource> resources = new HashSet<>(); OntResource r = ontModel.getOntClass(classUri); if (r == null) return new HashMap<>(); getParents(r, resources, recursive); return getResourcesLabels(resources); }
private void createIndividuals(OntModel ontModel, Model model) { for (BioPAXElement bp : model.getObjects()) { String name = bp.getModelInterface().getName(); name = name.substring(name.lastIndexOf('.') + 1); OntClass ontClass = ontModel.getOntClass(this.getLevel().getNameSpace() + name); if (log.isTraceEnabled()) { log.trace("ontClass = " + ontClass); } Individual individual = ontModel.createIndividual(bp.getRDFId(), ontClass); if (log.isTraceEnabled()) { log.trace("individual = " + individual); } objectToIndividualMap.put(bp, individual); } }
public OntClass getClass(String className) { for (Ontology ontology : getProfileDocument().getOntology()) { OntModel ontModel = getOntology(ontology.getId()); if (ontModel != null) { OntClass result = ontModel.getOntClass(className); if (result != null) return result; } } return null; }
public OntClass getClass(String className) { try { for (Ontology ontology : getProfileDocument().getOntology()) { OntModel ontModel = getOntology(ontology.getId()); if (ontModel != null) { OntClass result = ontModel.getOntClass(className); if (result != null) return result; } } } catch (RegistryException e) { } return null; }
return jenamodel.getOntClass(data.getIRI().toString()); } catch (OWLOntologyCreationException eoc) { System.err.print("ClassOwlToJena::: ");
OntClass c = this.ontHandler.getOntModel().getOntClass(r.getURI()); if(c != null) classes.put(c.getURI(), ontHandler.getResourceLabel(c));
public void testReasoning() throws Exception { JenaProvenanceOntology ontology = new JenaProvenanceOntology(new File( INSTANCES_DIR, "test.owl").toURI()); OntModel ontModel = ontology.getOntModel(); ontModel.write(System.out); ExtendedIterator instances = ontModel.getOntClass( ProvenanceVocab.DATA_OBJECT.getURI()).listInstances(); int i = 0; while (instances.hasNext()) { Individual nextIndividual = (Individual) instances.next(); System.out.println(nextIndividual.getURI()); i++; } instances.close(); assertEquals("expected runs", 2, i); // Model plain = ModelFactory.createModelForGraph( ontModel.getGraph() // ); // plain.write( System.out, "RDF/XML" ); }
OntClass rdfsClass = model.getOntClass(urlPrefixMetaData + cc.getId()); ConceptClass superClass = cc.getSpecialisationOf(); if (superClass != null) { rdfsClass.addSuperClass(model.getOntClass(urlPrefixMetaData + superClass.getId())); } else { rdfsClass.addSuperClass(rdfsSuperConceptClass);
provenanceOntology.addNestedWorkflow(workflowRun, nestedWorkflowRun); OntClass ontClass = provenanceOntology.model .getOntClass(ProvenanceVocab.NESTED_WORKFLOW_RUN.getURI()); Iterator iterator = ontClass.listInstances(); assertTrue("There is at least one NestedWorkflowRun", iterator
@Override public int generateLab(final String institutionURI, final String institutionLabel, final String labLabel, final String labURI, final String labURL, final String labTypeURI, final DataGenParams genParams) throws IOException { // retrieve the resource for the institution final Resource institution = model.getResource( institutionURI ); // create a resource for the lab final Resource lab = model.createResource( labURI ); final OntClass labTypeClass = ( (JenaEIOntModel)eagleiOntModel ).getOntModel().getOntClass( labTypeURI ); // add the direct type model.add( model.createStatement( lab, directType, labTypeClass ) ); // add all types (potentially with materialization) final String uri = labTypeClass.getURI(); final EIURI eiURI = EIURI.create( uri ); for (final EIClass type : getTypes( eagleiOntModel, eiURI, genParams.getMaterializeHierarchy() )) { model.add( model.createStatement( lab, RDF.type, model.getResource( type.getEntity().getURI().toString() ) ) ); } // add the label model.add( model.createStatement( lab, RDFS.label, labLabel ) ); // add located_in property from the lab to the university model.add( model.createStatement( lab, model.createProperty( LOCATED_IN_URI ), institution ) ); // add location_of property from the university to the lab model.add( model.createStatement( institution, model.createProperty( LOCATION_OF_URI ), lab ) ); return super.generateLab( institutionURI, institutionLabel, labLabel, labURI, labURL, labTypeURI, genParams ); }