public void writeOntology() throws OWLRendererException { if (ontologies.size() != 1) { throw new OWLRuntimeException("Can only render one ontology"); } OWLOntology ontology = getOntologies().iterator().next(); writePrefixMap(); writeNewLine(); writeOntologyHeader(ontology); for (OWLAnnotationProperty prop : ontology.getAnnotationPropertiesInSignature()) { write(prop); } for (OWLDatatype datatype : ontology.getDatatypesInSignature()) { write(datatype); } for (OWLObjectProperty prop : ontology.getObjectPropertiesInSignature()) { write(prop); OWLObjectPropertyExpression invProp = prop.getInverseProperty(); if (!ontology.getAxioms(invProp).isEmpty()) { write(invProp); } } for (OWLDataProperty prop : ontology.getDataPropertiesInSignature()) { write(prop); } for (OWLClass cls : ontology.getClassesInSignature()) { write(cls); } for (OWLNamedIndividual ind : ontology.getIndividualsInSignature()) { write(ind); } for (OWLAnonymousIndividual ind : ontology.getReferencedAnonymousIndividuals()) { write(ind); } // Nary disjoint classes axioms event = new RendererEvent(this, ontology); for (OWLDisjointClassesAxiom ax : ontology.getAxioms(AxiomType.DISJOINT_CLASSES)) { if (ax.getClassExpressions().size() > 2) { SectionMap map = new SectionMap(); map.add(ax.getClassExpressions(), ax); writeSection(DISJOINT_CLASSES, map, ",", false, ontology); } } // Nary equivalent classes axioms for (OWLEquivalentClassesAxiom ax : ontology.getAxioms(AxiomType.EQUIVALENT_CLASSES)) { if (ax.getClassExpressions().size() > 2) { SectionMap map = new SectionMap(); map.add(ax.getClassExpressions(), ax); writeSection(EQUIVALENT_CLASSES, map, ",", false, ontology); } } // Nary disjoint properties for (OWLDisjointObjectPropertiesAxiom ax : ontology.getAxioms(AxiomType.DISJOINT_OBJECT_PROPERTIES)) { if (ax.getProperties().size() > 2) { SectionMap map = new SectionMap(); map.add(ax.getProperties(), ax); writeSection(DISJOINT_PROPERTIES, map, ",", false, ontology); } } // Nary equivlant properties for (OWLEquivalentObjectPropertiesAxiom ax : ontology.getAxioms(AxiomType.EQUIVALENT_OBJECT_PROPERTIES)) { if (ax.getProperties().size() > 2) { SectionMap map = new SectionMap(); map.add(ax.getProperties(), ax); writeSection(EQUIVALENT_PROPERTIES, map, ",", false, ontology); } } // Nary disjoint properties for (OWLDisjointDataPropertiesAxiom ax : ontology.getAxioms(AxiomType.DISJOINT_DATA_PROPERTIES)) { if (ax.getProperties().size() > 2) { SectionMap map = new SectionMap(); map.add(ax.getProperties(), ax); writeSection(DISJOINT_PROPERTIES, map, ",", false, ontology); } } // Nary equivalent properties for (OWLEquivalentDataPropertiesAxiom ax : ontology.getAxioms(AxiomType.EQUIVALENT_DATA_PROPERTIES)) { if (ax.getProperties().size() > 2) { SectionMap map = new SectionMap(); map.add(ax.getProperties(), ax); writeSection(EQUIVALENT_PROPERTIES, map, ",", false, ontology); } } // Nary different individuals for (OWLDifferentIndividualsAxiom ax : ontology.getAxioms(AxiomType.DIFFERENT_INDIVIDUALS)) { if (ax.getIndividuals().size() > 2) { SectionMap map = new SectionMap(); map.add(ax.getIndividuals(), ax); writeSection(DIFFERENT_INDIVIDUALS, map, ",", false, ontology); } } for (SWRLRule rule : ontology.getAxioms(AxiomType.SWRL_RULE)) { writeSection(RULE, Collections.singleton(rule), ", ", false); } flush(); }
private OWLOntology parseWithReasoner(OWLOntologyManager manager, OWLOntology ontology) { try { PelletOptions.load(new URL("http://" + cssLocation + "pellet.properties")); PelletReasoner reasoner = PelletReasonerFactory.getInstance().createReasoner(ontology); reasoner.getKB().prepare(); List<InferredAxiomGenerator<? extends OWLAxiom>> generators = new ArrayList<InferredAxiomGenerator<? extends OWLAxiom>>(); generators.add(new InferredSubClassAxiomGenerator()); generators.add(new InferredClassAssertionAxiomGenerator()); generators.add(new InferredDisjointClassesAxiomGenerator()); generators.add(new InferredEquivalentClassAxiomGenerator()); generators.add(new InferredEquivalentDataPropertiesAxiomGenerator()); generators.add(new InferredEquivalentObjectPropertyAxiomGenerator()); generators.add(new InferredInverseObjectPropertiesAxiomGenerator()); generators.add(new InferredPropertyAssertionGenerator()); generators.add(new InferredSubDataPropertyAxiomGenerator()); generators.add(new InferredSubObjectPropertyAxiomGenerator()); InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, generators); OWLOntologyID id = ontology.getOntologyID(); Set<OWLImportsDeclaration> declarations = ontology.getImportsDeclarations(); Set<OWLAnnotation> annotations = ontology.getAnnotations(); Map<OWLEntity, Set<OWLAnnotationAssertionAxiom>> entityAnnotations = new HashMap<OWLEntity, Set<OWLAnnotationAssertionAxiom>>(); for (OWLClass aEntity : ontology.getClassesInSignature()) { entityAnnotations.put(aEntity, aEntity.getAnnotationAssertionAxioms(ontology)); } for (OWLObjectProperty aEntity : ontology.getObjectPropertiesInSignature()) { entityAnnotations.put(aEntity, aEntity.getAnnotationAssertionAxioms(ontology)); } for (OWLDataProperty aEntity : ontology.getDataPropertiesInSignature()) { entityAnnotations.put(aEntity, aEntity.getAnnotationAssertionAxioms(ontology)); } for (OWLNamedIndividual aEntity : ontology.getIndividualsInSignature()) { entityAnnotations.put(aEntity, aEntity.getAnnotationAssertionAxioms(ontology)); } for (OWLAnnotationProperty aEntity : ontology.getAnnotationPropertiesInSignature()) { entityAnnotations.put(aEntity, aEntity.getAnnotationAssertionAxioms(ontology)); } for (OWLDatatype aEntity : ontology.getDatatypesInSignature()) { entityAnnotations.put(aEntity, aEntity.getAnnotationAssertionAxioms(ontology)); } manager.removeOntology(ontology); OWLOntology inferred = manager.createOntology(id); iog.fillOntology(manager, inferred); for (OWLImportsDeclaration decl : declarations) { manager.applyChange(new AddImport(inferred, decl)); } for (OWLAnnotation ann : annotations) { manager.applyChange(new AddOntologyAnnotation(inferred, ann)); } for (OWLClass aEntity : inferred.getClassesInSignature()) { applyAnnotations(aEntity, entityAnnotations, manager, inferred); } for (OWLObjectProperty aEntity : inferred.getObjectPropertiesInSignature()) { applyAnnotations(aEntity, entityAnnotations, manager, inferred); } for (OWLDataProperty aEntity : inferred.getDataPropertiesInSignature()) { applyAnnotations(aEntity, entityAnnotations, manager, inferred); } for (OWLNamedIndividual aEntity : inferred.getIndividualsInSignature()) { applyAnnotations(aEntity, entityAnnotations, manager, inferred); } for (OWLAnnotationProperty aEntity : inferred.getAnnotationPropertiesInSignature()) { applyAnnotations(aEntity, entityAnnotations, manager, inferred); } for (OWLDatatype aEntity : inferred.getDatatypesInSignature()) { applyAnnotations(aEntity, entityAnnotations, manager, inferred); } return inferred; } catch (FileNotFoundException e1) { return ontology; } catch (MalformedURLException e1) { return ontology; } catch (IOException e1) { return ontology; } catch (OWLOntologyCreationException e) { return ontology; } }