public void writeOntologyHeader(OWLOntology ontology) {
event = new RendererEvent(this, ontology);
fireFrameRenderingPrepared(ONTOLOGY.toString());
write(ONTOLOGY.toString());
write(":");
writeSpace();
if (!ontology.isAnonymous()) {
int indent = getIndent();
writeFullURI(ontology.getOntologyID().getOntologyIRI().toString());
writeNewLine();
pushTab(indent);
if (ontology.getOntologyID().getVersionIRI() != null) {
writeFullURI(ontology.getOntologyID().getVersionIRI().toString());
}
popTab();
}
fireFrameRenderingStarted(ONTOLOGY.toString());
writeNewLine();
for (OWLImportsDeclaration decl : ontology.getImportsDeclarations()) {
fireSectionItemPrepared(IMPORT.toString());
write(IMPORT.toString());
write(":");
writeSpace();
fireSectionRenderingStarted(IMPORT.toString());
writeFullURI(decl.getURI().toString());
writeNewLine();
fireSectionRenderingFinished(IMPORT.toString());
}
writeNewLine();
writeSection(ANNOTATIONS, ontology.getAnnotations(), ",", true);
fireFrameRenderingFinished(ONTOLOGY.toString());
}
public void visit(OWLOntology ontology) {
checkOccurrence(ontology.getAnnotations());
for (AxiomType<?> t : AxiomType.AXIOM_TYPES) {
for (OWLAxiom ax : ontology.getAxioms(t)) {
checkOccurrence(ax.getAnnotations());
ax.accept(this);
}
}
singleAppearance.clear();
}
private OntologyManager() {
_manager = OWLManager.createOWLOntologyManager();
try {
_ontology = _manager.loadOntology(IRI.create(getClass().getResource(ONTOLOGY_RESOURCE_PATH)));
for (OWLAnnotation anon : _ontology.getAnnotations()) {
if (anon.getProperty().getIRI().toString().equals(DomainOntology.taxonomyDefinedBy)) {
_taxonomyType = anon.getValue().toString().replace("\"", "");
break;
}
}
_reasoner = new StructuralReasonerFactory().createReasoner(_ontology);
} catch (OWLOntologyCreationException ex) {
Log.e(TAG, "Error while loading the domain ontology");
_taxonomyType = null;
}
}
@Test
public void testConvert() throws Exception {
// PARSE TEST FILE
OWLOntology ontology = convert(parseOBOFile("synonym_test.obo"));
Set<OWLAnnotation> anns = ontology.getAnnotations();
for (OWLAnnotation ann : anns) {
// TODO
System.out.println("Ann=" + ann);
}
Set<OWLAnnotationProperty> aps = ontology.getAnnotationPropertiesInSignature();
for (OWLAnnotationProperty ap : aps) {
System.out.println("ap=" + ap);
}
// TODO
}
public void mergeOntologies() {
List<OWLOntologyChange> changes = new ArrayList<OWLOntologyChange>();
for (OWLOntology ont : ontologies) {
if (!ont.equals(targetOntology)) {
// move the axioms
for (OWLAxiom ax : ont.getAxioms()) {
changes.add(new AddAxiom(targetOntology, ax));
}
// move ontology annotations
for (OWLAnnotation annot : ont.getAnnotations()) {
changes.add(new AddOntologyAnnotation(targetOntology, annot));
}
if (!targetOntology.getOntologyID().isAnonymous()) {
// move ontology imports
for (OWLImportsDeclaration decl : ont.getImportsDeclarations()) {
if (ontologies.contains(ont.getOWLOntologyManager().getImportedOntology(decl))) {
continue;
}
Optional<IRI> defaultDocumentIRI =
targetOntology.getOntologyID().getDefaultDocumentIRI();
if (defaultDocumentIRI.isPresent() && !decl.getIRI().equals(defaultDocumentIRI.get())) {
changes.add(new AddImport(targetOntology, decl));
} else {
logger.warn(
"Merge: ignoring import declaration for ontology "
+ targetOntology.getOntologyID()
+ " (would result in target ontology importing itself).");
}
}
}
}
}
try {
owlOntologyManager.applyChanges(changes);
} catch (OWLOntologyChangeException e) {
ErrorLogPanel.showErrorDialog(e);
}
}
public void storeFromTo(OWLOntology from, HGDBOntology to) {
final Set<OWLAxiom> axioms = from.getAxioms();
int i = 0;
for (OWLAxiom axiom : axioms) {
to.applyChange(new AddAxiom(to, axiom));
i++;
if (i % 5000 == 0) {
System.out.println("storeFromTo: Axioms: " + i);
}
}
System.out.println("storeFromTo: Axioms: " + i);
// manager.addAxioms(newOnto, axioms);
// Add Ontology Annotations
for (OWLAnnotation a : from.getAnnotations()) {
to.applyChange(new AddOntologyAnnotation(to, a));
}
// Add Import Declarations
for (OWLImportsDeclaration im : from.getImportsDeclarations()) {
to.applyChange(new AddImport(to, im));
}
}
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;
}
}
