public OWLOntology getMergedOntology() {
final IRI mergedOntologyIRI =
IRI.create(queryOntology.getOntologyID().getDefaultDocumentIRI() + "-merged");
final OWLOntologyManager mm = controller.getOWLOntologyManager();
if (mm.contains(mergedOntologyIRI)) {
return mm.getOntology(mergedOntologyIRI);
} else {
try {
final OWLOntology mergedOntology = mm.createOntology(mergedOntologyIRI);
mm.setOntologyFormat(mergedOntology, new RDFXMLOntologyFormat());
final String mergedOntologyFileName =
mergedOntologyIRI
.toURI()
.toString()
.substring(mergedOntologyIRI.toURI().toString().lastIndexOf("/") + 1)
+ ".owl";
mm.setOntologyDocumentIRI(
mergedOntology,
IRI.create(
controller.getRuleSpec().getOutputDir().toURI() + "/" + mergedOntologyFileName));
mm.applyChange(
new AddImport(
mergedOntology,
mm.getOWLDataFactory()
.getOWLImportsDeclaration(
queryOntology.getOntologyID().getDefaultDocumentIRI())));
return mergedOntology;
} catch (OWLOntologyCreationException e) {
// TODO Auto-generated catch block
e.printStackTrace();
return null;
}
}
}
public KuabaRepository createNewRepository(String url, File destination) {
IRI iri;
if (url == null) iri = IRI.generateDocumentIRI();
else iri = IRI.create(url);
try {
OWLOntology inst = manager.createOntology(iri);
OWLImportsDeclaration imp =
manager.getOWLDataFactory().getOWLImportsDeclaration(IRI.create(ONTOLOGY_URL));
AddImport addi = new AddImport(inst, imp);
manager.applyChange(addi);
KuabaRepository repo = new OwlApiKuabaRepository(inst, manager.getOWLDataFactory());
repoMap.put(inst.getOntologyID().getOntologyIRI(), repo);
fileMap.put(repo, destination);
TemplateGenerator.generateRootQuestion(repo);
if (destination != null) this.save(repo);
return repo;
} catch (OWLOntologyCreationException ex) {
Logger.getLogger(OwlApiFileGateway.class.getName()).log(Level.SEVERE, null, ex);
}
return null;
}
@Override
public void removeSubDataProperty(String subDataPropertyName, String dataPropertyName) {
OWLDataFactory factory = manager.getOWLDataFactory();
OWLDataProperty dataProperty =
factory.getOWLDataProperty(IRI.create(prefix + dataPropertyName));
OWLDataProperty subDataProperty =
factory.getOWLDataProperty(IRI.create(prefix + subDataPropertyName));
OWLAxiom axiom = factory.getOWLSubDataPropertyOfAxiom(subDataProperty, dataProperty);
axiom = changeManager.getAnnotatedAxiom(axiom);
RemoveAxiom removeAxiom = new RemoveAxiom(localContext, axiom);
try {
synchronized (this) {
changeManager.validateRemovalChange(axiom);
manager.applyChange(removeAxiom);
}
} catch (RemovalException ex) {
logger.severe(
ex.getMessage()
+ " Change ( removeSubDataProperty "
+ subDataPropertyName
+ " of "
+ dataPropertyName
+ ") will not be applied.");
}
}
@Override
public void addDataPropertyFloatRange(String dataPropertyName) {
OWLDataFactory factory = manager.getOWLDataFactory();
OWLDataProperty dataProperty =
factory.getOWLDataProperty(IRI.create(prefix + dataPropertyName));
OWLDatatype floatDatatype = factory.getFloatOWLDatatype();
OWLAxiom axiom = factory.getOWLDataPropertyRangeAxiom(dataProperty, floatDatatype);
axiom = changeManager.getAnnotatedAxiom(axiom);
AddAxiom addAxiom = new AddAxiom(localContext, axiom);
manager.applyChange(addAxiom);
}
@Override
public void addDataPropertyDomain(String dataPropertyName, String domainName) {
OWLDataFactory factory = manager.getOWLDataFactory();
OWLDataProperty dataProperty =
factory.getOWLDataProperty(IRI.create(prefix + dataPropertyName));
OWLClass domain = factory.getOWLClass(IRI.create(prefix + domainName));
OWLAxiom axiom = factory.getOWLDataPropertyDomainAxiom(dataProperty, domain);
axiom = changeManager.getAnnotatedAxiom(axiom);
AddAxiom addAxiom = new AddAxiom(localContext, axiom);
manager.applyChange(addAxiom);
}
public HeD2OwlHelper(
OWLOntology ontology,
OWLOntologyManager manager,
OWLDataFactory factory,
PrefixManager prefixManager) {
super(ontology, manager, factory, prefixManager);
OWLImportsDeclaration imprt =
manager
.getOWLDataFactory()
.getOWLImportsDeclaration(IRI.create("http://asu.edu/sharpc2b/sharp"));
manager.applyChange(new AddImport(ontology, imprt));
}
@Override
public void addSubDataProperty(String subDataPropertyName, String dataPropertyName) {
OWLDataFactory factory = manager.getOWLDataFactory();
OWLDataProperty dataProperty =
factory.getOWLDataProperty(IRI.create(prefix + dataPropertyName));
OWLDataProperty subDataProperty =
factory.getOWLDataProperty(IRI.create(prefix + subDataPropertyName));
OWLAxiom axiom = factory.getOWLSubDataPropertyOfAxiom(subDataProperty, dataProperty);
axiom = changeManager.getAnnotatedAxiom(axiom);
AddAxiom addAxiom = new AddAxiom(localContext, axiom);
try {
synchronized (this) {
changeManager.validateAddSubDataPropertyChange(axiom, subDataProperty, dataProperty);
manager.applyChange(addAxiom);
}
} catch (DeclarationException ex) {
logger.info(
ex.getMessage()
+ " Change ( addSubDataProperty "
+ subDataPropertyName
+ " of "
+ dataPropertyName
+ " ) will not be applied.");
} catch (RedundancyException ex) {
synchronized (this) {
removeSubDataProperty(ex.getSubCls(), ex.getCls());
manager.applyChange(addAxiom);
}
} catch (CycleException ex) {
logger.severe(
ex.getMessage()
+ " Change ( addSubDataProperty "
+ subDataPropertyName
+ " of "
+ dataPropertyName
+ ") will not be applied.");
}
}
@Override
public void addDataProperty(String dataPropertyName) {
OWLDataFactory factory = manager.getOWLDataFactory();
OWLDataProperty dataProperty =
factory.getOWLDataProperty(IRI.create(prefix + dataPropertyName));
OWLAxiom axiom = factory.getOWLDeclarationAxiom(dataProperty);
axiom = changeManager.getAnnotatedAxiom(axiom);
AddAxiom addAxiom = new AddAxiom(localContext, axiom);
try {
synchronized (this) {
changeManager.validateAddChange(axiom);
manager.applyChange(addAxiom);
}
} catch (DeclarationException ex) {
logger.info(
ex.getMessage()
+ "Change ( addDataProperty "
+ dataPropertyName
+ " ) will not be applied.");
}
}
@Override
public void removeDataPropertyBooleanRange(String dataPropertyName) {
OWLDataFactory factory = manager.getOWLDataFactory();
OWLDataProperty dataProperty =
factory.getOWLDataProperty(IRI.create(prefix + dataPropertyName));
OWLDatatype booleanDatatype = factory.getBooleanOWLDatatype();
OWLAxiom axiom = factory.getOWLDataPropertyRangeAxiom(dataProperty, booleanDatatype);
axiom = changeManager.getAnnotatedAxiom(axiom);
RemoveAxiom removeAxiom = new RemoveAxiom(localContext, axiom);
try {
synchronized (this) {
changeManager.validateRemovalChange(axiom);
manager.applyChange(removeAxiom);
}
} catch (RemovalException ex) {
logger.severe(
ex.getMessage()
+ " Change ( removeDataPropertyBooleanRange"
+ dataPropertyName
+ ") will not be applied.");
}
}
public static void main(String[] args)
throws OWLOntologyCreationException, IOException, OWLOntologyStorageException {
OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
OWLOntology ontology = manager.createOntology(ontologyIRI);
OWLDataFactory factory = manager.getOWLDataFactory();
// create basic concepts with their IRIs
currentPhase = factory.getOWLClass(IRI.create(ontologyIRI + "#CurrentPhase"));
previousPhase = factory.getOWLObjectProperty(IRI.create(ontologyIRI + "#previousPhase"));
detectedPhase = factory.getOWLClass(IRI.create(ontologyIRI + "#DetectedPhase"));
// init the currentPhase-class with the "start"-individual
OWLNamedIndividual start1 = factory.getOWLNamedIndividual(IRI.create(ontologyIRI + "start"));
manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(currentPhase, start1));
// create rule1
SWRLRule rulePP = buildRule("port_placement", "port", "unknown", "place");
manager.applyChange(new AddAxiom(ontology, rulePP));
// create rule2
SWRLRule ruleMob1 =
buildRule("mobilisation", "atraumatic_grasper", "gallbladder_fundus", "grasp");
manager.applyChange(new AddAxiom(ontology, ruleMob1));
SWRLRule ruleMob2 =
buildRule("mobilisation", "atraumatic_grasper", "gastrocolic_ligament", "grasp");
manager.applyChange(new AddAxiom(ontology, ruleMob2));
SWRLRule ruleDis1 =
buildRule("dissection", "atraumatic_grasper", "hepatoduodenal_ligament", "grasp");
manager.applyChange(new AddAxiom(ontology, ruleDis1));
SWRLRule ruleDis2 =
buildRule("dissection", "atraumatic_grasper", "hepatoduodenal_ligament", "lift");
manager.applyChange(new AddAxiom(ontology, ruleDis2));
SWRLRule ruleDis3 =
buildRule("dissection", "instrument", "calot_triangle", "instrumental_property");
manager.applyChange(new AddAxiom(ontology, ruleDis3));
SWRLRule ruleDis4 =
buildRule("dissection", "sharp_instrument", "hepatoduodenal_ligament", "cutting_action");
manager.applyChange(new AddAxiom(ontology, ruleDis4));
SWRLRule ruleResCA1 =
buildRule("resection_cystic_artery", "sharp_instrument", "cystic_artery", "cutting_action");
manager.applyChange(new AddAxiom(ontology, ruleResCA1));
SWRLRule ruleResCA2 = buildRule("resection_cystic_artery", "clip", "cystic_artery", "clipping");
manager.applyChange(new AddAxiom(ontology, ruleResCA2));
SWRLRule ruleResCD1 =
buildRule("resection_cystic_duct", "sharp_instrument", "cystic_duct", "cutting_action");
manager.applyChange(new AddAxiom(ontology, ruleResCD1));
SWRLRule ruleResCD2 = buildRule("resection_cystic_duct", "clip", "cystic_duct", "clipping");
manager.applyChange(new AddAxiom(ontology, ruleResCD2));
SWRLRule ruleResG1 =
buildRule(
"resection_gallbladder", "sharp_instrument", "gallbladder_serosa", "cutting_action");
manager.applyChange(new AddAxiom(ontology, ruleResG1));
SWRLRule ruleResG2 =
buildRule("resection_gallbladder", "sharp_instrument", "gallbladder_serosa", "dissect");
manager.applyChange(new AddAxiom(ontology, ruleResG2));
SWRLRule ruleResG3 =
buildRule("resection_gallbladder", "sharp_instrument", "gallbladder", "cutting_action");
manager.applyChange(new AddAxiom(ontology, ruleResG3));
SWRLRule ruleResG4 =
buildRule(
"resection_gallbladder", "sharp_instrument", "gallbladder_liverbed", "cutting_action");
manager.applyChange(new AddAxiom(ontology, ruleResG4));
SWRLRule ruleClose1 = buildRule("closure", "specimen_bag", "unknown", "instrumental_property");
manager.applyChange(new AddAxiom(ontology, ruleClose1));
SWRLRule ruleClose2 = buildRule("closure", "specimen_bag", "organ", "instrumental_property");
manager.applyChange(new AddAxiom(ontology, ruleClose2));
// Strange rules with the instrument "drain". It should be called "drainage" as by the next two
// rules.
// SWRLRule ruleDrain1 = buildRule("drain", "drain", "unknown", "putting_action");
// manager.applyChange(new AddAxiom(ontology, ruleDrain1));
// SWRLRule ruleDrain2 = buildRule("drain", "drain", "unknown", "instrumental_property");
// manager.applyChange(new AddAxiom(ontology, ruleDrain2));
SWRLRule ruleDrainage1 = buildRule("drain", "drainage", "unknown", "instrumental_property");
manager.applyChange(new AddAxiom(ontology, ruleDrainage1));
SWRLRule ruleDrainage2 = buildRule("drain", "drainage", "organ", "instrumental_property");
manager.applyChange(new AddAxiom(ontology, ruleDrainage2));
// save in RDF/XML format
File output = new File("D:/DiplArbeit/OurWork/USECASE/RULES/CCE_rules.owl");
output.createNewFile();
manager.saveOntology(ontology, IRI.create(output.toURI()));
}
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;
}
}
/** @param args */
public static void main(String[] args) {
String external = "http://purl.obolibrary.org/obo/iao/dev/external.owl";
String externalDerived = "http://purl.obolibrary.org/obo/iao/dev/externalDerived.owl";
String externalByHand = "http://purl.obolibrary.org/obo/iao/dev/externalByHand.owl";
String metaData = "http://purl.obolibrary.org/obo/iao/dev/ontology-metadata.owl";
String reasonerName = "hermit";
String path = "C:/Documents and Settings/Jie/My Documents/Ontology/iao/releases/2012-01-05/";
String saveIaoFilename = path + "merged/iao-main-infer.owl";
String inferOntURIStr = "http://purl.obolibrary.org/obo/iao/dev/iao_inferredSuperClasses.owl";
String saveInferFilename = path + "merged/iao-inferredSuperClasses.owl";
// Get hold of an ontology manager
OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
AutoIRIMapper mapper = new AutoIRIMapper(new File(path + "ontology/"), false);
manager.addIRIMapper(mapper);
OWLOntology iaoOnt = OntologyManipulator.load(path + "ontology/iao-main.owl", manager);
// OntologyManipulator.printPrefixNSs(manager, iaoOnt);
OWLDataFactory df = manager.getOWLDataFactory();
// get all imported ontologies
Set<OWLOntology> importOnts = iaoOnt.getImports();
// remove imports statements from the loaded ontology
for (OWLOntology importOnt : importOnts) {
IRI importOntIRI = importOnt.getOntologyID().getOntologyIRI();
if (importOntIRI.equals(IRI.create(metaData))
|| importOntIRI.equals(IRI.create(external))
|| importOntIRI.equals(IRI.create(externalByHand))
|| importOntIRI.equals(IRI.create(externalDerived))) {
RemoveImport ri = new RemoveImport(iaoOnt, df.getOWLImportsDeclaration(importOntIRI));
manager.applyChange(ri);
}
}
// merge the removed imported ontologies to the loaded one
for (OWLOntology importOnt : importOnts) {
IRI importOntIRI = importOnt.getOntologyID().getOntologyIRI();
if (importOntIRI.equals(IRI.create(metaData))
|| importOntIRI.equals(IRI.create(external))
|| importOntIRI.equals(IRI.create(externalByHand))
|| importOntIRI.equals(IRI.create(externalDerived))) {
// OntologyManipulator.printPrefixNSs(manager, importOnt);
iaoOnt = OntologyManipulator.mergeToTargetOnt(manager, iaoOnt, importOnt);
}
}
// generate the inferred hierarchy and clean the super classes
OWLReasoner reasoner = OWLReasonerRunner.runReasoner(manager, iaoOnt, reasonerName);
iaoOnt =
OWLReasonerRunner.getCleanedOntologyWithInferredSuperClasses(
manager, iaoOnt, inferOntURIStr, reasoner);
OntologyManipulator.saveToFile(manager, iaoOnt, saveIaoFilename);
if (manager.contains(IRI.create(inferOntURIStr))) {
OWLOntology inferOnt = manager.getOntology(IRI.create(inferOntURIStr));
OntologyManipulator.saveToFile(manager, inferOnt, saveInferFilename);
}
}