public void classifyOntology(OWLOntology ontology, OWLReasonerFactory factory) {
ToStringRenderer.getInstance().setRenderer(new ManchesterOWLSyntaxOWLObjectRendererImpl());
OWLReasoner reasoner = factory.createNonBufferingReasoner(ontology);
// reasoner.precomputeInferences(InferenceType.values());
long time = System.currentTimeMillis();
boolean isConsistent = reasoner.isConsistent();
int numOfUnsatClasses = reasoner.getUnsatisfiableClasses().getEntitiesMinusBottom().size();
time = System.currentTimeMillis() - time;
DLExpressivityChecker checker = new DLExpressivityChecker(Collections.singleton(ontology));
String e = checker.getDescriptionLogicName();
String name = ontology.getOntologyID().getOntologyIRI().getFragment();
logger.info(
"ontology: "
+ name
+ ", reasoner: "
+ factory.getReasonerName()
+ ", expressivity: "
+ e
+ ", consistent: "
+ isConsistent
+ ", unsat classes: "
+ numOfUnsatClasses
+ ", time: "
+ time);
}
public static void main(String[] args) {
try {
SimpleRenderer renderer = new SimpleRenderer();
renderer.setShortFormProvider(
new DefaultPrefixManager("http://www.mindswap.org/ontologies/tambis-full.owl#"));
ToStringRenderer.getInstance().setRenderer(renderer);
OWLOntologyManager man = OWLManager.createOWLOntologyManager();
OWLOntology ont =
man.loadOntology(
IRI.create(
"http://owl.cs.manchester.ac.uk/repository/download?ontology=http://www.cs.manchester.ac.uk/owl/ontologies/tambis-patched.owl"));
System.out.println("Loaded!");
OWLReasonerFactory reasonerFactory = PelletReasonerFactory.getInstance();
OWLReasoner reasoner = reasonerFactory.createNonBufferingReasoner(ont);
reasoner.getUnsatisfiableClasses();
ExplanationBasedRootClassFinder rdr =
new ExplanationBasedRootClassFinder(man, reasoner, reasonerFactory);
for (OWLClass cls : rdr.getRootUnsatisfiableClasses()) System.out.println("ROOT! " + cls);
} catch (TimeOutException e) {
e.printStackTrace();
} catch (ReasonerInterruptedException e) {
e.printStackTrace();
} catch (OWLOntologyCreationException e) {
e.printStackTrace();
}
}
private void classifyWithJFact(OWLOntology ontology) {
System.out.println("\nUsing JFact ...");
long startTime = System.nanoTime();
OWLReasonerFactory reasonerFactory = new JFactFactory();
OWLReasoner jfactReasoner = reasonerFactory.createReasoner(ontology);
jfactReasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY);
jfactReasoner.dispose();
System.out.println("Time taken (secs): " + Util.getElapsedTimeSecs(startTime));
}
public void getELKIncrementalRuntime(String baseOnt, String ontDir) throws Exception {
GregorianCalendar start = new GregorianCalendar();
OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
IRI documentIRI = IRI.create(new File(baseOnt));
OWLOntology baseOntology = manager.loadOntology(documentIRI);
System.out.println("Logical axioms: " + baseOntology.getLogicalAxiomCount());
// findDataHasValueAxiom(baseOntology.getAxioms(AxiomType.SUBCLASS_OF));
OWLReasonerFactory reasonerFactory = new ElkReasonerFactory();
OWLReasoner reasoner = reasonerFactory.createReasoner(baseOntology);
reasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY);
File[] files = new File(ontDir).listFiles();
int count = 0;
OWLOntologyManager manager2 = OWLManager.createOWLOntologyManager();
addTripsBaseOntologies(manager2);
for (File file : files) {
System.out.println("File name: " + file.getName());
documentIRI = IRI.create(file);
OWLOntology ontology = manager2.loadOntology(documentIRI);
Set<OWLLogicalAxiom> axioms = ontology.getLogicalAxioms();
// findDataHasValueAxiom(ontology.getAxioms(AxiomType.SUBCLASS_OF));
manager.addAxioms(baseOntology, axioms);
reasoner.flush();
System.out.println("Logical axioms: " + baseOntology.getLogicalAxiomCount());
// From the ELK wiki, it seems ABox reasoning will trigger TBox reasoning
reasoner.precomputeInferences(InferenceType.CLASS_ASSERTIONS);
manager2.removeOntology(ontology);
count++;
System.out.println("Done with " + count);
// if(count == 5)
// break;
}
reasoner.dispose();
System.out.println("Time taken (millis): " + Util.getElapsedTime(start));
}
@SuppressWarnings({"unchecked", "rawtypes"})
private OWLReasoner createModuleReasoner() throws OWLOntologyCreationException {
LOG.info("Creating module reasoner for module: " + modelId);
ModuleType mtype = ModuleType.BOT;
OWLOntologyManager m =
OWLManager.createOWLOntologyManager(
aboxOntology.getOWLOntologyManager().getOWLDataFactory());
SyntacticLocalityModuleExtractor sme =
new SyntacticLocalityModuleExtractor(m, aboxOntology, mtype);
Set<OWLEntity> seeds = (Set) aboxOntology.getIndividualsInSignature();
OWLOntology module = sme.extractAsOntology(seeds, IRI.generateDocumentIRI());
OWLReasoner reasoner = reasonerFactory.createReasoner(module);
LOG.info("Done creating module reasoner module: " + modelId);
return reasoner;
}
/** @return current reasoner, operating over abox */
public OWLReasoner getReasoner() {
synchronized (reasonerMutex) {
if (reasoner == null) {
// reasoner -> query -> abox -> tbox
if (LOG.isDebugEnabled()) {
LOG.debug(
"Creating reasoner on "
+ queryOntology
+ " ImportsClosure="
+ queryOntology.getImportsClosure());
}
reasoner = reasonerFactory.createReasoner(queryOntology);
}
}
return reasoner;
}
public static void main(String[] args) {
try {
// Create our ontology manager in the usual way.
OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
// Load a copy of the people+pets ontology. We'll load the ontology from the web (it's
// acutally located
// in the TONES ontology repository).
IRI docIRI = IRI.create(DOCUMENT_IRI);
// We load the ontology from a document - our IRI points to it directly
OWLOntology ont = manager.loadOntologyFromOntologyDocument(docIRI);
System.out.println("Loaded " + ont.getOntologyID());
// We need to create an instance of OWLReasoner. An OWLReasoner provides the basic
// query functionality that we need, for example the ability obtain the subclasses
// of a class etc. To do this we use a reasoner factory.
// Create a reasoner factory. In this case, we will use HermiT, but we could also
// use FaCT++ (http://code.google.com/p/factplusplus/) or
// Pellet(http://clarkparsia.com/pellet)
// Note that (as of 03 Feb 2010) FaCT++ and Pellet OWL API 3.0.0 compatible libraries are
// expected to be available in the near future).
// For now, we'll use HermiT
// HermiT can be downloaded from http://hermit-reasoner.com
// Make sure you get the HermiT library and add it to your class path. You can then
// instantiate the HermiT reasoner factory:
// Comment out the first line below and uncomment the second line below to instantiate
// the HermiT reasoner factory. You'll also need to import the
// org.semanticweb.HermiT.Reasoner
// package.
OWLReasonerFactory reasonerFactory = null;
// OWLReasonerFactory reasonerFactory = new Reasoner.ReasonerFactory();
// We'll now create an instance of an OWLReasoner (the implementation being provided by HermiT
// as
// we're using the HermiT reasoner factory). The are two categories of reasoner, Buffering
// and
// NonBuffering. In our case, we'll create the buffering reasoner, which is the default kind
// of reasoner.
// We'll also attach a progress monitor to the reasoner. To do this we set up a configuration
// that
// knows about a progress monitor.
// Create a console progress monitor. This will print the reasoner progress out to the
// console.
ConsoleProgressMonitor progressMonitor = new ConsoleProgressMonitor();
// Specify the progress monitor via a configuration. We could also specify other setup
// parameters in
// the configuration, and different reasoners may accept their own defined parameters this
// way.
OWLReasonerConfiguration config = new SimpleConfiguration(progressMonitor);
// Create a reasoner that will reason over our ontology and its imports closure. Pass in the
// configuration.
OWLReasoner reasoner = reasonerFactory.createReasoner(ont, config);
// Ask the reasoner to do all the necessary work now
reasoner.precomputeInferences();
// We can determine if the ontology is actually consistent (in this case, it should be).
boolean consistent = reasoner.isConsistent();
System.out.println("Consistent: " + consistent);
System.out.println("\n");
// We can easily get a list of unsatisfiable classes. (A class is unsatisfiable if it
// can't possibly have any instances). Note that the getUnsatisfiableClasses method
// is really just a convenience method for obtaining the classes that are equivalent
// to owl:Nothing. In our case there should be just one unsatisfiable class - "mad_cow"
// We ask the reasoner for the unsatisfiable classes, which returns the bottom node
// in the class hierarchy (an unsatisfiable class is a subclass of every class).
Node<OWLClass> bottomNode = reasoner.getUnsatisfiableClasses();
// This node contains owl:Nothing and all the classes that are equivalent to owl:Nothing -
// i.e. the unsatisfiable classes.
// We just want to print out the unsatisfiable classes excluding owl:Nothing, and we can
// used a convenience method on the node to get these
Set<OWLClass> unsatisfiable = bottomNode.getEntitiesMinusBottom();
if (!unsatisfiable.isEmpty()) {
System.out.println("The following classes are unsatisfiable: ");
for (OWLClass cls : unsatisfiable) {
System.out.println(" " + cls);
}
} else {
System.out.println("There are no unsatisfiable classes");
}
System.out.println("\n");
// Now we want to query the reasoner for all descendants of vegetarian. Vegetarians are
// defined in the
// ontology to be animals that don't eat animals or parts of animals.
OWLDataFactory fac = manager.getOWLDataFactory();
// Get a reference to the vegetarian class so that we can as the reasoner about it.
// The full IRI of this class happens to be:
// <http://owl.man.ac.uk/2005/07/sssw/people#vegetarian>
OWLClass vegPizza =
fac.getOWLClass(IRI.create("http://owl.man.ac.uk/2005/07/sssw/people#vegetarian"));
// Now use the reasoner to obtain the subclasses of vegetarian.
// We can ask for the direct subclasses of vegetarian or all of the (proper) subclasses of
// vegetarian.
// In this case we just want the direct ones (which we specify by the "true" flag).
NodeSet<OWLClass> subClses = reasoner.getSubClasses(vegPizza, true);
// The reasoner returns a NodeSet, which represents a set of Nodes.
// Each node in the set represents a subclass of vegetarian pizza. A node of classes contains
// classes,
// where each class in the node is equivalent. For example, if we asked for the
// subclasses of some class A and got back a NodeSet containing two nodes {B, C} and {D}, then
// A would have
// two proper subclasses. One of these subclasses would be equivalent to the class D, and the
// other would
// be the class that is equivalent to class B and class C.
// In this case, we don't particularly care about the equivalences, so we will flatten this
// set of sets and print the result
Set<OWLClass> clses = subClses.getFlattened();
System.out.println("Subclasses of vegetarian: ");
for (OWLClass cls : clses) {
System.out.println(" " + cls);
}
System.out.println("\n");
// In this case, we should find that the classes, cow, sheep and giraffe are vegetarian. Note
// that in this
// ontology only the class cow had been stated to be a subclass of vegetarian. The fact that
// sheep and
// giraffe are subclasses of vegetarian was implicit in the ontology (through other things we
// had said)
// and this illustrates why it is important to use a reasoner for querying an ontology.
// We can easily retrieve the instances of a class. In this example we'll obtain the
// instances of
// the class pet. This class has a full IRI of <http://owl.man.ac.uk/2005/07/sssw/people#pet>
// We need to obtain a reference to this class so that we can ask the reasoner about it.
OWLClass country =
fac.getOWLClass(IRI.create("http://owl.man.ac.uk/2005/07/sssw/people#pet"));
// Ask the reasoner for the instances of pet
NodeSet<OWLNamedIndividual> individualsNodeSet = reasoner.getInstances(country, true);
// The reasoner returns a NodeSet again. This time the NodeSet contains individuals.
// Again, we just want the individuals, so get a flattened set.
Set<OWLNamedIndividual> individuals = individualsNodeSet.getFlattened();
System.out.println("Instances of pet: ");
for (OWLNamedIndividual ind : individuals) {
System.out.println(" " + ind);
}
System.out.println("\n");
// Again, it's worth noting that not all of the individuals that are returned were explicitly
// stated
// to be pets.
// Finally, we can ask for the property values (property assertions in OWL speak) for a given
// individual
// and property.
// Let's get the property values for the individual Mick, the full IRI of which is
// <http://owl.man.ac.uk/2005/07/sssw/people#Mick>
// Get a reference to the individual Mick
OWLNamedIndividual mick =
fac.getOWLNamedIndividual(IRI.create("http://owl.man.ac.uk/2005/07/sssw/people#Mick"));
// Let's get the pets of Mick
// Get hold of the has_pet property which has a full IRI of
// <http://owl.man.ac.uk/2005/07/sssw/people#has_pet>
OWLObjectProperty hasPet =
fac.getOWLObjectProperty(IRI.create("http://owl.man.ac.uk/2005/07/sssw/people#has_pet"));
// Now ask the reasoner for the has_pet property values for Mick
NodeSet<OWLNamedIndividual> petValuesNodeSet = reasoner.getObjectPropertyValues(mick, hasPet);
Set<OWLNamedIndividual> values = petValuesNodeSet.getFlattened();
System.out.println("The has_pet property values for Mick are: ");
for (OWLNamedIndividual ind : values) {
System.out.println(" " + ind);
}
// Notice that Mick has a pet Rex, which wasn't asserted in the ontology.
// Finally, let's print out the class hierarchy.
// Get hold of the top node in the class hierarchy (containing owl:Thing)
// Now print the hierarchy out
Node<OWLClass> topNode = reasoner.getTopClassNode();
print(topNode, reasoner, 0);
} catch (UnsupportedOperationException exception) {
System.out.println("Unsupported reasoner operation.");
} catch (OWLOntologyCreationException e) {
System.out.println("Could not load the pizza ontology: " + e.getMessage());
}
}
private void precomputeAndCheckResults(OWLOntology ontology) throws Exception {
System.out.println("Not Normalizing");
PropertyFileHandler propertyFileHandler = PropertyFileHandler.getInstance();
HostInfo resultNodeHostInfo = propertyFileHandler.getResultNode();
// port: 6489 for snapshot testing
Jedis resultStore =
new Jedis(
resultNodeHostInfo.getHost(), resultNodeHostInfo.getPort(), Constants.INFINITE_TIMEOUT);
Jedis resultStore2 =
new Jedis(
resultNodeHostInfo.getHost(), resultNodeHostInfo.getPort(), Constants.INFINITE_TIMEOUT);
resultStore2.select(2);
HostInfo localHostInfo = propertyFileHandler.getLocalHostInfo();
Jedis localStore = new Jedis(localHostInfo.getHost(), localHostInfo.getPort());
Set<String> idHosts =
localStore.zrange(
AxiomDistributionType.CONCEPT_ID.toString(),
Constants.RANGE_BEGIN,
Constants.RANGE_END);
// currently there is only one ID node
String[] idHostPort = idHosts.iterator().next().split(":");
Jedis idReader =
new Jedis(idHostPort[0], Integer.parseInt(idHostPort[1]), Constants.INFINITE_TIMEOUT);
GregorianCalendar cal1 = new GregorianCalendar();
try {
// OWLReasonerFactory reasonerFactory = new ElkReasonerFactory();
// OWLReasoner reasoner = reasonerFactory.createReasoner(ontology);
// reasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY);
// PelletReasoner reasoner = PelletReasonerFactory.getInstance().
// createReasoner( ontology );
// reasoner.prepareReasoner();
// Reasoner hermitReasoner = new Reasoner(ontology);
// hermitReasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY);
// OWLReasonerFactory reasonerFactory = new ElkReasonerFactory();
// OWLReasoner reasoner = reasonerFactory.createReasoner(ontology);
// reasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY);
// RELReasonerFactory relfactory = new RELReasonerFactory();
// RELReasoner reasoner = relfactory.createReasoner(ontology);
// reasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY);
// JcelReasoner reasoner = new JcelReasoner(ontology, false);
// reasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY);
OWLReasonerFactory reasonerFactory = new ElkReasonerFactory();
OWLReasoner reasoner = reasonerFactory.createReasoner(ontology);
reasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY);
System.out.println("Reasoner completed in (millis): " + Util.getElapsedTime(cal1));
System.out.println("Comparing results using ELK.....");
rearrangeAndCompareResults(ontology, reasoner, resultStore, resultStore2, idReader);
// pelletReasoner.dispose();
// reasonerELK.dispose();
reasoner.dispose();
} finally {
localStore.disconnect();
resultStore.disconnect();
resultStore2.disconnect();
idReader.disconnect();
}
}
public Set<NamingIssue> detectNonMatchingChildIssues(OWLOntology ontology, boolean directChild) {
long start = System.currentTimeMillis();
// get SubClass - SuperClass pairs
Set<NamingIssue> nonMatchingChildren = new HashSet<NamingIssue>();
if (directChild) {
Set<OWLSubClassOfAxiom> axioms = ontology.getAxioms(AxiomType.SUBCLASS_OF);
for (OWLSubClassOfAxiom ax : axioms) {
OWLClassExpression subClass = ax.getSubClass();
OWLClassExpression superClass = ax.getSuperClass();
if (!subClass.isAnonymous() && !superClass.isAnonymous()) {
String subClassURI = subClass.asOWLClass().toStringID();
String superClassURI = superClass.asOWLClass().toStringID();
if (ignoreSingleTokenSubClasses && !singleToken(subClassURI)) {
String subClassHead = getHeadNoun(subClassURI);
String superClassHead = getHeadNoun(superClassURI);
boolean matching =
subClassHead.equals(superClassHead) || isHypernymOf(superClassHead, subClassHead);
if (!matching) {
String newClassURI = buildNewURI(subClassURI, superClassHead);
nonMatchingChildren.add(
new NamingIssue(
subClassURI,
superClassURI,
new RenamingInstruction(subClassURI, newClassURI)));
}
}
}
}
} else {
OWLReasonerFactory reasonerFactory = PelletReasonerFactory.getInstance();
OWLReasoner reasoner = reasonerFactory.createNonBufferingReasoner(ontology);
Set<OWLClass> classes = ontology.getClassesInSignature();
for (OWLClass cls : classes) {
Set<OWLClass> superClasses = reasoner.getSuperClasses(cls, false).getFlattened();
superClasses.remove(OWL_THING);
for (OWLClass superClass : superClasses) {
String subClassURI = cls.asOWLClass().toStringID();
String superClassURI = superClass.asOWLClass().toStringID();
if (ignoreSingleTokenSubClasses && !singleToken(subClassURI)) {
String subClassHead = getHeadNoun(subClassURI);
String superClassHead = getHeadNoun(superClassURI);
boolean matching =
subClassHead.equals(superClassHead) || isHypernymOf(superClassHead, subClassHead);
if (!matching) {
String newClassURI = buildNewURI(subClassURI, superClassHead);
nonMatchingChildren.add(
new NamingIssue(
subClassURI,
superClassURI,
new RenamingInstruction(subClassURI, newClassURI)));
}
}
}
}
}
long end = System.currentTimeMillis();
logger.info("Operation took " + (end - start) + "ms");
return nonMatchingChildren;
}