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[DL-Learner SVN] SF.net SVN: dl-learner:[3602] trunk/components-core/src/main/java/org/ dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java
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From: <lor...@us...> - 2012-03-01 02:50:21
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Revision: 3602
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3602&view=rev
Author: lorenz_b
Date: 2012-03-01 02:50:14 +0000 (Thu, 01 Mar 2012)
Log Message:
-----------
Added workaround for problem in OWLAPI with user-defined datatypes.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java
Modified: trunk/components-core/src/main/java/org/dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java 2012-02-29 08:08:16 UTC (rev 3601)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java 2012-03-01 02:50:14 UTC (rev 3602)
@@ -2,6 +2,8 @@
import java.io.BufferedInputStream;
import java.io.BufferedOutputStream;
+import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
@@ -47,7 +49,6 @@
import org.semanticweb.owlapi.model.OWLDataFactory;
import org.semanticweb.owlapi.model.OWLEntity;
import org.semanticweb.owlapi.model.OWLLiteral;
-import org.semanticweb.owlapi.model.OWLLogicalAxiom;
import org.semanticweb.owlapi.model.OWLObjectProperty;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLOntologyCreationException;
@@ -64,13 +65,18 @@
import uk.ac.manchester.cs.owl.owlapi.OWLDataFactoryImpl;
import uk.ac.manchester.cs.owlapi.modularity.ModuleType;
-import com.clarkparsia.modularity.IncrementalClassifier;
import com.clarkparsia.modularity.ModularityUtils;
import com.clarkparsia.owlapi.explanation.BlackBoxExplanation;
import com.clarkparsia.owlapi.explanation.HSTExplanationGenerator;
import com.clarkparsia.owlapi.explanation.PelletExplanation;
import com.clarkparsia.pellet.owlapiv3.PelletReasoner;
import com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory;
+import com.hp.hpl.jena.rdf.model.Model;
+import com.hp.hpl.jena.rdf.model.ModelFactory;
+import com.hp.hpl.jena.rdf.model.RDFNode;
+import com.hp.hpl.jena.rdf.model.Statement;
+import com.hp.hpl.jena.rdf.model.StmtIterator;
+import com.hp.hpl.jena.vocabulary.RDFS;
public class JustificationBasedCoherentOntologyExtractor implements CoherentOntologyExtractor{
@@ -108,7 +114,7 @@
private OWLOntology dbpediaOntology;
- private String fileName = "dbpedia";
+ private String fileName;
private String diffFileName = "diff.owl";
public JustificationBasedCoherentOntologyExtractor() {
@@ -117,7 +123,7 @@
} catch (NoSuchAlgorithmException e) {
e.printStackTrace();
}
- dbpediaOntology = loadDBpediaOntology();
+ dbpediaOntology = loadDBpediaOntologyOWLDL();
}
static {PelletExplanation.setup();}
@@ -147,7 +153,8 @@
e1.printStackTrace();
}
- //only for debugging
+ /*only to avoid Pellet warnings during the process and this axioms are only removed from the ontology,
+ which is used during the debugging and not from the ontology which is always saved and returned finally*/
removedTransitiveAxioms = incoherentOntology.getAxioms(AxiomType.TRANSITIVE_OBJECT_PROPERTY);
incoherentOntology.getOWLOntologyManager().removeAxioms(incoherentOntology, removedTransitiveAxioms);
@@ -181,12 +188,6 @@
}
private OWLOntology computeCoherentOntologyRootBased(OWLOntology ontology) {
-
-// startTime = System.currentTimeMillis();
-// hermitReasoner = new Reasoner(incoherentOntology);
-// hermitReasoner.classifyClasses();
-// logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
-
OWLOntologyManager man = incoherentOntology.getOWLOntologyManager();
factory = man.getOWLDataFactory();
// man.addOntologyChangeListener(reasoner);
@@ -203,9 +204,9 @@
int derivedCnt = derivedUnsatClasses.size();
//if no roots are found we use all unsat classes
- if(rootCnt == 0){
- unsatClasses = derivedUnsatClasses;
- }
+ if(rootCnt == 0){
+ unsatClasses = derivedUnsatClasses;
+ }
// Set<OWLClass> unsatClasses = reasoner.getUnsatisfiableClasses().getEntitiesMinusBottom();
int cnt = rootCnt + derivedCnt;
@@ -333,6 +334,10 @@
unsatPropCnt = unsatObjectProperties.size();
}
+ if(unsatObjectProperties.isEmpty()){
+ break;
+ }
+
//recompute explanations if necessary
logger.info("Recomputing explanations...");
startTime = System.currentTimeMillis();
@@ -349,39 +354,42 @@
}
private OWLOntology computeCoherentOntology(OWLOntology ontology) {
+ OWLOntologyManager man = incoherentOntology.getOWLOntologyManager();
+ factory = man.getOWLDataFactory();
+// man.addOntologyChangeListener(reasoner);
+
//compute the unsatisfiable classes
logger.info("Computing unsatisfiable classes...");
long startTime = System.currentTimeMillis();
+ Set<OWLClass> unsatClasses = reasoner.getUnsatisfiableClasses().getEntitiesMinusBottom();
logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
- Set<OWLClass> unsatClasses = reasoner.getUnsatisfiableClasses().getEntitiesMinusBottom();
- int cnt = unsatClasses.size();
- logger.info("Detected " + cnt + " unsatisfiable classes.");
+ logger.info("Detected " + unsatClasses.size() + " unsatisfiable classes.");
//if the ontology is not incoherent we return it here
if(unsatClasses.isEmpty()){
return incoherentOntology;
}
- //compute the logical modules for each unsatisfiable class
- logger.info("Computing module for each unsatisfiable class...");
- startTime = System.currentTimeMillis();
- entity2ModuleMap = extractModules(unsatClasses);
- logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
//compute initial explanations for each unsatisfiable class
logger.info("Computing initial explanations...");
startTime = System.currentTimeMillis();
computeExplanations(unsatClasses);
-// entity2Explanations.putAll(getInitialExplanations(unsatObjectProperties));
+ if(computeParallel){
+ computeExplanations(unsatObjectProperties);
+ }
logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
- while(!unsatClasses.isEmpty()){// && !unsatObjectProperties.isEmpty()){
+ int cnt = unsatClasses.size();
+ if(computeParallel){
+ cnt += unsatObjectProperties.size();
+ }
+
+ while(cnt > 0){
//we remove the most appropriate axiom from the ontology
removeAppropriateAxiom();
- //recompute the unsatisfiable classes
- logger.info("Reclassifying...");
+ logger.info("Computing unsatisfiable classes...");
startTime = System.currentTimeMillis();
- reasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY);
unsatClasses = reasoner.getUnsatisfiableClasses().getEntitiesMinusBottom();
logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
logger.info("Remaining unsatisfiable classes: " + unsatClasses.size());
@@ -391,30 +399,75 @@
logger.info("Remaining unsatisfiable object properties: " + unsatObjectProperties.size());
//save
- if(cnt - unsatClasses.size() >= 10){
+ if((!computeParallel && (cnt-unsatClasses.size()>= 5))
+ || (computeParallel && (cnt-unsatClasses.size()+unsatObjectProperties.size())>=5)){
cnt = unsatClasses.size();
- save("log/" + fileName + "_" + cnt + "cls" + unsatObjectProperties.size() + "prop.owl");
+ save("log/" + fileName + "_" + unsatClasses.size() + "cls" + unsatObjectProperties.size() + "prop.owl");
+ if(computeParallel){
+ cnt += unsatObjectProperties.size();
+ }
}
+ if(unsatClasses.isEmpty() && (!computeParallel || (computeParallel && unsatObjectProperties.isEmpty()))){
+ cnt = 0;
+ break;
+ }
//recompute explanations if necessary
logger.info("Recomputing explanations...");
startTime = System.currentTimeMillis();
- refillExplanations(unsatClasses, entity2Explanations);
- //refillExplanations(unsatObjectProperties, entity2Explanations);
+ computeExplanations(unsatClasses);
+ if(computeParallel){
+ computeExplanations(unsatObjectProperties);
+ }
logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
System.gc();
}
- try {
- incoherentOntology.getOWLOntologyManager().saveOntology(getOntologyWithAnnotations(incoherentOntology), new RDFXMLOntologyFormat(), new BufferedOutputStream(new FileOutputStream("log/dbpedia_coherent.owl")));
- } catch (OWLOntologyStorageException e) {
- e.printStackTrace();
- } catch (FileNotFoundException e) {
- e.printStackTrace();
+ entity2Explanations.clear();
+ entity2ModuleMap.clear();
+
+ save("log/" + fileName + "_" + unsatClasses.size() + "cls" + unsatObjectProperties.size() + "prop.owl");
+
+
+ if(!computeParallel){
+ unsatObjectProperties = getUnsatisfiableObjectProperties();
+ int unsatPropCnt = unsatObjectProperties.size();
+ logger.info("Remaining unsatisfiable object properties: " + unsatObjectProperties.size());
+
+ logger.info("Recomputing explanations...");
+ startTime = System.currentTimeMillis();
+ computeExplanations(unsatObjectProperties);
+ logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
+ while(unsatPropCnt > 0){
+ //we remove the most appropriate axiom from the ontology
+ removeAppropriateAxiom();
+
+ //recompute unsatisfiable object properties
+ unsatObjectProperties = getUnsatisfiableObjectProperties();
+ logger.info("Remaining unsatisfiable object properties: " + unsatObjectProperties.size());
+
+ //save
+ if((unsatPropCnt - unsatObjectProperties.size()) >= 5){
+ save("log/" + fileName + "_" + unsatClasses.size() + "cls" + unsatPropCnt + "prop.owl");
+ unsatPropCnt = unsatObjectProperties.size();
+ }
+ if(unsatObjectProperties.isEmpty()){
+ break;
+ }
+
+ //recompute explanations if necessary
+ logger.info("Recomputing explanations...");
+ startTime = System.currentTimeMillis();
+ computeExplanations(unsatObjectProperties);
+ logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
+
+ System.gc();
+ }
}
- System.out.println(incoherentOntology.getLogicalAxiomCount());
- return getOntologyWithAnnotations(incoherentOntology);
+ save("log/" + fileName + "_coherent.owl");
+
+ return ontology;
}
private OWLOntology computeCoherentOntology2(OWLOntology ontology) {
@@ -473,16 +526,9 @@
logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
}
- try {
- incoherentOntology.getOWLOntologyManager().saveOntology(getOntologyWithAnnotations(incoherentOntology), new RDFXMLOntologyFormat(), new BufferedOutputStream(new FileOutputStream("log/dbpedia_coherent.owl")));
- } catch (OWLOntologyStorageException e) {
- e.printStackTrace();
- } catch (FileNotFoundException e) {
- e.printStackTrace();
- }
- System.out.println(incoherentOntology.getLogicalAxiomCount());
+ save("log/" + fileName + "_coherent.owl");
- return getOntologyWithAnnotations(incoherentOntology);
+ return ontology;
}
private void removeAppropriateAxiom(){
@@ -491,6 +537,12 @@
Map<OWLAxiom, Integer> axiom2CountMap = getAxiomFrequency(entity2Explanations);
//get a sorted list of entries with the highest axiom count first
List<Entry<OWLAxiom, Integer>> sortedEntries = sort(axiom2CountMap);
+ logger.info("Candidates: " + sortedEntries.size());
+ if(sortedEntries.size() >= 2){
+ logger.info("First: " + sortedEntries.get(0) + "(" + getConfidence(sortedEntries.get(0).getKey()) + ")");
+ logger.info("Second: " + sortedEntries.get(1) + "(" + getConfidence(sortedEntries.get(1).getKey()) + ")");
+ }
+
//we remove the most frequent axiom from the ontology which is not contained in the original DBpedia ontology
for(Entry<OWLAxiom, Integer> e : sortedEntries){
OWLAxiom axiom = e.getKey();
@@ -511,6 +563,8 @@
}
private void save(String fileName){
+ logger.info("Writing to disk...");
+ long startTime = System.currentTimeMillis();
try {
ontology.getOWLOntologyManager().saveOntology(ontology, new RDFXMLOntologyFormat(), new BufferedOutputStream(new FileOutputStream(fileName)));
diffOntology.getOWLOntologyManager().saveOntology(diffOntology, new RDFXMLOntologyFormat(), new BufferedOutputStream(new FileOutputStream("log/" + diffFileName)));
@@ -519,6 +573,7 @@
} catch (FileNotFoundException e) {
e.printStackTrace();
}
+ logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
}
private Set<OWLObjectProperty> getUnsatisfiableObjectProperties(){
@@ -526,13 +581,20 @@
long startTime = System.currentTimeMillis();
SortedSet<OWLObjectProperty> properties = new TreeSet<OWLObjectProperty>();
OWLDataFactory f = OWLManager.createOWLOntologyManager().getOWLDataFactory();
- for(OWLObjectProperty p : reasoner.getRootOntology().getObjectPropertiesInSignature()){
+ for(OWLObjectProperty p : incoherentOntology.getObjectPropertiesInSignature()){
// boolean satisfiable = reasoner.isSatisfiable(f.getOWLObjectExactCardinality(1, p));
boolean satisfiable = reasoner.isSatisfiable(f.getOWLObjectSomeValuesFrom(p, factory.getOWLThing()));
if(!satisfiable){
properties.add(p);
}
}
+ /*
+ * this method down't seem to work TODO ask Pellet developers why
+ for(OWLObjectPropertyExpression p : reasoner.getEquivalentObjectProperties(factory.getOWLBottomObjectProperty()).getEntitiesMinusBottom()){
+ if(!p.isAnonymous()){
+ properties.add(p.asOWLObjectProperty());
+ }
+ }*/
logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
return properties;
}
@@ -556,17 +618,6 @@
}
}
- private void refillExplanations(Set<? extends OWLEntity> unsatEntities, Map<OWLEntity, Set<Set<OWLAxiom>>> entity2Explanations){
- for(OWLEntity unsatClass : unsatEntities){
- Set<Set<OWLAxiom>> precomputedExplanations = entity2Explanations.get(unsatClass);
- if(precomputedExplanations == null || precomputedExplanations.size() < numberOfJustifications){
- Set<Set<OWLAxiom>> newExplanations = computeExplanations(unsatClass, numberOfJustifications);
- logger.info(unsatClass + ": " + newExplanations.size());
- entity2Explanations.put(unsatClass, newExplanations);
- }
- }
- }
-
private Map<OWLAxiom, Integer> getAxiomFrequency(Map<OWLEntity, Set<Set<OWLAxiom>>> entity2Explanations){
Map<OWLAxiom, Integer> axiom2CountMap = new HashMap<OWLAxiom, Integer>();
@@ -632,18 +683,6 @@
return null;
}
- private OWLOntology getOntologyWithAnnotations(OWLOntology ontologyWithOutAnnotations){
- logger.info("BEFORE: "+ ontology.getSubClassAxiomsForSubClass(factory.getOWLClass(IRI.create("http://dbpedia.org/ontology/Award"))));
- OWLOntologyManager man = ontology.getOWLOntologyManager();
- for (Iterator<OWLLogicalAxiom> iterator = ontology.getLogicalAxioms().iterator(); iterator.hasNext();) {
- OWLLogicalAxiom axiom = iterator.next();
- if(!ontologyWithOutAnnotations.containsAxiomIgnoreAnnotations(axiom)){
- man.removeAxiom(ontology, axiom);
- }
- }logger.info("AFTER: "+ ontology.getSubClassAxiomsForSubClass(factory.getOWLClass(IRI.create("http://dbpedia.org/ontology/Award"))));
- return ontology;
- }
-
private Set<Set<OWLAxiom>> computeExplanations(OWLEntity unsatEntity){
return computeExplanations(unsatEntity, numberOfJustifications);
}
@@ -675,7 +714,7 @@
private double getConfidence(OWLAxiom axiom){
Set<OWLAxiom> axiomsWithAnnotations = ontology.getAxiomsIgnoreAnnotations(axiom);
- if(axiomsWithAnnotations.isEmpty()){
+ if(axiomsWithAnnotations.isEmpty()){//this should never happen
logger.info("Axiom with annotations not found: " + axiom);
return 2;
}
@@ -768,6 +807,62 @@
return ontology;
}
+ /**
+ * First try to clean up ontology with JENA as original ontology is in OWL Full because of some user-defined datatypes.
+ * We could either (1) return the rdfs:range triples of the properties with user-defined datatypes or (2) remove all triples about the property.
+ * @return
+ */
+ private OWLOntology loadDBpediaOntologyOWLDL() {
+ long startTime = System.currentTimeMillis();
+ logger.info("Loading DBpedia reference ontology...");
+ OWLOntology ontology = null;
+ try {
+ URL dbpediaURL = new URL("http://downloads.dbpedia.org/3.7/dbpedia_3.7.owl.bz2");
+ InputStream is = dbpediaURL.openStream();
+ is = new CompressorStreamFactory().createCompressorInputStream("bzip2", is);
+ Model model = ModelFactory.createDefaultModel();
+ model.read(is, null);
+ //get all subjects where URI of RDFS:range starts with http://dbpedia.org/datatype/
+ for(StmtIterator iter = model.listStatements(null, RDFS.range, (RDFNode)null); iter.hasNext();){
+ Statement st = iter.next();
+ if(st.getObject().asResource().getURI().startsWith("http://dbpedia.org/datatype/")){
+ iter.remove();
+ }
+ //solution 2
+// for(StmtIterator iter2 = model.listStatements(iter.next().getSubject(), null, (RDFNode)null); iter2.hasNext();){
+// iter2.remove();
+// }
+ }
+
+
+
+ return convert(model);
+
+ } catch (MalformedURLException e) {
+ e.printStackTrace();
+ } catch (IOException e) {
+ e.printStackTrace();
+ } catch (CompressorException e) {
+ e.printStackTrace();
+ }
+ logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
+ return ontology;
+ }
+
+ private OWLOntology convert(Model model) {
+ ByteArrayOutputStream baos = new ByteArrayOutputStream();
+ model.write(baos, "N-TRIPLE");
+ ByteArrayInputStream bais = new ByteArrayInputStream(baos.toByteArray());
+ OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
+ OWLOntology retOnt = null;
+ try {
+ retOnt = manager.loadOntologyFromOntologyDocument(bais);
+ } catch (OWLOntologyCreationException e) {
+
+ }
+ return retOnt;
+ }
+
private Map<OWLEntity, OWLOntology> extractModules(Set<? extends OWLEntity> entities){
logger.info("Computing modules...");
long startTime = System.currentTimeMillis();
@@ -843,8 +938,6 @@
is = new CompressorStreamFactory().createCompressorInputStream("bzip2", is);
}
OWLOntology schema = man.loadOntologyFromOntologyDocument(is);
- Set<OWLTransitiveObjectPropertyAxiom> removedAxioms = schema.getAxioms(AxiomType.TRANSITIVE_OBJECT_PROPERTY);
- man.removeAxioms(schema, removedAxioms);
System.out.println("...done.");
JustificationBasedCoherentOntologyExtractor extractor = new JustificationBasedCoherentOntologyExtractor();
@@ -854,10 +947,9 @@
if(filename.indexOf('/') >= 0){
filename = filename.substring( filename.lastIndexOf('/')+1, filename.length() );
}
-
extractor.setFileName(filename);
+
OWLOntology coherentOntology = extractor.getCoherentOntology(schema, preferRoots);
- man.addAxioms(coherentOntology, removedAxioms);
System.out.println("Coherent ontology contains " + coherentOntology.getLogicalAxiomCount() + " logical axioms.");
}
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