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[DL-Learner SVN] SF.net SVN: dl-learner:[3556] trunk/components-core/src/main/java/org/ dllearner
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From: <lor...@us...> - 2012-01-25 13:31:31
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Revision: 3556
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3556&view=rev
Author: lorenz_b
Date: 2012-01-25 13:31:24 +0000 (Wed, 25 Jan 2012)
Log Message:
-----------
Small improvements.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/algorithms/properties/DisjointDataPropertyAxiomLearner.java
trunk/components-core/src/main/java/org/dllearner/algorithms/properties/DisjointObjectPropertyAxiomLearner.java
trunk/components-core/src/main/java/org/dllearner/algorithms/properties/EquivalentDataPropertyAxiomLearner.java
trunk/components-core/src/main/java/org/dllearner/algorithms/properties/EquivalentObjectPropertyAxiomLearner.java
trunk/components-core/src/main/java/org/dllearner/utilities/CoherentOntologyExtractor.java
trunk/components-core/src/main/java/org/dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/properties/DisjointDataPropertyAxiomLearner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/properties/DisjointDataPropertyAxiomLearner.java 2012-01-20 02:53:33 UTC (rev 3555)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/properties/DisjointDataPropertyAxiomLearner.java 2012-01-25 13:31:24 UTC (rev 3556)
@@ -154,6 +154,8 @@
oldCnt = result.get(prop);
if(oldCnt == null){
oldCnt = Integer.valueOf(newCnt);
+ } else {
+ oldCnt += newCnt;
}
result.put(prop, oldCnt);
repeat = true;
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/properties/DisjointObjectPropertyAxiomLearner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/properties/DisjointObjectPropertyAxiomLearner.java 2012-01-20 02:53:33 UTC (rev 3555)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/properties/DisjointObjectPropertyAxiomLearner.java 2012-01-25 13:31:24 UTC (rev 3556)
@@ -161,14 +161,15 @@
oldCnt = result.get(prop);
if(oldCnt == null){
oldCnt = Integer.valueOf(newCnt);
+ } else {
+ oldCnt += newCnt;
}
result.put(prop, oldCnt);
- qs.getLiteral("count").getInt();
repeat = true;
}
if(!result.isEmpty()){
currentlyBestAxioms = buildAxioms(result, allObjectProperties);
- offset += 1000;
+ offset += limit;
}
}
@@ -185,7 +186,7 @@
EvaluatedAxiom evalAxiom;
//first create disjoint axioms with properties which not occur and give score of 1
- for(ObjectProperty p : completeDisjointProperties){
+ for(ObjectProperty p : completeDisjointProperties){System.out.println(p);
if(usePropertyPopularity){
int popularity = reasoner.getPropertyCount(p);
//skip if property is not used in kb
@@ -217,10 +218,10 @@
public static void main(String[] args) throws Exception{
DisjointObjectPropertyAxiomLearner l = new DisjointObjectPropertyAxiomLearner(new SparqlEndpointKS(new SparqlEndpoint(
new URL("http://dbpedia.aksw.org:8902/sparql"), Collections.singletonList("http://dbpedia.org"), Collections.<String>emptyList())));//.getEndpointDBpediaLiveAKSW()));
- l.setPropertyToDescribe(new ObjectProperty("http://dbpedia.org/ontology/engineType"));
+ l.setPropertyToDescribe(new ObjectProperty("http://dbpedia.org/ontology/state"));
l.setMaxExecutionTimeInSeconds(10);
l.init();
l.start();
- System.out.println(l.getCurrentlyBestEvaluatedAxioms(5));
+ System.out.println(l.getCurrentlyBestEvaluatedAxioms(Integer.MAX_VALUE));
}
}
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/properties/EquivalentDataPropertyAxiomLearner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/properties/EquivalentDataPropertyAxiomLearner.java 2012-01-20 02:53:33 UTC (rev 3555)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/properties/EquivalentDataPropertyAxiomLearner.java 2012-01-25 13:31:24 UTC (rev 3556)
@@ -145,8 +145,10 @@
prop = new DatatypeProperty(qs.getResource("p").getURI());
int newCnt = qs.getLiteral("count").getInt();
oldCnt = result.get(prop);
- if (oldCnt == null) {
+ if(oldCnt == null){
oldCnt = Integer.valueOf(newCnt);
+ } else {
+ oldCnt += newCnt;
}
result.put(prop, oldCnt);
qs.getLiteral("count").getInt();
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/properties/EquivalentObjectPropertyAxiomLearner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/properties/EquivalentObjectPropertyAxiomLearner.java 2012-01-20 02:53:33 UTC (rev 3555)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/properties/EquivalentObjectPropertyAxiomLearner.java 2012-01-25 13:31:24 UTC (rev 3556)
@@ -151,9 +151,10 @@
oldCnt = result.get(prop);
if(oldCnt == null){
oldCnt = Integer.valueOf(newCnt);
+ } else {
+ oldCnt += newCnt;
}
result.put(prop, oldCnt);
- qs.getLiteral("count").getInt();
repeat = true;
}
if(!result.isEmpty()){
Modified: trunk/components-core/src/main/java/org/dllearner/utilities/CoherentOntologyExtractor.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/CoherentOntologyExtractor.java 2012-01-20 02:53:33 UTC (rev 3555)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/CoherentOntologyExtractor.java 2012-01-25 13:31:24 UTC (rev 3556)
@@ -5,5 +5,7 @@
public interface CoherentOntologyExtractor {
OWLOntology getCoherentOntology(OWLOntology incoherentOntology);
+
+ OWLOntology getCoherentOntology(OWLOntology ontology, boolean preferRoots);
}
Modified: trunk/components-core/src/main/java/org/dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java 2012-01-20 02:53:33 UTC (rev 3555)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java 2012-01-25 13:31:24 UTC (rev 3556)
@@ -4,6 +4,8 @@
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
+import java.security.MessageDigest;
+import java.security.NoSuchAlgorithmException;
import java.util.Collections;
import java.util.HashMap;
import java.util.Iterator;
@@ -14,12 +16,17 @@
import java.util.logging.Level;
import java.util.logging.Logger;
+import openlink.util.MD5;
+
import org.mindswap.pellet.RBox;
+import org.semanticweb.HermiT.Configuration;
+import org.semanticweb.HermiT.Reasoner;
import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.io.RDFXMLOntologyFormat;
import org.semanticweb.owlapi.model.AxiomType;
import org.semanticweb.owlapi.model.OWLAxiom;
import org.semanticweb.owlapi.model.OWLClass;
+import org.semanticweb.owlapi.model.OWLDataFactory;
import org.semanticweb.owlapi.model.OWLEntity;
import org.semanticweb.owlapi.model.OWLLogicalAxiom;
import org.semanticweb.owlapi.model.OWLOntology;
@@ -27,11 +34,17 @@
import org.semanticweb.owlapi.model.OWLOntologyManager;
import org.semanticweb.owlapi.model.OWLOntologyStorageException;
import org.semanticweb.owlapi.model.RemoveAxiom;
+import org.semanticweb.owlapi.reasoner.IllegalConfigurationException;
+import org.semanticweb.owlapi.reasoner.OWLReasoner;
+import org.semanticweb.owlapi.reasoner.OWLReasonerConfiguration;
+import org.semanticweb.owlapi.reasoner.OWLReasonerFactory;
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.owlapiv3.OntologyUtils;
@@ -39,35 +52,72 @@
private static final org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(JustificationBasedCoherentOntologyExtractor.class);
- private static final int NUMBER_OF_JUSTIFICATIONS = 5;
+ private int numberOfJustifications = 10;
// private PelletReasoner reasoner;
private IncrementalClassifier reasoner;
+ private Reasoner hermitReasoner;
private OWLOntology incoherentOntology;
private OWLOntology ontology;
+ private OWLDataFactory factory;
private Map<OWLClass, OWLOntology> cls2ModuleMap = new HashMap<OWLClass, OWLOntology>();
+ private OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
+ MessageDigest md5;
+
+ public JustificationBasedCoherentOntologyExtractor() {
+ try {
+ md5 = MessageDigest.getInstance("MD5");
+ } catch (NoSuchAlgorithmException e) {
+ e.printStackTrace();
+ }
+ }
+
static {PelletExplanation.setup();}
@Override
- public OWLOntology getCoherentOntology(OWLOntology ontology) {
- this.ontology = ontology;ontology.getOWLOntologyManager().removeAxioms(ontology, ontology.getAxioms(AxiomType.TRANSITIVE_OBJECT_PROPERTY));
+ public OWLOntology getCoherentOntology(OWLOntology ontology){
+ return getCoherentOntology(ontology, false);
+ }
+
+ @Override
+ public OWLOntology getCoherentOntology(OWLOntology ontology, boolean preferRoots){
+ if(preferRoots){
+ return computeCoherentOntologyRootBased(ontology);
+ } else {
+ return computeCoherentOntology(ontology);
+ }
+ }
+
+ private OWLOntology computeCoherentOntologyRootBased(OWLOntology ontology) {
+ this.ontology = ontology;
this.incoherentOntology = getOntologyWithoutAnnotations(ontology);
-// reasoner = PelletReasonerFactory.getInstance().createNonBufferingReasoner(incoherentOntology);
-// reasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY);
+ //only for debugging
+ ontology.getOWLOntologyManager().removeAxioms(ontology, ontology.getAxioms(AxiomType.TRANSITIVE_OBJECT_PROPERTY));
+
+ long startTime = System.currentTimeMillis();
reasoner = new IncrementalClassifier(incoherentOntology);
reasoner.classify();
+ logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
+// 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);
//compute the unsatisfiable classes
+ logger.info("Computing root/derived unsatisfiable classes...");
+ startTime = System.currentTimeMillis();
StructureBasedRootClassFinder rootFinder = new StructureBasedRootClassFinder(reasoner);
- rootFinder.computeRootDerivedClasses();
Set<OWLClass> unsatClasses = rootFinder.getRootUnsatisfiableClasses();
Set<OWLClass> derivedUnsatClasses = rootFinder.getDerivedUnsatisfiableClasses();
+ logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
int rootCnt = unsatClasses.size();
int derivedCnt = derivedUnsatClasses.size();
// Set<OWLClass> unsatClasses = reasoner.getUnsatisfiableClasses().getEntitiesMinusBottom();
@@ -80,13 +130,15 @@
}
//compute the logical modules for each unsatisfiable class
logger.info("Computing module for each unsatisfiable class...");
+ startTime = System.currentTimeMillis();
cls2ModuleMap = extractModules(unsatClasses);
- logger.info("...done.");
+ logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
//compute initial explanations for each unsatisfiable class
logger.info("Computing initial explanations...");
+ startTime = System.currentTimeMillis();
Map<OWLClass, Set<Set<OWLAxiom>>> cls2Explanations = getInitialExplanationsForUnsatClasses(unsatClasses);
- logger.info("...done.");
+ logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
while(!unsatClasses.isEmpty()){
//get frequency for each axiom
@@ -95,7 +147,7 @@
//get a sorted list of entries with the highest axiom count first
List<Entry<OWLAxiom, Integer>> sortedEntries = MapUtils.sortByValues(axiom2CountMap);
for(Entry<OWLAxiom, Integer> entry : sortedEntries){
- System.out.println(entry.getKey() + ":" + entry.getValue());
+// System.out.println(entry.getKey() + ":" + entry.getValue());
}
//we remove the most frequent axiom from the ontology
OWLAxiom toRemove = sortedEntries.get(0).getKey();
@@ -106,15 +158,22 @@
removeFromModules(toRemove);
//recompute the unsatisfiable classes
+ logger.info("Reclassifying...");
+ startTime = System.currentTimeMillis();
reasoner.classify();
+// hermitReasoner.classifyClasses();
// unsatClasses = reasoner.getUnsatisfiableClasses().getEntitiesMinusBottom();
+ logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
+ logger.info("Computing root/derived unsatisfiable classes...");
+ startTime = System.currentTimeMillis();
rootFinder = new StructureBasedRootClassFinder(reasoner);
- rootFinder.computeRootDerivedClasses();
unsatClasses = rootFinder.getRootUnsatisfiableClasses();
+ derivedUnsatClasses = rootFinder.getDerivedUnsatisfiableClasses();
rootCnt = unsatClasses.size();
- derivedUnsatClasses = rootFinder.getDerivedUnsatisfiableClasses();
derivedCnt = derivedUnsatClasses.size();
+ logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
+
logger.info("Remaining unsatisfiable classes: " + (rootCnt + derivedCnt) + "(" + rootCnt + " roots).");
//save
@@ -133,13 +192,14 @@
//recompute explanations if necessary
logger.info("Recomputing explanations...");
+ startTime = System.currentTimeMillis();
refillExplanations(unsatClasses, cls2Explanations);
- logger.info("...done.");
+ logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
System.gc();
}
try {
- incoherentOntology.getOWLOntologyManager().saveOntology(incoherentOntology, new RDFXMLOntologyFormat(), new BufferedOutputStream(new FileOutputStream("log/dbpedia_coherent.owl")));
+ incoherentOntology.getOWLOntologyManager().saveOntology(getOntologyWithAnnotations(incoherentOntology), new RDFXMLOntologyFormat(), new BufferedOutputStream(new FileOutputStream("log/dbpedia_coherent.owl")));
} catch (OWLOntologyStorageException e) {
e.printStackTrace();
} catch (FileNotFoundException e) {
@@ -150,6 +210,103 @@
return getOntologyWithAnnotations(incoherentOntology);
}
+ private OWLOntology computeCoherentOntology(OWLOntology ontology) {
+ this.ontology = ontology;
+ this.incoherentOntology = getOntologyWithoutAnnotations(ontology);
+
+ //only for debugging
+ ontology.getOWLOntologyManager().removeAxioms(ontology, ontology.getAxioms(AxiomType.TRANSITIVE_OBJECT_PROPERTY));
+
+ long startTime = System.currentTimeMillis();
+ reasoner = new IncrementalClassifier(incoherentOntology);
+ reasoner.classify();
+ logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
+
+ OWLOntologyManager man = incoherentOntology.getOWLOntologyManager();
+ factory = man.getOWLDataFactory();
+
+ //compute the unsatisfiable classes
+ logger.info("Computing unsatisfiable classes...");
+ startTime = System.currentTimeMillis();
+ logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
+ Set<OWLClass> unsatClasses = reasoner.getUnsatisfiableClasses().getEntitiesMinusBottom();
+ int cnt = unsatClasses.size();
+ logger.info("Detected " + cnt + " 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();
+ cls2ModuleMap = 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();
+ Map<OWLClass, Set<Set<OWLAxiom>>> cls2Explanations = getInitialExplanationsForUnsatClasses(unsatClasses);
+ logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
+
+ while(!unsatClasses.isEmpty()){
+ //get frequency for each axiom
+ Map<OWLAxiom, Integer> axiom2CountMap = getAxiomFrequency(cls2Explanations);
+
+ //get a sorted list of entries with the highest axiom count first
+ List<Entry<OWLAxiom, Integer>> sortedEntries = MapUtils.sortByValues(axiom2CountMap);
+ for(Entry<OWLAxiom, Integer> entry : sortedEntries){
+// System.out.println(entry.getKey() + ":" + entry.getValue());
+ }
+ //we remove the most frequent axiom from the ontology
+ OWLAxiom toRemove = sortedEntries.get(0).getKey();
+ logger.info("Removing axiom " + toRemove + ".");
+ man.removeAxiom(incoherentOntology, toRemove);
+ man.applyChange(new RemoveAxiom(incoherentOntology, toRemove));
+ removeFromExplanations(cls2Explanations, toRemove);
+ removeFromModules(toRemove);
+
+ //recompute the unsatisfiable classes
+ logger.info("Reclassifying...");
+ startTime = System.currentTimeMillis();
+ reasoner.classify();
+ unsatClasses = reasoner.getUnsatisfiableClasses().getEntitiesMinusBottom();
+ logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
+ logger.info("Remaining unsatisfiable classes: " + unsatClasses.size());
+
+ //save
+ if(cnt - unsatClasses.size() >= 10){
+ cnt = unsatClasses.size();
+ OWLOntology toSave = getOntologyWithAnnotations(incoherentOntology);
+ try {
+ toSave.getOWLOntologyManager().saveOntology(incoherentOntology, new RDFXMLOntologyFormat(), new BufferedOutputStream(new FileOutputStream("log/dbpedia_" + cnt + ".owl")));
+ } catch (OWLOntologyStorageException e) {
+ e.printStackTrace();
+ } catch (FileNotFoundException e) {
+ e.printStackTrace();
+ }
+ }
+
+ //recompute explanations if necessary
+ logger.info("Recomputing explanations...");
+ startTime = System.currentTimeMillis();
+ refillExplanations(unsatClasses, cls2Explanations);
+ 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();
+ }
+ System.out.println(incoherentOntology.getLogicalAxiomCount());
+
+ return getOntologyWithAnnotations(incoherentOntology);
+ }
+
private void removeFromModules(OWLAxiom axiom){
OWLOntology module;
for(Entry<OWLClass, OWLOntology> entry : cls2ModuleMap.entrySet()){
@@ -172,8 +329,8 @@
private void refillExplanations(Set<OWLClass> unsatClasses, Map<OWLClass, Set<Set<OWLAxiom>>> cls2Explanations){
for(OWLClass unsatClass : unsatClasses){
Set<Set<OWLAxiom>> precomputedExplanations = cls2Explanations.get(unsatClass);
- if(precomputedExplanations == null || precomputedExplanations.size() < NUMBER_OF_JUSTIFICATIONS){
- Set<Set<OWLAxiom>> newExplanations = computeExplanations(unsatClass, NUMBER_OF_JUSTIFICATIONS);
+ if(precomputedExplanations == null || precomputedExplanations.size() < numberOfJustifications){
+ Set<Set<OWLAxiom>> newExplanations = computeExplanations(unsatClass, numberOfJustifications);
cls2Explanations.put(unsatClass, newExplanations);
}
}
@@ -237,24 +394,65 @@
private Set<Set<OWLAxiom>> computeExplanations(OWLClass unsatClass){
PelletExplanation expGen = new PelletExplanation(getModule(unsatClass));
- return expGen.getUnsatisfiableExplanations(unsatClass, NUMBER_OF_JUSTIFICATIONS);
+ return expGen.getUnsatisfiableExplanations(unsatClass, numberOfJustifications);
}
private Set<Set<OWLAxiom>> computeExplanations(OWLClass unsatClass, int limit){
PelletExplanation expGen = new PelletExplanation(getModule(unsatClass));
- return expGen.getUnsatisfiableExplanations(unsatClass, NUMBER_OF_JUSTIFICATIONS);
+ return expGen.getUnsatisfiableExplanations(unsatClass, numberOfJustifications);
}
- private OWLOntology getModule(OWLClass cls){
+ private Set<Set<OWLAxiom>> computeExplanationsBlackBox(OWLClass unsatClass, int limit){
+ BlackBoxExplanation singleExpGen = new BlackBoxExplanation(incoherentOntology, new HermiTReasonerFactory(), hermitReasoner);
+ HSTExplanationGenerator expGen = new HSTExplanationGenerator(singleExpGen);
+ return expGen.getExplanations(unsatClass, limit);
+ }
+
+// private Set<Set<OWLAxiom>> computeExplanationsBlackbox(OWLClass unsatClass, int limit){
+// BlackBoxExplanation b = new BlackBoxExplanation(incoherentOntology, reasonerFactory, hermitReasoner)
+// MultipleExplanationGenerator expGen = new HSTExplanationGenerator(b);
+// PelletExplanation expGen = new PelletExplanation(getModule(unsatClass));
+// return expGen.getUnsatisfiableExplanations(unsatClass, NUMBER_OF_JUSTIFICATIONS);
+// }
+
+ private OWLOntology getModule(OWLClass cls){System.out.println(cls);
OWLOntology module = cls2ModuleMap.get(cls);
+ new File("log").mkdir();
if(module == null){
- module = OntologyUtils.getOntologyFromAxioms(
- ModularityUtils.extractModule(incoherentOntology, Collections.singleton((OWLEntity)cls), ModuleType.TOP_OF_BOT));
+ md5.reset();
+ md5.update((ontology.getOWLOntologyManager().getOntologyDocumentIRI(ontology).toString() + cls.toStringID()).getBytes());
+ String hash = MD5.asHex(md5.digest());
+ String filename = "log/" + hash + ".owl";
+ File file = new File(filename);
+ if(file.exists()){
+ module = loadModule(file);
+ } else {
+ module = OntologyUtils.getOntologyFromAxioms(
+ ModularityUtils.extractModule(incoherentOntology, Collections.singleton((OWLEntity)cls), ModuleType.TOP_OF_BOT));
+ try {
+ manager.saveOntology(module, new RDFXMLOntologyFormat(), new BufferedOutputStream(new FileOutputStream(filename)));
+ } catch (OWLOntologyStorageException e) {
+ e.printStackTrace();
+ } catch (FileNotFoundException e) {
+ e.printStackTrace();
+ }
+ }
+
cls2ModuleMap.put(cls, module);
}
return module;
}
+ private OWLOntology loadModule(File file){
+ OWLOntology module = null;
+ try {
+ module = manager.loadOntologyFromOntologyDocument(file);
+ } catch (OWLOntologyCreationException e) {
+ e.printStackTrace();
+ }
+ return module;
+ }
+
private Map<OWLClass, OWLOntology> extractModules(Set<OWLClass> classes){
Map<OWLClass, OWLOntology> cls2ModuleMap = new HashMap<OWLClass, OWLOntology>();
for(OWLClass cls : classes){
@@ -264,17 +462,81 @@
return cls2ModuleMap;
}
+ public void setNumberOfJustifications(int numberOfJustifications) {
+ this.numberOfJustifications = numberOfJustifications;
+ }
+
public static void main(String[] args) throws Exception{
Logger.getLogger(RBox.class.getName()).setLevel(Level.OFF);
OWLOntologyManager man = OWLManager.createOWLOntologyManager();
-// OWLOntology schema = man.loadOntologyFromOntologyDocument(new File("/home/lorenz/dbpedia_0.75_no_datapropaxioms.owl"));
- OWLOntology schema = man.loadOntologyFromOntologyDocument(new File("log/dbpedia_95.owl"));
+
+ if(args.length != 3){
+ System.out.println("USAGE: JustificationBasedCoherentOntologyExtractor <incoherent.owl> <numberOfJustifcations> <preferRootClasses(true|false)>");
+ System.exit(0);
+ }
+ String filename = args[0];
+ int numberOfJustifications = Integer.parseInt(args[1]);
+ boolean preferRoots = Boolean.valueOf(args[2]);
+
+ System.out.println("Loading ontology...");
+ File file = new File(filename);
+ OWLOntology schema = man.loadOntologyFromOntologyDocument(file);
+ man.removeAxioms(schema, schema.getAxioms(AxiomType.TRANSITIVE_OBJECT_PROPERTY));
+
+// OWLOntology cleaned = man.createOntology(IRI.create("http://dbpedia_cleaned.owl"));
+// man.addAxioms(cleaned, schema.getLogicalAxioms());
+// man.removeAxioms(cleaned, cleaned.getAxioms(AxiomType.TRANSITIVE_OBJECT_PROPERTY));
+// man.removeAxioms(cleaned, cleaned.getAxioms(AxiomType.REFLEXIVE_OBJECT_PROPERTY));
+// man.removeAxioms(cleaned, cleaned.getAxioms(AxiomType.IRREFLEXIVE_OBJECT_PROPERTY));
+// man.removeAxioms(cleaned, cleaned.getAxioms(AxiomType.SYMMETRIC_OBJECT_PROPERTY));
+// man.removeAxioms(cleaned, cleaned.getAxioms(AxiomType.ASYMMETRIC_OBJECT_PROPERTY));
+// man.removeAxioms(cleaned, cleaned.getAxioms(AxiomType.FUNCTIONAL_OBJECT_PROPERTY));
+// man.removeAxioms(cleaned, cleaned.getAxioms(AxiomType.INVERSE_FUNCTIONAL_OBJECT_PROPERTY));
+// man.saveOntology(cleaned, new RDFXMLOntologyFormat(), new BufferedOutputStream(new FileOutputStream(file.getParent() + "/cleaned.owl")));
+// OWLOntology schema = man.loadOntologyFromOntologyDocument(new File("log/dbpedia_95.owl"));
+// OWLOntology schema = man.loadOntologyFromOntologyDocument(new File("/home/lorenz/arbeit/dbpedia_0.75_no_datapropaxioms.owl"));
// System.out.println(schema.getLogicalAxiomCount());
// OWLOntology schema = man.loadOntologyFromOntologyDocument(new File("log/dbpedia_coherent.owl"));
- System.out.println(schema.getLogicalAxiomCount());
+// System.out.println(schema.getLogicalAxiomCount());
+ System.out.println("...done.");
JustificationBasedCoherentOntologyExtractor extractor = new JustificationBasedCoherentOntologyExtractor();
- OWLOntology coherentOntology = extractor.getCoherentOntology(schema);System.out.println(coherentOntology.getLogicalAxiomCount());
+ extractor.setNumberOfJustifications(numberOfJustifications);
+ OWLOntology coherentOntology = extractor.getCoherentOntology(schema, preferRoots);
+ System.out.println("Coherent ontology contains " + coherentOntology.getLogicalAxiomCount() + " logical axioms.");
}
+
+ class HermiTReasonerFactory implements OWLReasonerFactory{
+ @Override
+ public OWLReasoner createNonBufferingReasoner(OWLOntology ontology) {
+ return new Reasoner(ontology);
+ }
+
+ @Override
+ public OWLReasoner createNonBufferingReasoner(OWLOntology ontology,
+ OWLReasonerConfiguration config)
+ throws IllegalConfigurationException {
+ return new Reasoner((Configuration) config, ontology);
+ }
+
+ @Override
+ public OWLReasoner createReasoner(OWLOntology ontology) {
+ return new Reasoner(ontology);
+ }
+
+ @Override
+ public OWLReasoner createReasoner(OWLOntology ontology,
+ OWLReasonerConfiguration config)
+ throws IllegalConfigurationException {
+ return new Reasoner((Configuration) config, ontology);
+ }
+
+ @Override
+ public String getReasonerName() {
+ return "HermiT Reasoner";
+ }
+
+ }
+
}
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