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[DL-Learner SVN] SF.net SVN: dl-learner:[3597] trunk/components-core/src/main/java/org/ dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java
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From: <lor...@us...> - 2012-02-28 15:56:27
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Revision: 3597
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3597&view=rev
Author: lorenz_b
Date: 2012-02-28 15:56:18 +0000 (Tue, 28 Feb 2012)
Log Message:
-----------
Many modifications to work for eval.
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 2012-02-28 15:46:01 UTC (rev 3596)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java 2012-02-28 15:56:18 UTC (rev 3597)
@@ -14,7 +14,9 @@
import java.security.NoSuchAlgorithmException;
import java.util.ArrayList;
import java.util.Collections;
+import java.util.Comparator;
import java.util.HashMap;
+import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
@@ -24,25 +26,29 @@
import java.util.TreeSet;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
-import java.util.concurrent.Future;
-import java.util.logging.Level;
-import java.util.logging.Logger;
import openlink.util.MD5;
import org.apache.commons.compress.compressors.CompressorException;
import org.apache.commons.compress.compressors.CompressorStreamFactory;
-import org.mindswap.pellet.RBox;
+import org.apache.log4j.ConsoleAppender;
+import org.apache.log4j.FileAppender;
+import org.apache.log4j.Level;
+import org.apache.log4j.Logger;
+import org.apache.log4j.SimpleLayout;
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.IRI;
+import org.semanticweb.owlapi.model.OWLAnnotation;
+import org.semanticweb.owlapi.model.OWLAnnotationProperty;
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.OWLLiteral;
import org.semanticweb.owlapi.model.OWLLogicalAxiom;
import org.semanticweb.owlapi.model.OWLObjectProperty;
import org.semanticweb.owlapi.model.OWLOntology;
@@ -56,6 +62,7 @@
import org.semanticweb.owlapi.reasoner.OWLReasonerConfiguration;
import org.semanticweb.owlapi.reasoner.OWLReasonerFactory;
+import uk.ac.manchester.cs.owl.owlapi.OWLDataFactoryImpl;
import uk.ac.manchester.cs.owlapi.modularity.ModuleType;
import com.clarkparsia.modularity.IncrementalClassifier;
@@ -63,7 +70,6 @@
import com.clarkparsia.owlapi.explanation.BlackBoxExplanation;
import com.clarkparsia.owlapi.explanation.HSTExplanationGenerator;
import com.clarkparsia.owlapi.explanation.PelletExplanation;
-import com.clarkparsia.owlapiv3.OntologyUtils;
import com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory;
public class JustificationBasedCoherentOntologyExtractor implements CoherentOntologyExtractor{
@@ -78,7 +84,7 @@
private OWLOntology incoherentOntology;
private OWLOntology ontology;
- private OWLDataFactory factory;
+ private OWLDataFactory factory = new OWLDataFactoryImpl();;
//we store the removed axioms in it
private OWLOntology diffOntology;
@@ -86,6 +92,8 @@
private Map<OWLEntity, OWLOntology> entity2ModuleMap = new HashMap<OWLEntity, OWLOntology>();
private Map<OWLEntity, Set<Set<OWLAxiom>>> entity2Explanations = new HashMap<OWLEntity, Set<Set<OWLAxiom>>>();
private Map<OWLEntity, PelletExplanation> entity2ExpGen = new HashMap<OWLEntity, PelletExplanation>();
+ private Set<OWLEntity> entitiesWithLessExplanations = new HashSet<OWLEntity>();
+
private OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
MessageDigest md5;
@@ -96,6 +104,8 @@
//whether to debug classes and properties in parallel
private boolean computeParallel = false;
+ private OWLAnnotationProperty confidenceProperty;
+
private OWLOntology dbpediaOntology;
private String fileName = "dbpedia";
@@ -119,6 +129,8 @@
@Override
public OWLOntology getCoherentOntology(OWLOntology ontology, boolean preferRoots){
+ ontology.getOWLOntologyManager().addAxioms(ontology, dbpediaOntology.getLogicalAxioms());
+
this.ontology = ontology;
this.incoherentOntology = getOntologyWithoutAnnotations(ontology);
@@ -218,7 +230,7 @@
startTime = System.currentTimeMillis();
computeExplanations(unsatClasses);
if(computeParallel){
- entity2Explanations.putAll(getInitialExplanations(unsatObjectProperties));
+ computeExplanations(unsatObjectProperties);
}
logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
@@ -235,12 +247,12 @@
startTime = System.currentTimeMillis();
reasoner.classify();
// hermitReasoner.classifyClasses();
-// unsatClasses = reasoner.getUnsatisfiableClasses().getEntitiesMinusBottom();
+ //Set<OWLClass> unsatClasses2 = 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 = new StructureBasedRootClassFinder(reasoner, this);
unsatClasses = rootFinder.getRootUnsatisfiableClasses();
derivedUnsatClasses = rootFinder.getDerivedUnsatisfiableClasses();
rootCnt = unsatClasses.size();
@@ -253,19 +265,19 @@
}
logger.info("Remaining unsatisfiable classes: " + (rootCnt + derivedCnt) + "(" + rootCnt + " roots).");
-
+
if(unsatClasses.isEmpty()){
unsatClasses = derivedUnsatClasses;
}
//recompute unsatisfiable object properties
- if(computeParallel){
+ // if(computeParallel){
unsatObjectProperties = getUnsatisfiableObjectProperties(reasoner);
logger.info("Remaining unsatisfiable object properties: " + unsatObjectProperties.size());
- }
+ // }
//save
- if(cnt - (rootCnt+derivedCnt) >= 1 || (unsatPropCnt - unsatObjectProperties.size()) >= 1){
+ if(cnt - (rootCnt+derivedCnt) >= 5 || (unsatPropCnt - unsatObjectProperties.size()) >= 5){
cnt = rootCnt + derivedCnt;
save("log/" + fileName + "_" + cnt + "cls" + unsatPropCnt + "prop.owl");
cnt = rootCnt + derivedCnt;
@@ -362,11 +374,11 @@
//compute initial explanations for each unsatisfiable class
logger.info("Computing initial explanations...");
startTime = System.currentTimeMillis();
- entity2Explanations.putAll(getInitialExplanations(unsatClasses));
- entity2Explanations.putAll(getInitialExplanations(unsatObjectProperties));
+ computeExplanations(unsatClasses);
+// entity2Explanations.putAll(getInitialExplanations(unsatObjectProperties));
logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
- while(!unsatClasses.isEmpty() && !unsatObjectProperties.isEmpty()){
+ while(!unsatClasses.isEmpty()){// && !unsatObjectProperties.isEmpty()){
//we remove the most appropriate axiom from the ontology
removeAppropriateAxiom();
@@ -392,7 +404,7 @@
logger.info("Recomputing explanations...");
startTime = System.currentTimeMillis();
refillExplanations(unsatClasses, entity2Explanations);
- refillExplanations(unsatObjectProperties, entity2Explanations);
+ //refillExplanations(unsatObjectProperties, entity2Explanations);
logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
System.gc();
@@ -478,10 +490,11 @@
}
private void removeAppropriateAxiom(){
+ logger.info("Searching for appropriate axiom to remove...");
//get frequency for each axiom
Map<OWLAxiom, Integer> axiom2CountMap = getAxiomFrequency(entity2Explanations);
//get a sorted list of entries with the highest axiom count first
- List<Entry<OWLAxiom, Integer>> sortedEntries = MapUtils.sortByValues(axiom2CountMap);
+ List<Entry<OWLAxiom, Integer>> sortedEntries = sort(axiom2CountMap);
//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();
@@ -500,7 +513,7 @@
private void save(String fileName){
OWLOntology toSave = getOntologyWithAnnotations(incoherentOntology);
try {
- toSave.getOWLOntologyManager().saveOntology(incoherentOntology, new RDFXMLOntologyFormat(), new BufferedOutputStream(new FileOutputStream(fileName)));
+ toSave.getOWLOntologyManager().saveOntology(toSave, new RDFXMLOntologyFormat(), new BufferedOutputStream(new FileOutputStream(fileName)));
toSave.getOWLOntologyManager().saveOntology(diffOntology, new RDFXMLOntologyFormat(), new BufferedOutputStream(new FileOutputStream("log/" + diffFileName)));
} catch (OWLOntologyStorageException e) {
e.printStackTrace();
@@ -549,6 +562,7 @@
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);
}
}
@@ -576,17 +590,20 @@
private void computeExplanations(Set<? extends OWLEntity> unsatEntities){
ExecutorService executor = Executors.newFixedThreadPool(Runtime.getRuntime().availableProcessors());
- List<Future<Void>> list = new ArrayList<Future<Void>>();
for(final OWLEntity unsatEntity : unsatEntities){
Set<Set<OWLAxiom>> precomputedExplanations = entity2Explanations.get(unsatEntity);
- if(precomputedExplanations == null || precomputedExplanations.size() < numberOfJustifications){
+ if(precomputedExplanations == null || (!entitiesWithLessExplanations.contains(unsatEntity) && precomputedExplanations.size() < numberOfJustifications)){
executor.execute(new Runnable(){
@Override
public void run() {
Set<Set<OWLAxiom>> explanations = computeExplanations(unsatEntity);
+ logger.info("Computed "+ explanations.size() + " explanations for " + unsatEntity);
entity2Explanations.put(unsatEntity, explanations);
+ if(explanations.size() < numberOfJustifications){
+ entitiesWithLessExplanations.add(unsatEntity);
+ }
}
});
@@ -601,22 +618,10 @@
}
- private Map<OWLEntity, Set<Set<OWLAxiom>>> getInitialExplanations(Set<? extends OWLEntity> unsatEntities){
- Map<OWLEntity, Set<Set<OWLAxiom>>> cls2Explanations = new HashMap<OWLEntity, Set<Set<OWLAxiom>>>();
-
- Set<Set<OWLAxiom>> explanations;
- for(OWLEntity unsatEntity : unsatEntities){
- explanations = computeExplanations(unsatEntity);
- cls2Explanations.put(unsatEntity, explanations);
- }
-
- return cls2Explanations;
- }
-
private OWLOntology getOntologyWithoutAnnotations(OWLOntology ontology){
try {
- OWLOntologyManager man = ontology.getOWLOntologyManager();
- OWLOntology ontologyWithoutAnnotations = ontology.getOWLOntologyManager().createOntology();
+ OWLOntologyManager man = OWLManager.createOWLOntologyManager();
+ OWLOntology ontologyWithoutAnnotations = man.createOntology();
for(OWLAxiom ax : ontology.getLogicalAxioms()){
man.addAxiom(ontologyWithoutAnnotations, ax.getAxiomWithoutAnnotations());
}
@@ -640,7 +645,6 @@
}
private Set<Set<OWLAxiom>> computeExplanations(OWLEntity unsatEntity){
- logger.info(unsatEntity);
return computeExplanations(unsatEntity, numberOfJustifications);
}
@@ -656,10 +660,10 @@
private PelletExplanation getExplanationGenerator(OWLEntity entity){
PelletExplanation expGen = entity2ExpGen.get(entity);
- if(expGen == null){
+// if(expGen == null){
expGen = new PelletExplanation(PelletReasonerFactory.getInstance().createNonBufferingReasoner(getModule(entity)));
- entity2ExpGen.put(entity, expGen);
- }
+// entity2ExpGen.put(entity, expGen);
+// }
return expGen;
}
@@ -668,42 +672,27 @@
HSTExplanationGenerator expGen = new HSTExplanationGenerator(singleExpGen);
return expGen.getExplanations(unsatClass, limit);
}
+
+ private double getConfidence(OWLAxiom axiom){
+ Set<OWLAxiom> axiomsWithAnnotations = ontology.getAxiomsIgnoreAnnotations(axiom);
+ if(axiomsWithAnnotations.isEmpty()){
+ logger.info("Axiom with annotations not found: " + axiom);
+ logger.info("Ontology contains axiom: " + incoherentOntology.containsAxiomIgnoreAnnotations(axiom));
+ logger.info("Original loaded ontology contains axiom: " + ontology.containsAxiomIgnoreAnnotations(axiom));
+ System.out.println(ontology.getSubClassAxiomsForSubClass(factory.getOWLClass(IRI.create("http://dbpedia.org/ontology/Award"))));
+ }
+ OWLAxiom axiomWithAnnotations = axiomsWithAnnotations.iterator().next();
+ Set<OWLAnnotation> annotations = axiomWithAnnotations.getAnnotations(confidenceProperty);
+ if(!annotations.isEmpty()){
+ OWLAnnotation anno = annotations.iterator().next();
+ OWLLiteral literal = (OWLLiteral) anno.getValue();
+ return literal.parseDouble();
+ }
+ return 2;
+
+ }
-// 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){
-// OWLOntology module = cls2ModuleMap.get(cls);
-// new File("log").mkdir();
-// if(module == null){
-// 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;
-// }
-
public OWLOntology getModule(OWLEntity entity){
OWLOntology module = entity2ModuleMap.get(entity);
new File("log").mkdir();
@@ -713,21 +702,29 @@
String hash = MD5.asHex(md5.digest());
String filename = "log/" + hash + ".owl";
File file = new File(filename);
- if(file.exists()){
+ boolean load = false;
+ if(load){//file.exists()){
module = loadModule(file);
} else {
+ try {
+ module = OWLManager.createOWLOntologyManager().createOntology(ModularityUtils.extractModule(incoherentOntology, Collections.singleton(entity), ModuleType.TOP_OF_BOT));
+ } catch (OWLOntologyCreationException e) {
+ e.printStackTrace();
+ }
+ /*
module = OntologyUtils.getOntologyFromAxioms(
ModularityUtils.extractModule(incoherentOntology, Collections.singleton(entity), 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();
- }
+ }*/
}
- entity2ModuleMap.put(entity, module);
+ //entity2ModuleMap.put(entity, module);
}
return module;
}
@@ -765,24 +762,6 @@
return ontology;
}
-// private Map<OWLClass, OWLOntology> extractModules(Set<OWLClass> classes){
-// Map<OWLClass, OWLOntology> cls2ModuleMap = new HashMap<OWLClass, OWLOntology>();
-// for(OWLClass cls : classes){
-// OWLOntology module = getModule(cls);
-// cls2ModuleMap.put(cls, module);
-// }
-// return cls2ModuleMap;
-// }
-//
-// private Map<OWLObjectProperty, OWLOntology> extractModules(Set<OWLObjectProperty> objectProperties){
-// Map<OWLObjectProperty, OWLOntology> prop2ModuleMap = new HashMap<OWLObjectProperty, OWLOntology>();
-// for(OWLObjectProperty prop : objectProperties){
-// OWLOntology module = getModule(prop);
-// prop2ModuleMap.put(prop, module);
-// }
-// return prop2ModuleMap;
-// }
-
private Map<OWLEntity, OWLOntology> extractModules(Set<? extends OWLEntity> entities){
logger.info("Computing modules...");
long startTime = System.currentTimeMillis();
@@ -803,19 +782,54 @@
public void setComputeParallel(boolean computeParallel) {
this.computeParallel = computeParallel;
}
+
+ public void setConfidencePropertyIRI(String iri){
+ this.confidenceProperty = factory.getOWLAnnotationProperty(IRI.create(iri));
+ }
+ private List<Entry<OWLAxiom, Integer>> sort(Map<OWLAxiom, Integer> map){
+ List<Entry<OWLAxiom, Integer>> entries = new ArrayList<Entry<OWLAxiom, Integer>>(map.entrySet());
+ Collections.sort(entries, new Comparator<Entry<OWLAxiom, Integer>>() {
+
+ @Override
+ public int compare(Entry<OWLAxiom, Integer> o1, Entry<OWLAxiom, Integer> o2) {
+ int cmp = o2.getValue().compareTo(o1.getValue());
+ //use as tie breaker the confidence value
+ if(cmp == 0){
+ double conf1 = getConfidence(o1.getKey());
+ double conf2 = getConfidence(o2.getKey());
+ double diff = conf1-conf2;
+ if(diff > 0){
+ return 1;
+ } else if(diff < 0){
+ return -1;
+ } else {
+ return 0;
+ }
+// return Double.compare(conf2, conf1);
+ }
+ return cmp;
+ }
+ });
+ return entries;
+ }
+
public static void main(String[] args) throws Exception{
- Logger.getLogger(RBox.class.getName()).setLevel(Level.OFF);
+ Logger.getRootLogger().setLevel(Level.INFO);
+ Logger.getRootLogger().removeAllAppenders();
+ Logger.getRootLogger().addAppender(new ConsoleAppender(new SimpleLayout()));
+ Logger.getRootLogger().addAppender(new FileAppender(new SimpleLayout(), "log/out.log"));
OWLOntologyManager man = OWLManager.createOWLOntologyManager();
- if(args.length != 4){
- System.out.println("USAGE: JustificationBasedCoherentOntologyExtractor <incoherent.owl> <numberOfJustifcations> <preferRootClasses(true|false)> <computeParallel(true|false)>");
+ if(args.length != 5){
+ System.out.println("USAGE: JustificationBasedCoherentOntologyExtractor <incoherent.owl> <confidencePropertyIRI> <numberOfJustifcations> <preferRootClasses(true|false)> <computeParallel(true|false)>");
System.exit(0);
}
String filename = args[0];
- int numberOfJustifications = Integer.parseInt(args[1]);
- boolean preferRoots = Boolean.valueOf(args[2]);
- boolean computeParallel = Boolean.valueOf(args[3]);
+ String confidenceIRI = args[1];
+ int numberOfJustifications = Integer.parseInt(args[2]);
+ boolean preferRoots = Boolean.valueOf(args[3]);
+ boolean computeParallel = Boolean.valueOf(args[4]);
System.out.println("Loading ontology...");
InputStream is = new BufferedInputStream(new FileInputStream(filename));
@@ -823,34 +837,22 @@
is = new CompressorStreamFactory().createCompressorInputStream("bzip2", is);
}
OWLOntology schema = man.loadOntologyFromOntologyDocument(is);
- 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());
+ Set<OWLTransitiveObjectPropertyAxiom> removedAxioms = schema.getAxioms(AxiomType.TRANSITIVE_OBJECT_PROPERTY);
+ man.removeAxioms(schema, removedAxioms);
System.out.println("...done.");
JustificationBasedCoherentOntologyExtractor extractor = new JustificationBasedCoherentOntologyExtractor();
extractor.setNumberOfJustifications(numberOfJustifications);
extractor.setComputeParallel(computeParallel);
+ extractor.setConfidencePropertyIRI(confidenceIRI);
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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