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[DL-Learner SVN] SF.net SVN: dl-learner:[3576] trunk/components-core/src/main/java/org/ dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java
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From: <lor...@us...> - 2012-02-08 11:49:26
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Revision: 3576
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3576&view=rev
Author: lorenz_b
Date: 2012-02-08 11:49:16 +0000 (Wed, 08 Feb 2012)
Log Message:
-----------
Remove only axioms not contained in the original DBpedia ontology.
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 2012-02-07 21:43:20 UTC (rev 3575)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java 2012-02-08 11:49:16 UTC (rev 3576)
@@ -4,6 +4,10 @@
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.net.MalformedURLException;
+import java.net.URL;
import java.security.MessageDigest;
import java.security.NoSuchAlgorithmException;
import java.util.Collections;
@@ -20,6 +24,8 @@
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.semanticweb.HermiT.Configuration;
import org.semanticweb.HermiT.Reasoner;
@@ -39,6 +45,7 @@
import org.semanticweb.owlapi.model.OWLOntologyStorageException;
import org.semanticweb.owlapi.model.OWLTransitiveObjectPropertyAxiom;
import org.semanticweb.owlapi.model.RemoveAxiom;
+import org.semanticweb.owlapi.owllink.builtin.requests.LoadOntologies;
import org.semanticweb.owlapi.reasoner.IllegalConfigurationException;
import org.semanticweb.owlapi.reasoner.OWLReasoner;
import org.semanticweb.owlapi.reasoner.OWLReasonerConfiguration;
@@ -83,12 +90,15 @@
//whether to debug classes and properties in parallel
private boolean computeParallel = false;
+ private OWLOntology dbpediaOntology;
+
public JustificationBasedCoherentOntologyExtractor() {
try {
md5 = MessageDigest.getInstance("MD5");
} catch (NoSuchAlgorithmException e) {
e.printStackTrace();
}
+ dbpediaOntology = loadDBpediaOntology();
}
static {PelletExplanation.setup();}
@@ -185,19 +195,14 @@
}
logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
- while(!unsatClasses.isEmpty()){
- //get frequency for each axiom
- Map<OWLAxiom, Integer> axiom2CountMap = getAxiomFrequency(entity2Explanations);
+ if(computeParallel){
+ cnt += unsatPropCnt;
+ }
+
+ while(cnt >= 0){
+ //we remove the most appropriate axiom from the ontology
+ removeAppropriateAxiom();
- //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();
- removeAxiom(toRemove);
-
//recompute the unsatisfiable classes
logger.info("Reclassifying...");
startTime = System.currentTimeMillis();
@@ -229,6 +234,9 @@
save("log/dbpedia_" + cnt + "cls" + unsatPropCnt + "prop.owl");
cnt = rootCnt + derivedCnt;
unsatPropCnt = unsatObjectProperties.size();
+ if(computeParallel){
+ cnt += unsatPropCnt;
+ }
}
//recompute explanations if necessary
@@ -251,15 +259,9 @@
entity2ModuleMap.putAll(extractModules(unsatObjectProperties));
while(!unsatObjectProperties.isEmpty()){
- //get frequency for each axiom
- Map<OWLAxiom, Integer> axiom2CountMap = getAxiomFrequency(entity2Explanations);
+ //we remove the most appropriate axiom from the ontology
+ removeAppropriateAxiom();
- //get a sorted list of entries with the highest axiom count first
- List<Entry<OWLAxiom, Integer>> sortedEntries = MapUtils.sortByValues(axiom2CountMap);
- //we remove the most frequent axiom from the ontology
- OWLAxiom toRemove = sortedEntries.get(0).getKey();
- removeAxiom(toRemove);
-
//recompute the unsatisfiable classes
logger.info("Reclassifying...");
startTime = System.currentTimeMillis();
@@ -324,18 +326,9 @@
logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
while(!unsatClasses.isEmpty()){
- //get frequency for each axiom
- Map<OWLAxiom, Integer> axiom2CountMap = getAxiomFrequency(entity2Explanations);
+ //we remove the most appropriate axiom from the ontology
+ removeAppropriateAxiom();
- //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();
- removeAxiom(toRemove);
-
//recompute the unsatisfiable classes
logger.info("Reclassifying...");
startTime = System.currentTimeMillis();
@@ -375,13 +368,24 @@
return getOntologyWithAnnotations(incoherentOntology);
}
- private void removeAxiom(OWLAxiom axiom){
- logger.info("Removing axiom " + axiom + ".");
- manager.removeAxiom(incoherentOntology, axiom);
- manager.addAxiom(diffOntology, axiom);
- manager.applyChange(new RemoveAxiom(incoherentOntology, axiom));
- removeFromExplanations(entity2Explanations, axiom);
- removeFromModules(axiom);
+ private void removeAppropriateAxiom(){
+ //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);
+ //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();
+ if(!dbpediaOntology.containsAxiomIgnoreAnnotations(axiom)){
+ logger.info("Removing axiom " + axiom + ".");
+ manager.removeAxiom(incoherentOntology, axiom);
+ manager.addAxiom(diffOntology, axiom);
+ manager.applyChange(new RemoveAxiom(incoherentOntology, axiom));
+ removeFromExplanations(entity2Explanations, axiom);
+ removeFromModules(axiom);
+ return;
+ }
+ }
}
private void save(String fileName){
@@ -603,6 +607,28 @@
return module;
}
+ private OWLOntology loadDBpediaOntology() {
+ 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);
+ ontology = OWLManager.createOWLOntologyManager().loadOntologyFromOntologyDocument(is);
+ } catch (MalformedURLException e) {
+ e.printStackTrace();
+ } catch (OWLOntologyCreationException e) {
+ e.printStackTrace();
+ } catch (IOException e) {
+ e.printStackTrace();
+ } catch (CompressorException e) {
+ e.printStackTrace();
+ }
+ logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
+ return ontology;
+ }
+
// private Map<OWLClass, OWLOntology> extractModules(Set<OWLClass> classes){
// Map<OWLClass, OWLOntology> cls2ModuleMap = new HashMap<OWLClass, OWLOntology>();
// for(OWLClass cls : classes){
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