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From: <lor...@us...> - 2012-01-26 13:43:24
|
Revision: 3557
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3557&view=rev
Author: lorenz_b
Date: 2012-01-26 13:43:13 +0000 (Thu, 26 Jan 2012)
Log Message:
-----------
Added constructor to give some basic datastructures as arguments.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/reasoning/FastInstanceChecker.java
Modified: trunk/components-core/src/main/java/org/dllearner/reasoning/FastInstanceChecker.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/FastInstanceChecker.java 2012-01-25 13:31:24 UTC (rev 3556)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/FastInstanceChecker.java 2012-01-26 13:43:13 UTC (rev 3557)
@@ -20,6 +20,7 @@
package org.dllearner.reasoning;
import java.io.File;
+import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
@@ -143,7 +144,65 @@
public FastInstanceChecker() {
}
- public FastInstanceChecker(Set<AbstractKnowledgeSource> sources) {
+ public FastInstanceChecker(TreeSet<Individual> individuals,
+ Map<NamedClass, TreeSet<Individual>> classInstancesPos,
+ Map<ObjectProperty, Map<Individual, SortedSet<Individual>>> opPos,
+ Map<DatatypeProperty, Map<Individual, SortedSet<Integer>>> id,
+ Map<DatatypeProperty, TreeSet<Individual>> bdPos,
+ Map<DatatypeProperty, TreeSet<Individual>> bdNeg,
+ AbstractKnowledgeSource... sources) {
+ super(new HashSet<AbstractKnowledgeSource>(Arrays.asList(sources)));
+ this.individuals = individuals;
+ this.classInstancesPos = classInstancesPos;
+ this.opPos = opPos;
+ this.id = id;
+ this.bdPos = bdPos;
+ this.bdNeg = bdNeg;
+
+ if(rc == null){
+ rc = new OWLAPIReasoner(new HashSet<AbstractKnowledgeSource>(Arrays.asList(sources)));
+ try {
+ rc.init();
+ } catch (ComponentInitException e) {
+ e.printStackTrace();
+ }
+ }
+
+ atomicConcepts = rc.getNamedClasses();
+ datatypeProperties = rc.getDatatypeProperties();
+ booleanDatatypeProperties = rc.getBooleanDatatypeProperties();
+ doubleDatatypeProperties = rc.getDoubleDatatypeProperties();
+ intDatatypeProperties = rc.getIntDatatypeProperties();
+ stringDatatypeProperties = rc.getStringDatatypeProperties();
+ atomicRoles = rc.getObjectProperties();
+
+ for (NamedClass atomicConcept : rc.getNamedClasses()) {
+ TreeSet<Individual> pos = classInstancesPos.get(atomicConcept);
+ if(pos != null){
+ classInstancesNeg.put(atomicConcept, (TreeSet<Individual>) Helper.difference(individuals, pos));
+ } else {
+ classInstancesPos.put(atomicConcept, new TreeSet<Individual>());
+ classInstancesNeg.put(atomicConcept, individuals);
+ }
+ }
+ for(ObjectProperty p : atomicRoles){
+ if(opPos.get(p) == null){
+ opPos.put(p, new HashMap<Individual, SortedSet<Individual>>());
+ }
+ }
+
+ for (DatatypeProperty dp : booleanDatatypeProperties) {
+ if(bdPos.get(dp) == null){
+ bdPos.put(dp, new TreeSet<Individual>());
+ }
+ if(bdNeg.get(dp) == null){
+ bdNeg.put(dp, new TreeSet<Individual>());
+ }
+
+ }
+ }
+
+ public FastInstanceChecker(Set<AbstractKnowledgeSource> sources) {
super(sources);
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lor...@us...> - 2012-01-25 13:31:31
|
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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|
|
From: <lor...@us...> - 2012-01-20 02:53:39
|
Revision: 3555
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3555&view=rev
Author: lorenz_b
Date: 2012-01-20 02:53:33 +0000 (Fri, 20 Jan 2012)
Log Message:
-----------
Fixed bug.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/kb/sparql/SPARQLTasks.java
Modified: trunk/components-core/src/main/java/org/dllearner/kb/sparql/SPARQLTasks.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/kb/sparql/SPARQLTasks.java 2012-01-16 10:35:18 UTC (rev 3554)
+++ trunk/components-core/src/main/java/org/dllearner/kb/sparql/SPARQLTasks.java 2012-01-20 02:53:33 UTC (rev 3555)
@@ -712,8 +712,8 @@
}
//remove trivial classes
- classes.remove(OWL.Nothing.toStringID());
- classes.remove(OWL.Thing.toStringID());
+ classes.remove(new NamedClass(OWL.Nothing.toStringID()));
+ classes.remove(new NamedClass(OWL.Thing.toStringID()));
return classes;
}
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|
|
From: <lor...@us...> - 2012-01-16 10:35:29
|
Revision: 3554
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3554&view=rev
Author: lorenz_b
Date: 2012-01-16 10:35:18 +0000 (Mon, 16 Jan 2012)
Log Message:
-----------
Fixed small bugs.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/algorithms/DisjointClassesLearner.java
trunk/components-core/src/main/java/org/dllearner/algorithms/properties/DisjointObjectPropertyAxiomLearner.java
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/DisjointClassesLearner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/DisjointClassesLearner.java 2012-01-13 14:41:55 UTC (rev 3553)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/DisjointClassesLearner.java 2012-01-16 10:35:18 UTC (rev 3554)
@@ -165,7 +165,7 @@
int limit = 1000;
int offset = 0;
String baseQuery = "CONSTRUCT {?s a <%s>. ?s a ?type.} WHERE {?s a <%s>. ?s a ?type.} LIMIT %d OFFSET %d";
- String query = String.format(baseQuery, classToDescribe.getName(), classToDescribe.getName(), limit, offset);System.out.println(query);
+ String query = String.format(baseQuery, classToDescribe.getName(), classToDescribe.getName(), limit, offset);
Model newModel = executeConstructQuery(query);
Map<NamedClass, Integer> result = new HashMap<NamedClass, Integer>();
NamedClass cls;
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 2012-01-13 14:41:55 UTC (rev 3553)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/properties/DisjointObjectPropertyAxiomLearner.java 2012-01-16 10:35:18 UTC (rev 3554)
@@ -130,7 +130,7 @@
offset += limit;
- query = String.format(baseQuery, propertyToDescribe.getName(), propertyToDescribe.getName(), limit, offset);
+ query = String.format(baseQuery, propertyToDescribe.getName(), limit, offset);
newModel = executeConstructQuery(query);
}
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|
|
From: <ku...@us...> - 2012-01-13 14:42:06
|
Revision: 3553
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3553&view=rev
Author: kurzum
Date: 2012-01-13 14:41:55 +0000 (Fri, 13 Jan 2012)
Log Message:
-----------
added new parameter limit to rest interface
Modified Paths:
--------------
trunk/interfaces/src/main/java/org/dllearner/server/Rest.java
Modified: trunk/interfaces/src/main/java/org/dllearner/server/Rest.java
===================================================================
--- trunk/interfaces/src/main/java/org/dllearner/server/Rest.java 2012-01-11 15:32:31 UTC (rev 3552)
+++ trunk/interfaces/src/main/java/org/dllearner/server/Rest.java 2012-01-13 14:41:55 UTC (rev 3553)
@@ -61,14 +61,16 @@
JSONObject learningResult = new JSONObject();
try {
String conf = null;
+ int limit = 5;
if (!isSet("conf", httpServletRequest)) {
throw new IllegalArgumentException("Missing parameter: conf is required. ");
} else {
conf = httpServletRequest.getParameter("conf");
+ if(isSet("limit" , httpServletRequest)){
+ limit = Integer.parseInt(httpServletRequest.getParameter("limit")) ;
+ }
}
- /*todo learn*/
-
if (isSet("debug", httpServletRequest) && httpServletRequest.getParameter("debug").equalsIgnoreCase("true")) {
@@ -91,6 +93,8 @@
EvaluatedDescriptionPosNeg ed = learn(conf);
SparqlQueryDescriptionConvertVisitor sqd = new SparqlQueryDescriptionConvertVisitor();
+ sqd.setLimit(limit);
+
learningResult.put("success", "1");
learningResult.put("manchester", ed.getDescription().toManchesterSyntaxString(null, null));
learningResult.put("kbsyntax", ed.getDescription().toKBSyntaxString());
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|
|
From: <lor...@us...> - 2012-01-11 15:32:37
|
Revision: 3552
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3552&view=rev
Author: lorenz_b
Date: 2012-01-11 15:32:31 +0000 (Wed, 11 Jan 2012)
Log Message:
-----------
Started script to extract some relevant metrics from SPARQL endpoints.
Added Paths:
-----------
trunk/scripts/src/main/java/org/dllearner/scripts/SPARQLEndpointMetrics.java
Added: trunk/scripts/src/main/java/org/dllearner/scripts/SPARQLEndpointMetrics.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/SPARQLEndpointMetrics.java (rev 0)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/SPARQLEndpointMetrics.java 2012-01-11 15:32:31 UTC (rev 3552)
@@ -0,0 +1,133 @@
+package org.dllearner.scripts;
+
+import java.net.URL;
+import java.util.Map;
+import java.util.TreeMap;
+import java.util.Map.Entry;
+import java.util.concurrent.ArrayBlockingQueue;
+import java.util.concurrent.ThreadPoolExecutor;
+import java.util.concurrent.TimeUnit;
+
+import org.apache.log4j.ConsoleAppender;
+import org.apache.log4j.Level;
+import org.apache.log4j.Logger;
+import org.apache.log4j.SimpleLayout;
+import org.dllearner.kb.sparql.SparqlEndpoint;
+import org.dllearner.kb.sparql.SparqlQuery;
+
+import com.hp.hpl.jena.query.QuerySolution;
+import com.hp.hpl.jena.query.ResultSet;
+import com.hp.hpl.jena.rdf.model.Resource;
+
+public class SPARQLEndpointMetrics {
+
+ //parameters for thread pool
+ //Parallel running Threads(Executor) on System
+ private static int corePoolSize = 1;
+ //Maximum Threads allowed in Pool
+ private static int maximumPoolSize = 20;
+ //Keep alive time for waiting threads for jobs(Runnable)
+ private static long keepAliveTime = 10;
+
+ /**
+ * @param args
+ */
+ public static void main(String[] args) throws Exception{
+ SimpleLayout layout = new SimpleLayout();
+ ConsoleAppender consoleAppender = new ConsoleAppender(layout);
+ Logger.getRootLogger().setLevel(Level.WARN);
+ Logger.getLogger("org.dllearner").setLevel(Level.WARN); // seems to be needed for some reason (?)
+ Logger.getRootLogger().removeAllAppenders();
+ Logger.getRootLogger().addAppender(consoleAppender);
+
+ // get all SPARQL endpoints and their graphs - the key is a name-identifier
+ Map<String,SparqlEndpoint> endpoints = new TreeMap<String,SparqlEndpoint>();
+ Map<SparqlEndpoint, String> namespaces = new TreeMap<SparqlEndpoint, String>();
+
+ String query = "";
+ query += "PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> \n";
+ query += "PREFIX void: <http://rdfs.org/ns/void#> \n";
+ query += "PREFIX dcterms: <http://purl.org/dc/terms/> \n";
+ query += "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> \n";
+ query += "PREFIX ov: <http://open.vocab.org/terms/> \n";
+ query += "SELECT * \n";
+ query += "WHERE { \n";
+ query += " ?item rdf:type void:Dataset . \n";
+ query += " ?item dcterms:isPartOf <http://ckan.net/group/lodcloud> . \n";
+ query += " ?item void:sparqlEndpoint ?endpoint . \n";
+// query += " ?item dcterms:subject ?subject . \n";
+// query += " ?item rdfs:label ?label . \n";
+ query += " ?item ov:shortName ?shortName . \n";
+ query += " OPTIONAL{?item <http://www.w3.org/ns/sparql-service-description#namedGraph> ?defaultGraph} \n";
+ query += "}";
+// query += "LIMIT 20";
+ System.out.println("Getting list of SPARQL endpoints from LATC DSI:");
+ System.out.println(query);
+
+ // contact LATC DSI/MDS
+ SparqlEndpoint dsi = new SparqlEndpoint(new URL("http://api.talis.com/stores/latc-mds/services/sparql"));
+ SparqlQuery sq = new SparqlQuery(query, dsi);
+ ResultSet rs = sq.send();
+ while(rs.hasNext()) {
+ QuerySolution qs = rs.next();
+ String endpoint = qs.get("endpoint").toString();
+ String shortName = qs.get("shortName").toString();
+ Resource r = qs.getResource("defaultGraph");
+ if(r != null){
+ String defaultGraph = qs.get("defaultGraph").toString();System.out.println(defaultGraph);
+ }
+
+ endpoints.put(shortName, new SparqlEndpoint(new URL(endpoint)));
+ }
+ System.out.println(endpoints.size() + " endpoints detected.");
+
+ ArrayBlockingQueue<Runnable> workQueue = new ArrayBlockingQueue<Runnable>(endpoints.size());
+ ThreadPoolExecutor threadPool = new ThreadPoolExecutor(corePoolSize, maximumPoolSize, keepAliveTime, TimeUnit.SECONDS, workQueue);
+
+ final StringBuffer sb = new StringBuffer();
+ sb.append("<table border=\"1\">");
+ sb.append("<tr><th>#classes</th><th>#op</th><th>#dp</th><th>#individuals</th></tr>");
+
+ // perform enrichment on endpoints
+ for(final Entry<String,SparqlEndpoint> endpoint : endpoints.entrySet()) {
+
+ threadPool.execute(new Runnable() {
+
+ @Override
+ public void run() {
+ SparqlEndpoint se = endpoint.getValue();
+// System.out.println(se);
+
+ String filter = "FILTER()";
+
+ try {
+ //count classes
+ String query = "SELECT (COUNT(DISTINCT ?type) AS ?cnt) WHERE {?s a ?type.}";
+ int classCnt = new SparqlQuery(query, se).send().next().getLiteral("cnt").getInt();
+
+ //count object properties
+ query = "SELECT (COUNT(DISTINCT ?p) AS ?cnt) WHERE {?s ?p ?o.}";
+ int opCnt = new SparqlQuery(query, se).send().next().getLiteral("cnt").getInt();
+
+ //count data properties
+ query = "SELECT (COUNT(DISTINCT ?p) AS ?cnt) WHERE {?s ?p ?o.}";
+ int dpCnt = new SparqlQuery(query, se).send().next().getLiteral("cnt").getInt();
+
+ //count individuals
+ query = "SELECT (COUNT(DISTINCT ?s) AS ?cnt) WHERE {?s a ?type.}";
+ int indCnt = new SparqlQuery(query, se).send().next().getLiteral("cnt").getInt();
+
+ sb.append("<tr><td>" + classCnt + "</td><td>" + opCnt + "</td>" + "</td><td>" + dpCnt + "</td><td>" + indCnt + "</td></tr>\n");
+ } catch (Exception e) {
+ sb.append("");
+ }
+
+ }
+ });
+ }
+ threadPool.shutdown();
+ System.out.println(sb);
+
+ }
+
+}
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|
|
From: <km...@us...> - 2012-01-11 14:58:35
|
Revision: 3551
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3551&view=rev
Author: kmpf
Date: 2012-01-11 14:58:24 +0000 (Wed, 11 Jan 2012)
Log Message:
-----------
Modified Paths:
--------------
trunk/test/pdb/Original data sets/plp273.list
trunk/test/pdb/Original data sets/plp364.list
trunk/test/pdb/Original data sets/plp399.list
Added Paths:
-----------
trunk/test/pdb/Original data sets/bt426.list
Added: trunk/test/pdb/Original data sets/bt426.list
===================================================================
--- trunk/test/pdb/Original data sets/bt426.list (rev 0)
+++ trunk/test/pdb/Original data sets/bt426.list 2012-01-11 14:58:24 UTC (rev 3551)
@@ -0,0 +1,426 @@
+1LMB.3.
+8ABP..
+1MRP..
+1G3P..
+1GVP..
+1AT0..
+1AOP..
+1AMP..
+1AK0..
+1BGP..
+2CYP..
+1LAT.B.
+1LUC.B.
+1MTY.B.
+1NBA.B.
+1NCI.B.
+1KVE.B.
+1KWA.B.
+1EDM.B.
+1FMT.B.
+1GOT.B.
+1ATZ.B.
+1APY.B.
+1AQZ.B.
+1A28.B.
+1BDM.B.
+1BEN.B.
+1BTK.B.
+1CPC.B.
+1VWL.B.
+1WPO.B.
+1PNK.B.
+1RYP.2.
+5P21..
+1HA1..
+1ECA..
+1FUA..
+1FNA..
+1GSA..
+1A6Q..
+1AK1..
+1ABA..
+1BV1..
+1BA1..
+1TCA..
+1WBA..
+1POA..
+1QBA..
+2BAA..
+3CLA..
+2KIN.B.
+5HPG.A.
+1LKK.A.
+1LTS.A.
+1MLD.A.
+1MOL.A.
+1MKA.A.
+1MUG.A.
+1MUC.A.
+1MPG.A.
+1NBC.A.
+1NP1.A.
+1ONR.A.
+1HGX.A.
+1HAV.A.
+1HCR.A.
+1HSB.A.
+1IIB.A.
+1IDA.A.
+1IAK.A.
+1ISU.A.
+1JET.A.
+1JFR.A.
+1KVE.A.
+1KPT.A.
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+1DOK.A.
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+1DUP.A.
+1ECP.A.
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+1FVK.A.
+1FWC.A.
+1GIF.A.
+1XFF.A.
+1GAR.A.
+1GUQ.A.
+1ALV.A.
+1ALI.A.
+1AMU.A.
+1AOZ.A.
+1AOQ.A.
+1AOH.A.
+1AOC.A.
+1AJS.A.
+1ADO.A.
+1AFW.A.
+1AGJ.A.
+1AT1.A.
+1AVM.A.
+1AWS.A.
+1AQ6.A.
+1AQ0.A.
+1A7T.A.
+1A2Z.A.
+1A2Y.A.
+1A2P.A.
+1A34.A.
+1BKR.A.
+1BEB.A.
+1BFT.A.
+1BBP.A.
+1CHM.A.
+1CKA.A.
+1CYD.A.
+1XIK.A.
+1XGS.A.
+1YTB.A.
+1TVX.A.
+1VCA.A.
+1PHN.A.
+1RGE.A.
+1SLT.A.
+1SLU.A.
+1SPU.A.
+1IG5..
+1NAR..
+1JER..
+1KNB..
+1FDR..
+1A62..
+1ARB..
+1AQB..
+1AJ2..
+1AD2..
+1BYB..
+1C52..
+1CFB..
+1YER..
+1WAB..
+2POR..
+3CYR..
+3SEB..
+3SDH.A.
+2HMZ.A.
+2ARC.A.
+2PSP.A.
+8RXN.A.
+1HTR.P.
+1LIS..
+1MSC..
+1NLS..
+1ORC..
+1HFC..
+1IFC..
+1JPC..
+1FUS..
+1FDS..
+1A9S..
+1AL3..
+1AAC..
+1BGC..
+1C1C..
+1YCC..
+1TYS..
+1VCC..
+1POC..
+1PGS..
+1RHS..
+2CTC..
+2PLC..
+2SNS..
+2SN3..
+3TSS..
+1MTY.G.
+1GOT.G.
+1LIT..
+1MBD..
+1OPD..
+1IGD..
+1KID..
+1DAD..
+1EDT..
+1FIT..
+1GND..
+1AWD..
+1BRT..
+1BFD..
+1CHD..
+1VSD..
+1VID..
+1PUD..
+1POT..
+1SMD..
+2LBD..
+2HFT..
+2END..
+1RYP.F.
+1LBU..
+1MWE..
+1NEU..
+1HOE..
+1KVU..
+1EDE..
+1A8E..
+1ALU..
+1TFE..
+1UAE..
+1PHE..
+1RIE..
+1CSE.E.
+1NIF..
+1KPF..
+1ERV..
+1ARV..
+1ANF..
+1BKF..
+1CNV..
+1THV..
+1QNF..
+1LT5.D.
+1MTY.D.
+1AGQ.D.
+1JDW..
+1EDG..
+1AH7..
+1AF7..
+1BFG..
+1RMG..
+2HBG..
+1NOX..
+1IXH..
+1KUH..
+1A68..
+1A1X..
+1AMX..
+1CSH..
+1CEX..
+1THX..
+1VHH..
+2AYH..
+3COX..
+1RYP.J.
+1LKI..
+1MSI..
+1MAI..
+1OPY..
+1DXY..
+1GKY..
+1GAI..
+1A8I..
+1ALY..
+1UBI..
+1R69..
+2DRI..
+1FLE.I.
+1CEW.I.
+1CSE.I.
+1YVE.I.
+1RYP.I.
+1MRJ..
+1AJJ..
+1AKZ..
+1CTJ..
+8RUC.I.
+1MSK..
+1NPK..
+1IDK..
+2BBK.H.
+1GD1.O.
+1LML..
+1LCL..
+1MML..
+1ECL..
+1AYL..
+1AOL..
+153L..
+119L..
+2SIL..
+1LAM..
+1MZM..
+1EZM..
+1AMM..
+1CEM..
+2MCM..
+2GDM..
+1NFN..
+1HXN..
+1DUN..
+1AXN..
+1BTN..
+1CSN..
+1CBN..
+1ISO..
+1IDO..
+1AZO..
+1VLB..
+1AKO..
+1AHO..
+1BDO..
+1CPO..
+1CEO..
+1XJO..
+1PDO..
+1YAI.C.
+1TAD.C.
+1TSP..
+1WHT.B.
+7RSA..
+1PTQ..
+1PDA..
+2FHA..
+2CBA..
+2WEA..
+2PIA..
+5CSM.A.
+4PGA.A.
+7AHL.A.
+6GSV.A.
+1XYZ.A.
+1YAS.A.
+1TRK.A.
+1URN.A.
+1VPS.A.
+1PCF.A.
+1RYP.1.
+1RVA.A.
+1SVP.A.
+2I1B..
+2A0B..
+2KIN.A.
+2FIV.A.
+2CHS.A.
+2CCY.A.
+2SCP.A.
+4XIS..
+1ONC..
+1OIS..
+1VLS..
+1VJS..
+1CYO..
+1PNE..
+3PTE..
+1REQ.D.
+1UXY..
+1V39..
+1WHI..
+1PTY..
+1PMI..
+2ACY..
+2PHY..
+2PII..
+3CHY..
+1REG.Y.
+1SGP.I.
+1SKZ..
+2SIC.I.
+2ILK..
+2ABK..
+2SAK..
+1TML..
+3NUL..
+2FDN..
+3PCG.M.
+1WHO..
+5PTP..
+1PHP..
+1SFP..
+1SBP..
+1NUL.B.
+1PRX.B.
+1SFT.B.
+1SRA..
+2MSB.B.
+2VHB.B.
+2RSP.B.
+1NWP.A.
+1OVA.A.
+1XSO.A.
+1UNK.A.
+1WDC.A.
+1STM.A.
+4MT2..
+1NXB..
+1XNB..
+1TIB..
+1WER..
+1SVB..
+2RN2..
+3VUB..
+3DAA.A.
+2NAC.A.
+2HPD.A.
+2BOP.A.
+2TYS.A.
+256B.A.
+1OYC..
+1PLC..
+1RSS..
+1REC..
+2HTS..
+3GRS..
+1PPT..
+2PGD..
+3LZT..
+1TIF..
+1VIF..
+1RCF..
+2ENG..
+1UCH..
+2PTH..
+5PTI..
+1PII..
+1RSY..
+1RA9..
+2TGI..
+1OSP.O.
+4BCL..
+6CEL..
+2ERL..
+1ZIN..
+1VIN..
+1PPN..
+1RRO..
+2BBK.L.
Modified: trunk/test/pdb/Original data sets/plp273.list
===================================================================
--- trunk/test/pdb/Original data sets/plp273.list 2012-01-11 13:03:48 UTC (rev 3550)
+++ trunk/test/pdb/Original data sets/plp273.list 2012-01-11 14:58:24 UTC (rev 3551)
@@ -1,273 +1,273 @@
-2W8X.A
-2W9Y.A
-2WCJ.A
-2WCR.A
-2WFB.A
-2WFO.A
-2WJ5.A
-2WJ9.A
-2WJR.A
-2WL1.A
-2WNF.A
-2WPV.B
-2WQF.A
-2WTP.A
-2WUJ.A
-2WUU.A
-2WUX.A
-2WVX.A
-2WY3.B
-2WZO.A
-2ZXY.A
-3A0Z.A
-3A4R.A
-3A57.A
-3A5P.A
-3AAP.A
-3FOT.A
-3FOV.A
-3FQG.A
-3FRR.A
-3FSO.A
-3FSS.A
-3FWK.A
-3FWZ.A
-3FX7.A
-3FYB.A
-3FYM.A
-3G02.A
-3G0M.A
-3G1J.A
-3G21.A
-3G2B.A
-3G2S.A
-3G36.A
-3G3T.A
-3G5B.A
-3G7G.A
-3GA3.A
-3GA4.A
-3GAE.A
-3GBW.A
-3GBY.A
-3GDW.A
-3GE3.E
-3GFP.A
-3GI7.A
-3GIX.A
-3GKJ.A
-3GMG.A
-3GN6.A
-3GNE.A
-3GNZ.P
-3GOE.A
-3GP4.A
-3GP6.A
-3GQQ.A
-3GWH.A
-3GWN.A
-3GXW.A
-3GY9.A
-3GZB.A
-3H05.A
-3H0W.A
-3H20.A
-3H3L.A
-3H51.A
-3H5J.A
-3H6P.C
-3H6R.A
-3H7H.B
-3H8T.A
-3H96.A
-3H9W.A
-3HA2.A
-3HE5.B
-3HFO.A
-3HH1.A
-3HL1.A
-3HN0.A
-3HN5.A
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-3HOI.A
-3HPC.X
-3HR0.A
-3HRL.A
-3HRR.A
-3HSH.A
-3HTV.A
-3HVS.A
-3HWP.A
-3HWU.A
-3HX8.A
-3HXL.A
-3HYN.A
-3HZP.A
-3I0W.A
-3I1A.A
-3I2V.A
-3I4O.A
-3I7M.A
-3I84.A
-3IBM.A
-3IC3.A
-3ID1.A
-3IDF.A
-3IDU.A
-3IE4.A
-3IEE.A
-3IG9.A
-3IHT.A
-3IJM.A
-3IKB.A
-3IKW.A
-3ILW.A
-3IM3.A
-3IMK.A
-3IP4.C
-3IPF.A
-3IPJ.A
-3IR4.A
-3IT5.A
-3IU6.A
-3IUF.A
-3IUO.A
-3IUW.A
-3IVV.A
-3IWF.A
-3IX3.A
-3JQY.A
-3JRN.A
-3JSZ.A
-3JTW.A
-3JU0.A
-3JUD.A
-3JXO.A
-3JYG.A
-3JYZ.A
-3JZ9.A
-3K0X.A
-3K0Z.A
-3K2O.A
-3K5J.A
-3K69.A
-3K6O.A
-3K7X.A
-3KD3.A
-3KDE.C
-3KDF.A
-3KDF.B
-3KDG.A
-3KE7.A
-3KG9.A
-3KGK.A
-3KK4.A
-3KKF.A
-3KKG.A
-3KLQ.A
-3KMI.A
-3KOG.A
-3KOS.A
-3KPE.A
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-3L15.A
-3L23.A
-3L29.A
-3L3E.A
-3L4H.A
-3L51.B
-3L6T.A
-3L7H.A
-2X2S.A
-2X2U.A
-2X32.A
-2X3G.A
-2X4J.A
-2X4K.A
-2X4W.A
-2X55.A
-2X5N.A
-2XCJ.A
-2XDG.A
-2XDH.A
-2XF7.A
-2XFV.A
-2XG5.B
-2XLG.A
-2XMJ.A
-3AG3.D
-3L9A.X
-3LAX.A
-3LDC.A
-3LDU.A
-3LE4.A
-3LFR.A
-3LGB.A
-3LHE.A
-3LHO.A
-3LHR.A
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-3LR2.A
-3LR4.A
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-3LYG.A
-3LYH.A
-3LYY.A
-3M1T.A
-3M66.A
-3M6J.A
-3M7K.A
-3M7O.A
-3M8J.A
-3M9Q.A
-3MAB.A
-3MAL.A
-3MCB.A
-3MCB.B
-3MCQ.A
-3MDP.A
-3MG1.A
-3MHS.B
-3MR0.A
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-3MZO.A
-3N0R.A
-3N1E.A
-3N6Y.A
-3N9B.A
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-3NZN.A
-3O6C.A
-3OAJ.A
+2W8X.A.
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+3FOT.A.
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+3FQG.A.
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+3FWZ.A.
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+3G3T.A.
+3G5B.A.
+3G7G.A.
+3GA3.A.
+3GA4.A.
+3GAE.A.
+3GBW.A.
+3GBY.A.
+3GDW.A.
+3GE3.E.
+3GFP.A.
+3GI7.A.
+3GIX.A.
+3GKJ.A.
+3GMG.A.
+3GN6.A.
+3GNE.A.
+3GNZ.P.
+3GOE.A.
+3GP4.A.
+3GP6.A.
+3GQQ.A.
+3GWH.A.
+3GWN.A.
+3GXW.A.
+3GY9.A.
+3GZB.A.
+3H05.A.
+3H0W.A.
+3H20.A.
+3H3L.A.
+3H51.A.
+3H5J.A.
+3H6P.C.
+3H6R.A.
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+3H8T.A.
+3H96.A.
+3H9W.A.
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+3HE5.B.
+3HFO.A.
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+3IEE.A.
+3IG9.A.
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+3IJM.A.
+3IKB.A.
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+3JU0.A.
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+3JZ9.A.
+3K0X.A.
+3K0Z.A.
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+3KDE.C.
+3KDF.A.
+3KDF.B.
+3KDG.A.
+3KE7.A.
+3KG9.A.
+3KGK.A.
+3KK4.A.
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+3KLQ.A.
+3KMI.A.
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+3KPE.A.
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+3KWS.A.
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+3KYZ.A.
+3KZ5.A.
+3KZD.A.
+3KZP.A.
+3L0Q.B.
+3L15.A.
+3L23.A.
+3L29.A.
+3L3E.A.
+3L4H.A.
+3L51.B.
+3L6T.A.
+3L7H.A.
+2X2S.A.
+2X2U.A.
+2X32.A.
+2X3G.A.
+2X4J.A.
+2X4K.A.
+2X4W.A.
+2X55.A.
+2X5N.A.
+2XCJ.A.
+2XDG.A.
+2XDH.A.
+2XF7.A.
+2XFV.A.
+2XG5.B.
+2XLG.A.
+2XMJ.A.
+3AG3.D.
+3L9A.X.
+3LAX.A.
+3LDC.A.
+3LDU.A.
+3LE4.A.
+3LFR.A.
+3LGB.A.
+3LHE.A.
+3LHO.A.
+3LHR.A.
+3LLO.A.
+3LM3.A.
+3LQ9.A.
+3LR2.A.
+3LR4.A.
+3LS0.A.
+3LUC.A.
+3LUM.A.
+3LUR.A.
+3LUU.A.
+3LWC.A.
+3LWG.A.
+3LXR.F.
+3LYD.A.
+3LYG.A.
+3LYH.A.
+3LYY.A.
+3M1T.A.
+3M66.A.
+3M6J.A.
+3M7K.A.
+3M7O.A.
+3M8J.A.
+3M9Q.A.
+3MAB.A.
+3MAL.A.
+3MCB.A.
+3MCB.B.
+3MCQ.A.
+3MDP.A.
+3MG1.A.
+3MHS.B.
+3MR0.A.
+3MSW.A.
+3MT0.A.
+3MW8.A.
+3MWZ.A.
+3MZO.A.
+3N0R.A.
+3N1E.A.
+3N6Y.A.
+3N9B.A.
+3NE8.A.
+3NFT.A.
+3NKE.A.
+3NKG.A.
+3NKL.A.
+3NO2.A.
+3NOH.A.
+3NPD.A.
+3NQI.A.
+3NRF.A.
+3NRW.A.
+3NS2.A.
+3NY3.A.
+3NZN.A.
+3O6C.A.
+3OAJ.A.
Modified: trunk/test/pdb/Original data sets/plp364.list
===================================================================
--- trunk/test/pdb/Original data sets/plp364.list 2012-01-11 13:03:48 UTC (rev 3550)
+++ trunk/test/pdb/Original data sets/plp364.list 2012-01-11 14:58:24 UTC (rev 3551)
@@ -1,364 +1,364 @@
-2JK9.A
-2V4X.A
-2VQ4.A
-2VTC.A
-2VV6.A
-2VXT.I
-2VXZ.A
-2VZC.A
-2W2R.A
-2W61.A
-2W6A.A
-2W7A.A
-2W7N.A
-2ZK9.X
-2ZNR.A
-2ZQ5.A
-2ZQE.A
-2ZSI.B
-2ZX0.A
-3BYP.A
-3BYQ.A
-3C1Q.A
-3C7T.A
-3C8L.A
-3C8W.A
-3CHM.A
-3CKK.A
-3CNY.A
-3CP7.A
-3CT6.A
-3CZ6.A
-3D1R.A
-3D2Q.A
-3D34.A
-3D3B.J
-3D59.A
-3D85.C
-3DAN.A
-3DD7.A
-3DS2.A
-3DSB.A
-3E7H.A
-3E7U.X
-3E8O.A
-3E8T.A
-3EBT.A
-3ECF.A
-3ECH.A
-3EDO.A
-3EEH.A
-3EER.A
-3EF8.A
-3EHG.A
-3EHM.A
-3EKI.A
-3EMF.A
-3EMI.A
-3ENU.A
-3EO6.A
-3ER7.A
-3ES4.A
-3EYT.A
-3EZI.A
-3F0P.A
-3F2E.A
-3F40.A
-3F4M.A
-3F62.A
-3F7E.A
-3F7Q.A
-3F8X.A
-3F95.A
-3F9S.A
-3FAU.A
-3FB9.A
-3FBL.A
-3FCN.A
-3FF2.A
-3FF5.A
-3FFV.A
-3FG9.A
-3FGR.B
-3FGV.A
-3FH1.A
-3FIA.A
-3FID.A
-3FJU.B
-3FK8.A
-3FKA.A
-3FM2.A
-3FMY.A
-2W8X.A
-2W9Y.A
-2WCJ.A
-2WCR.A
-2WFB.A
-2WFO.A
-2WJ5.A
-2WJ9.A
-2WJR.A
-2WL1.A
-2WNF.A
-2WPV.B
-2WQF.A
-2WTP.A
-2WUJ.A
-2WUU.A
-2WUX.A
-2WVX.A
-2WY3.B
-2WZO.A
-2ZXY.A
-3A0Z.A
-3A4R.A
-3A57.A
-3A5P.A
-3AAP.A
-3FOT.A
-3FOV.A
-3FQG.A
-3FRR.A
-3FSO.A
-3FSS.A
-3FWK.A
-3FWZ.A
-3FX7.A
-3FYB.A
-3FYM.A
-3G02.A
-3G0M.A
-3G1J.A
-3G21.A
-3G2B.A
-3G2S.A
-3G36.A
-3G3T.A
-3G5B.A
-3G7G.A
-3GA3.A
-3GA4.A
-3GAE.A
-3GBW.A
-3GBY.A
-3GDW.A
-3GE3.E
-3GFP.A
-3GI7.A
-3GIX.A
-3GKJ.A
-3GMG.A
-3GN6.A
-3GNE.A
-3GNZ.P
-3GOE.A
-3GP4.A
-3GP6.A
-3GQQ.A
-3GWH.A
-3GWN.A
-3GXW.A
-3GY9.A
-3GZB.A
-3H05.A
-3H0W.A
-3H20.A
-3H3L.A
-3H51.A
-3H5J.A
-3H6P.C
-3H6R.A
-3H7H.B
-3H8T.A
-3H96.A
-3H9W.A
-3HA2.A
-3HE5.B
-3HFO.A
-3HH1.A
-3HL1.A
-3HN0.A
-3HN5.A
-3HO6.A
-3HOI.A
-3HPC.X
-3HR0.A
-3HRL.A
-3HRR.A
-3HSH.A
-3HTV.A
-3HVS.A
-3HWP.A
-3HWU.A
-3HX8.A
-3HXL.A
-3HYN.A
-3HZP.A
-3I0W.A
-3I1A.A
-3I2V.A
-3I4O.A
-3I7M.A
-3I84.A
-3IBM.A
-3IC3.A
-3ID1.A
-3IDF.A
-3IDU.A
-3IE4.A
-3IEE.A
-3IG9.A
-3IHT.A
-3IJM.A
-3IKB.A
-3IKW.A
-3ILW.A
-3IM3.A
-3IMK.A
-3IP4.C
-3IPF.A
-3IPJ.A
-3IR4.A
-3IT5.A
-3IU6.A
-3IUF.A
-3IUO.A
-3IUW.A
-3IVV.A
-3IWF.A
-3IX3.A
-3JQY.A
-3JRN.A
-3JSZ.A
-3JTW.A
-3JU0.A
-3JUD.A
-3JXO.A
-3JYG.A
-3JYZ.A
-3JZ9.A
-3K0X.A
-3K0Z.A
-3K2O.A
-3K5J.A
-3K69.A
-3K6O.A
-3K7X.A
-3KD3.A
-3KDE.C
-3KDF.A
-3KDF.B
-3KDG.A
-3KE7.A
-3KG9.A
-3KGK.A
-3KK4.A
-3KKF.A
-3KKG.A
-3KLQ.A
-3KMI.A
-3KOG.A
-3KOS.A
-3KPE.A
-3KUC.B
-3KWS.A
-3KXT.A
-3KYZ.A
-3KZ5.A
-3KZD.A
-3KZP.A
-3L0Q.B
-3L15.A
-3L23.A
-3L29.A
-3L3E.A
-3L4H.A
-3L51.B
-3L6T.A
-3L7H.A
-2X2S.A
-2X2U.A
-2X32.A
-2X3G.A
-2X4J.A
-2X4K.A
-2X4W.A
-2X55.A
-2X5N.A
-2XCJ.A
-2XDG.A
-2XDH.A
-2XF7.A
-2XFV.A
-2XG5.B
-2XLG.A
-2XMJ.A
-3AG3.D
-3L9A.X
-3LAX.A
-3LDC.A
-3LDU.A
-3LE4.A
-3LFR.A
-3LGB.A
-3LHE.A
-3LHO.A
-3LHR.A
-3LLO.A
-3LM3.A
-3LQ9.A
-3LR2.A
-3LR4.A
-3LS0.A
-3LUC.A
-3LUM.A
-3LUR.A
-3LUU.A
-3LWC.A
-3LWG.A
-3LXR.F
-3LYD.A
-3LYG.A
-3LYH.A
-3LYY.A
-3M1T.A
-3M66.A
-3M6J.A
-3M7K.A
-3M7O.A
-3M8J.A
-3M9Q.A
-3MAB.A
-3MAL.A
-3MCB.A
-3MCB.B
-3MCQ.A
-3MDP.A
-3MG1.A
-3MHS.B
-3MR0.A
-3MSW.A
-3MT0.A
-3MW8.A
-3MWZ.A
-3MZO.A
-3N0R.A
-3N1E.A
-3N6Y.A
-3N9B.A
-3NE8.A
-3NFT.A
-3NKE.A
-3NKG.A
-3NKL.A
-3NO2.A
-3NOH.A
-3NPD.A
-3NQI.A
-3NRF.A
-3NRW.A
-3NS2.A
-3NY3.A
-3NZN.A
-3O6C.A
-3OAJ.A
+2JK9.A.
+2V4X.A.
+2VQ4.A.
+2VTC.A.
+2VV6.A.
+2VXT.I.
+2VXZ.A.
+2VZC.A.
+2W2R.A.
+2W61.A.
+2W6A.A.
+2W7A.A.
+2W7N.A.
+2ZK9.X.
+2ZNR.A.
+2ZQ5.A.
+2ZQE.A.
+2ZSI.B.
+2ZX0.A.
+3BYP.A.
+3BYQ.A.
+3C1Q.A.
+3C7T.A.
+3C8L.A.
+3C8W.A.
+3CHM.A.
+3CKK.A.
+3CNY.A.
+3CP7.A.
+3CT6.A.
+3CZ6.A.
+3D1R.A.
+3D2Q.A.
+3D34.A.
+3D3B.J.
+3D59.A.
+3D85.C.
+3DAN.A.
+3DD7.A.
+3DS2.A.
+3DSB.A.
+3E7H.A.
+3E7U.X.
+3E8O.A.
+3E8T.A.
+3EBT.A.
+3ECF.A.
+3ECH.A.
+3EDO.A.
+3EEH.A.
+3EER.A.
+3EF8.A.
+3EHG.A.
+3EHM.A.
+3EKI.A.
+3EMF.A.
+3EMI.A.
+3ENU.A.
+3EO6.A.
+3ER7.A.
+3ES4.A.
+3EYT.A.
+3EZI.A.
+3F0P.A.
+3F2E.A.
+3F40.A.
+3F4M.A.
+3F62.A.
+3F7E.A.
+3F7Q.A.
+3F8X.A.
+3F95.A.
+3F9S.A.
+3FAU.A.
+3FB9.A.
+3FBL.A.
+3FCN.A.
+3FF2.A.
+3FF5.A.
+3FFV.A.
+3FG9.A.
+3FGR.B.
+3FGV.A.
+3FH1.A.
+3FIA.A.
+3FID.A.
+3FJU.B.
+3FK8.A.
+3FKA.A.
+3FM2.A.
+3FMY.A.
+2W8X.A.
+2W9Y.A.
+2WCJ.A.
+2WCR.A.
+2WFB.A.
+2WFO.A.
+2WJ5.A.
+2WJ9.A.
+2WJR.A.
+2WL1.A.
+2WNF.A.
+2WPV.B.
+2WQF.A.
+2WTP.A.
+2WUJ.A.
+2WUU.A.
+2WUX.A.
+2WVX.A.
+2WY3.B.
+2WZO.A.
+2ZXY.A.
+3A0Z.A.
+3A4R.A.
+3A57.A.
+3A5P.A.
+3AAP.A.
+3FOT.A.
+3FOV.A.
+3FQG.A.
+3FRR.A.
+3FSO.A.
+3FSS.A.
+3FWK.A.
+3FWZ.A.
+3FX7.A.
+3FYB.A.
+3FYM.A.
+3G02.A.
+3G0M.A.
+3G1J.A.
+3G21.A.
+3G2B.A.
+3G2S.A.
+3G36.A.
+3G3T.A.
+3G5B.A.
+3G7G.A.
+3GA3.A.
+3GA4.A.
+3GAE.A.
+3GBW.A.
+3GBY.A.
+3GDW.A.
+3GE3.E.
+3GFP.A.
+3GI7.A.
+3GIX.A.
+3GKJ.A.
+3GMG.A.
+3GN6.A.
+3GNE.A.
+3GNZ.P.
+3GOE.A.
+3GP4.A.
+3GP6.A.
+3GQQ.A.
+3GWH.A.
+3GWN.A.
+3GXW.A.
+3GY9.A.
+3GZB.A.
+3H05.A.
+3H0W.A.
+3H20.A.
+3H3L.A.
+3H51.A.
+3H5J.A.
+3H6P.C.
+3H6R.A.
+3H7H.B.
+3H8T.A.
+3H96.A.
+3H9W.A.
+3HA2.A.
+3HE5.B.
+3HFO.A.
+3HH1.A.
+3HL1.A.
+3HN0.A.
+3HN5.A.
+3HO6.A.
+3HOI.A.
+3HPC.X.
+3HR0.A.
+3HRL.A.
+3HRR.A.
+3HSH.A.
+3HTV.A.
+3HVS.A.
+3HWP.A.
+3HWU.A.
+3HX8.A.
+3HXL.A.
+3HYN.A.
+3HZP.A.
+3I0W.A.
+3I1A.A.
+3I2V.A.
+3I4O.A.
+3I7M.A.
+3I84.A.
+3IBM.A.
+3IC3.A.
+3ID1.A.
+3IDF.A.
+3IDU.A.
+3IE4.A.
+3IEE.A.
+3IG9.A.
+3IHT.A.
+3IJM.A.
+3IKB.A.
+3IKW.A.
+3ILW.A.
+3IM3.A.
+3IMK.A.
+3IP4.C.
+3IPF.A.
+3IPJ.A.
+3IR4.A.
+3IT5.A.
+3IU6.A.
+3IUF.A.
+3IUO.A.
+3IUW.A.
+3IVV.A.
+3IWF.A.
+3IX3.A.
+3JQY.A.
+3JRN.A.
+3JSZ.A.
+3JTW.A.
+3JU0.A.
+3JUD.A.
+3JXO.A.
+3JYG.A.
+3JYZ.A.
+3JZ9.A.
+3K0X.A.
+3K0Z.A.
+3K2O.A.
+3K5J.A.
+3K69.A.
+3K6O.A.
+3K7X.A.
+3KD3.A.
+3KDE.C.
+3KDF.A.
+3KDF.B.
+3KDG.A.
+3KE7.A.
+3KG9.A.
+3KGK.A.
+3KK4.A.
+3KKF.A.
+3KKG.A.
+3KLQ.A.
+3KMI.A.
+3KOG.A.
+3KOS.A.
+3KPE.A.
+3KUC.B.
+3KWS.A.
+3KXT.A.
+3KYZ.A.
+3KZ5.A.
+3KZD.A.
+3KZP.A.
+3L0Q.B.
+3L15.A.
+3L23.A.
+3L29.A.
+3L3E.A.
+3L4H.A.
+3L51.B.
+3L6T.A.
+3L7H.A.
+2X2S.A.
+2X2U.A.
+2X32.A.
+2X3G.A.
+2X4J.A.
+2X4K.A.
+2X4W.A.
+2X55.A.
+2X5N.A.
+2XCJ.A.
+2XDG.A.
+2XDH.A.
+2XF7.A.
+2XFV.A.
+2XG5.B.
+2XLG.A.
+2XMJ.A.
+3AG3.D.
+3L9A.X.
+3LAX.A.
+3LDC.A.
+3LDU.A.
+3LE4.A.
+3LFR.A.
+3LGB.A.
+3LHE.A.
+3LHO.A.
+3LHR.A.
+3LLO.A.
+3LM3.A.
+3LQ9.A.
+3LR2.A.
+3LR4.A.
+3LS0.A.
+3LUC.A.
+3LUM.A.
+3LUR.A.
+3LUU.A.
+3LWC.A.
+3LWG.A.
+3LXR.F.
+3LYD.A.
+3LYG.A.
+3LYH.A.
+3LYY.A.
+3M1T.A.
+3M66.A.
+3M6J.A.
+3M7K.A.
+3M7O.A.
+3M8J.A.
+3M9Q.A.
+3MAB.A.
+3MAL.A.
+3MCB.A.
+3MCB.B.
+3MCQ.A.
+3MDP.A.
+3MG1.A.
+3MHS.B.
+3MR0.A.
+3MSW.A.
+3MT0.A.
+3MW8.A.
+3MWZ.A.
+3MZO.A.
+3N0R.A.
+3N1E.A.
+3N6Y.A.
+3N9B.A.
+3NE8.A.
+3NFT.A.
+3NKE.A.
+3NKG.A.
+3NKL.A.
+3NO2.A.
+3NOH.A.
+3NPD.A.
+3NQI.A.
+3NRF.A.
+3NRW.A.
+3NS2.A.
+3NY3.A.
+3NZN.A.
+3O6C.A.
+3OAJ.A.
Modified: trunk/test/pdb/Original data sets/plp399.list
===================================================================
--- trunk/test/pdb/Original data sets/plp399.list 2012-01-11 13:03:48 UTC (rev 3550)
+++ trunk/test/pdb/Original data sets/plp399.list 2012-01-11 14:58:24 UTC (rev 3551)
@@ -1,399 +1,399 @@
-3JU0.A
-3JUD.A
-2WQF.A
-3F8X.A
-2X4W.A
-2X4J.A
-2X4K.A
-3LM3.A
-3FQG.A
-3A57.A
-3A5P.A
-3FJU.B
-2ZQ5.A
-2ZQE.A
-2ZNR.A
-2G1P.A
-3G1J.A
-3K7X.A
-3LLO.A
-3IVV.A
-3ES4.A
-3K0X.A
-3K0Z.A
-3IWF.A
-3MW8.A
-3MWZ.A
-3FKA.A
-3FK8.A
-3GMG.A
-3I1A.A
-3FBL.A
-3FB9.A
-2WY3.B
-3MG1.A
-3HA2.A
-3H20.A
-3LFR.A
-2RIV.B
-3H5J.A
-3H51.A
-2VXZ.A
-2VXT.I
-1US5.A
-2WCJ.A
-2WCR.A
-1EG3.A
-3G02.A
-3G0M.A
-3HOI.A
-3HO6.A
-3KMI.A
-3HRR.A
-3HR0.A
-3HRL.A
-3G21.A
-3G2B.A
-3G2S.A
-3KOS.A
-3KOG.A
-3C7T.A
-2RH3.A
-3F62.A
-3H0W.A
-3H05.A
-1DC1.A
-3NE8.A
-3GDW.A
-3L4H.A
-3GY9.A
-2XMJ.A
-2XCJ.A
-3IM3.A
-3IMK.A
-3I2V.A
-2WJ5.A
-2WJR.A
-2WJ9.A
-3JSZ.A
-3JTW.A
-3D59.A
-3H9W.A
-3H96.A
-3FH1.A
-3CP7.A
-3LYD.A
-3LYY.A
-3LYG.A
-3LYH.A
-3I7M.A
-3F2E.A
-3HZP.A
-2XF7.A
-2XFV.A
-3KZP.A
-3KZ5.A
-3KZD.A
-2WL1.A
-3MT0.A
-3GFP.A
-3KYZ.A
-3N0R.A
-3EO6.A
-3HWU.A
-3HWP.A
-2WNF.A
-3GWH.A
-3GWN.A
-3K2O.A
-2R16.A
-3DAN.A
-3GNE.A
-3GN6.A
-3GNZ.P
-3OAJ.A
-3I0W.A
-3C1Q.A
-2QL8.A
-3CHM.A
-3CZ6.A
-3EYT.A
-2WZO.A
-2VZC.A
-3FF2.A
-3FFV.A
-3FF5.A
-3NQI.A
-2XG5.B
-3HH1.A
-2VE8.A
-3D2Q.A
-3NS2.A
-3E7U.X
-3E7H.A
-2P4F.A
-3IKB.A
-3IKW.A
-3NZN.A
-3GI7.A
-3GIX.A
-3KWS.A
-3IP4.C
-3IPJ.A
-3IPF.A
-3KUC.B
-3ENU.A
-2AQ6.A
-3KLQ.A
-3L15.A
-3N9B.A
-3NO2.A
-3NOH.A
-3KDF.A
-3KDF.B
-3KDE.C
-3KDG.A
-3KD3.A
-3CT6.A
-3IG9.A
-3L9A.X
-3LDC.A
-3LDU.A
-3FWK.A
-3FWZ.A
-3A4R.A
-3BFQ.G
-3GE3.E
-3LUM.A
-3LUU.A
-3LUC.A
-3LUR.A
-3IU6.A
-3IUO.A
-3IUW.A
-3IUF.A
-2OX7.A
-3LHR.A
-3LHE.A
-3LHO.A
-3ER7.A
-2QZQ.A
-3N1E.A
-3LQ9.A
-2WTP.A
-3IC3.A
-3M8J.A
-2ZCA.A
-3F7Q.A
-3F7E.A
-3MHS.C
-3HSH.A
-3KKG.A
-3KK4.A
-3KKF.A
-3NRF.A
-3NRW.A
-3HYN.A
-3EMF.A
-3EMI.A
-3C8L.A
-3C8W.A
-3IR4.A
-3L23.A
-3L29.A
-3BO6.A
-2P1M.A
-2ZF9.A
-2X32.A
-2X3G.A
-2QPX.A
-3G5B.A
-2ZK9.X
-3M66.A
-3M6J.A
-3E8O.A
-3E8T.A
-3ILW.A
-2ILR.A
-3BCY.A
-3LWG.A
-3LWC.A
-3H7H.B
-2W9Y.A
-2JK9.A
-3NPD.A
-3H8T.A
-3M7K.A
-3M7O.A
-3L6T.A
-3JXO.A
-2WUU.A
-2WUJ.A
-2WUX.A
-3L51.B
-3FAU.A
-3L0Q.B
-3D85.C
-3MCQ.A
-3MCB.A
-3MCB.B
-2R2A.A
-3DD7.A
-3L3E.A
-3N6Y.A
-3GZB.A
-3FM2.A
-3FMY.A
-3I84.A
-2F1N.A
-3LAX.A
-3IX3.A
-3KE7.A
-2XLG.A
-3IDU.A
-3IDF.A
-3ID1.A
-3FOV.A
-3FOT.A
-3FCN.A
-3D1R.A
-3IBM.A
-3EZI.A
-3AG3.D
-3H6P.C
-3H6R.A
-3NFT.A
-2VQ4.A
-3L7H.A
-3GXW.A
-2VTC.A
-3IJM.A
-3GOE.A
-3EDO.A
-3FGR.B
-3FG9.A
-3FGV.A
-3JQY.A
-3K69.A
-3K6O.A
-3BMZ.A
-3BM3.A
-2WVX.A
-3ECH.A
-3ECF.A
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This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <km...@us...> - 2012-01-11 13:03:59
|
Revision: 3550
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3550&view=rev
Author: kmpf
Date: 2012-01-11 13:03:48 +0000 (Wed, 11 Jan 2012)
Log Message:
-----------
Corrected format for .list files
Modified Paths:
--------------
trunk/test/pdb/bt426.list
trunk/test/pdb/plp273.list
trunk/test/pdb/plp364.list
trunk/test/pdb/plp399.list
Modified: trunk/test/pdb/bt426.list
===================================================================
--- trunk/test/pdb/bt426.list 2012-01-11 13:00:18 UTC (rev 3549)
+++ trunk/test/pdb/bt426.list 2012-01-11 13:03:48 UTC (rev 3550)
@@ -1,345 +1,4 @@
-1LMB.3.
-8ABP..
-1MRP..
-1G3P..
-1GVP..
-1AT0..
-1AOP..
-1AMP..
-1AK0..
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-2CYP..
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-1KVE.B.
-1KWA.B.
-1EDM.B.
-1FMT.B.
-1GOT.B.
-1ATZ.B.
-1APY.B.
-1AQZ.B.
-1A28.B.
-1BDM.B.
-1BEN.B.
-1BTK.B.
-1CPC.B.
-1VWL.B.
-1WPO.B.
-1PNK.B.
-1RYP.2.
-5P21..
-1HA1..
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-1FNA..
-1GSA..
-1A6Q..
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-1POA..
-1QBA..
-2BAA..
-3CLA..
-2KIN.B.
-5HPG.A.
-1LKK.A.
-1LTS.A.
-1MLD.A.
-1MOL.A.
-1MKA.A.
-1MUG.A.
-1MUC.A.
-1MPG.A.
-1NBC.A.
-1NP1.A.
-1ONR.A.
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-1GDO.A.
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-1GUQ.A.
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-1PHN.A.
-1RGE.A.
-1SLT.A.
-1SLU.A.
-1SPU.A.
-5ICB..
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-1KNB..
-1FDR..
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-3SDH.A.
-2HMZ.A.
-2ARC.A.
-2PSP.A.
-8RXN.A.
-1HTR.P.
-1LIS..
-1MSC..
-1NLS..
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-1IFC..
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-1CPO..
-1CEO..
-1XJO..
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-1TAD.C.
-1TSP..
-1WHT.B.
-7RSA..
-1PTQ..
-1PDA..
-2FHA..
-2CBA..
-2WEA..
-2PIA..
-5CSM.A.
-4PGA.A.
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-6GSV.A.
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-1VPS.A.
-1PCF.A.
-1RYP.1.
-1RVA.A.
-1SVP.A.
-2I1B..
-2A0B..
-2KIN.A.
-2FIV.A.
-2CHS.A.
-2CCY.A.
-2SCP.A.
-4XIS..
-1ONC..
-1OIS..
-1VLS..
-1VJS..
-3B5C..
+1CYO..
1PNE..
3PTE..
1REQ.D.
Modified: trunk/test/pdb/plp273.list
===================================================================
--- trunk/test/pdb/plp273.list 2012-01-11 13:00:18 UTC (rev 3549)
+++ trunk/test/pdb/plp273.list 2012-01-11 13:03:48 UTC (rev 3550)
@@ -270,4 +270,4 @@
3NY3.A.
3NZN.A.
3O6C.A.
-3OAJ.A
+3OAJ.A.
Modified: trunk/test/pdb/plp364.list
===================================================================
--- trunk/test/pdb/plp364.list 2012-01-11 13:00:18 UTC (rev 3549)
+++ trunk/test/pdb/plp364.list 2012-01-11 13:03:48 UTC (rev 3550)
@@ -361,4 +361,4 @@
3NY3.A.
3NZN.A.
3O6C.A.
-3OAJ.A
+3OAJ.A.
Modified: trunk/test/pdb/plp399.list
===================================================================
--- trunk/test/pdb/plp399.list 2012-01-11 13:00:18 UTC (rev 3549)
+++ trunk/test/pdb/plp399.list 2012-01-11 13:03:48 UTC (rev 3550)
@@ -396,4 +396,4 @@
3H3L.A.
2RBG.A.
3HE5.B.
-3CKK.A
+3CKK.A.
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <km...@us...> - 2012-01-11 13:00:31
|
Revision: 3549
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3549&view=rev
Author: kmpf
Date: 2012-01-11 13:00:18 +0000 (Wed, 11 Jan 2012)
Log Message:
-----------
Added individuals to represent amino acid properties.
Modified Paths:
--------------
trunk/test/pdb/AA_properties.owl
Modified: trunk/test/pdb/AA_properties.owl
===================================================================
--- trunk/test/pdb/AA_properties.owl 2012-01-09 16:05:33 UTC (rev 3548)
+++ trunk/test/pdb/AA_properties.owl 2012-01-11 13:00:18 UTC (rev 3549)
@@ -2,31 +2,31 @@
<!DOCTYPE rdf:RDF [
+ <!ENTITY pdb "http://bio2rdf.org/pdb:" >
<!ENTITY owl "http://www.w3.org/2002/07/owl#" >
<!ENTITY xsd "http://www.w3.org/2001/XMLSchema#" >
<!ENTITY owl2xml "http://www.w3.org/2006/12/owl2-xml#" >
<!ENTITY rdfs "http://www.w3.org/2000/01/rdf-schema#" >
<!ENTITY rdf "http://www.w3.org/1999/02/22-rdf-syntax-ns#" >
- <!ENTITY AA_properties "http://dl-learner.org/Projects/DLLearner/Protein_Secondary_Structure_Prediction/AA_properties.owl#" >
]>
-<rdf:RDF xmlns="http://dl-learner.org/Projects/DLLearner/Protein_Secondary_Structure_Prediction/AA_properties.owl#"
- xml:base="http://dl-learner.org/Projects/DLLearner/Protein_Secondary_Structure_Prediction/AA_properties.owl"
+<rdf:RDF xmlns="http://dl-learner.org/pdb:"
+ xml:base="http://dl-learner.org/pdb:"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:owl2xml="http://www.w3.org/2006/12/owl2-xml#"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
- xmlns:AA_properties="http://dl-learner.org/Projects/DLLearner/Protein_Secondary_Structure_Prediction/AA_properties.owl#">
- <owl:Ontology rdf:about=""/>
+ xmlns:pdb="http://bio2rdf.org/pdb:">
+ <owl:Ontology rdf:about="http://dl-learner.org/Projects/DLLearner/Protein_Secondary_Structure_Prediction/AA_properties.owl"/>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
- // Object Properties
+ // Annotation properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->
@@ -34,80 +34,72 @@
- <!-- http://dl-learner.org/Projects/DLLearner/Protein_Secondary_Structure_Prediction/AA_properties.owl#relational_property -->
+ <!--
+ ///////////////////////////////////////////////////////////////////////////////////////
+ //
+ // Datatypes
+ //
+ ///////////////////////////////////////////////////////////////////////////////////////
+ -->
- <owl:ObjectProperty rdf:about="#relational_property">
- <rdfs:label
- >relational_property</rdfs:label>
- </owl:ObjectProperty>
- <!-- http://dl-learner.org/Projects/DLLearner/Protein_Secondary_Structure_Prediction/AA_properties.owl#modifier_property -->
+ <!--
+ ///////////////////////////////////////////////////////////////////////////////////////
+ //
+ // Object Properties
+ //
+ ///////////////////////////////////////////////////////////////////////////////////////
+ -->
- <owl:ObjectProperty rdf:about="#modifier_property">
- <rdfs:label
- >modifier_property</rdfs:label>
- </owl:ObjectProperty>
- <!-- http://dl-learner.org/Projects/DLLearner/Protein_Secondary_Structure_Prediction/AA_properties.owl#has_hydrophobicity -->
+ <!-- http://dl-learner.org/pdb:has_hydrophobicity -->
- <owl:ObjectProperty rdf:about="#has_hydrophobicity">
- <rdfs:label
- >has_hydrophobicity</rdfs:label>
- <rdfs:subPropertyOf rdf:resource="#modifier_property"/>
+ <owl:ObjectProperty rdf:about="http://dl-learner.org/pdb:has_hydrophobicity">
+ <rdfs:label>has_hydrophobicity</rdfs:label>
+ <rdfs:domain rdf:resource="http://dl-learner.org/pdb:Hydrophobicity"/>
+ <rdfs:subPropertyOf rdf:resource="http://dl-learner.org/pdb:modifier_property"/>
</owl:ObjectProperty>
- <!-- http://dl-learner.org/Projects/DLLearner/Protein_Secondary_Structure_Prediction/AA_properties.owl#has_size -->
+ <!-- http://dl-learner.org/pdb:has_polarity -->
- <owl:ObjectProperty rdf:about="#has_size">
- <rdfs:label>has_size</rdfs:label>
- <rdfs:subPropertyOf rdf:resource="#modifier_property"/>
+ <owl:ObjectProperty rdf:about="http://dl-learner.org/pdb:has_polarity">
+ <rdfs:label>has_polarity</rdfs:label>
+ <rdfs:subPropertyOf rdf:resource="http://dl-learner.org/pdb:modifier_property"/>
</owl:ObjectProperty>
- <!-- http://dl-learner.org/Projects/DLLearner/Protein_Secondary_Structure_Prediction/AA_properties.owl#has_polarity -->
+ <!-- http://dl-learner.org/pdb:has_size -->
- <owl:ObjectProperty rdf:about="#has_polarity">
- <rdfs:label>c</rdfs:label>
- <rdfs:subPropertyOf rdf:resource="#modifier_property"/>
+ <owl:ObjectProperty rdf:about="http://dl-learner.org/pdb:has_size">
+ <rdfs:label>has_size</rdfs:label>
+ <rdfs:subPropertyOf rdf:resource="http://dl-learner.org/pdb:modifier_property"/>
</owl:ObjectProperty>
- <!-- http://dl-learner.org/Projects/DLLearner/Protein_Secondary_Structure_Prediction/AA_properties.owl#has_aromaticity -->
+ <!-- http://dl-learner.org/pdb:modifier_property -->
- <owl:ObjectProperty rdf:about="#has_aromaticity">
- <rdfs:label>has_aromaticity</rdfs:label>
- <rdfs:subPropertyOf rdf:resource="#modifier_property"/>
+ <owl:ObjectProperty rdf:about="http://dl-learner.org/pdb:modifier_property">
+ <rdfs:label>modifier_property</rdfs:label>
</owl:ObjectProperty>
- <!-- http://dl-learner.org/Projects/DLLearner/Protein_Secondary_Structure_Prediction/AA_properties.owl#has_charge -->
+ <!-- http://dl-learner.org/pdb:relational_property -->
- <owl:ObjectProperty rdf:about="#has_charge">
- <rdfs:label>has_charge</rdfs:label>
- <rdfs:subPropertyOf rdf:resource="#modifier_property"/>
+ <owl:ObjectProperty rdf:about="http://dl-learner.org/pdb:relational_property">
+ <rdfs:label>relational_property</rdfs:label>
</owl:ObjectProperty>
- <!-- http://dl-learner.org/Projects/DLLearner/Protein_Secondary_Structure_Prediction/AA_properties.owl#is_in_hydrogen_bond -->
-
- <owl:ObjectProperty rdf:about="#is_in_hydrogen_bond">
- <rdfs:label
- >is_in_hydrogen_bond</rdfs:label>
- <rdfs:subPropertyOf rdf:resource="#modifier_property"/>
- </owl:ObjectProperty>
-
-
-
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
@@ -119,1310 +111,735 @@
- <!-- http://dl-learner.org/Projects/DLLearner/Protein_Secondary_Structure_Prediction/AA_properties.owl#Domain_entity -->
+ <!-- http://bio2rdf.org/pdb:Alanine -->
- <owl:Class rdf:about="#Domain_entity">
- <rdfs:label>Domain_entity</rdfs:label>
- <rdfs:subClassOf rdf:resource="&owl;Thing"/>
- </owl:Class>
-
-
-
- <!-- http://dl-learner.org/Projects/DLLearner/Protein_Secondary_Structure_Prediction/AA_properties.owl#Independent_entity -->
-
- <owl:Class rdf:about="#Independent_entity">
- <rdfs:label
- >Independent_entity</rdfs:label>
- <rdfs:subClassOf rdf:resource="#Domain_entity"/>
- <owl:disjointWith rdf:resource="#Value"/>
- </owl:Class>
-
-
-
- <!-- http://dl-learner.org/Projects/DLLearner/Protein_Secondary_Structure_Prediction/AA_properties.owl#Value -->
-
- <owl:Class rdf:about="#Value">
- <rdfs:label>Value</rdfs:label>
- <rdfs:subClassOf rdf:resource="#Domain_entity"/>
- </owl:Class>
-
-
-
- <!-- http://dl-learner.org/Projects/DLLearner/Protein_Secondary_Structure_Prediction/AA_properties.owl#Amino_acid -->
-
- <owl:Class rdf:about="#Amino_acid">
- <rdfs:label>Amino_acid</rdfs:label>
- <rdfs:subClassOf rdf:resource="#Independent_entity"/>
- </owl:Class>
-
-
-
- <!-- http://dl-learner.org/Projects/DLLearner/Protein_Secondary_Structure_Prediction/AA_properties.owl#Alanine -->
-
- <owl:Class rdf:about="http://bio2rdf.org/pdb:Alanine">
+ <owl:Class rdf:about="&pdb;Alanine">
<rdfs:label>Alanine</rdfs:label>
- <rdfs:subClassOf rdf:resource="#Amino_acid"/>
+ <rdfs:subClassOf rdf:resource="http://dl-learner.org/pdb:Amino_acid"/>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty rdf:resource="#has_aromaticity"/>
- <owl:someValuesFrom rdf:resource="#not_aromatic"/>
+ <owl:onProperty rdf:resource="http://dl-learner.org/pdb:has_polarity"/>
+ <owl:hasValue rdf:resource="http://dl-learner.org/pdb:unpolar"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty rdf:resource="#has_charge"/>
- <owl:someValuesFrom rdf:resource="#neutral_charge"/>
+ <owl:onProperty rdf:resource="http://dl-learner.org/pdb:has_hydrophobicity"/>
+ <owl:hasValue rdf:resource="http://dl-learner.org/pdb:hydrophobic"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty rdf:resource="#has_size"/>
- <owl:allValuesFrom>
- <owl:Class>
- <owl:unionOf rdf:parseType="Collection">
- <rdf:Description rdf:about="#small"/>
- <rdf:Description rdf:about="#tiny"/>
- </owl:unionOf>
- </owl:Class>
- </owl:allValuesFrom>
+ <owl:onProperty rdf:resource="http://dl-learner.org/pdb:has_size"/>
+ <owl:hasValue rdf:resource="http://dl-learner.org/pdb:tiny"/>
</owl:Restriction>
</rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_polarity"/>
- <owl:someValuesFrom rdf:resource="#unpolar"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_size"/>
- <owl:someValuesFrom rdf:resource="#tiny"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_aromaticity"/>
- <owl:someValuesFrom rdf:resource="#not_aliphatic"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_hydrophobicity"/>
- <owl:someValuesFrom rdf:resource="#very_hydrophobic"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_size"/>
- <owl:someValuesFrom rdf:resource="#small"/>
- </owl:Restriction>
- </rdfs:subClassOf>
</owl:Class>
- <!-- http://dl-learner.org/Projects/DLLearner/Protein_Secondary_Structure_Prediction/AA_properties.owl#Arginine -->
+ <!-- http://bio2rdf.org/pdb:Arginine -->
- <owl:Class rdf:about="http://bio2rdf.org/pdb:Arginine">
+ <owl:Class rdf:about="&pdb;Arginine">
<rdfs:label>Arginine</rdfs:label>
- <rdfs:subClassOf rdf:resource="#Amino_acid"/>
+ <rdfs:subClassOf rdf:resource="http://dl-learner.org/pdb:Amino_acid"/>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty rdf:resource="#has_aromaticity"/>
- <owl:someValuesFrom rdf:resource="#not_aromatic"/>
+ <owl:onProperty rdf:resource="http://dl-learner.org/pdb:has_size"/>
+ <owl:hasValue rdf:resource="http://dl-learner.org/pdb:large"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty rdf:resource="#has_size"/>
- <owl:someValuesFrom rdf:resource="#large"/>
+ <owl:onProperty rdf:resource="http://dl-learner.org/pdb:has_polarity"/>
+ <owl:hasValue rdf:resource="http://dl-learner.org/pdb:positive"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty rdf:resource="#has_charge"/>
- <owl:someValuesFrom rdf:resource="#positive_charge"/>
+ <owl:onProperty rdf:resource="http://dl-learner.org/pdb:has_hydrophobicity"/>
+ <owl:hasValue rdf:resource="http://dl-learner.org/pdb:hydrophilic"/>
</owl:Restriction>
</rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_hydrophobicity"/>
- <owl:someValuesFrom rdf:resource="#hydrophilic"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_aromaticity"/>
- <owl:someValuesFrom rdf:resource="#not_aliphatic"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#is_in_hydrogen_bond"/>
- <owl:someValuesFrom rdf:resource="#hydrogen_bond_donor"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_polarity"/>
- <owl:someValuesFrom rdf:resource="#polar"/>
- </owl:Restriction>
- </rdfs:subClassOf>
</owl:Class>
- <!-- http://dl-learner.org/Projects/DLLearner/Protein_Secondary_Structure_Prediction/AA_properties.owl#Asparagine -->
+ <!-- http://bio2rdf.org/pdb:Asparagine -->
- <owl:Class rdf:about="http://bio2rdf.org/pdb:Asparagine">
+ <owl:Class rdf:about="&pdb;Asparagine">
<rdfs:label>Asparagine</rdfs:label>
- <rdfs:subClassOf rdf:resource="#Amino_acid"/>
+ <rdfs:subClassOf rdf:resource="http://dl-learner.org/pdb:Amino_acid"/>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty rdf:resource="#has_polarity"/>
- <owl:someValuesFrom rdf:resource="#polar"/>
+ <owl:onProperty rdf:resource="http://dl-learner.org/pdb:has_hydrophobicity"/>
+ <owl:hasValue rdf:resource="http://dl-learner.org/pdb:hydrophilic"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty rdf:resource="#is_in_hydrogen_bond"/>
- <owl:someValuesFrom rdf:resource="#hydrogen_bond_donor"/>
+ <owl:onProperty rdf:resource="http://dl-learner.org/pdb:has_size"/>
+ <owl:hasValue rdf:resource="http://dl-learner.org/pdb:small"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty rdf:resource="#has_aromaticity"/>
- <owl:someValuesFrom rdf:resource="#not_aliphatic"/>
+ <owl:onProperty rdf:resource="http://dl-learner.org/pdb:has_polarity"/>
+ <owl:hasValue rdf:resource="http://dl-learner.org/pdb:polar"/>
</owl:Restriction>
</rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_size"/>
- <owl:someValuesFrom rdf:resource="#small"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_aromaticity"/>
- <owl:someValuesFrom rdf:resource="#not_aromatic"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_charge"/>
- <owl:someValuesFrom rdf:resource="#neutral_charge"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#is_in_hydrogen_bond"/>
- <owl:someValuesFrom rdf:resource="#hydrogen_bond_acceptor"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_hydrophobicity"/>
- <owl:someValuesFrom rdf:resource="#hydrophilic"/>
- </owl:Restriction>
- </rdfs:subClassOf>
</owl:Class>
- <!-- http://dl-learner.org/Projects/DLLearner/Protein_Secondary_Structure_Prediction/AA_properties.owl#Aspartic_acid -->
+ <!-- http://bio2rdf.org/pdb:Aspartic_acid -->
- <owl:Class rdf:about="http://bio2rdf.org/pdb:Aspartic_acid">
+ <owl:Class rdf:about="&pdb;Aspartic_acid">
<rdfs:label>Aspartic_acid</rdfs:label>
- <rdfs:subClassOf rdf:resource="#Amino_acid"/>
+ <rdfs:subClassOf rdf:resource="http://dl-learner.org/pdb:Amino_acid"/>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty rdf:resource="#has_hydrophobicity"/>
- <owl:someValuesFrom rdf:resource="#hydrophilic"/>
+ <owl:onProperty rdf:resource="http://dl-learner.org/pdb:has_polarity"/>
+ <owl:hasValue rdf:resource="http://dl-learner.org/pdb:negative"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty rdf:resource="#has_aromaticity"/>
- <owl:someValuesFrom rdf:resource="#not_aliphatic"/>
+ <owl:onProperty rdf:resource="http://dl-learner.org/pdb:has_size"/>
+ <owl:hasValue rdf:resource="http://dl-learner.org/pdb:small"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty rdf:resource="#has_polarity"/>
- <owl:someValuesFrom rdf:resource="#polar"/>
+ <owl:onProperty rdf:resource="http://dl-learner.org/pdb:has_hydrophobicity"/>
+ <owl:hasValue rdf:resource="http://dl-learner.org/pdb:hydrophilic"/>
</owl:Restriction>
</rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_aromaticity"/>
- <owl:someValuesFrom rdf:resource="#not_aromatic"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_size"/>
- <owl:someValuesFrom rdf:resource="#small"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_charge"/>
- <owl:someValuesFrom rdf:resource="#negative_charge"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#is_in_hydrogen_bond"/>
- <owl:someValuesFrom rdf:resource="#hydrogen_bond_acceptor"/>
- </owl:Restriction>
- </rdfs:subClassOf>
</owl:Class>
- <!-- http://dl-learner.org/Projects/DLLearner/Protein_Secondary_Structure_Prediction/AA_properties.owl#Cysteine -->
+ <!-- http://bio2rdf.org/pdb:Cysteine -->
- <owl:Class rdf:about="http://bio2rdf.org/pdb:Cysteine">
+ <owl:Class rdf:about="&pdb;Cysteine">
<rdfs:label>Cysteine</rdfs:label>
- <rdfs:subClassOf rdf:resource="#Amino_acid"/>
+ <rdfs:subClassOf rdf:resource="http://dl-learner.org/pdb:Amino_acid"/>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty rdf:resource="#has_size"/>
- <owl:someValuesFrom rdf:resource="#small"/>
+ <owl:onProperty rdf:resource="http://dl-learner.org/pdb:has_size"/>
+ <owl:hasValue rdf:resource="http://dl-learner.org/pdb:tiny"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty rdf:resource="#is_in_hydrogen_bond"/>
- <owl:someValuesFrom rdf:resource="#hydrogen_bond_donor"/>
+ <owl:onProperty rdf:resource="http://dl-learner.org/pdb:has_hydrophobicity"/>
+ <owl:hasValue rdf:resource="http://dl-learner.org/pdb:hydrophobic"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty rdf:resource="#has_aromaticity"/>
- <owl:someValuesFrom rdf:resource="#not_aromatic"/>
+ <owl:onProperty rdf:resource="http://dl-learner.org/pdb:has_polarity"/>
+ <owl:hasValue rdf:resource="http://dl-learner.org/pdb:polar"/>
</owl:Restriction>
</rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#is_in_hydrogen_bond"/>
- <owl:someValuesFrom rdf:resource="#hydrogen_bond_acceptor"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_aromaticity"/>
- <owl:someValuesFrom rdf:resource="#not_aliphatic"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_polarity"/>
- <owl:someValuesFrom rdf:resource="#unpolar"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_hydrophobicity"/>
- <owl:someValuesFrom rdf:resource="#hydrophobic"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_charge"/>
- <owl:someValuesFrom rdf:resource="#neutral_charge"/>
- </owl:Restriction>
- </rdfs:subClassOf>
</owl:Class>
- <!-- http://dl-learner.org/Projects/DLLearner/Protein_Secondary_Structure_Prediction/AA_properties.owl#Glutamic_acid -->
+ <!-- http://bio2rdf.org/pdb:Glutamic_acid -->
- <owl:Class rdf:about="http://bio2rdf.org/pdb:Glutamic_acid">
+ <owl:Class rdf:about="&pdb;Glutamic_acid">
<rdfs:label>Glutamic_acid</rdfs:label>
- <rdfs:subClassOf rdf:resource="#Amino_acid"/>
+ <rdfs:subClassOf rdf:resource="http://dl-learner.org/pdb:Amino_acid"/>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty rdf:resource="#has_hydrophobicity"/>
- <owl:someValuesFrom rdf:resource="#hydrophilic"/>
+ <owl:onProperty rdf:resource="http://dl-learner.org/pdb:has_polarity"/>
+ <owl:hasValue rdf:resource="http://dl-learner.org/pdb:negative"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty rdf:resource="#has_aromaticity"/>
- <owl:someValuesFrom rdf:resource="#not_aromatic"/>
+ <owl:onProperty rdf:resource="http://dl-learner.org/pdb:has_size"/>
+ <owl:hasValue rdf:resource="http://dl-learner.org/pdb:large"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty rdf:resource="#has_polarity"/>
- <owl:someValuesFrom rdf:resource="#polar"/>
+ <owl:onProperty rdf:resource="http://dl-learner.org/pdb:has_hydrophobicity"/>
+ <owl:hasValue rdf:resource="http://dl-learner.org/pdb:hydrophilic"/>
</owl:Restriction>
</rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_charge"/>
- <owl:someValuesFrom rdf:resource="#negative_charge"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#is_in_hydrogen_bond"/>
- <owl:someValuesFrom rdf:resource="#hydrogen_bond_acceptor"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_aromaticity"/>
- <owl:someValuesFrom rdf:resource="#not_aliphatic"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_size"/>
- <owl:someValuesFrom rdf:resource="#large"/>
- </owl:Restriction>
- </rdfs:subClassOf>
</owl:Class>
- <!-- http://dl-learner.org/Projects/DLLearner/Protein_Secondary_Structure_Prediction/AA_properties.owl#Glutamine -->
+ <!-- http://bio2rdf.org/pdb:Glutamine -->
- <owl:Class rdf:about="http://bio2rdf.org/pdb:Glutamine">
+ <owl:Class rdf:about="&pdb;Glutamine">
<rdfs:label>Glutamine</rdfs:label>
- <rdfs:subClassOf rdf:resource="#Amino_acid"/>
+ <rdfs:subClassOf rdf:resource="http://dl-learner.org/pdb:Amino_acid"/>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty rdf:resource="#is_in_hydrogen_bond"/>
- <owl:someValuesFrom rdf:resource="#hydrogen_bond_donor"/>
+ <owl:onProperty rdf:resource="http://dl-learner.org/pdb:has_hydrophobicity"/>
+ <owl:hasValue rdf:resource="http://dl-learner.org/pdb:hydrophilic"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty rdf:resource="#has_aromaticity"/>
- <owl:someValuesFrom rdf:resource="#not_aliphatic"/>
+ <owl:onProperty rdf:resource="http://dl-learner.org/pdb:has_size"/>
+ <owl:hasValue rdf:resource="http://dl-learner.org/pdb:large"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty rdf:resource="#has_hydrophobicity"/>
- <owl:someValuesFrom rdf:resource="#hydrophilic"/>
+ <owl:onProperty rdf:resource="http://dl-learner.org/pdb:has_polarity"/>
+ <owl:hasValue rdf:resource="http://dl-learner.org/pdb:polar"/>
</owl:Restriction>
</rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_charge"/>
- <owl:someValuesFrom rdf:resource="#neutral_charge"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_polarity"/>
- <owl:someValuesFrom rdf:resource="#polar"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_size"/>
- <owl:someValuesFrom rdf:resource="#large"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_aromaticity"/>
- <owl:someValuesFrom rdf:resource="#not_aromatic"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#is_in_hydrogen_bond"/>
- <owl:someValuesFrom rdf:resource="#hydrogen_bond_acceptor"/>
- </owl:Restriction>
- </rdfs:subClassOf>
</owl:Class>
- <!-- http://dl-learner.org/Projects/DLLearner/Protein_Secondary_Structure_Prediction/AA_properties.owl#Glycine -->
+ <!-- http://bio2rdf.org/pdb:Glycine -->
- <owl:Class rdf:about="http://bio2rdf.org/pdb:Glycine">
+ <owl:Class rdf:about="&pdb;Glycine">
<rdfs:label>Glycine</rdfs:label>
- <rdfs:subClassOf rdf:resource="#Amino_acid"/>
+ <rdfs:subClassOf rdf:resource="http://dl-learner.org/pdb:Amino_acid"/>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty rdf:resource="#has_aromaticity"/>
- <owl:someValuesFrom rdf:resource="#not_aromatic"/>
+ <owl:onProperty rdf:resource="http://dl-learner.org/pdb:has_polarity"/>
+ <owl:hasValue rdf:resource="http://dl-learner.org/pdb:unpolar"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty rdf:resource="#has_hydrophobicity"/>
- <owl:someValuesFrom rdf:resource="#very_hydrophobic"/>
+ <owl:onProperty rdf:resource="http://dl-learner.org/pdb:has_size"/>
+ <owl:hasValue rdf:resource="http://dl-learner.org/pdb:tiny"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty rdf:resource="#has_aromaticity"/>
- <owl:someValuesFrom rdf:resource="#not_aliphatic"/>
+ <owl:onProperty rdf:resource="http://dl-learner.org/pdb:has_hydrophobicity"/>
+ <owl:hasValue rdf:resource="http://dl-learner.org/pdb:hydrophobic"/>
</owl:Restriction>
</rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_size"/>
- <owl:someValuesFrom rdf:resource="#small"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_charge"/>
- <owl:someValuesFrom rdf:resource="#neutral_charge"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_size"/>
- <owl:someValuesFrom rdf:resource="#tiny"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_polarity"/>
- <owl:someValuesFrom rdf:resource="#unpolar"/>
- </owl:Restriction>
- </rdfs:subClassOf>
</owl:Class>
- <!-- http://dl-learner.org/Projects/DLLearner/Protein_Secondary_Structure_Prediction/AA_properties.owl#Histidine -->
+ <!-- http://bio2rdf.org/pdb:Histidine -->
- <owl:Class rdf:about="http://bio2rdf.org/pdb:Histidine">
+ <owl:Class rdf:about="&pdb;Histidine">
<rdfs:label>Histidine</rdfs:label>
- <rdfs:subClassOf rdf:resource="#Amino_acid"/>
+ <rdfs:subClassOf rdf:resource="http://dl-learner.org/pdb:Amino_acid"/>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty rdf:resource="#has_charge"/>
- <owl:someValuesFrom rdf:resource="#positive_charge"/>
+ <owl:onProperty rdf:resource="http://dl-learner.org/pdb:has_polarity"/>
+ <owl:hasValue rdf:resource="http://dl-learner.org/pdb:positive"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty rdf:resource="#has_hydrophobicity"/>
- <owl:someValuesFrom rdf:resource="#hydrophobic"/>
+ <owl:onProperty rdf:resource="http://dl-learner.org/pdb:has_size"/>
+ <owl:hasValue rdf:resource="http://dl-learner.org/pdb:large"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty rdf:resource="#has_aromaticity"/>
- <owl:someValuesFrom rdf:resource="#not_aliphatic"/>
+ <owl:onProperty rdf:resource="http://dl-learner.org/pdb:has_hydrophobicity"/>
+ <owl:hasValue rdf:resource="http://dl-learner.org/pdb:aromatic"/>
</owl:Restriction>
</rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_polarity"/>
- <owl:someValuesFrom rdf:resource="#polar"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_size"/>
- <owl:someValuesFrom rdf:resource="#large"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_aromaticity"/>
- <owl:someValuesFrom rdf:resource="#aromatic"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#is_in_hydrogen_bond"/>
- <owl:someValuesFrom rdf:resource="#hydrogen_bond_donor"/>
- </owl:Restriction>
- </rdfs:subClassOf>
</owl:Class>
- <!-- http://dl-learner.org/Projects/DLLearner/Protein_Secondary_Structure_Prediction/AA_properties.owl#Isoleucine -->
+ <!-- http://bio2rdf.org/pdb:Isoleucine -->
- <owl:Class rdf:about="http://bio2rdf.org/pdb:Isoleucine">
+ <owl:Class rdf:about="&pdb;Isoleucine">
<rdfs:label>Isoleucine</rdfs:label>
- <rdfs:subClassOf rdf:resource="#Amino_acid"/>
+ <rdfs:subClassOf rdf:resource="http://dl-learner.org/pdb:Amino_acid"/>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty rdf:resource="#has_hydrophobicity"/>
- <owl:someValuesFrom rdf:resource="#very_hydrophobic"/>
+ <owl:onProperty rdf:resource="http://dl-learner.org/pdb:has_size"/>
+ <owl:hasValue rdf:resource="http://dl-learner.org/pdb:large"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty rdf:resource="#has_aromaticity"/>
- <owl:someValuesFrom rdf:resource="#aliphatic"/>
+ <owl:onProperty rdf:resource="http://dl-learner.org/pdb:has_hydrophobicity"/>
+ <owl:hasValue rdf:resource="http://dl-learner.org/pdb:aliphatic"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty rdf:resource="#has_charge"/>
- <owl:someValuesFrom rdf:resource="#neutral_charge"/>
+ <owl:onProperty rdf:resource="http://dl-learner.org/pdb:has_polarity"/>
+ <owl:hasValue rdf:resource="http://dl-learner.org/pdb:unpolar"/>
</owl:Restriction>
</rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_polarity"/>
- <owl:someValuesFrom rdf:resource="#unpolar"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_size"/>
- <owl:someValuesFrom rdf:resource="#large"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_aromaticity"/>
- <owl:someValuesFrom rdf:resource="#not_aromatic"/>
- </owl:Restriction>
- </rdfs:subClassOf>
</owl:Class>
- <!-- http://dl-learner.org/Projects/DLLearner/Protein_Secondary_Structure_Prediction/AA_properties.owl#Leucine -->
+ <!-- http://bio2rdf.org/pdb:Leucine -->
- <owl:Class rdf:about="http://bio2rdf.org/pdb:Leucine">
+ <owl:Class rdf:about="&pdb;Leucine">
<rdfs:label>Leucine</rdfs:label>
- <rdfs:subClassOf rdf:resource="#Amino_acid"/>
+ <rdfs:subClassOf rdf:resource="http://dl-learner.org/pdb:Amino_acid"/>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty rdf:resource="#has_aromaticity"/>
- <owl:someValuesFrom rdf:resource="#not_aromatic"/>
+ <owl:onProperty rdf:resource="http://dl-learner.org/pdb:has_hydrophobicity"/>
+ <owl:hasValue rdf:resource="http://dl-learner.org/pdb:aliphatic"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty rdf:resource="#has_hydrophobicity"/>
- <owl:someValuesFrom rdf:resource="#very_hydrophobic"/>
+ <owl:onProperty rdf:resource="http://dl-learner.org/pdb:has_polarity"/>
+ <owl:hasValue rdf:resource="http://dl-learner.org/pdb:unpolar"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty rdf:resource="#has_aromaticity"/>
- <owl:someValuesFrom rdf:resource="#not_aliphatic"/>
+ <owl:onProperty rdf:resource="http://dl-learner.org/pdb:has_size"/>
+ <owl:hasValue rdf:resource="http://dl-learner.org/pdb:large"/>
</owl:Restriction>
</rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_charge"/>
- <owl:someValuesFrom rdf:resource="#neutral_charge"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_polarity"/>
- <owl:someValuesFrom rdf:resource="#unpolar"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_size"/>
- <owl:someValuesFrom rdf:resource="#large"/>
- </owl:Restriction>
- </rdfs:subClassOf>
</owl:Class>
- <!-- http://dl-learner.org/Projects/DLLearner/Protein_Secondary_Structure_Prediction/AA_properties.owl#Lysine -->
+ <!-- http://bio2rdf.org/pdb:Lysine -->
- <owl:Class rdf:about="http://bio2rdf.org/pdb:Lysine">
+ <owl:Class rdf:about="&pdb;Lysine">
<rdfs:label>Lysine</rdfs:label>
- <rdfs:subClassOf rdf:resource="#Amino_acid"/>
+ <rdfs:subClassOf rdf:resource="http://dl-learner.org/pdb:Amino_acid"/>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty rdf:resource="#has_aromaticity"/>
- <owl:someValuesFrom rdf:resource="#not_aromatic"/>
+ <owl:onProperty rdf:resource="http://dl-learner.org/pdb:has_size"/>
+ <owl:hasValue rdf:resource="http://dl-learner.org/pdb:large"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty rdf:resource="#has_hydrophobicity"/>
- <owl:someValuesFrom rdf:resource="#hydrophobic"/>
+ <owl:onProperty rdf:resource="http://dl-learner.org/pdb:has_polarity"/>
+ <owl:hasValue rdf:resource="http://dl-learner.org/pdb:positive"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty rdf:resource="#has_aromaticity"/>
- <owl:someValuesFrom rdf:resource="#aliphatic"/>
+ <owl:onProperty rdf:resource="http://dl-learner.org/pdb:has_hydrophobicity"/>
+ <owl:hasValue rdf:resource="http://dl-learner.org/pdb:hydrophobic"/>
</owl:Restriction>
</rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_size"/>
- <owl:someValuesFrom rdf:resource="#large"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_charge"/>
- <owl:someValuesFrom rdf:resource="#positive_charge"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#is_in_hydrogen_bond"/>
- <owl:someValuesFrom rdf:resource="#hydrogen_bond_donor"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_polarity"/>
- <owl:someValuesFrom rdf:resource="#polar"/>
- </owl:Restriction>
- </rdfs:subClassOf>
</owl:Class>
- <!-- http://dl-learner.org/Projects/DLLearner/Protein_Secondary_Structure_Prediction/AA_properties.owl#Methionine -->
+ <!-- http://bio2rdf.org/pdb:Methionine -->
- <owl:Class rdf:about="http://bio2rdf.org/pdb:Methionine">
+ <owl:Class rdf:about="&pdb;Methionine">
<rdfs:label>Methionine</rdfs:label>
- <rdfs:subClassOf rdf:resource="#Amino_acid"/>
+ <rdfs:subClassOf rdf:resource="http://dl-learner.org/pdb:Amino_acid"/>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty rdf:resource="#has_size"/>
- <owl:someValuesFrom rdf:resource="#large"/>
+ <owl:onProperty rdf:resource="http://dl-learner.org/pdb:has_polarity"/>
+ <owl:hasValue rdf:resource="http://dl-learner.org/pdb:unpolar"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty rdf:resource="#has_aromaticity"/>
- <owl:someValuesFrom rdf:resource="#not_aromatic"/>
+ <owl:onProperty rdf:resource="http://dl-learner.org/pdb:has_hydrophobicity"/>
+ <owl:hasValue rdf:resource="http://dl-learner.org/pdb:hydrophobic"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty rdf:resource="#has_aromaticity"/>
- <owl:someValuesFrom rdf:resource="#not_aliphatic"/>
+ <owl:onProperty rdf:resource="http://dl-learner.org/pdb:has_size"/>
+ <owl:hasValue rdf:resource="http://dl-learner.org/pdb:large"/>
</owl:Restriction>
</rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_hydrophobicity"/>
- <owl:someValuesFrom rdf:resource="#very_hydrophobic"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_polarity"/>
- <owl:someValuesFrom rdf:resource="#unpolar"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_charge"/>
- <owl:someValuesFrom rdf:resource="#neutral_charge"/>
- </owl:Restriction>
- </rdfs:subClassOf>
</owl:Class>
- <!-- http://dl-learner.org/Projects/DLLearner/Protein_Secondary_Structure_Prediction/AA_properties.owl#Phenylalanine -->
+ <!-- http://bio2rdf.org/pdb:Phenylalanine -->
- <owl:Class rdf:about="http://bio2rdf.org/pdb:Phenylalanine">
+ <owl:Class rdf:about="&pdb;Phenylalanine">
<rdfs:label>Phenylalanine</rdfs:label>
- <rdfs:subClassOf rdf:resource="#Amino_acid"/>
+ <rdfs:subClassOf rdf:resource="http://dl-learner.org/pdb:Amino_acid"/>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty rdf:resource="#has_charge"/>
- <owl:someValuesFrom rdf:resource="#neutral_charge"/>
+ <owl:onProperty rdf:resource="http://dl-learner.org/pdb:has_polarity"/>
+ <owl:hasValue rdf:resource="http://dl-learner.org/pdb:unpolar"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty rdf:resource="#has_aromaticity"/>
- <owl:someValuesFrom rdf:resource="#not_aliphatic"/>
+ <owl:onProperty rdf:resource="http://dl-learner.org/pdb:has_hydrophobicity"/>
+ <owl:hasValue rdf:resource="http://dl-learner.org/pdb:aromatic"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty rdf:resource="#has_hydrophobicity"/>
- <owl:someValuesFrom rdf:resource="#very_hydrophobic"/>
+ <owl:onProperty rdf:resource="http://dl-learner.org/pdb:has_size"/>
+ <owl:hasValue rdf:resource="http://dl-learner.org/pdb:large"/>
</owl:Restriction>
</rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_size"/>
- <owl:someValuesFrom rdf:resource="#large"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_polarity"/>
- <owl:someValuesFrom rdf:resource="#unpolar"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_aromaticity"/>
- <owl:someValuesFrom rdf:resource="#aromatic"/>
- </owl:Restriction>
- </rdfs:subClassOf>
</owl:Class>
- <!-- http://dl-learner.org/Projects/DLLearner/Protein_Secondary_Structure_Prediction/AA_properties.owl#Proline -->
+ <!-- http://bio2rdf.org/pdb:Proline -->
- <owl:Class rdf:about="http://bio2rdf.org/pdb:Proline">
+ <owl:Class rdf:about="&pdb;Proline">
<rdfs:label>Proline</rdfs:label>
- <rdfs:subClassOf rdf:resource="#Amino_acid"/>
+ <rdfs:subClassOf rdf:resource="http://dl-learner.org/pdb:Amino_acid"/>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty rdf:resource="#has_charge"/>
- <owl:someValuesFrom rdf:resource="#neutral_charge"/>
+ <owl:onProperty rdf:resource="http://dl-learner.org/pdb:has_hydrophobicity"/>
+ <owl:hasValue rdf:resource="http://dl-learner.org/pdb:hydrophilic"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty rdf:resource="#has_aromaticity"/>
- <owl:someValuesFrom rdf:resource="#not_aromatic"/>
+ <owl:onProperty rdf:resource="http://dl-learner.org/pdb:has_polarity"/>
+ <owl:hasValue rdf:resource="http://dl-learner.org/pdb:unpolar"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty rdf:resource="#has_polarity"/>
- <owl:someValuesFrom rdf:resource="#unpolar"/>
+ <owl:onProperty rdf:resource="http://dl-learner.org/pdb:has_size"/>
+ <owl:hasValue rdf:resource="http://dl-learner.org/pdb:small"/>
</owl:Restriction>
</rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_aromaticity"/>
- <owl:someValuesFrom rdf:resource="#not_aliphatic"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_size"/>
- <owl:someValuesFrom rdf:resource="#small"/>
- </owl:Restriction>
- </rdfs:subClassOf>
</owl:Class>
- <!-- http://dl-learner.org/Projects/DLLearner/Protein_Secondary_Structure_Prediction/AA_properties.owl#Serine -->
+ <!-- http://bio2rdf.org/pdb:Serine -->
- <owl:Class rdf:about="http://bio2rdf.org/pdb:Serine">
+ <owl:Class rdf:about="&pdb;Serine">
<rdfs:label>Serine</rdfs:label>
- <rdfs:subClassOf rdf:resource="#Amino_acid"/>
+ <rdfs:subClassOf rdf:resource="http://dl-learner.org/pdb:Amino_acid"/>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty rdf:resource="#has_aromaticity"/>
- <owl:someValuesFrom rdf:resource="#not_aliphatic"/>
+ <owl:onProperty rdf:resource="http://dl-learner.org/pdb:has_hydrophobicity"/>
+ <owl:hasValue rdf:resource="http://dl-learner.org/pdb:hydrophilic"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty rdf:resource="#is_in_hydrogen_bond"/>
- <owl:someValuesFrom rdf:resource="#hydrogen_bond_acceptor"/>
+ <owl:onProperty rdf:resource="http://dl-learner.org/pdb:has_polarity"/>
+ <owl:hasValue rdf:resource="http://dl-learner.org/pdb:polar"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty rdf:resource="#has_size"/>
- <owl:someValuesFrom rdf:resource="#small"/>
+ <owl:onProperty rdf:resource="http://dl-learner.org/pdb:has_size"/>
+ <owl:hasValue rdf:resource="http://dl-learner.org/pdb:tiny"/>
</owl:Restriction>
</rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_polarity"/>
- <owl:someValuesFrom rdf:resource="#polar"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_size"/>
- <owl:someValuesFrom rdf:resource="#tiny"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_charge"/>
- <owl:someValuesFrom rdf:resource="#neutral_charge"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_hydrophobicity"/>
- <owl:someValuesFrom rdf:resource="#hydrophilic"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#is_in_hydrogen_bond"/>
- <owl:someValuesFrom rdf:resource="#hydrogen_bond_donor"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_aromaticity"/>
- <owl:someValuesFrom rdf:resource="#not_aromatic"/>
- </owl:Restriction>
- </rdfs:subClassOf>
</owl:Class>
- <!-- http://dl-learner.org/Projects/DLLearner/Protein_Secondary_Structure_Prediction/AA_properties.owl#Threonine -->
+ <!-- http://bio2rdf.org/pdb:Threonine -->
- <owl:Class rdf:about="http://bio2rdf.org/pdb:Threonine">
+ <owl:Class rdf:about="&pdb;Threonine">
<rdfs:label>Threonine</rdfs:label>
- <rdfs:subClassOf rdf:resource="#Amino_acid"/>
+ <rdfs:subClassOf rdf:resource="http://dl-learner.org/pdb:Amino_acid"/>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty rdf:resource="#has_charge"/>
- <owl:someValuesFrom rdf:resource="#neutral_charge"/>
+ <owl:onProperty rdf:resource="http://dl-learner.org/pdb:has_polarity"/>
+ <owl:hasValue rdf:resource="http://dl-learner.org/pdb:polar"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty rdf:resource="#is_in_hydrogen_bond"/>
- <owl:someValuesFrom rdf:resource="#hydrogen_bond_acceptor"/>
+ <owl:onProperty rdf:resource="http://dl-learner.org/pdb:has_size"/>
+ <owl:hasValue rdf:resource="http://dl-learner.org/pdb:small"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty rdf:resource="#has_size"/>
- <owl:someValuesFrom rdf:resource="#small"/>
+ <owl:onProperty rdf:resource="http://dl-learner.org/pdb:has_hydrophobicity"/>
+ <owl:hasValue rdf:resource="http://dl-learner.org/pdb:hydrophobic"/>
</owl:Restriction>
</rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#is_in_hydrogen_bond"/>
- <owl:someValuesFrom rdf:resource="#hydrogen_bond_donor"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_aromaticity"/>
- <owl:someValuesFrom rdf:resource="#not_aromatic"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_aromaticity"/>
- <owl:someValuesFrom rdf:resource="#aromatic"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_aromaticity"/>
- <owl:someValuesFrom rdf:resource="#not_aliphatic"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_polarity"/>
- <owl:someValuesFrom rdf:resource="#polar"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_hydrophobicity"/>
- <owl:someValuesFrom rdf:resource="#hydrophobic"/>
- </owl:Restriction>
- </rdfs:subClassOf>
</owl:Class>
- <!-- http://dl-learner.org/Projects/DLLearner/Protein_Secondary_Structure_Prediction/AA_properties.owl#Tryptophan -->
+ <!-- http://bio2rdf.org/pdb:Tryptophan -->
- <owl:Class rdf:about="http://bio2rdf.org/pdb:Tryptophan">
+ <owl:Class rdf:about="&pdb;Tryptophan">
<rdfs:label>Tryptophan</rdfs:label>
- <rdfs:subClassOf rdf:resource="#Amino_acid"/>
+ <rdfs:subClassOf rdf:resource="http://dl-learner.org/pdb:Amino_acid"/>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty rdf:resource="#has_hydrophobicity"/>
- <owl:someValuesFrom rdf:resource="#hydrophobic"/>
+ <owl:onProperty rdf:resource="http://dl-learner.org/pdb:has_size"/>
+ <owl:hasValue rdf:resource="http://dl-learner.org/pdb:large"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty rdf:resource="#has_polarity"/>
- <owl:someValuesFrom rdf:resource="#polar"/>
+ <owl:onProperty rdf:resource="http://dl-learner.org/pdb:has_hydrophobicity"/>
+ <owl:hasValue rdf:resource="http://dl-learner.org/pdb:aromatic"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty rdf:resource="#is_in_hydrogen_bond"/>
- <owl:someValuesFrom rdf:resource="#hydrogen_bond_donor"/>
+ <owl:onProperty rdf:resource="http://dl-learner.org/pdb:has_polarity"/>
+ <owl:hasValue rdf:resource="http://dl-learner.org/pdb:polar"/>
</owl:Restriction>
</rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_aromaticity"/>
- <owl:someValuesFrom rdf:resource="#aromatic"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_charge"/>
- <owl:someValuesFrom rdf:resource="#neutral_charge"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_size"/>
- <owl:someValuesFrom rdf:resource="#large"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_aromaticity"/>
- <owl:someValuesFrom rdf:resource="#not_aliphatic"/>
- </owl:Restriction>
- </rdfs:subClassOf>
</owl:Class>
- <!-- http://dl-learner.org/Projects/DLLearner/Protein_Secondary_Structure_Prediction/AA_properties.owl#Tyrosine -->
+ <!-- http://bio2rdf.org/pdb:Tyrosine -->
- <owl:Class rdf:about="http://bio2rdf.org/pdb:Tyrosine">
+ <owl:Class rdf:about="&pdb;Tyrosine">
<rdfs:label>Tyrosine</rdfs:label>
- <rdfs:subClassOf rdf:resource="#Amino_acid"/>
+ <rdfs:subClassOf rdf:resource="http://dl-learner.org/pdb:Amino_acid"/>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty rdf:resource="#has_hydrophobicity"/>
- <owl:someValuesFrom rdf:resource="#hydrophobic"/>
+ <owl:onProperty rdf:resource="http://dl-learner.org/pdb:has_polarity"/>
+ <owl:hasValue rdf:resource="http://dl-learner.org/pdb:polar"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty rdf:resource="#has_aromaticity"/>
- <owl:someValuesFrom rdf:resource="#not_aliphatic"/>
+ <owl:onProperty rdf:resource="http://dl-learner.org/pdb:has_hydrophobicity"/>
+ <owl:hasValue rdf:resource="http://dl-learner.org/pdb:aromatic"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty rdf:resource="#has_polarity"/>
- <owl:someValuesFrom rdf:resource="#polar"/>
+ <owl:onProperty rdf:resource="http://dl-learner.org/pdb:has_size"/>
+ <owl:hasValue rdf:resource="http://dl-learner.org/pdb:large"/>
</owl:Restriction>
</rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#is_in_hydrogen_bond"/>
- <owl:someValuesFrom rdf:resource="#hydrogen_bond_acceptor"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="#has_charge"/>
- <owl:someValuesFrom rdf:resource="...
[truncated message content] |
|
From: <jen...@us...> - 2012-01-09 16:05:39
|
Revision: 3548
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3548&view=rev
Author: jenslehmann
Date: 2012-01-09 16:05:33 +0000 (Mon, 09 Jan 2012)
Log Message:
-----------
fixed a bug when self configuring a heuristic
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/CELOE.java
trunk/components-core/src/main/java/org/dllearner/algorithms/ocel/OCEL.java
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/CELOE.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/CELOE.java 2012-01-09 15:29:14 UTC (rev 3547)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/CELOE.java 2012-01-09 16:05:33 UTC (rev 3548)
@@ -1014,6 +1014,7 @@
return heuristic;
}
+ @Autowired(required=false)
public void setHeuristic(OEHeuristicRuntime heuristic) {
this.heuristic = heuristic;
}
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/ocel/OCEL.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/ocel/OCEL.java 2012-01-09 15:29:14 UTC (rev 3547)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/ocel/OCEL.java 2012-01-09 16:05:33 UTC (rev 3548)
@@ -145,7 +145,7 @@
private int maxClassDescriptionTests = CommonConfigOptions.maxClassDescriptionTestsDefault;
private double negativeWeight = 1.0;
- private double startNodeBonus = 1.0;
+ private double startNodeBonus = 0.1; // 1.0;
private double expansionPenaltyFactor = 0.02;
private int negationPenalty = 0;
private boolean terminateOnNoiseReached = true;
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lor...@us...> - 2012-01-09 15:29:23
|
Revision: 3547
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3547&view=rev
Author: lorenz_b
Date: 2012-01-09 15:29:14 +0000 (Mon, 09 Jan 2012)
Log Message:
-----------
Refined output to distinguish between different problems.
Modified Paths:
--------------
trunk/interfaces/src/main/java/org/dllearner/cli/GlobalEnrichment.java
Modified: trunk/interfaces/src/main/java/org/dllearner/cli/GlobalEnrichment.java
===================================================================
--- trunk/interfaces/src/main/java/org/dllearner/cli/GlobalEnrichment.java 2012-01-09 14:58:40 UTC (rev 3546)
+++ trunk/interfaces/src/main/java/org/dllearner/cli/GlobalEnrichment.java 2012-01-09 15:29:14 UTC (rev 3547)
@@ -19,14 +19,18 @@
*/
package org.dllearner.cli;
+import java.io.BufferedReader;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
+import java.io.FileReader;
+import java.io.FileWriter;
+import java.io.IOException;
import java.io.PrintStream;
import java.lang.reflect.InvocationTargetException;
import java.net.MalformedURLException;
import java.net.URL;
-import java.util.HashMap;
+import java.util.ArrayList;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
@@ -37,6 +41,8 @@
import java.util.concurrent.ThreadPoolExecutor;
import java.util.concurrent.TimeUnit;
+import javax.servlet.jsp.SkipPageException;
+
import org.apache.log4j.ConsoleAppender;
import org.apache.log4j.Level;
import org.apache.log4j.Logger;
@@ -53,8 +59,6 @@
import com.hp.hpl.jena.query.QuerySolution;
import com.hp.hpl.jena.query.ResultSet;
import com.hp.hpl.jena.rdf.model.Model;
-import com.hp.hpl.jena.sparql.engine.http.QueryExceptionHTTP;
-import com.hp.hpl.jena.sparql.resultset.ResultSetException;
/**
* Enriches all of the LOD cloud.
@@ -63,6 +67,13 @@
*
*/
public class GlobalEnrichment {
+
+ //whether or not to skip endpoints which caused exceptions in a run before
+ private static boolean skipFailedEndpoints = true;
+ //whether or not to skip endpoints which returned no axioms during the learning process
+ private static boolean skipEmptyEndpoints = true;
+ //whether or not to skip endpoints on which we could learn something
+ private static boolean skipSuccessfulEndpoints = true;
// parameters
private static double threshold = 0.8;
@@ -75,7 +86,7 @@
//parameters for thread pool
//Parallel running Threads(Executor) on System
- private static int corePoolSize = 1;
+ private static int corePoolSize = 5;
//Maximum Threads allowed in Pool
private static int maximumPoolSize = 20;
//Keep alive time for waiting threads for jobs(Runnable)
@@ -131,7 +142,7 @@
ResultSet rs = sq.send();
while(rs.hasNext()) {
QuerySolution qs = rs.next();
- String endpoint = qs.get("endpoint").toString();System.out.println(endpoint);
+ String endpoint = qs.get("endpoint").toString();
String shortName = qs.get("shortName").toString();
endpoints.put(shortName, new SparqlEndpoint(new URL(endpoint)));
}
@@ -140,6 +151,23 @@
TreeSet<String> blacklist = new TreeSet<String>();
blacklist.add("rkb-explorer-crime"); // computation never completes
+ //remove endpoints which failed in a run before
+ if(skipFailedEndpoints){
+ for(String name : getErrorList()){
+ endpoints.remove(name);
+ }
+ }
+ if(skipEmptyEndpoints){
+ for(String name : getEmptyList()){
+ endpoints.remove(name);
+ }
+ }
+ if(skipSuccessfulEndpoints){
+ for(String name : getSuccessList()){
+ endpoints.remove(name);
+ }
+ }
+
ArrayBlockingQueue<Runnable> workQueue = new ArrayBlockingQueue<Runnable>(endpoints.size());
ThreadPoolExecutor threadPool = new ThreadPoolExecutor(corePoolSize, maximumPoolSize, keepAliveTime, TimeUnit.SECONDS, workQueue);
@@ -155,8 +183,8 @@
SparqlEndpoint se = endpoint.getValue();
String name = endpoint.getKey();
- File f = new File(baseDir + name + ".ttl");
- File log = new File(baseDir + name + ".log");
+ File f = new File(baseDir + File.separator + "success" + File.separator + name + ".ttl");
+ File log = new File(baseDir + File.separator + "failed" + File.separator + name + ".log");
System.out.println("Enriching " + name + " using " + se.getURL());
Enrichment e = new Enrichment(se, null, threshold, nrOfAxiomsToLearn, useInference, false);
@@ -175,6 +203,8 @@
e.start();
success = true;
} catch (Exception ex){
+ write2File(ex, se);
+ ex.printStackTrace();
ex.printStackTrace(new PrintStream(log));
} catch(StackOverflowError error) {
error.printStackTrace(new PrintStream(log));
@@ -212,11 +242,16 @@
SparqlEndpointKS ks = new SparqlEndpointKS(se);
List<AlgorithmRun> runs = e.getAlgorithmRuns();
List<OWLAxiom> axioms = new LinkedList<OWLAxiom>();
+ int axiomCnt = 0;
for(AlgorithmRun run : runs) {
+ axiomCnt += e.getGeneratedOntology().getLogicalAxiomCount();
axioms.addAll(e.toRDF(run.getAxioms(), run.getAlgorithm(), run.getParameters(), ks));
}
Model model = e.getModel(axioms);
try {
+ if(axiomCnt == 0){
+ f = f = new File(baseDir + File.separator + "success/empty" + File.separator + name + ".ttl");
+ }
model.write(new FileOutputStream(f), "TURTLE");
} catch (FileNotFoundException e1) {
// TODO Auto-generated catch block
@@ -228,6 +263,49 @@
});
}
+ threadPool.shutdown();
}
+
+ public static void write2File(Exception e, SparqlEndpoint endpoint) {
+ try {
+ File file = new File(baseDir + File.separator + "errors" + File.separator + e.getClass().getName());
+ if(!file.exists()){
+ file.createNewFile();
+ }
+ FileWriter fw = new FileWriter(file, true);
+ fw.append(endpoint.getURL().toString() + "\n");
+ fw.flush();
+ fw.close();
+ } catch (Exception ex) {
+ ex.printStackTrace();
+ }
+ }
+
+ public static List<String> getErrorList(){
+ List<String> errorNames = new ArrayList<String>();
+ File dir = new File(baseDir + "/failed/");
+ for(File file : dir.listFiles()){
+ errorNames.add(file.getName().replace(".log", ""));
+ }
+ return errorNames;
+ }
+
+ public static List<String> getEmptyList(){
+ List<String> errorNames = new ArrayList<String>();
+ File dir = new File(baseDir + "/success/empty/");
+ for(File file : dir.listFiles()){
+ errorNames.add(file.getName().replace(".ttl", ""));
+ }
+ return errorNames;
+ }
+
+ public static List<String> getSuccessList(){
+ List<String> errorNames = new ArrayList<String>();
+ File dir = new File(baseDir + "/success/");
+ for(File file : dir.listFiles()){
+ errorNames.add(file.getName().replace(".ttl", ""));
+ }
+ return errorNames;
+ }
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lor...@us...> - 2012-01-09 14:58:51
|
Revision: 3546
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3546&view=rev
Author: lorenz_b
Date: 2012-01-09 14:58:40 +0000 (Mon, 09 Jan 2012)
Log Message:
-----------
Made option configurable in *.conf files.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/PCELOE.java
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/PCELOE.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/PCELOE.java 2012-01-09 08:34:46 UTC (rev 3545)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/PCELOE.java 2012-01-09 14:58:40 UTC (rev 3546)
@@ -205,12 +205,15 @@
@ConfigOption(name = "maxDepth", defaultValue="7", description="maximum depth of description")
private double maxDepth = 7;
+
+ @ConfigOption(name = "nrOfThreads", defaultValue="2", description="number of threads running in parallel")
+ private int nrOfThreads = 2;
private int expressionTestCountLastImprovement;
private long timeLastImprovement = 0;
private Set<OENode> currentlyProcessedNodes = Collections.synchronizedSet(new HashSet<OENode>());
- private double highestAccuracy = 0.0;
+ private volatile double highestAccuracy = 0.0;
// public CELOEConfigurator getConfigurator() {
// return configurator;
@@ -451,13 +454,15 @@
addNode(startClass, null);
- int nrOfThreads = Runtime.getRuntime().availableProcessors();
- nrOfThreads = 4;//only for tests TODO make number of threads configurable
- ExecutorService service = Executors.newFixedThreadPool(nrOfThreads);
+ int nrOfWorkers = nrOfThreads;
+ if(nrOfWorkers == 0){
+ nrOfWorkers = Runtime.getRuntime().availableProcessors();
+ }
+ ExecutorService service = Executors.newFixedThreadPool(nrOfWorkers);
List<Runnable> tasks = new ArrayList<Runnable>();
- for(int i = 0; i < nrOfThreads; i++){
+ for(int i = 0; i < nrOfWorkers; i++){
tasks.add(new Worker());
}
@@ -633,7 +638,9 @@
if(!shorterDescriptionExists) {
if(!filterFollowsFromKB || !((ClassLearningProblem)learningProblem).followsFromKB(niceDescription)) {
// System.out.println("Test2");
- bestEvaluatedDescriptions.add(niceDescription, accuracy, learningProblem);
+ synchronized (bestEvaluatedDescriptions) {
+ bestEvaluatedDescriptions.add(niceDescription, accuracy, learningProblem);
+ }
// System.out.println("acc: " + accuracy);
// System.out.println(bestEvaluatedDescriptions);
}
@@ -1011,19 +1018,33 @@
this.maxExecutionTimeInSecondsAfterImprovement = maxExecutionTimeInSecondsAfterImprovement;
}
+
+
+ public int getNrOfThreads() {
+ return nrOfThreads;
+ }
+
+ public void setNrOfThreads(int nrOfThreads) {
+ this.nrOfThreads = nrOfThreads;
+ }
+
+ private synchronized double getHighestAccuracy(){
+ return highestAccuracy;
+ }
+
+
class Worker implements Runnable{
@Override
public void run() {
int loop = 0;
-
// highest accuracy so far
// double highestAccuracy = 0.0;
OENode nextNode;
while (!terminationCriteriaSatisfied()) {
// System.out.println("loop " + loop);
- if(!singleSuggestionMode && bestEvaluatedDescriptions.getBestAccuracy() > highestAccuracy) {
+ if(!singleSuggestionMode && bestEvaluatedDescriptions.getBestAccuracy() > getHighestAccuracy()) {
highestAccuracy = bestEvaluatedDescriptions.getBestAccuracy();
expressionTestCountLastImprovement = expressionTests;
timeLastImprovement = System.nanoTime();
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|
|
From: <lor...@us...> - 2012-01-09 08:34:53
|
Revision: 3545
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3545&view=rev
Author: lorenz_b
Date: 2012-01-09 08:34:46 +0000 (Mon, 09 Jan 2012)
Log Message:
-----------
Updated logging.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/PCELOE.java
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/PCELOE.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/PCELOE.java 2012-01-08 18:42:27 UTC (rev 3544)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/PCELOE.java 2012-01-09 08:34:46 UTC (rev 3545)
@@ -1106,8 +1106,8 @@
public static void main(String[] args) throws Exception{
Logger.getRootLogger().setLevel(Level.INFO);
- Logger.getLogger(PCELOE2.class).setLevel(Level.DEBUG);
- Logger.getLogger(PCELOE2.class).addAppender(new FileAppender(new PatternLayout( "[%t] %c: %m%n" ), "log/parallel_run.txt", false));
+ Logger.getLogger(PCELOE.class).setLevel(Level.DEBUG);
+ Logger.getLogger(PCELOE.class).addAppender(new FileAppender(new PatternLayout( "[%t] %c: %m%n" ), "log/parallel_run.txt", false));
AbstractKnowledgeSource ks = new OWLFile("../examples/family/father_oe.owl");
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|
|
From: <lor...@us...> - 2012-01-08 18:42:33
|
Revision: 3544
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3544&view=rev
Author: lorenz_b
Date: 2012-01-08 18:42:27 +0000 (Sun, 08 Jan 2012)
Log Message:
-----------
Registered component.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/core/AnnComponentManager.java
Modified: trunk/components-core/src/main/java/org/dllearner/core/AnnComponentManager.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/AnnComponentManager.java 2012-01-08 18:40:18 UTC (rev 3543)
+++ trunk/components-core/src/main/java/org/dllearner/core/AnnComponentManager.java 2012-01-08 18:42:27 UTC (rev 3544)
@@ -51,6 +51,7 @@
// (CLI, GUI, Web Service) and scripts (HTML documentation generator)
private static List<String> componentClassNames = new ArrayList<String> ( Arrays.asList(new String[]{
"org.dllearner.algorithms.celoe.CELOE",
+ "org.dllearner.algorithms.celoe.PCELOE",
"org.dllearner.algorithms.el.ELLearningAlgorithm",
"org.dllearner.algorithms.el.ELLearningAlgorithmDisjunctive",
"org.dllearner.algorithms.fuzzydll.FuzzyCELOE",
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lor...@us...> - 2012-01-08 18:40:25
|
Revision: 3543
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3543&view=rev
Author: lorenz_b
Date: 2012-01-08 18:40:18 +0000 (Sun, 08 Jan 2012)
Log Message:
-----------
Optimized tests.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/PCELOE.java
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/PCELOE.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/PCELOE.java 2012-01-08 13:42:22 UTC (rev 3542)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/PCELOE.java 2012-01-08 18:40:18 UTC (rev 3543)
@@ -24,7 +24,6 @@
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
-import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.LinkedList;
@@ -33,18 +32,16 @@
import java.util.Set;
import java.util.SortedSet;
import java.util.TreeSet;
-import java.util.concurrent.ArrayBlockingQueue;
+import java.util.concurrent.ExecutionException;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
-import java.util.concurrent.ThreadPoolExecutor;
-import java.util.concurrent.TimeUnit;
+import java.util.concurrent.Future;
-import org.apache.log4j.ConsoleAppender;
import org.apache.log4j.FileAppender;
import org.apache.log4j.Level;
import org.apache.log4j.Logger;
import org.apache.log4j.PatternLayout;
-import org.apache.log4j.SimpleLayout;
+import org.dllearner.algorithms.celoe.PCELOE.Worker;
import org.dllearner.core.AbstractCELA;
import org.dllearner.core.AbstractKnowledgeSource;
import org.dllearner.core.AbstractLearningProblem;
@@ -91,15 +88,6 @@
*/
@ComponentAnn(name="PCELOE", shortName="pceloe", version=1.0, description="CELOE is an adapted and extended version of the OCEL algorithm applied for the ontology engineering use case. See http://jens-lehmann.org/files/2011/celoe.pdf for reference.")
public class PCELOE extends AbstractCELA {
-
- //parameters for thread pool
- //Parallel running Threads(Executor) on System
- private static int corePoolSize = 5;
- //Maximum Threads allowed in Pool
- private static int maximumPoolSize = 20;
- //Keep alive time for waiting threads for jobs(Runnable)
- private static long keepAliveTime = 10;
-
private static Logger logger = Logger.getLogger(PCELOE.class);
// private CELOEConfigurator configurator;
@@ -117,6 +105,7 @@
// all nodes in the search tree (used for selecting most promising node)
private SortedSet<OENode> nodes;
+// private TreeSet<OENode> nodes;
private OEHeuristicRuntime heuristic; // = new OEHeuristicRuntime();
// root of search tree
private OENode startNode;
@@ -125,7 +114,8 @@
private Description startClass;
// all descriptions in the search tree plus those which were too weak (for fast redundancy check)
- private TreeSet<Description> descriptions;
+// private TreeSet<Description> descriptions;
+ private SortedSet<Description> descriptions;
private EvaluatedDescriptionSet bestEvaluatedDescriptions;
@@ -198,19 +188,29 @@
@ConfigOption(name = "reuseExistingDescription", defaultValue="false", description="If true, the algorithm tries to find a good starting point close to an existing definition/super class of the given class in the knowledge base.")
private boolean reuseExistingDescription = false;
- @ConfigOption(name = "maxClassDescriptionTests", defaultValue="0", description="The maximum number of candidate hypothesis the algorithm is allowed to test (0 = no limit). The algorithm will stop afterwards. (The real number of tests can be slightly higher, because this criterion usually won't be checked after each single test.)")
- private int maxClassDescriptionTests = 0;
+ @ConfigOption(name = "maxClassExpressionTests", defaultValue="0", description="The maximum number of candidate hypothesis the algorithm is allowed to test (0 = no limit). The algorithm will stop afterwards. (The real number of tests can be slightly higher, because this criterion usually won't be checked after each single test.)")
+ private int maxClassExpressionTests = 0;
+ @ConfigOption(name = "maxClassExpressionTestsAfterImprovement", defaultValue="0", description = "The maximum number of candidate hypothesis the algorithm is allowed after an improvement in accuracy (0 = no limit). The algorithm will stop afterwards. (The real number of tests can be slightly higher, because this criterion usually won't be checked after each single test.)")
+ private int maxClassExpressionTestsAfterImprovement = 0;
+
@ConfigOption(defaultValue = "10", name = "maxExecutionTimeInSeconds", description = "maximum execution of the algorithm in seconds")
private int maxExecutionTimeInSeconds = 10;
+ @ConfigOption(defaultValue = "0", name = "maxExecutionTimeInSecondsAfterImprovement", description = "maximum execution of the algorithm in seconds")
+ private int maxExecutionTimeInSecondsAfterImprovement = 0;
+
@ConfigOption(name = "terminateOnNoiseReached", defaultValue="false", description="specifies whether to terminate when noise criterion is met")
private boolean terminateOnNoiseReached = false;
@ConfigOption(name = "maxDepth", defaultValue="7", description="maximum depth of description")
private double maxDepth = 7;
+
+ private int expressionTestCountLastImprovement;
+ private long timeLastImprovement = 0;
private Set<OENode> currentlyProcessedNodes = Collections.synchronizedSet(new HashSet<OENode>());
+ private double highestAccuracy = 0.0;
// public CELOEConfigurator getConfigurator() {
// return configurator;
@@ -232,12 +232,16 @@
// }
public static String getName() {
- return "CELOE";
+ return "PCELOE";
}
@Override
public void init() throws ComponentInitException {
+ if(maxExecutionTimeInSeconds != 0 && maxExecutionTimeInSecondsAfterImprovement != 0) {
+ maxExecutionTimeInSeconds = Math.min(maxExecutionTimeInSeconds, maxExecutionTimeInSecondsAfterImprovement);
+ }
+
// compute used concepts/roles from allowed/ignored
// concepts/roles
Set<NamedClass> usedConcepts;
@@ -443,109 +447,89 @@
reset();
nanoStartTime = System.nanoTime();
+
+
addNode(startClass, null);
int nrOfThreads = Runtime.getRuntime().availableProcessors();
- nrOfThreads = 8;//only for tests TODO make number of threads configurable
+ nrOfThreads = 4;//only for tests TODO make number of threads configurable
ExecutorService service = Executors.newFixedThreadPool(nrOfThreads);
List<Runnable> tasks = new ArrayList<Runnable>();
for(int i = 0; i < nrOfThreads; i++){
- RhoDRDown operator = new RhoDRDown();
- operator.setStartClass(startClass);
- operator.setReasoner(reasoner);
- try {
- operator.init();
- } catch (ComponentInitException e) {
- e.printStackTrace();
- }
- operator.setSubHierarchy(reasoner.getClassHierarchy().clone());
- operator.setObjectPropertyHierarchy(reasoner.getObjectPropertyHierarchy());
- operator.setDataPropertyHierarchy(reasoner.getDatatypePropertyHierarchy());
-
- tasks.add(new Worker(operator));
+ tasks.add(new Worker());
}
+ //needed to block until all threads have been finished, because otherwise the main thread outputs the result to early
+ List<Future> futures = new ArrayList<Future>();
for(Runnable task : tasks){
- service.submit(task);
+ futures.add(service.submit(task));
}
-
- try {
- service.awaitTermination(maxExecutionTimeInSeconds, TimeUnit.SECONDS);
- } catch (InterruptedException e) {
- e.printStackTrace();
+ for(Future future : futures){
+ try {
+ future.get();
+ } catch (InterruptedException e) {
+ e.printStackTrace();
+ } catch (ExecutionException e) {
+ e.printStackTrace();
+ }
}
- if(singleSuggestionMode) {
- bestEvaluatedDescriptions.add(bestDescription, bestAccuracy, learningProblem);
- }
-
if (stop) {
logger.info("Algorithm stopped ("+expressionTests+" descriptions tested). " + nodes.size() + " nodes in the search tree.\n");
} else {
- logger.info("Algorithm terminated successfully ("+expressionTests+" descriptions tested). " + nodes.size() + " nodes in the search tree.\n");
+ logger.info("Algorithm terminated successfully (time: " + Helper.prettyPrintNanoSeconds(System.nanoTime()-nanoStartTime) + ", "+expressionTests+" descriptions tested, " + nodes.size() + " nodes in the search tree).\n");
logger.info(reasoner.toString());
}
+
+ if(singleSuggestionMode) {
+ bestEvaluatedDescriptions.add(bestDescription, bestAccuracy, learningProblem);
+ }
// print solution(s)
-
-// System.out.println("isRunning: " + isRunning);
-
logger.info("solutions:\n" + getSolutionString());
// System.out.println(startNode.toTreeString(baseURI));
isRunning = false;
service.shutdown();
-
+// System.out.println("isRunning: " + isRunning);
}
- synchronized private OENode getNextNodeToExpand() {
+ private OENode getNextNodeToExpand() {
// we expand the best node of those, which have not achieved 100% accuracy
// already and have a horizontal expansion equal to their length
// (rationale: further extension is likely to add irrelevant syntactical constructs)
- synchronized (nodes) {
- logger.debug("in 1.lock of getNextNodeToExpand method");
- Iterator<OENode> it = nodes.iterator();//logger.info(nodes.size());
- logger.debug("search tree size: " + nodes.size());
- while(it.hasNext()) {
- OENode node = it.next();
- logger.debug("Checking node " + node + "...");
- if(!currentlyProcessedNodes.contains(node) && (node.getAccuracy() < 1.0 || node.getHorizontalExpansion() < node.getDescription().getLength())) {
- currentlyProcessedNodes.add(node);
- logger.debug("...checked and return node.");
- return node;
- }
- logger.debug("...checked.");
+// Iterator<OENode> it = nodes.descendingIterator();
+ synchronized(nodes){
+ Iterator<OENode> it = nodes.iterator();
+ while(it.hasNext()) {
+ OENode node = it.next();
+ if(!currentlyProcessedNodes.contains(node) && (node.getAccuracy() < 1.0 || node.getHorizontalExpansion() < node.getDescription().getLength())) {
+ currentlyProcessedNodes.add(node);
+ return node;
}
+ }
}
-
// this should practically never be called, since for any reasonable learning
// task, we will always have at least one node with less than 100% accuracy
return null;
}
// expand node horizontically
- private TreeSet<Description> refineNode(OENode node, RhoDRDown operator) {
+ private TreeSet<Description> refineNode(OENode node) {
// we have to remove and add the node since its heuristic evaluation changes through the expansion
// (you *must not* include any criteria in the heuristic which are modified outside of this method,
// otherwise you may see rarely occurring but critical false ordering in the nodes set)
- synchronized (nodes) {
- nodes.remove(node);
- }
-
+ nodes.remove(node);
// System.out.println("refining: " + node);
int horizExp = node.getHorizontalExpansion();
-// TreeSet<Description> refinements = (TreeSet<Description>) operator.refine(node.getDescription(), horizExp+1);
TreeSet<Description> refinements = (TreeSet<Description>) operator.refine(node.getDescription(), horizExp+1);
node.incHorizontalExpansion();
node.setRefinementCount(refinements.size());
- synchronized (nodes) {
- nodes.add(node);
- }
-
+ nodes.add(node);
return refinements;
}
@@ -560,17 +544,15 @@
if(!nonRedundant) {
return false;
}
- logger.debug("Check if description is allowed...");
+
// check whether the description is allowed
if(!isDescriptionAllowed(description, parentNode)) {
return false;
}
- logger.debug("...done");
// System.out.println("Test " + new Date());
// quality of description (return if too weak)
double accuracy = learningProblem.getAccuracyOrTooWeak(description, noise);
- logger.debug("Accuracy: " + accuracy);
// issue a warning if accuracy is not between 0 and 1 or -1 (too weak)
if(accuracy > 1.0 || (accuracy < 0.0 && accuracy != -1)) {
logger.warn("Invalid accuracy value " + accuracy + " for description " + description + ". This could be caused by a bug in the heuristic measure and should be reported to the DL-Learner bug tracker.");
@@ -614,7 +596,6 @@
// we need to make sure that this does not get called more often than
// necessary since rewriting is expensive
boolean isCandidate = !bestEvaluatedDescriptions.isFull();
- logger.debug("Is candidate:" + isCandidate);
if(!isCandidate) {
EvaluatedDescription worst = bestEvaluatedDescriptions.getWorst();
double accThreshold = worst.getAccuracy();
@@ -638,33 +619,25 @@
// A is not a candidate; on the other hand this suppresses many meaningless extensions of A
boolean shorterDescriptionExists = false;
if(forceMutualDifference) {
- synchronized (bestEvaluatedDescriptions) {
- for(EvaluatedDescription ed : bestEvaluatedDescriptions.getSet()) {
- if(Math.abs(ed.getAccuracy()-accuracy) <= 0.00001 && ConceptTransformation.isSubdescription(niceDescription, ed.getDescription())) {
-// System.out.println("shorter: " + ed.getDescription());
- shorterDescriptionExists = true;
- break;
- }
- }
- }
-
+ for(EvaluatedDescription ed : bestEvaluatedDescriptions.getSet()) {
+ if(Math.abs(ed.getAccuracy()-accuracy) <= 0.00001 && ConceptTransformation.isSubdescription(niceDescription, ed.getDescription())) {
+// System.out.println("shorter: " + ed.getDescription());
+ shorterDescriptionExists = true;
+ break;
+ }
+ }
}
- logger.debug("Point 2");
// System.out.println("shorter description? " + shorterDescriptionExists + " nice: " + niceDescription);
- filterFollowsFromKB = false;
+
if(!shorterDescriptionExists) {
if(!filterFollowsFromKB || !((ClassLearningProblem)learningProblem).followsFromKB(niceDescription)) {
// System.out.println("Test2");
- synchronized (bestEvaluatedDescriptions) {
- bestEvaluatedDescriptions.add(niceDescription, accuracy, learningProblem);
- }
-
+ bestEvaluatedDescriptions.add(niceDescription, accuracy, learningProblem);
// System.out.println("acc: " + accuracy);
// System.out.println(bestEvaluatedDescriptions);
}
}
- logger.debug("Point 3");
// System.out.println(bestEvaluatedDescriptions.getSet().size());
}
@@ -763,9 +736,11 @@
private Description rewriteNode(OENode node) {
Description description = node.getDescription();
// minimize description (expensive!) - also performes some human friendly rewrites
- Description niceDescription;
+ Description niceDescription = description;
if(useMinimizer) {
- niceDescription = minimizer.minimizeClone(description);
+ synchronized (minimizer) {
+ niceDescription = minimizer.minimizeClone(description);
+ }
} else {
niceDescription = description;
}
@@ -775,22 +750,24 @@
}
private boolean terminationCriteriaSatisfied() {
- boolean ret = stop ||
- (maxClassDescriptionTests != 0 && (expressionTests >= maxClassDescriptionTests)) ||
- (maxExecutionTimeInSeconds != 0 && ((System.nanoTime() - nanoStartTime) >= (maxExecutionTimeInSeconds*1000000000l))) ||
- (terminateOnNoiseReached && (100*getCurrentlyBestAccuracy()>=100-noisePercentage));
- logger.debug("terminate: " + ret);
- return ret;
-
+ return
+ stop ||
+ (maxClassExpressionTestsAfterImprovement != 0 && (expressionTests - expressionTestCountLastImprovement >= maxClassExpressionTestsAfterImprovement)) ||
+ (maxClassExpressionTests != 0 && (expressionTests >= maxClassExpressionTests)) ||
+ (maxExecutionTimeInSecondsAfterImprovement != 0 && ((System.nanoTime() - nanoStartTime) >= (maxExecutionTimeInSecondsAfterImprovement*1000000000l))) ||
+ (maxExecutionTimeInSeconds != 0 && ((System.nanoTime() - nanoStartTime) >= (maxExecutionTimeInSeconds*1000000000l))) ||
+ (terminateOnNoiseReached && (100*getCurrentlyBestAccuracy()>=100-noisePercentage));
}
private void reset() {
// set all values back to their default values (used for running
// the algorithm more than once)
- nodes = Collections.synchronizedSortedSet(new TreeSet<OENode>(heuristic));
- descriptions = new TreeSet<Description>(new ConceptComparator());
+// nodes = new TreeSet<OENode>(heuristic);
+ nodes = Collections.synchronizedSortedSet(new TreeSet<OENode>(Collections.reverseOrder(heuristic)));
+ descriptions = Collections.synchronizedSortedSet(new TreeSet<Description>(new ConceptComparator()));
bestEvaluatedDescriptions.getSet().clear();
expressionTests = 0;
+ highestAccuracy = 0.0;
}
@Override
@@ -852,6 +829,7 @@
double scoreThreshold = heuristic.getNodeScore(node) + 1 - node.getAccuracy();
for(OENode n : nodes) {
+// for(OENode n : nodes.descendingSet()) {
if(n != node) {
if(n.getHorizontalExpansion() == minHorizExp) {
// we can stop instantly when another node with min.
@@ -968,11 +946,11 @@
}
public int getMaxClassDescriptionTests() {
- return maxClassDescriptionTests;
+ return maxClassExpressionTests;
}
public void setMaxClassDescriptionTests(int maxClassDescriptionTests) {
- this.maxClassDescriptionTests = maxClassDescriptionTests;
+ this.maxClassExpressionTests = maxClassDescriptionTests;
}
public int getMaxExecutionTimeInSeconds() {
@@ -1013,78 +991,63 @@
public void setHeuristic(OEHeuristicRuntime heuristic) {
this.heuristic = heuristic;
+ }
+
+ public int getMaxClassExpressionTestsWithoutImprovement() {
+ return maxClassExpressionTestsAfterImprovement;
+ }
+
+ public void setMaxClassExpressionTestsWithoutImprovement(
+ int maxClassExpressionTestsWithoutImprovement) {
+ this.maxClassExpressionTestsAfterImprovement = maxClassExpressionTestsWithoutImprovement;
+ }
+
+ public int getMaxExecutionTimeInSecondsAfterImprovement() {
+ return maxExecutionTimeInSecondsAfterImprovement;
+ }
+
+ public void setMaxExecutionTimeInSecondsAfterImprovement(
+ int maxExecutionTimeInSecondsAfterImprovement) {
+ this.maxExecutionTimeInSecondsAfterImprovement = maxExecutionTimeInSecondsAfterImprovement;
}
-
- public static void main(String[] args) throws Exception{
- Logger.getRootLogger().setLevel(Level.INFO);
- Logger.getLogger(PCELOE.class).setLevel(Level.DEBUG);
- Logger.getLogger(PCELOE.class).addAppender(new FileAppender(new PatternLayout( "[%t] %c: %m%n" ), "log/parallel_run.txt", false));
-
-
- AbstractKnowledgeSource ks = new OWLFile("../examples/family/father_oe.owl");
- ks.init();
-
- AbstractReasonerComponent rc = new FastInstanceChecker(ks);
- rc.init();
-
- ClassLearningProblem lp = new ClassLearningProblem(rc);
- lp.setClassToDescribe(new NamedClass("http://example.com/father#father"));
- lp.setCheckConsistency(false);
- lp.init();
-
- PCELOE alg = new PCELOE(lp, rc);
- alg.setMaxExecutionTimeInSeconds(10);
-// alg.setMaxClassDescriptionTests(200);
- alg.init();
-
- alg.start();
-
- }
-
class Worker implements Runnable{
-
- private RhoDRDown operator;
-
- public Worker(RhoDRDown operator) {
- this.operator = operator;
- }
@Override
public void run() {
- logger.debug("Started thread...");
+ int loop = 0;
+ // highest accuracy so far
+// double highestAccuracy = 0.0;
OENode nextNode;
- double highestAccuracy = 0.0;
- int loop = 0;
while (!terminationCriteriaSatisfied()) {
+// System.out.println("loop " + loop);
-
if(!singleSuggestionMode && bestEvaluatedDescriptions.getBestAccuracy() > highestAccuracy) {
highestAccuracy = bestEvaluatedDescriptions.getBestAccuracy();
- logger.info("more accurate (" + dfPercent.format(highestAccuracy) + ") class expression found: " + descriptionToString(bestEvaluatedDescriptions.getBest().getDescription()));
+ expressionTestCountLastImprovement = expressionTests;
+ timeLastImprovement = System.nanoTime();
+ logger.info("more accurate (" + dfPercent.format(highestAccuracy) + ") class expression found: " + descriptionToString(bestEvaluatedDescriptions.getBest().getDescription()));
}
// chose best node according to heuristics
- logger.debug("Get next node to expand...");
nextNode = getNextNodeToExpand();
- logger.debug("...done");
- try {
- Thread.sleep(10);
- } catch (InterruptedException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- logger.debug("next Node: " + nextNode);
if(nextNode != null){
int horizExp = nextNode.getHorizontalExpansion();
// apply operator
Monitor mon = MonitorFactory.start("refineNode");
- logger.debug("Refine node...");
- TreeSet<Description> refinements = refineNode(nextNode, operator);
+ TreeSet<Description> refinements = refineNode(nextNode);
mon.stop();
- logger.debug("...done");
+
+// System.out.println("next node: " + nextNode);
+// for(Description refinement : refinements) {
+// System.out.println("refinement: " + refinement);
+// }
+// if((loop+1) % 500 == 0) {
+// System.out.println(getMinimumHorizontalExpansion() + " - " + getMaximumHorizontalExpansion());
+// System.exit(0);
+// }
while(refinements.size() != 0) {
// pick element from set
@@ -1097,10 +1060,8 @@
// System.out.println("potentially adding " + refinement + " to search tree as child of " + nextNode + " " + new Date());
Monitor mon2 = MonitorFactory.start("addNode");
- logger.debug("Add node...");
addNode(refinement, nextNode);
mon2.stop();
- logger.debug("...done");
// adding nodes is potentially computationally expensive, so we have
// to check whether max time is exceeded
if(terminationCriteriaSatisfied()) {
@@ -1113,7 +1074,26 @@
}
// updateMinMaxHorizExp(nextNode);
-
+
+ // writing the search tree (if configured)
+ if (writeSearchTree) {
+ String treeString = "best node: " + bestEvaluatedDescriptions.getBest() + "\n";
+ if (refinements.size() > 1) {
+ treeString += "all expanded nodes:\n";
+ for (Description n : refinements) {
+ treeString += " " + n + "\n";
+ }
+ }
+ treeString += startNode.toTreeString(baseURI);
+ treeString += "\n";
+
+ if (replaceSearchTree)
+ Files.createFile(new File(searchTreeFile), treeString);
+ else
+ Files.appendToFile(new File(searchTreeFile), treeString);
+ }
+
+// System.out.println(loop);
loop++;
currentlyProcessedNodes.remove(nextNode);
}
@@ -1124,4 +1104,29 @@
}
+ public static void main(String[] args) throws Exception{
+ Logger.getRootLogger().setLevel(Level.INFO);
+ Logger.getLogger(PCELOE2.class).setLevel(Level.DEBUG);
+ Logger.getLogger(PCELOE2.class).addAppender(new FileAppender(new PatternLayout( "[%t] %c: %m%n" ), "log/parallel_run.txt", false));
+
+
+ AbstractKnowledgeSource ks = new OWLFile("../examples/family/father_oe.owl");
+ ks.init();
+
+ AbstractReasonerComponent rc = new FastInstanceChecker(ks);
+ rc.init();
+
+ ClassLearningProblem lp = new ClassLearningProblem(rc);
+ lp.setClassToDescribe(new NamedClass("http://example.com/father#father"));
+ lp.setCheckConsistency(false);
+ lp.init();
+
+ PCELOE alg = new PCELOE(lp, rc);
+ alg.setMaxExecutionTimeInSeconds(10);
+// alg.setMaxClassDescriptionTests(200);
+ alg.init();
+
+ alg.start();
+ }
+
}
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|
|
From: <seb...@us...> - 2012-01-08 13:42:31
|
Revision: 3542
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3542&view=rev
Author: sebastianwtr
Date: 2012-01-08 13:42:22 +0000 (Sun, 08 Jan 2012)
Log Message:
-----------
[tbsl exploration] changed function for server connection and some other minor functions
Modified Paths:
--------------
trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/exploration/Sparql/GetRessourcePropertys.java
trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/exploration/Sparql/SparqlObject.java
trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/exploration/Sparql/mySQLDictionary.java
trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/exploration/Sparql/queryInformation.java
trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/exploration/exploration_main/exploration_main.java
Modified: trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/exploration/Sparql/GetRessourcePropertys.java
===================================================================
--- trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/exploration/Sparql/GetRessourcePropertys.java 2012-01-06 14:24:45 UTC (rev 3541)
+++ trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/exploration/Sparql/GetRessourcePropertys.java 2012-01-08 13:42:22 UTC (rev 3542)
@@ -6,6 +6,8 @@
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
+import java.io.OutputStreamWriter;
+import java.net.HttpURLConnection;
import java.net.MalformedURLException;
import java.net.URL;
import java.util.ArrayList;
@@ -17,12 +19,12 @@
public class GetRessourcePropertys {
//String Prefix="http://greententacle.techfak.uni-bielefeld.de:5171/sparql";
- //String Prefix="http://dbpedia.org/sparql";
- String Prefix="http://purpurtentacle.techfak.uni-bielefeld.de:8892/sparql";
+ String Prefix="http://dbpedia.org/sparql";
+ //String Prefix="http://purpurtentacle.techfak.uni-bielefeld.de:8892/sparql";
- public HashMap<String,String> getPropertys(String element, String side) throws IOException{
+ public HashMap<String,String> getPropertys(String element, String side, int timeToTimeoutOnServer) throws IOException{
- return sendServerPropertyRequest(element,side);
+ return sendServerPropertyRequest(element,side, timeToTimeoutOnServer);
@@ -34,7 +36,7 @@
* @return
* @throws IOException
*/
- private HashMap<String,String> sendServerPropertyRequest(String vergleich, String side) throws IOException{
+ private HashMap<String,String> sendServerPropertyRequest(String vergleich, String side, int timeToTimeoutOnServer) throws IOException{
//System.out.println("Resource die gesucht wird: "+ vergleich);
//System.out.println("Seite die gesucht wird: "+side);
@@ -64,43 +66,65 @@
//System.out.println("property right!!! : " +tmp_right);
String tmp_right=Prefix+"?default-graph-uri=&query="+createServerRequest("PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> SELECT DISTINCT ?s ?p WHERE {<"+vergleichorig+"> ?p ?y. ?p rdfs:label ?s.}")+"%0D%0A&format=text%2Fhtml&debug=on&timeout=";
+ String tmp_both=Prefix+"?default-graph-uri=&query="+createServerRequest("PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> SELECT DISTINCT ?s ?p WHERE {{?y ?p <"+vergleichorig+">. ?p rdfs:label ?s.} UNION {<"+vergleichorig+"> ?p ?y. ?p rdfs:label ?s.}}")+"%0D%0A&format=text%2Fhtml&debug=on&timeout=";
String verarbeitungsurl=null;
- if(side.contains("RIGHT")) verarbeitungsurl=tmp_right;
+ /*Original*/
+ if(side.contains("RIGHT")) verarbeitungsurl=tmp_right;
if(side.contains("LEFT")) verarbeitungsurl=tmp_left;
+
+ /*if(side.contains("LEFT")) verarbeitungsurl=tmp_both;
+ if(side.contains("RIGHT")) verarbeitungsurl=tmp_both;*/
//System.out.println(verarbeitungsurl);
//just in case.....
if(!side.contains("LEFT") && !side.contains("RIGHT")) verarbeitungsurl=tmp_left;
- //String verarbeitungsstring="http://greententacle.techfak.uni-bielefeld.de:5171/sparql?default-graph-uri=&query=PREFIX+rdfs%3A+%3Chttp%3A%2F%2Fwww.w3.org%2F2000%2F01%2Frdf-schema%23%3E%0D%0APREFIX+res%3A+%3Chttp%3A%2F%2Fdbpedia.org%2Fresource%2F%3E%0D%0A%0D%0ASELECT+DISTINCT+%3Fp+%3Fl+WHERE++{%0D%0A+{+res%3A"+vergleich+"+%3Fp+%3Fo+.+}%0D%0A+UNION%0D%0A+{+%3Fs+%3Fp+res%3A"+vergleich+"+.+}%0D%0A+{+%3Fp+rdfs%3Alabel+%3Fl+.+}%0D%0A}%0D%0A&format=text%2Fhtml&debug=on&timeout=";
- URL url;
- InputStream is;
- InputStreamReader isr;
- BufferedReader r;
- String str;
String result="";
-
- try {
- url = new URL(verarbeitungsurl);
- is = url.openStream();
- isr = new InputStreamReader(is);
- r = new BufferedReader(isr);
- do {
- str = r.readLine();
- if (str != null)
- result=result+str;
- } while (str != null);
- } catch (MalformedURLException e) {
- System.out.println("Must enter a valid URL");
- } catch (IOException e) {
- System.out.println("Can not connect");
- }
+ HttpURLConnection connection = null;
+ BufferedReader rd = null;
+ StringBuilder sb = null;
+ String line = null;
- /* FileWriter w = new FileWriter("answer_property");
- w.write(result);
- w.close();
- */
+ URL serverAddress = null;
+ try {
+ serverAddress = new URL(verarbeitungsurl);
+ //set up out communications stuff
+ connection = null;
+
+ //Set up the initial connection
+ connection = (HttpURLConnection)serverAddress.openConnection();
+ connection.setRequestMethod("GET");
+ connection.setDoOutput(true);
+ connection.setReadTimeout(timeToTimeoutOnServer);
+
+ connection.connect();
+ rd = new BufferedReader(new InputStreamReader(connection.getInputStream()));
+ sb = new StringBuilder();
+
+ while ((line = rd.readLine()) != null)
+ {
+ sb.append(line + '\n');
+ }
+
+ //System.out.println(sb.toString());
+ result=sb.toString();
+
+ } catch (MalformedURLException e) {
+ System.out.println("Must enter a valid URL");
+ } catch (IOException e) {
+ System.out.println("Can not connect or timeout");
+ }
+ finally
+ {
+ //close the connection, set all objects to null
+ connection.disconnect();
+ rd = null;
+ sb = null;
+ Object wr = null;
+ connection = null;
+ }
+
HashMap<String,String> hm = new HashMap();
result=result.replace("<th>s</th>","");
result=result.replace("<th>p</th>","");
Modified: trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/exploration/Sparql/SparqlObject.java
===================================================================
--- trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/exploration/Sparql/SparqlObject.java 2012-01-06 14:24:45 UTC (rev 3541)
+++ trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/exploration/Sparql/SparqlObject.java 2012-01-08 13:42:22 UTC (rev 3542)
@@ -9,8 +9,10 @@
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.OutputStreamWriter;
+import java.net.HttpURLConnection;
import java.net.MalformedURLException;
import java.net.URL;
+import java.net.URLConnection;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
@@ -26,15 +28,18 @@
import net.didion.jwnl.data.POS;
import org.dllearner.algorithm.tbsl.exploration.sax.ParseXmlHtml;
+import org.dllearner.algorithm.tbsl.nlp.StanfordLemmatizer;
import org.dllearner.algorithm.tbsl.nlp.WordNet;
import org.dllearner.algorithm.tbsl.sparql.BasicQueryTemplate;
import org.dllearner.algorithm.tbsl.sparql.Path;
import org.dllearner.algorithm.tbsl.sparql.SPARQL_Filter;
+import org.dllearner.algorithm.tbsl.sparql.SPARQL_Having;
import org.dllearner.algorithm.tbsl.sparql.SPARQL_Term;
import org.dllearner.algorithm.tbsl.sparql.Slot;
import org.dllearner.algorithm.tbsl.sparql.Template;
import org.dllearner.algorithm.tbsl.templator.BasicTemplator;
import org.dllearner.algorithm.tbsl.templator.Templator;
+import org.xml.sax.InputSource;
import java.sql.Connection;
import java.sql.DriverManager;
@@ -53,17 +58,20 @@
static int explorationdepthwordnet=2;
static int iterationdepth =0;
static int numberofanswers=1;
- static double LevenstheinMin = 0.8;
+ static double LevenstheinMin = 0.9;
static WordNet wordnet;
BasicTemplator btemplator;
Templator templator;
private static mySQLDictionary myindex;
boolean only_best_levensthein_query;
+ static StanfordLemmatizer lemmatiser;
+ //one Minute
+ private static int timeToTimeoutOnServer=60000;
//change here and in getRessourcePropertys
//String Prefix="http://greententacle.techfak.uni-bielefeld.de:5171/sparql";
- //String Prefix="http://dbpedia.org/sparql";
- String Prefix="http://purpurtentacle.techfak.uni-bielefeld.de:8892/sparql";
+ String Prefix="http://dbpedia.org/sparql";
+ //String Prefix="http://purpurtentacle.techfak.uni-bielefeld.de:8892/sparql";
//Konstruktor
@@ -88,6 +96,7 @@
setNumberofanswers(1);
only_best_levensthein_query=false;
+ lemmatiser = new StanfordLemmatizer();
}
/*
@@ -133,12 +142,19 @@
* "Main" Method of this Class.
*
*/
- public queryInformation create_Sparql_query(queryInformation query_struct) throws JWNLException, IOException, SQLException{
+ public queryInformation create_Sparql_query(queryInformation queryObject) throws JWNLException, IOException, SQLException{
//create_Sparql_query_new(string);
ArrayList<ArrayList<String>> lstquery = new ArrayList<ArrayList<String>>();
long startParsingTime = System.currentTimeMillis();
- lstquery=getQuery(query_struct.getQuery());
+ //lstquery=getQuery(queryObject.getQuery(),queryObject);
+ queryObject=getQuery(queryObject);
+ lstquery=queryObject.getQueryInformation();
+ queryObject.setQueryInformation(lstquery);
+ /*BufferedReader in1 = new BufferedReader(new InputStreamReader(System.in));
+ String line;
+
+ line = in1.readLine();*/
long endParsingTime = System.currentTimeMillis();
long startIterationTime = System.currentTimeMillis();
System.out.println("The Questionparsing took "+ (endParsingTime-startParsingTime)+ " ms");
@@ -146,7 +162,7 @@
Set<String> final_query_hash = new HashSet<String>();
if(lstquery.isEmpty()){
- saveNotParsedQuestions(query_struct.getQuery());
+ saveNotParsedQuestions(queryObject.getQuery());
}
for(ArrayList<String> querylist : lstquery){
@@ -188,7 +204,7 @@
String out=null;
if (query.equals("") || query.equals(" ")||query.length()==0) query="Could not parse";
- out=tmp + "\n" + query_struct.getQuery() + ":\n"+query+"\n";
+ out=tmp + "\n" + queryObject.getQuery() + ":\n"+query+"\n";
BufferedWriter outfile = new BufferedWriter(
new OutputStreamWriter(
@@ -243,19 +259,23 @@
ArrayList<String> final_answer_tmp = new ArrayList<String>();
ArrayList<String> final_query_tmp=new ArrayList<String>();
- if(querylist.size()==4){
+ if(querylist.size()==4&&!query.contains("rdf:type")){
- final_query_tmp=simpleCase(querylist, query, "LEVENSTHEIN");
+ final_query_tmp=simpleCase(querylist, query, "LEVENSTHEIN",queryObject);
for(String i: final_query_tmp){
final_query_hash.add(i);
}
}
+ //e.g. Select ßy Where (?y rdf:type <http://..../ontology/School>
+ if(querylist.size()==4&&query.contains("rdf:type")){
+ final_query_hash.add(query);
+ }
if(querylist.size()>4&&query.contains("rdf:type")){
- final_query_tmp=isAIteration(querylist, query,"LEVENSTHEIN");
+ final_query_tmp=isAIteration(querylist, query,"LEVENSTHEIN",queryObject.getIsaResource());
for(String i: final_query_tmp){
final_query_hash.add(i);
@@ -285,17 +305,21 @@
ArrayList<String> final_query_tmp = new ArrayList<String>();
//isAIteration(querylist, query);
- if(querylist.size()==4){
+ if(querylist.size()==4&&!query.contains("rdf:type")){
- final_query_tmp=simpleCase(querylist, query, "WORDNET");
+ final_query_tmp=simpleCase(querylist, query, "WORDNET",queryObject);
for(String i: final_query_tmp){
final_query_hash.add(i);
}
}
+ //e.g. Select ßy Where (?y rdf:type <http://..../ontology/School>
+ if(querylist.size()==4&&query.contains("rdf:type")){
+ final_query_hash.add(query);
+ }
if(querylist.size()>4&&query.contains("rdf:type")){
- final_query_tmp=isAIteration(querylist, query,"WORDNET");
+ final_query_tmp=isAIteration(querylist, query,"WORDNET",queryObject.getIsaResource());
for(String i: final_query_tmp){
final_query_hash.add(i);
}
@@ -323,48 +347,60 @@
- Iterator it = final_query_hash.iterator();
+ Iterator<String> it = final_query_hash.iterator();
while (it.hasNext()) {
System.out.println(it.next());
- String answer_tmp;
+ ArrayList<String> answer= new ArrayList<String>();
try{
String anfrage=it.next().toString();
- answer_tmp=sendServerQuestionRequest(anfrage);
+ answer=sendServerQuestionRequestArray(anfrage);
+ // @en is also in the ML
+ /*
answer_tmp=answer_tmp.replace("\"@en", "");
- answer_tmp=answer_tmp.replace("\"", "");
+ answer_tmp=answer_tmp.replace("\"", "");*/
//filter answers!
- if(query_struct.isHint()){
- System.out.println("Using hint!");
- /*
- * Answertyps: resource, string, boolean, num, date
- */
- if(query_struct.getType().contains("boolean")){
- if(answer_tmp.contains("true")||answer_tmp.contains("false")) final_answer.add(answer_tmp);
-
- }
- else if (query_struct.getType().contains("resource")){
- final_answer.add(answer_tmp);
- }
- else if (query_struct.getType().contains("string")){
- if(!answer_tmp.contains("http")&&!answer_tmp.contains("EmtyAnswer")) {
- String[] tmparray = answer_tmp.split("\n");
- for(String z : tmparray)final_answer.add(z);
- }
-
- }
- else if (query_struct.getType().contains("num")){
- if(answer_tmp.matches("[0-9]*")) final_answer.add(answer_tmp);
-
- }
- else if (query_struct.getType().contains("date")){
- final_answer.add(answer_tmp);
- }
+ for(String answer_tmp : answer ){
+ if(answer_tmp!="EmtyAnswer"){
+ if(queryObject.isHint()){
+ //System.out.println("Using hint!");
+ /*
+ * Answertyps: resource, string, boolean, num, date
+ */
+ if(queryObject.getType().contains("boolean")){
+ if(answer_tmp.contains("true")||answer_tmp.contains("false")) final_answer.add(answer_tmp);
+
+ }
+ else if (queryObject.getType().contains("resource")){
+ try{
+ String[] tmparray = answer_tmp.split("\n");
+ for(String z : tmparray)final_answer.add(z);
+ }
+ catch(Exception e){
+ final_answer.add(answer_tmp);
+ }
+ }
+ else if (queryObject.getType().contains("string")||queryObject.getType().contains("uri")){
+ if(!answer_tmp.contains("EmtyAnswer")) {
+ String[] tmparray = answer_tmp.split("\n");
+ for(String z : tmparray)final_answer.add(z);
+ }
+
+ }
+ else if (queryObject.getType().contains("num")){
+ if(answer_tmp.matches("[0-9]*")) final_answer.add(answer_tmp);
+
+ }
+ else if (queryObject.getType().contains("date")){
+ final_answer.add(answer_tmp);
+ }
+ }
+ else{
+ //final_answer.add("Begin:\n"+anfrage +"\n"+answer_tmp+" \n End");
+ final_answer.add(answer_tmp);
+ }
+ }
}
- else{
- //final_answer.add("Begin:\n"+anfrage +"\n"+answer_tmp+" \n End");
- final_answer.add(answer_tmp);
- }
}
catch (Exception e){
@@ -372,13 +408,20 @@
}
+ long stopIterationTime = System.currentTimeMillis();
+ /*
+ * Set time
+ */
+
+ queryObject.setTimeGesamt(stopIterationTime-startParsingTime);
+ queryObject.setTimeParser(endParsingTime-startParsingTime);
+ queryObject.setTimeWithoutParser(stopIterationTime-startIterationTime);
+ queryObject.setResult(final_answer);
- query_struct.setResult(final_answer);
-
- return query_struct;
+ return queryObject;
}
- private ArrayList<String> newIteration(ArrayList<String> querylist, String query) throws SQLException,
+ private ArrayList<String> newIteration(ArrayList<String> querylist, String query, queryInformation queryObject) throws SQLException,
JWNLException {
//only for special case, that the first condition has a resource
ArrayList<String> final_answer=new ArrayList<String>();
@@ -439,7 +482,7 @@
querylist_new.add("PROPERTY"+firstProperty);
querylist_new.add(sideOfProperty+firstResource);
if(answer_tmp.isEmpty()){
- answer_tmp=simpleCase(querylist_new,firstquery,"WORDNET");
+ answer_tmp=simpleCase(querylist_new,firstquery,"WORDNET",queryObject);
}
//if answer_tmp is still empty return null and exit function
if(answer_tmp.isEmpty()){final_answer.add("new Iteration didnt work");
@@ -481,7 +524,7 @@
for(ArrayList as: secondquerylist){
ArrayList<String> answer_tmp_two=new ArrayList<String>();
//answer_tmp_two=sendServerQuestionRequestArray(s);
- answer_tmp=simpleCase(as,as.get(0).toString(),"WORDNET");
+ answer_tmp=simpleCase(as,as.get(0).toString(),"WORDNET",queryObject);
for(String t :answer_tmp_two){
final_answer.add(t);
System.out.println("Answer from advanced Iteration: "+ t);
@@ -495,7 +538,7 @@
- private ArrayList<String> isAIteration(ArrayList<String> querylist, String query, String fall) throws SQLException,
+ private ArrayList<String> isAIteration(ArrayList<String> querylist, String query, String fall, String uri_isA_Resource) throws SQLException,
JWNLException {
ArrayList<String> new_queries= new ArrayList<String>();
//TODO: in get Query change, that there will be a second query, but only with the part of the condition upsidedown, which doesnt contains an isA
@@ -506,29 +549,17 @@
*/
- //take query and use regex, to take only the part beween the {}
- Pattern p = Pattern.compile (".*\\{(.*\\<http.*)\\}.*");
- Matcher m = p.matcher (query);
ArrayList<String> list_of_x=new ArrayList<String>();
String query_for_x=null;
- while(m.find()){
- String tmp=m.group(1);
-
- Pattern p2=Pattern.compile (".*(http://dbpedia.org/ontology/[A-Z].*)\\>\\W.*");
- Matcher m2 = p2.matcher (tmp);
- //now we know, that we are in the part with the rdf type thing
- while(m2.find()){
- query_for_x="PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> SELECT ?x WHERE { ?x rdf:type <"+m2.group(1)+">}";
- //System.out.println("Done: "+ query_for_x);
- }
-
- }
+
+
+
+ query_for_x="PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> SELECT ?x WHERE { ?x rdf:type <"+uri_isA_Resource+">}";
//now send query_for_x to the server, to get all x
System.out.println("IsA x-query: "+query_for_x);
if(query_for_x!=null)list_of_x=sendServerQuestionRequestArray(query_for_x);
-
/*
* Zweiter Schritt:
* alle Propertys z.B. der ersten 5 xe holen und in eine Liste packen
@@ -543,6 +574,7 @@
/*
* First use left and also right Propertys
*/
+
tmpcounter++;
if(tmpcounter <=number_of_x_used){
HashMap<String,String> propertiesleft = new HashMap<String, String>();
@@ -550,8 +582,8 @@
GetRessourcePropertys property = new GetRessourcePropertys();
try {
- propertiesleft=property.getPropertys(s,"LEFT");
- propertiesright=property.getPropertys(s,"RIGHT");
+ propertiesleft=property.getPropertys(s,"LEFT",timeToTimeoutOnServer);
+ propertiesright=property.getPropertys(s,"RIGHT",timeToTimeoutOnServer);
}
catch (Exception e){
@@ -565,7 +597,14 @@
}
}
- //System.out.println(list_of_properties);
+ /* System.out.println("List of Properties: ");
+ for (Entry<String, String> entry : list_of_properties.entrySet()) {
+ String key = entry.getKey();
+ key=key.replace("\"","");
+ key=key.replace("@en","");
+ String value = entry.getValue();
+ System.out.println("Key: "+ key + " Value: "+value);
+ }*/
/*
* get Property used in the original query
@@ -577,47 +616,44 @@
//http://dbpedia.org/ontology/officialLanguage
//look for property
- Pattern p3=Pattern.compile (".*\\<(http://dbpedia.org/property/.*)\\>\\W\\?.*");
+ Pattern p3=Pattern.compile (".*\\<(http://dbpedia.org/property/.*)\\>\\W\\W*\\?.*");
Matcher m3 = p3.matcher(query);
- while(m3.find()) System.out.println("Property in IsA: "+m3.group(1));
+ String property_to_compare_with_uri="";
+ while(m3.find()) {
+ property_to_compare_with_uri=m3.group(1);
+ System.out.println("Property in IsA: "+m3.group(1));
+ }
- //look for ontology, which is NO class
- //Pattern p4=Pattern.compile (".*\\<(http://dbpedia.org/ontology/^[A-Z].*)\\>\\W.*");
- Pattern p4=Pattern.compile (".*\\<(http://dbpedia.org/ontology/[a-z].*)\\>\\W\\?.*");
- Matcher m4 = p4.matcher(query);
- String uri_property=null;
- while(m4.find()) {
- uri_property=m4.group(1);
- System.out.println("Uri_Property: "+ uri_property);
+ //if there is no property but an ontology-property
+ if(property_to_compare_with_uri==""){
+ Pattern p4=Pattern.compile (".*\\<(http://dbpedia.org/ontology/[a-z].*)\\>\\W\\W*\\?.*");
+ Matcher m4 = p4.matcher(query);
+ while(m4.find()) {
+ property_to_compare_with_uri=m4.group(1);
+ System.out.println("Property in IsA: "+m4.group(1));
+ }
}
- /*
- * Nice, now i get http://dbpedia.org/ontology/officialLanguage
- */
- if(uri_property!=null){
- String property=uri_property.replace("http://dbpedia.org/ontology/", "").replace("http://dbpedia.org/property/", "");
- String property_to_compare_with="";
-
+ String property_to_compare_with=property_to_compare_with_uri.replace("http://dbpedia.org/property/","").replace("http://dbpedia.org/ontology/","");
+
+ /* BufferedReader in = new BufferedReader(new InputStreamReader(System.in));
+ String line;
- for(String s : querylist){
- if(s.contains("PROPERTY")){
- property_to_compare_with=s.replace("PROPERTY","");
- }
-
- }
-
-
- /*
- * Dritter Schritt: original Query nehmen und über die Liste mit den Propertys laufen und normal mit wordnet/levensthein vergleichen
- */
-
- //I think, i dont need here the last part of the uri but the original word from the query!
- //new_queries=doWordnet(query,property,uri_property,list_of_properties);
-
- //if you want to use wordnet:
- if(fall.contains("WORDNET")) new_queries=doWordnet(query,property_to_compare_with,uri_property,list_of_properties);
- if(fall.contains("LEVENSTHEIN")) new_queries=doLevensthein(query,property_to_compare_with,uri_property,list_of_properties);
- }
+ System.out.println("############################");
+ System.out.println("query: "+query);
+ System.out.println("property_to_compare_with: "+property_to_compare_with);
+ System.out.println("property_to_compare_with_uri: "+property_to_compare_with_uri);
+ System.out.println("############################");
+ try {
+ line = in.readLine();
+ } catch (IOException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }*/
+ if(fall.contains("WORDNET")) new_queries=doWordnet(query,property_to_compare_with,property_to_compare_with_uri,list_of_properties);
+ if(fall.contains("LEVENSTHEIN")) new_queries=doLevensthein(query,property_to_compare_with_uri,property_to_compare_with_uri,list_of_properties);
+
+
return new_queries;
@@ -625,7 +661,7 @@
- private ArrayList<String> simpleCase(ArrayList<String> querylist, String query, String fall) throws SQLException,
+ private ArrayList<String> simpleCase(ArrayList<String> querylist, String query, String fall, queryInformation queryObject) throws SQLException,
JWNLException {
System.out.println("In Simpe levensthein case!!");
@@ -655,6 +691,7 @@
}
}
+ System.out.println("ARRAY LIST: "+querylist);
System.out.println("Property to compare:: "+ property_to_compare_with);
System.out.println("Resource: "+ resource);
@@ -664,11 +701,12 @@
Boolean goOnAfterProperty = true;
- System.out.println("URI from Resource "+ resource +": "+getUriFromIndex(resource.toLowerCase(),0));
+ //System.out.println("URI from Resource "+ resource +": "+getUriFromIndex(resource.toLowerCase(),0));
+ System.out.println("URI from Resource "+ resource +": "+queryObject.getHashValue(resource.toLowerCase()));
//gets Propertys left or right from the resource!
try {
- properties=property.getPropertys(getUriFromIndex(resource.toLowerCase(),0),sideOfProperty);
+ properties=property.getPropertys(queryObject.getHashValue(resource.toLowerCase()),sideOfProperty,timeToTimeoutOnServer);
if (properties==null){
System.out.println("Begin:\n"+query +"\nError in getting Properties \n End");
@@ -684,8 +722,8 @@
}
if(goOnAfterProperty==true){
- if(fall.contains("WORDNET")) new_queries=doWordnet(query, property_to_compare_with,getUriFromIndex(property_to_compare_with.toLowerCase(),1),properties);
- if(fall.contains("LEVENSTHEIN")) new_queries=doLevensthein(query, property_to_compare_with,getUriFromIndex(property_to_compare_with.toLowerCase(),1),properties);
+ if(fall.contains("WORDNET")) new_queries=doWordnet(query, property_to_compare_with,queryObject.getHashValue(property_to_compare_with.toLowerCase()),properties);
+ if(fall.contains("LEVENSTHEIN")) new_queries=doLevensthein(query, property_to_compare_with,queryObject.getHashValue(property_to_compare_with.toLowerCase()),properties);
//new_queries=doLevensthein(query, property_to_compare_with,getUriFromIndex(property_to_compare_with.toLowerCase(),1),properties);
//add original query
@@ -797,8 +835,8 @@
//Get Properties for Resource in condition One and Two from Server
try {
- propertiesOne=property.getPropertys(getUriFromIndex(resourceOne.toLowerCase(),0),sideOfPropertyOne);
- propertiesTwo=property.getPropertys(getUriFromIndex(resourceTwo.toLowerCase(),0),sideOfPropertyTwo);
+ propertiesOne=property.getPropertys(getUriFromIndex(resourceOne.toLowerCase(),0),sideOfPropertyOne,timeToTimeoutOnServer);
+ propertiesTwo=property.getPropertys(getUriFromIndex(resourceTwo.toLowerCase(),0),sideOfPropertyTwo,timeToTimeoutOnServer);
if (propertiesOne==null){
System.out.println("Begin:\n"+query +"\nError in getting Properties \n End");
@@ -1128,7 +1166,8 @@
-
+
+ //TODO: Write function new!!!!!
/**
* Iterates thrue the conditions and returns an array, where one can see, if the Property is left or right from the resource
* @param query
@@ -1140,31 +1179,83 @@
Matcher m = p.matcher (query);
ArrayList<String> lstquery = new ArrayList<String>();
while (m.find()) {
- String tmp= m.group(1);
+ System.out.println("In While Loop!");
+ String workingQuery= m.group(1);
//if there is an .../ontology/C, dann ist das eine Klasse und das ganze soll dann nicht ersetzt reingepackt werden, sondern so bleiben, wie es ist.
- System.out.println("Before new pattern and checking "+tmp);
- Pattern p1=Pattern.compile (".*(http://dbpedia.org/ontology/[A-Z].*)\\>\\W.*");
- Matcher m1 = p1.matcher (tmp);
+ System.out.println("Before new pattern and checking "+workingQuery);
+
+ //take the Filter out, so you only have the conditions left
+ Pattern p2=Pattern.compile (".*(\\.FILTER\\(.*\\)).*");
+ Matcher m2 = p2.matcher (workingQuery);
+ while(m2.find()){
+ System.out.println("FIlter: "+m2.group(1));
+ workingQuery=workingQuery.replace(m2.group(1), "");
+ System.out.println("Without Filter: "+workingQuery);
+ }
+
String resourceTemp="";
- while(m1.find()){
- resourceTemp="RESOURCE"+m1.group(1);
- tmp=tmp.replace("<"+m1.group(1)+">", "SKIP");
- System.out.println("New temp: "+tmp);
+ if(workingQuery.contains("ontologie")){
+ Pattern p1=Pattern.compile (".*\\<(http://dbpedia.org/ontology/[A-Z].*)\\>\\W\\W*.*");
+ Matcher m1 = p1.matcher (workingQuery);
+
+
+ /*
+ * Das darf nicht sein:
+ * Replacment: <http://dbpedia.org/ontology/Caves> rdf:type ?x .?y <http://dbpedia.org/property/entrances>
+ */
+ while(m1.find()){
+ resourceTemp="RESOURCE"+m1.group(1);
+ String replacment="<"+m1.group(1)+">";
+ //TODO: Make it nice!!!
+ //if he doesnt find the ontolokg party, kind of skip
+ if(!replacment.contains("property")&&!replacment.contains("resource")){
+ System.out.println("Replacment: "+replacment);
+ workingQuery=workingQuery.replace(replacment, "SKIP");
+ System.out.println("New temp: "+workingQuery);
+ }
+
+ }
+
}
- /* if(m1.find()){
- System.out.println("YEAHHHHHHHHHHHHHHHHHHHH "+m1.group(1));
+
+ /*
+ * dbpedia.org/class/yago/
+ */
+ if(workingQuery.contains("yago")){
+ Pattern p3=Pattern.compile (".*\\<(http://dbpedia.org/class/yago//[A-Z].*)\\>\\W.*");
+ Matcher m3 = p3.matcher (workingQuery);
+
+
+ /*
+ * Das darf nicht sein:
+ * Replacment: <http://dbpedia.org/ontology/Caves> rdf:type ?x .?y <http://dbpedia.org/property/entrances>
+ */
+ while(m3.find()){
+ resourceTemp="RESOURCE"+m3.group(1);
+ String replacment="<"+m3.group(1)+">";
+ //TODO: Make it nice!!!
+ //if he doesnt find the ontolokg party, kind of skip
+ if(!replacment.contains("property")&&!replacment.contains("resource")){
+ System.out.println("Replacment: "+replacment);
+ workingQuery=workingQuery.replace(replacment, "SKIP");
+ System.out.println("New temp: "+workingQuery);
+ }
+
+ }
+
}
- else{*/
-
+
+ System.out.println("TMP before replace :"+workingQuery);
+ workingQuery=workingQuery.replace("http://dbpedia.org/resource/","").replace("http://dbpedia.org/property/", "").replace("http://dbpedia.org/ontology/", "");
- tmp=tmp.replace("http://dbpedia.org/resource/","").replace("http://dbpedia.org/property/", "").replace("http://dbpedia.org/ontology/", "");
-
+ System.out.println("TMP After replace :"+workingQuery);
//split on . for sign for end of conditions
- String[] firstArray=tmp.split("\\.");
+ String[] firstArray=workingQuery.split("\\.");
for(String i : firstArray){
String[] secondArray=i.split(" ");
+
//always in three counts
int counter=0;
for(String j : secondArray){
@@ -1189,7 +1280,7 @@
else if(j.contains("SKIP"))lstquery.add(resourceTemp);
else if(j.contains("rdf:type"))lstquery.add("IsA");
}
- if(counter==0)counter=0;
+ if(counter==3)counter=0;
}
@@ -1202,6 +1293,7 @@
}
+
//TODO: Plural Singual abfragen über die Wordnetdatei...
/**
@@ -1210,8 +1302,9 @@
* @return ArrayList of Sparql queries.
* @throws SQLException
*/
- private ArrayList<ArrayList<String>> getQuery(String question) throws SQLException {
+ private queryInformation getQuery(queryInformation queryObject) throws SQLException {
ArrayList<ArrayList<String>> lstquery = new ArrayList<ArrayList<String>>();
+ String question=queryObject.getQuery();
Set<BasicQueryTemplate> querytemps = btemplator.buildBasicQueries(question);
for (BasicQueryTemplate temp : querytemps) {
@@ -1219,6 +1312,8 @@
ArrayList<String> lstquerupsidedown = new ArrayList<String>();
String query;
String selTerms ="";
+ String yago_query="";
+ String yago_query_upside_down="";
boolean addQuery=true;
//sometimes there isnt an Selectterm, so dont use this query
@@ -1248,6 +1343,14 @@
filters="";
addQuery=false;
}
+ String having="";
+ try{
+ for(SPARQL_Having tmp : temp.getHavings()) having=having+tmp+" ";
+ }
+ catch(Exception e){
+ having="";
+ addQuery=false;
+ }
//if there is no order by, replace with ""
String orderdBy="ORDER BY ";
@@ -1276,7 +1379,7 @@
}
if(addQuery==true){
- query="PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> "+temp.getQt().toString()+" "+selTerms+" WHERE {"+ conditions.replace("--","") + filters+"}"+orderdBy +" "+limit;
+ query="PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> "+temp.getQt().toString()+" "+selTerms+" WHERE {"+ conditions.replace("--","") + filters+"}"+orderdBy+" "+having +" "+limit;
String conditions_new = "";
for(Path condition: temp.getConditions()){
@@ -1300,7 +1403,7 @@
System.out.println("Conditions_new: " + conditions_new);
- String query_upside_down = "PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> "+temp.getQt().toString()+" "+selTerms+" WHERE {"+ conditions_new.replace("--","") +filters+ "}" + orderdBy +" "+limit;
+ String query_upside_down = "PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> "+temp.getQt().toString()+" "+selTerms+" WHERE {"+ conditions_new.replace("--","") +filters+"}" + orderdBy +" "+having+" "+limit;
String[] slots= null;
@@ -1313,7 +1416,7 @@
int slotcounter=1;
/*
- * the one after the isA, has to be an ontology Class!!!
+ * the one after the isA, has to be an ontology Class or an Yago Class!!!
* so first find out, which one is behind the isA
* best with regex or so.... take the condition, regex the thing between isA and . for End of Condition
* kind of regex=[*a IsA (\\?*a.)*a]
@@ -1381,6 +1484,10 @@
System.out.println("Property "+property);*/
boolean skip=false;
+
+ /*
+ * Der geht hier garnicht in die Schleife.
+ */
if(resource.contains(isaComponent.replace("?", "")) || property.contains(isaComponent.replace("?", ""))){
skip=true;
@@ -1402,8 +1509,40 @@
catch(Exception e){
}
- String hm_result=myindex.getontologyClassURI(array[1]);
- if(hm_result==null)hm_result="http://dbpedia.org/ontology/"+Character.toUpperCase(array[1].charAt(0)) + array[1].substring(1, array[1].length());
+
+ /*
+ * Here lookup in ontology and in Yago, if ontology doesnt exist, use Yago, if not, use Ontology
+ * if both exist, add yago_query and yago_query upsideDown, but also change the isACase function for Yago
+ */
+ //first look in Hasmap, if there is already an entry, if not, add founded result
+ String hm_result="";
+ hm_result=queryObject.getHashValue(array[1]);
+ if(hm_result.contains("NONE")){
+ //hm_result=myindex.getontologyClassURI(array[1]);
+ hm_result=getUriFromIndex(array[1].toLowerCase(),2);
+ System.out.println("direkt gefunden URI: "+hm_result);
+ if(hm_result.contains("NONE")){
+ hm_result=getUriFromIndex(array[1].toLowerCase(),3);
+ if(hm_result.contains("NONE"))hm_result="http://dbpedia.org/ontology/"+Character.toUpperCase(array[1].charAt(0)) + array[1].substring(1, array[1].length());
+ }
+ queryObject.setHashValue(array[1], hm_result);
+ }
+
+ //check for Yago!
+ String hm_result_new=getUriFromIndex(array[1].toLowerCase(),3);
+ /*if(!hm_result_new.contains("NONE")){
+ //set identefire
+ yago_query="YAGO"+query.replace(replace, "<"+hm_result_new+">");
+ yago_query_upside_down="YAGO"+query_upside_down.replace(replace, "<"+hm_result_new+">");
+ }
+ else{*/
+ yago_query="NONE";
+ yago_query_upside_down="NONE";
+ //}
+ //add the uri for the Resource in isA case, so I dont have to search for it again
+ queryObject.setIsaResource(hm_result);
+
+
System.out.println(array[1]+" for getOntologyClass "+hm_result);
//System.out.print("URI for_ThingGettingURIfor: "+hm_result);
try
@@ -1431,8 +1570,13 @@
if(array[0].length()<2)replace = "?"+array[0]+" ";
else replace="?"+array[0];
- String hm_result=getUriFromIndex(array[1],0);
- //System.out.print("URI for_ThingGettingURIfor: "+hm_result);
+ String hm_result="";
+ hm_result=queryObject.getHashValue(array[1]);
+ if(hm_result.contains("NONE")){
+ hm_result=getUriFromIndex(array[1],0);
+ queryObject.setHashValue(array[1], hm_result);
+ }
+
try
{
if(hm_result.contains("Category:")) hm_result=hm_result.replace("Category:","");
@@ -1446,6 +1590,10 @@
//System.out.println("Query: "+query);
query_upside_down=query_upside_down.replace(replace, "<"+hm_result+">");
//System.out.println("Query Up Side Down: "+query_upside_down);
+ /* if(!yago_query.contains("NONE")){
+ yago_query=yago_query.replace(replace, "<"+hm_result+">");
+ yago_query_upside_down=yago_query_upside_down.replace(replace, "<"+hm_result+">");
+ }*/
}
@@ -1455,12 +1603,21 @@
if(array[0].length()<2)replace = "?"+array[0]+" ";
else replace="?"+array[0];
- String hm_result=getUriFromIndex(array[1],1);
+ String hm_result="";
+ hm_result=queryObject.getHashValue(array[1]);
+ if(hm_result.contains("NONE")){
+ hm_result=getUriFromIndex(array[1],1);
+ queryObject.setHashValue(array[1], hm_result);
+ }
query=query.replace(replace, "<"+hm_result+">");
//System.out.println("Query: "+query);
query_upside_down=query_upside_down.replace(replace, "<"+hm_result+">");
//System.out.println("Query Up Side Down: "+query_upside_down);
+ /* if(!yago_query.contains("NONE")){
+ yago_query=yago_query.replace(replace, "<"+hm_result+">");
+ yago_query_upside_down=yago_query_upside_down.replace(replace, "<"+hm_result+">");
+ }*/
}
@@ -1470,6 +1627,12 @@
query=query.replace("><","> <").replace(">?", "> ?");
query=query.replace("/__", "/");
query_upside_down=query_upside_down.replace("/__", "/");
+ /*if(!yago_query.contains("NONE")){
+ yago_query_upside_down=yago_query_upside_down.replace("><","> <").replace(">?", "> ?");
+ yago_query=yago_query.replace("><","> <").replace(">?", "> ?");
+ yago_query=yago_query.replace("/__", "/");
+ yago_query_upside_down=yago_query_upside_down.replace("/__", "/");
+ }*/
lstquerupsidedown.add(query_upside_down);
lstquerynew.add(query);
System.out.println("Query: "+query);
@@ -1484,6 +1647,7 @@
ArrayList<String> lsttmp=createLeftAndRightPropertyArray(query);
//if its lower than three, we dont have any conditions and dont need to check it.
//also if the size%3 isnt 0, than something else is wrong and we dont need to test the query
+ System.out.println("lsttmp :"+lsttmp);
if(lsttmp.size()>=3&&lsttmp.size()%3==0){
for(String i : lsttmp) lstquerynew.add(i.replace("__",""));
lstquery.add(lstquerynew);
@@ -1515,7 +1679,8 @@
}
System.out.println("List of Query: "+lstquery);
- return lstquery;
+ queryObject.setQueryInformation(lstquery);
+ return queryObject;
}
@@ -1558,7 +1723,7 @@
/**
*
* @param string
- * @param fall 1 Property 0 no Property
+ * @param fall 1=Property, 0=Resource, 2=OntologyClass, 3=Yago
* @return
* @throws SQLException
*/
@@ -1574,25 +1739,114 @@
String result=null;
String tmp1=null;
String tmp2 = null;
- //just to be sure its only 0 or 1
- if(fall!=0 && fall!=1) fall=0;
+
if(fall==0){
- //first try: take always the ontology if existing and not the Resource
- tmp1=myindex.getResourceURI(string.toLowerCase());
- tmp2=myindex.getontologyClassURI(string.toLowerCase());
- /*System.out.println("URI from resource: "+tmp1);
- System.out.println("URI from ontologyClass: "+tmp2);*/
+ result=myindex.getResourceURI(string.toLowerCase());
+ if(result==null){
+ /*
+ * Second try lemmatised one
+ */
+ result=myindex.getResourceURI(lemmatiser.stem(string.toLowerCase()));
+ if(result==null){
+ /*
+ * Third try lemmatised with like
+ */
+ ArrayList<String> tmp=myindex.getResourceURILike(lemmatiser.stem(string.toLowerCase()));
+ double highestNLD=0;
+ String bestWord="";
+ try{
+ if(!tmp.isEmpty()){
+ for(String i : tmp){
+ double nld_tmp=Levenshtein.nld(string.toLowerCase(), i);
+ if(nld_tmp>highestNLD) bestWord=i;
+ }
+ result=bestWord;
+ }
+ else{
+ result="NONE";
+ }
+ }
+ catch(Exception e){
+ result="NONE";
+ }
+ }
+ }
+
+ }
+ if(fall==2){
+ System.out.println("Im Ontology Fall");
+ result=myindex.getontologyClassURI(string.toLowerCase());
+ if(result==null){
+ /*
+ * Second try lemmatised one
+ */
+ result=myindex.getontologyClassURI(lemmatiser.stem(string.toLowerCase()));
+ if(result==null){
+ /*
+ * Third try lemmatised with like
+ */
+ ArrayList<String> tmp=myindex.getontologyClassURILike(lemmatiser.stem(string.toLowerCase()));
+ double highestNLD=0;
+ String bestWord="";
+ try{
+ if(!tmp.isEmpty()){
+ for(String i : tmp){
+ double nld_tmp=Levenshtein.nld(string.toLowerCase(), i);
+ if(nld_tmp>highestNLD) bestWord=i;
+ }
+ result=bestWord;
+ }
+ else{
+ result="NONE";
+ }
+ }
+ catch(Exception e){
+ result="NONE";
+ }
+ }
+ }
+ System.out.println("URi in Ontology: "+result);
+
+ }
+ if(fall==3){
-
- if(tmp1!=null && tmp2!=null) result=tmp2;
- if(tmp1!=null && tmp2==null) result=tmp1;
- if(tmp1==null && tmp2!=null) result=tmp2;
-
- //result=myindex.getResourceURI(string.toLowerCase());
- if(result==null)result=myindex.getPropertyURI(string.toLowerCase());
+ System.out.println("Im Yago Fall");
+ result=myindex.getYagoURI(string.toLowerCase());
+ if(result==null){
+ /*
+ * Second try lemmatised one
+ */
+ result=myindex.getYagoURI(lemmatiser.stem(string.toLowerCase()));
+ if(result==null){
+ /*
+ * Third try lemmatised with like
+ */
+ ArrayList<String> tmp=myindex.getYagoURILike(lemmatiser.stem(string.toLowerCase()));
+ double highestNLD=0;
+ String bestWord="";
+ try{
+ if(!tmp.isEmpty()){
+ for(String i : tmp){
+ double nld_tmp=Levenshtein.nld(string.toLowerCase(), i);
+ if(nld_tmp>highestNLD) bestWord=i;
+ }
+ result=bestWord;
+ }
+ else{
+ result="NONE";
+ }
+ }
+ catch(Exception e){
+ result="NONE";
+ }
+ }
+ }
+ System.out.println("URi in Ontology: "+result);
+
}
+
if(fall==1){
tmp1=myindex.getPropertyURI(string.toLowerCase());
tmp2=myindex.getontologyURI(string.toLowerCase());
@@ -1600,7 +1854,10 @@
if(tmp1!=null && tmp2==null) result=tmp1;
if(tmp1==null && tmp2!=null) result=tmp2;
if(result==null){
+ //kann ich mir sparen
result=myindex.getResourceURI(string.toLowerCase());
+
+
if(result!=null) result=result.replace("resource", "property");
}
@@ -1653,25 +1910,11 @@
ArrayList<String> semantics = new ArrayList<String>();
semantics=semanticsOrig;
- /*//check out, if in the semantics are still terms, with _ or ,
- //if so, split on _ and , and add them to the semantic list
- for(String id :semanticsOrig){
- if(id.contains("_")){
- System.out.println("in _");
- String[] tmp=id.split("_");
- for(String i: tmp) if(!semantics.contains(i))semantics.add(i);
-
- //and also add a term without _
- if(!semantics.contains(id.replace("_"," ")))semantics.add(id.replace("_"," "));
- //remove old id
- //semantics.remove(id);
- }
- if(id.contains(",")){
- System.out.println("in ,");
- String[] tmp=id.split(",");
- for(String i: tmp) if(!semantics.contains(i))semantics.add(i);
- //semantics.remove(id);
- }
+ //also look at the stemmt part!
+ /*for(String s: semanticsOrig){
+ String bla=lemmatiser.stem(s);
+ semantics.add(bla);
+ semantics.add(s);
}*/
try{
@@ -1802,35 +2045,59 @@
* change to dbpedia http://dbpedia.org/sparql
*/
//String tmp="http://greententacle.techfak.uni-bielefeld.de:5171/sparql?default-graph-uri=&query="+createServerRequest(query)+"&format=text%2Fhtml&debug=on&timeout=";
- String tmp=Prefix+"?default-graph-uri=&query="+createServerRequest(query)+"&format=text%2Fhtml&debug=on&timeout="; System.out.println(tmp);
- URL url;
- InputStream is;
- InputStreamReader isr;
- BufferedReader r;
- String str="";
- String result="";
+ String tmp=Prefix+"?default-graph-uri=&query="+createServerRequest(query)+"&format=text%2Fhtml&debug=on&timeout=";
+ //System.out.println(tmp);
+ String result="";
+ HttpURLConnection connection = null;
+ OutputStreamWriter wr = null;
+ BufferedReader rd = null;
+ StringBuilder sb = null;
+ String line = null;
+
+ URL serverAddress = null;
+
+ try {
+ serverAddress = new URL(tmp);
+ //set up out communications stuff
+ connection = null;
+
+ //Set up the initial connection
+ connection = (HttpURLConnection)serverAddress.openConnection();
+ connection.setRequestMethod("GET");
+ connection.setDoOutput(true);
+ connection.setReadTimeout(timeToTimeoutOnServer);
+
+ connection.connect();
+ rd = new BufferedReader(new InputStreamReader(connection.getInputStream()));
+ sb = new StringBuilder();
+
+ while ((line = rd.readLine()) != null)
+ {
+ sb.append(line + '\n');
+ }
+
+ //System.out.println(sb.toString());
+ result=sb.toString();
+
+ } catch (MalformedURLException e) {
+ System.out.println("Must enter a valid URL");
+ } catch (IOException e) {
+ System.out.println("Can not connect or timeout");
+ }
+ finally
+ {
+ //close the connection, set all objects to null
+ connection.disconnect();
+ rd = null;
+ sb = null;
+ wr = null;
+ connection = null;
+ }
+
- try {
- url = new URL(tmp);
- is = url.openStream();
- isr = new InputStreamReader(is);
- r = new BufferedReader(isr);
- int counter=0;
- do {
- str = r.readLine();
- if (str != null){
- result=result.concat(str);
- counter=counter+1;}
- } while (str != null);
-
- } catch (MalformedURLException e) {
- System.out.println("Must enter a valid URL");
- } catch (IOException e) {
- System.out.println("Can not connect");
- }
+
-
return createAnswer(result);
}
@@ -1842,35 +2109,56 @@
//String tmp="http://greententacle.techfak.uni-bielefeld.de:5171/sparql?default-graph-uri=&query="+createServerRequest(query)+"&format=text%2Fhtml&debug=on&timeout=";
String tmp=Prefix+"?default-graph-uri=&query="+createServerRequest(query)+"&format=text%2Fhtml&debug=on&timeout=";
- System.out.println(tmp);
- URL url;
- InputStream is;
- InputStreamReader isr;
- BufferedReader r;
- String str="";
- String result="";
-
- try {
- url = new URL(tmp);
- is = url.openStream();
- isr = new InputStreamReader(is);
- r = new BufferedReader(isr);
- int counter=0;
- do {
- str = r.readLine();
- if (str != null){
- result=result.concat(str);
- counter=counter+1;}
- } while (str != null);
-
- } catch (MalformedURLException e) {
- System.out.println("Must enter a valid URL");
- } catch (IOException e) {
- System.out.println("Can not connect");
- }
+ //System.out.println(tmp);
+ String result="";
+ HttpURLConnection connection = null;
+ OutputStreamWriter wr = null;
+ BufferedReader rd = null;
+ StringBuilder sb = null;
+ String line = null;
+ URL serverAddress = null;
+ try {
+ serverAddress = new URL(tmp);
+ //set up out communications stuff
+ connection = null;
+
+ //Set up the initial connection
+ connection = (HttpURLConnection)serverAddress.openConnection();
+ connection.setRequestMethod("GET");
+ connection.setDoOutput(true);
+ connection.setReadTimeout(timeToTimeoutOnServer);
+
+ connection.connect();
+ rd = new BufferedReader(new InputStreamReader(connection.getInputStream()));
+ sb = new StringBuilder();
+
+ while ((line = rd.readLine()) != null)
+ {
+ sb.append(line + '\n');
+ }
+
+ //System.out.println(sb.toString());
+ result=sb.toString();
+
+ } catch (MalformedURLException e) {
+ System.out.println("Must enter a valid URL");
+ } catch (IOException e) {
+ System.out.println("Can not connect or timeout");
+ }
+ finally
+ {
+ //close the connection, set all objects to null
+ connection.disconnect();
+ rd = null;
+ sb = null;
+ wr = null;
+ connection = null;
+ }
+
+
return createAnswerArray(result);
}
Modified: trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/exploration/Sparql/mySQLDictionary.java
===================================================================
--- trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/exploration/Sparql/mySQLDictionary.java 2012-01-06 14:24:45 UTC (rev 3541)
+++ trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/exploration/Sparql/mySQLDictionary.java 2012-01-08 13:42:22 UTC (rev 3542)
@@ -11,9 +11,13 @@
import java.sql.ResultSet;
import java.sql.SQLException;
import java.sql.Statement;
+import java.util.ArrayList;
+import org.dllearner.algorithm.tbsl.nlp.StanfordLemmatizer;
+
public class mySQLDictionary {
private Connection conn;
+ StanfordLemmatizer lemma;
public mySQLDictionary() throws ClassNotFoundException, SQLException {
// TODO Auto-generated constructor stub
@@ -23,18 +27,33 @@
createIndexResource();
createWordnetHelp();
createIndexOntology();
- createIndexoOntologyClass();
+ createIndexOntologyClass();
+ createIndexofYago();
+ lemma = new StanfordLemmatizer();
//optional!!
//createIndexWikipedia();
}
+ /*
+ * Next, we want to select the persons living in a city that contains the pattern "tav" from the "Persons" table.
+
+We use the following SELECT statement:
+SELECT * FROM Persons
+WHERE City LIKE '%tav%'
+ */
+
public String getResourceURI(String string) throws SQLException{
+ /* while(rs.next())
+ {*/
Statement stat = conn.createStatement();
ResultSet rs;
try {
rs = stat.executeQuery("select uri from resource where name='"+string.toLowerCase()+"';");
+ /*while(rs.next()){
+ System.out.println("Next: "+rs.getString("uri"));
+ }*/
return rs.getString("uri");
} catch (Exception e) {
// TODO Auto-generated catch block
@@ -43,6 +62,66 @@
}
}
+
+ public ArrayList<String> getResourceURILike(String string) throws SQLException{
+ /* while(rs.next())
+ {*/
+ Statement stat = conn.createStatement();
+ ResultSet rs;
+ ArrayList<String> result= new ArrayList<String>();
+ try {
+ rs = stat.executeQuery("select uri from resource where name like'"+string.toLowerCase()+"%';");
+ while(rs.next()){
+ System.out.println("Next: "+rs.getString("uri"));
+ result.add(rs.getString("uri"));
+ }
+ return result;
+ } catch (Exception e) {
+ // TODO Auto-generated catch block
+ //e.printStackTrace();
+ return null;
+ }
+
+ }
+
+ public ArrayList<String> getYagoURILike(String string) throws SQLException{
+ /* while(rs.next())
+ {*/
+ Statement stat = conn.createStatement();
+ ResultSet rs;
+ ArrayList<String> result= new ArrayList<String>();
+ try {
+ rs = stat.executeQuery("select uri from yago where name like'"+string.toLowerCase()+"%';");
+ while(rs.next()){
+ System.out.println("Next: "+rs.getString("uri"));
+ result.add(rs.getString("uri"));
+ }
+ return result;
+ } catch (Exception e) {
+ // TODO Auto-generated catch block
+ //e.printStackTrace();
+ return null;
+ }
+
+ }
+
+
+ public String getYagoURI(String string) throws SQLException{
+ /* while(rs.next())
+ {*/
+ Statement stat = conn.createStatement();
+ ResultSet rs;
+ try {
+ rs = stat.executeQuery("select uri from yago where name='"+string.toLowerCase()+"';");
+ return rs.getString("uri");
+ } catch (Exception e) {
+ // TODO Auto-generated catch block
+ //e.printStackTrace();
+ return null;
+ }
+
+ }
+
public String getPropertyURI(String string) throws SQLException{
Statement stat = conn.createStatement();
@@ -88,9 +167,28 @@
}
+ public ArrayList<String> getontologyClassURILike(String string) throws SQLException{
+ Statement stat = conn.createStatement();
+ ResultSet rs;
+ ArrayList<String> result= new ArrayList<String>();
+ try {
+ rs = stat.executeQuery("select uri from ontologyClass where name like'"+string.toLowerCase()+"%';");
+ while(rs.next()){
+ System.out.println("Next: "+rs.getString("uri"));
+ result.add(rs.getString("uri"));
+ }
+ return result;
+ } catch (Exception e) {
+ // TODO Auto-generated catch block
+ //e.printStackTrace();
+ return null;
+ }
+
+ }
+
public String getWikipediaURI(String string) throws SQLException{
Statement stat = conn.createStatement();
ResultSet rs;
@@ -233,16 +331,12 @@
System.out.println("Done");
}
private void createIndexPropertys() throws ClassNotFoundException, SQLException{
- /*System.out.println("Start SQL test");
- Class.forName( "org.sqlite.JDBC" );
- conn = DriverManager.getConnection("jdbc:sqlite::memory:");*/
System.out.println("start indexing Properties");
Statement stat = conn.createStatement();
stat.executeUpdate("drop table if exists property;");
stat.executeUpdate("create table property (name, uri);");
PreparedStatement prep = conn.prepareStatement("insert into property values (?, ?);");
BufferedReader in=null;
- // conn.setAutoCommit(false);
int zaehler=0;
try {
in = new BufferedReader(
@@ -256,12 +350,11 @@
prep.setString(2, tmp_array[1]);
prep.addBatch();
zaehler=zaehler+1;
- //if(zaehler%10000==0) System.out.println(zaehler);
if(zaehler%1000000==0){
conn.setAutoCommit(false);
prep.executeBatch();
conn.setAutoCommit(false);
- System.out.println("done");
+ // System.out.println(zaehler+" done");
}
}
@@ -282,18 +375,17 @@
conn.setAutoCommit(false);
prep.executeBatch();
conn.setAutoCommit(true);
+ System.out.println("Number of Property: "+zaehler);
System.out.println("Done");
}
private void createIndexResource() throws ClassNotFoundException, SQLException{
- /*System.out.println("Start SQL test");*/
System.out.println("start indexing Resources");
Statement stat = conn.createStatement();
stat.executeUpdate("drop table if exists resource;");
stat.executeUpdate("create table resource (name, uri);");
PreparedStatement prep = conn.prepareStatement("insert into resource values (?, ?);");
BufferedReader in=null;
- // conn.setAutoCommit(false);
int zaehler=0;
try {
in = new BufferedReader(
@@ -307,12 +399,10 @@
prep.setString(2, tmp_array[1]);
prep.addBatch();
zaehler=zaehler+1;
- // if(zaehler%10000==0) System.out.println(zaehler);
if(zaehler%1000000==0){
conn.setAutoCommit(false);
prep.executeBatch();
conn.setAutoCommit(false);
- System.out.println("done"+zaehler);
}
}
@@ -333,6 +423,7 @@
conn.setAutoCommit(false);
prep.executeBatch();
conn.setAutoCommit(true);
+ System.out.println("Number of Resources: "+zaehler);
System.out.println("Done");
@@ -365,7 +456,7 @@
conn.setAutoCommit(false);
prep.executeBatch();
conn.setAutoCommit(false);
- System.out.println("done" + zaehler);
+ //System.out.println("done" + zaehler);
}
}
@@ -386,11 +477,12 @@
conn.setAutoCommit(false);
prep.executeBatch();
conn.setAutoCommit(true);
+ System.out.println("Number of Ontologys: "+zaehler);
System.out.println("Done");
}
-private void createIndexoOntologyClass() throws ClassNotFoundException, SQLException{
+private void createIndexOntologyClass() throws ClassNotFoundException, SQLException{
/*System.out.println("Start SQL test");*/
System.out.println("start indexing ontologyClass");
Statement stat = conn.createStatement();
@@ -417,7 +509,7 @@
conn.setAutoCommit(false);
prep.executeBatch();
conn.setAutoCommit(false);
- System.out.println("done" + zaehler);
+ //System.out.println("done" + zaehler);
}
}
@@ -438,9 +530,65 @@
conn.setAutoCommit(false);
prep.executeBatch();
conn.setAutoCommit(true);
+ System.out.println("Number of OntologyClass: "+zaehler);
System.out.println("Done");
}
+private void createIndexofYago() throws ClassNotFoundException, SQLException{
+ /*System.out.println("Start SQL test");*/
+ System.out.println("start indexing yago");
+ Statement stat = conn.createStatement();
+ stat.executeUpdate("dro...
[truncated message content] |
|
From: <lor...@us...> - 2012-01-06 14:24:55
|
Revision: 3541
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3541&view=rev
Author: lorenz_b
Date: 2012-01-06 14:24:45 +0000 (Fri, 06 Jan 2012)
Log Message:
-----------
Small improvement in test case.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/PCELOE.java
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/PCELOE.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/PCELOE.java 2012-01-06 12:08:06 UTC (rev 3540)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/PCELOE.java 2012-01-06 14:24:45 UTC (rev 3541)
@@ -39,7 +39,9 @@
import java.util.concurrent.ThreadPoolExecutor;
import java.util.concurrent.TimeUnit;
+import org.apache.log4j.ConsoleAppender;
import org.apache.log4j.FileAppender;
+import org.apache.log4j.Level;
import org.apache.log4j.Logger;
import org.apache.log4j.PatternLayout;
import org.apache.log4j.SimpleLayout;
@@ -114,7 +116,7 @@
private boolean useMinimizer = true;
// all nodes in the search tree (used for selecting most promising node)
- private TreeSet<OENode> nodes;
+ private SortedSet<OENode> nodes;
private OEHeuristicRuntime heuristic; // = new OEHeuristicRuntime();
// root of search tree
private OENode startNode;
@@ -503,18 +505,20 @@
// we expand the best node of those, which have not achieved 100% accuracy
// already and have a horizontal expansion equal to their length
// (rationale: further extension is likely to add irrelevant syntactical constructs)
- synchronized (nodes) {logger.info("in 1.lock of getNextNodeToExpand method");
- Iterator<OENode> it = nodes.descendingIterator();//logger.info(nodes.size());
- logger.info("search tree size: " + nodes.size());
- while(it.hasNext()) {
- OENode node = it.next();
- logger.info("Checking node " + node + "...");
- if(!currentlyProcessedNodes.contains(node) && (node.getAccuracy() < 1.0 || node.getHorizontalExpansion() < node.getDescription().getLength())) {
- currentlyProcessedNodes.add(node);
- return node;
+ synchronized (nodes) {
+ logger.debug("in 1.lock of getNextNodeToExpand method");
+ Iterator<OENode> it = nodes.iterator();//logger.info(nodes.size());
+ logger.debug("search tree size: " + nodes.size());
+ while(it.hasNext()) {
+ OENode node = it.next();
+ logger.debug("Checking node " + node + "...");
+ if(!currentlyProcessedNodes.contains(node) && (node.getAccuracy() < 1.0 || node.getHorizontalExpansion() < node.getDescription().getLength())) {
+ currentlyProcessedNodes.add(node);
+ logger.debug("...checked and return node.");
+ return node;
+ }
+ logger.debug("...checked.");
}
- logger.info("...checked.");
- }
}
@@ -538,7 +542,7 @@
TreeSet<Description> refinements = (TreeSet<Description>) operator.refine(node.getDescription(), horizExp+1);
node.incHorizontalExpansion();
node.setRefinementCount(refinements.size());
- synchronized (refinements) {
+ synchronized (nodes) {
nodes.add(node);
}
@@ -556,17 +560,17 @@
if(!nonRedundant) {
return false;
}
- logger.info("Check if description is allowed...");
+ logger.debug("Check if description is allowed...");
// check whether the description is allowed
if(!isDescriptionAllowed(description, parentNode)) {
return false;
}
- logger.info("...done");
+ logger.debug("...done");
// System.out.println("Test " + new Date());
// quality of description (return if too weak)
double accuracy = learningProblem.getAccuracyOrTooWeak(description, noise);
- logger.info("Accuracy: " + accuracy);
+ logger.debug("Accuracy: " + accuracy);
// issue a warning if accuracy is not between 0 and 1 or -1 (too weak)
if(accuracy > 1.0 || (accuracy < 0.0 && accuracy != -1)) {
logger.warn("Invalid accuracy value " + accuracy + " for description " + description + ". This could be caused by a bug in the heuristic measure and should be reported to the DL-Learner bug tracker.");
@@ -610,7 +614,7 @@
// we need to make sure that this does not get called more often than
// necessary since rewriting is expensive
boolean isCandidate = !bestEvaluatedDescriptions.isFull();
- logger.info("Is candidate:" + isCandidate);
+ logger.debug("Is candidate:" + isCandidate);
if(!isCandidate) {
EvaluatedDescription worst = bestEvaluatedDescriptions.getWorst();
double accThreshold = worst.getAccuracy();
@@ -645,7 +649,7 @@
}
}
- logger.info("Point 2");
+ logger.debug("Point 2");
// System.out.println("shorter description? " + shorterDescriptionExists + " nice: " + niceDescription);
filterFollowsFromKB = false;
@@ -660,7 +664,7 @@
// System.out.println(bestEvaluatedDescriptions);
}
}
- logger.info("Point 3");
+ logger.debug("Point 3");
// System.out.println(bestEvaluatedDescriptions.getSet().size());
}
@@ -775,7 +779,7 @@
(maxClassDescriptionTests != 0 && (expressionTests >= maxClassDescriptionTests)) ||
(maxExecutionTimeInSeconds != 0 && ((System.nanoTime() - nanoStartTime) >= (maxExecutionTimeInSeconds*1000000000l))) ||
(terminateOnNoiseReached && (100*getCurrentlyBestAccuracy()>=100-noisePercentage));
- logger.info("terminate: " + ret);
+ logger.debug("terminate: " + ret);
return ret;
}
@@ -783,7 +787,7 @@
private void reset() {
// set all values back to their default values (used for running
// the algorithm more than once)
- nodes = new TreeSet<OENode>(heuristic);
+ nodes = Collections.synchronizedSortedSet(new TreeSet<OENode>(heuristic));
descriptions = new TreeSet<Description>(new ConceptComparator());
bestEvaluatedDescriptions.getSet().clear();
expressionTests = 0;
@@ -847,7 +851,7 @@
// the best accuracy that a node can achieve
double scoreThreshold = heuristic.getNodeScore(node) + 1 - node.getAccuracy();
- for(OENode n : nodes.descendingSet()) {
+ for(OENode n : nodes) {
if(n != node) {
if(n.getHorizontalExpansion() == minHorizExp) {
// we can stop instantly when another node with min.
@@ -1013,8 +1017,11 @@
public static void main(String[] args) throws Exception{
+ Logger.getRootLogger().setLevel(Level.INFO);
+ Logger.getLogger(PCELOE.class).setLevel(Level.DEBUG);
Logger.getLogger(PCELOE.class).addAppender(new FileAppender(new PatternLayout( "[%t] %c: %m%n" ), "log/parallel_run.txt", false));
+
AbstractKnowledgeSource ks = new OWLFile("../examples/family/father_oe.owl");
ks.init();
@@ -1045,7 +1052,7 @@
@Override
public void run() {
- logger.info("Started thread...");
+ logger.debug("Started thread...");
OENode nextNode;
double highestAccuracy = 0.0;
@@ -1059,25 +1066,25 @@
}
// chose best node according to heuristics
- logger.info("Get next node to expand...");
+ logger.debug("Get next node to expand...");
nextNode = getNextNodeToExpand();
- logger.info("...done");
+ logger.debug("...done");
try {
Thread.sleep(10);
} catch (InterruptedException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
- logger.info("next Node: " + nextNode);
+ logger.debug("next Node: " + nextNode);
if(nextNode != null){
int horizExp = nextNode.getHorizontalExpansion();
// apply operator
Monitor mon = MonitorFactory.start("refineNode");
- logger.info("Refine node...");
+ logger.debug("Refine node...");
TreeSet<Description> refinements = refineNode(nextNode, operator);
mon.stop();
- logger.info("...done");
+ logger.debug("...done");
while(refinements.size() != 0) {
// pick element from set
@@ -1090,10 +1097,10 @@
// System.out.println("potentially adding " + refinement + " to search tree as child of " + nextNode + " " + new Date());
Monitor mon2 = MonitorFactory.start("addNode");
- logger.info("Add node...");
+ logger.debug("Add node...");
addNode(refinement, nextNode);
mon2.stop();
- logger.info("...done");
+ logger.debug("...done");
// adding nodes is potentially computationally expensive, so we have
// to check whether max time is exceeded
if(terminationCriteriaSatisfied()) {
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <jen...@us...> - 2012-01-06 11:38:27
|
Revision: 3539
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3539&view=rev
Author: jenslehmann
Date: 2012-01-06 11:38:20 +0000 (Fri, 06 Jan 2012)
Log Message:
-----------
adapted ELTL to new component system; fixed a bug in disjunctive ELTL
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/algorithms/el/ELLearningAlgorithm.java
trunk/components-core/src/main/java/org/dllearner/algorithms/el/ELLearningAlgorithmDisjunctive.java
trunk/components-core/src/main/java/org/dllearner/core/AnnComponentManager.java
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/el/ELLearningAlgorithm.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/el/ELLearningAlgorithm.java 2012-01-06 11:37:27 UTC (rev 3538)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/el/ELLearningAlgorithm.java 2012-01-06 11:38:20 UTC (rev 3539)
@@ -25,6 +25,7 @@
import java.util.TreeSet;
import org.apache.log4j.Logger;
+import org.dllearner.core.ComponentAnn;
import org.dllearner.core.ComponentInitException;
import org.dllearner.core.EvaluatedDescription;
import org.dllearner.core.AbstractCELA;
@@ -38,10 +39,11 @@
import org.dllearner.learningproblems.PosNegLP;
import org.dllearner.learningproblems.ScorePosNeg;
import org.dllearner.refinementoperators.ELDown2;
+import org.dllearner.utilities.Helper;
import org.dllearner.utilities.owl.EvaluatedDescriptionSet;
/**
- * A learning algorithm for EL, which will be based on a (hopefully)
+ * A learning algorithm for EL, which is based on an
* ideal refinement operator.
*
* TODO redundancy check
@@ -49,6 +51,7 @@
* @author Jens Lehmann
*
*/
+@ComponentAnn(name="ELTL", shortName="eltl", version=0.5, description="ELTL is an algorithm based on the refinement operator in http://jens-lehmann.org/files/2009/el_ilp.pdf.")
public class ELLearningAlgorithm extends AbstractCELA {
private static Logger logger = Logger.getLogger(ELLearningAlgorithm.class);
@@ -73,6 +76,10 @@
private ELHeuristic heuristic;
private TreeSet<SearchTreeNode> candidates;
+ public ELLearningAlgorithm() {
+
+ }
+
public ELLearningAlgorithm(PosNegLP problem, AbstractReasonerComponent reasoner) {
super(problem, reasoner);
// configurator = new ELLearningAlgorithmConfigurator(this);
@@ -144,7 +151,7 @@
}
// print solution(s)
- logger.info("solution : " + bestEvaluatedDescriptions.getBest());
+ logger.info("solution : " + bestEvaluatedDescriptions.getBest() + " [time: " + Helper.prettyPrintNanoSeconds(System.nanoTime()-treeStartTime) + "]");
isRunning = false;
}
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/el/ELLearningAlgorithmDisjunctive.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/el/ELLearningAlgorithmDisjunctive.java 2012-01-06 11:37:27 UTC (rev 3538)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/el/ELLearningAlgorithmDisjunctive.java 2012-01-06 11:38:20 UTC (rev 3539)
@@ -19,6 +19,7 @@
package org.dllearner.algorithms.el;
+import java.text.DecimalFormat;
import java.util.Collection;
import java.util.Iterator;
import java.util.LinkedList;
@@ -31,11 +32,10 @@
import org.dllearner.core.AbstractCELA;
import org.dllearner.core.AbstractLearningProblem;
import org.dllearner.core.AbstractReasonerComponent;
+import org.dllearner.core.ComponentAnn;
import org.dllearner.core.ComponentInitException;
import org.dllearner.core.EvaluatedDescription;
-import org.dllearner.core.options.CommonConfigOptions;
-import org.dllearner.core.options.ConfigOption;
-import org.dllearner.core.options.StringConfigOption;
+import org.dllearner.core.config.ConfigOption;
import org.dllearner.core.owl.Description;
import org.dllearner.core.owl.Individual;
import org.dllearner.core.owl.Thing;
@@ -80,6 +80,7 @@
* @author Jens Lehmann
*
*/
+@ComponentAnn(name="Disjunctive ELTL", shortName="deltl", version=0.5, description="Disjunctive ELTL is an algorithm based on the refinement operator in http://jens-lehmann.org/files/2009/el_ilp.pdf with support for disjunctions.")
public class ELLearningAlgorithmDisjunctive extends AbstractCELA {
private static Logger logger = Logger.getLogger(ELLearningAlgorithmDisjunctive.class);
@@ -100,8 +101,12 @@
// all trees (for fast redundancy check)
private TreeSet<ELDescriptionTree> trees;
- // tree search
+ @ConfigOption(name = "treeSearchTimeSeconds", defaultValue = "1.0", description="Specifies how long the algorithm should search for a partial solution (a tree).")
private double treeSearchTimeSeconds = 1.0;
+
+ @ConfigOption(name = "tryFullCoverage", defaultValue = "false", description="If yes, then the algorithm tries to cover all positive examples. Note that while this improves accuracy on the testing set, it may lead to overfitting.")
+ private boolean tryFullCoverage = false;
+
// private double noise = 0;
private List<ELDescriptionTree> currentSolution = new LinkedList<ELDescriptionTree>();
private EvaluatedDescription bestEvaluatedDescription;
@@ -117,8 +122,14 @@
// minimum score a tree must have to be part of the solution
private double minimumTreeScore = -1;
- private boolean instanceBasedDisjoints;
+ private boolean instanceBasedDisjoints;
+
+ private DecimalFormat df = new DecimalFormat("0.00");
+ public ELLearningAlgorithmDisjunctive() {
+
+ }
+
public ELLearningAlgorithmDisjunctive(PosNegLP problem, AbstractReasonerComponent reasoner) {
super(problem, reasoner);
}
@@ -134,13 +145,13 @@
}
- public static Collection<ConfigOption<?>> createConfigOptions() {
- Collection<ConfigOption<?>> options = new LinkedList<ConfigOption<?>>();
- options.add(CommonConfigOptions.getNoisePercentage());
- options.add(new StringConfigOption("startClass", "the named class which should be used to start the algorithm (GUI: needs a widget for selecting a class)"));
- options.add(CommonConfigOptions.getInstanceBasedDisjoints());
- return options;
- }
+// public static Collection<ConfigOption<?>> createConfigOptions() {
+// Collection<ConfigOption<?>> options = new LinkedList<ConfigOption<?>>();
+// options.add(CommonConfigOptions.getNoisePercentage());
+// options.add(new StringConfigOption("startClass", "the named class which should be used to start the algorithm (GUI: needs a widget for selecting a class)"));
+// options.add(CommonConfigOptions.getInstanceBasedDisjoints());
+// return options;
+// }
@Override
public void init() throws ComponentInitException {
@@ -210,12 +221,13 @@
// we found a tree (partial solution)
currentSolution.add(bestCurrentNode.getDescriptionTree());
Description bestDescription = bestCurrentNode.getDescriptionTree().transformToDescription();
+ Description bestCombinedDescription = bestDescription;
// form union of trees found so far with
if(treeCount==0) {
bestEvaluatedDescription = learningProblem.evaluate(bestDescription);
} else {
- Union union = new Union(bestEvaluatedDescription.getDescription(), bestDescription);
- bestEvaluatedDescription = learningProblem.evaluate(union);
+ bestCombinedDescription = new Union(bestEvaluatedDescription.getDescription(), bestDescription);
+ bestEvaluatedDescription = learningProblem.evaluate(bestCombinedDescription);
}
// remove already covered examples
@@ -224,6 +236,7 @@
while(it.hasNext()) {
Individual ind = it.next();
if(reasoner.hasType(bestDescription, ind)) {
+// System.out.println("covered pos: " + ind);
it.remove();
posCov++;
}
@@ -233,11 +246,13 @@
while(it.hasNext()) {
Individual ind = it.next();
if(reasoner.hasType(bestDescription, ind)) {
+// System.out.println("covered neg: " + ind);
it.remove();
negCov++;
}
}
- logger.info("tree found: " + bestDescription.toManchesterSyntaxString(baseURI, prefixes) + " (" + posCov + " pos covered, " + currentPosExamples.size() + " remaining, " + negCov + " neg covered, " + currentNegExamples.size() + " remaining, score: " + bestCurrentNode.getScore() + ")");
+ logger.info("tree found: " + bestDescription.toManchesterSyntaxString(baseURI, prefixes) + " (" + posCov + " pos covered, " + currentPosExamples.size() + " remaining, " + negCov + " neg covered, " + currentNegExamples.size() + " remaining, score: " + bestCurrentNode.getScore() + ")");
+ logger.info("combined accuracy: " + df .format(bestEvaluatedDescription.getAccuracy()));
} else {
logger.info("no tree found, which satisfies the minimum criteria - the best was: " + bestCurrentNode.getDescriptionTree().transformToDescription().toManchesterSyntaxString(baseURI, prefixes) + " with score " + bestCurrentNode.getScore());
}
@@ -372,6 +387,11 @@
// SearchTreeNode bestNode = candidates.last();
// return (bestNode.getCoveredNegatives() == 0);
+ // stop if there are no more positive examples to cover
+ if(currentPosExamples.size()==0) {
+ return true;
+ }
+
// we stop when the score of the last tree added is too low
// (indicating that the algorithm could not find anything appropriate
// in the timeframe set)
@@ -380,8 +400,12 @@
}
// stop when almost all positive examples have been covered
- int maxPosRemaining = (int) Math.ceil(startPosExamplesSize * 0.05d);
- return (currentPosExamples.size()<=maxPosRemaining);
+ if(tryFullCoverage) {
+ return false;
+ } else {
+ int maxPosRemaining = (int) Math.ceil(startPosExamplesSize * 0.05d);
+ return (currentPosExamples.size()<=maxPosRemaining);
+ }
}
private void reset() {
@@ -391,8 +415,9 @@
trees.clear();
currentSolution.clear();
bestEvaluatedDescription = learningProblem.evaluate(Thing.instance);
- currentPosExamples = ((PosNegLP)getLearningProblem()).getPositiveExamples();
- currentNegExamples = ((PosNegLP)getLearningProblem()).getNegativeExamples();
+ // we need to clone in order not to modify the learning problem
+ currentPosExamples = new TreeSet<Individual>(((PosNegLP)getLearningProblem()).getPositiveExamples());
+ currentNegExamples = new TreeSet<Individual>(((PosNegLP)getLearningProblem()).getNegativeExamples());
startPosExamplesSize = currentPosExamples.size();
// startNegExamplesSize = currentNegExamples.size();
}
@@ -438,6 +463,22 @@
public void setInstanceBasedDisjoints(boolean instanceBasedDisjoints) {
this.instanceBasedDisjoints = instanceBasedDisjoints;
+ }
+
+ public double getTreeSearchTimeSeconds() {
+ return treeSearchTimeSeconds;
+ }
+
+ public void setTreeSearchTimeSeconds(double treeSearchTimeSeconds) {
+ this.treeSearchTimeSeconds = treeSearchTimeSeconds;
+ }
+
+ public boolean isTryFullCoverage() {
+ return tryFullCoverage;
+ }
+
+ public void setTryFullCoverage(boolean tryFullCoverage) {
+ this.tryFullCoverage = tryFullCoverage;
}
}
Modified: trunk/components-core/src/main/java/org/dllearner/core/AnnComponentManager.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/AnnComponentManager.java 2012-01-06 11:37:27 UTC (rev 3538)
+++ trunk/components-core/src/main/java/org/dllearner/core/AnnComponentManager.java 2012-01-06 11:38:20 UTC (rev 3539)
@@ -51,6 +51,8 @@
// (CLI, GUI, Web Service) and scripts (HTML documentation generator)
private static List<String> componentClassNames = new ArrayList<String> ( Arrays.asList(new String[]{
"org.dllearner.algorithms.celoe.CELOE",
+ "org.dllearner.algorithms.el.ELLearningAlgorithm",
+ "org.dllearner.algorithms.el.ELLearningAlgorithmDisjunctive",
"org.dllearner.algorithms.fuzzydll.FuzzyCELOE",
"org.dllearner.algorithms.BruteForceLearner",
"org.dllearner.algorithms.RandomGuesser",
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <jen...@us...> - 2012-01-06 11:37:34
|
Revision: 3538
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3538&view=rev
Author: jenslehmann
Date: 2012-01-06 11:37:27 +0000 (Fri, 06 Jan 2012)
Log Message:
-----------
included ELTL (disjunctive or normal) configurations for all family benchmark examples
Modified Paths:
--------------
trunk/test/family-benchmark/Aunt.conf
trunk/test/family-benchmark/Brother.conf
trunk/test/family-benchmark/Cousin.conf
trunk/test/family-benchmark/Daughter.conf
trunk/test/family-benchmark/Father.conf
trunk/test/family-benchmark/Granddaughter.conf
trunk/test/family-benchmark/Grandfather.conf
trunk/test/family-benchmark/Grandgranddaughter.conf
trunk/test/family-benchmark/Grandgrandfather.conf
trunk/test/family-benchmark/Grandgrandmother.conf
trunk/test/family-benchmark/Grandgrandson.conf
trunk/test/family-benchmark/Grandmother.conf
trunk/test/family-benchmark/Grandson.conf
trunk/test/family-benchmark/Mother.conf
trunk/test/family-benchmark/PersonWithASibling.conf
trunk/test/family-benchmark/Sister.conf
trunk/test/family-benchmark/Son.conf
trunk/test/family-benchmark/Uncle.conf
Removed Paths:
-------------
trunk/test/family-benchmark/Female.conf
trunk/test/family-benchmark/Male.conf
Modified: trunk/test/family-benchmark/Aunt.conf
===================================================================
--- trunk/test/family-benchmark/Aunt.conf 2012-01-06 10:56:39 UTC (rev 3537)
+++ trunk/test/family-benchmark/Aunt.conf 2012-01-06 11:37:27 UTC (rev 3538)
@@ -25,6 +25,9 @@
// OCEL configuration
alg.type = "ocel"
+// Disjunctive ELTL
+// alg.type = "deltl"
+
// learning problem
lp.type = "posNegStandard"
lp.positiveExamples = {
Modified: trunk/test/family-benchmark/Brother.conf
===================================================================
--- trunk/test/family-benchmark/Brother.conf 2012-01-06 10:56:39 UTC (rev 3537)
+++ trunk/test/family-benchmark/Brother.conf 2012-01-06 11:37:27 UTC (rev 3538)
@@ -10,10 +10,18 @@
reasoner.type = "fast instance checker"
reasoner.sources = { ks }
-// create learning algorithm to run
+// CELOE
+/*
alg.type = "celoe"
alg.terminateOnNoiseReached = true
+*/
+// OCEL
+alg.type = "ocel"
+
+// ELTL
+// alg.type = "eltl"
+
// learning problem
lp.type = "posNegStandard"
lp.positiveExamples = {
Modified: trunk/test/family-benchmark/Cousin.conf
===================================================================
--- trunk/test/family-benchmark/Cousin.conf 2012-01-06 10:56:39 UTC (rev 3537)
+++ trunk/test/family-benchmark/Cousin.conf 2012-01-06 11:37:27 UTC (rev 3538)
@@ -25,6 +25,10 @@
alg.type = "ocel"
+// Disjunctive ELTL
+// alg.type = "deltl"
+// alg.tryFullCoverage = true
+
// learning problem
lp.type = "posNegStandard"
lp.positiveExamples = {
Modified: trunk/test/family-benchmark/Daughter.conf
===================================================================
--- trunk/test/family-benchmark/Daughter.conf 2012-01-06 10:56:39 UTC (rev 3537)
+++ trunk/test/family-benchmark/Daughter.conf 2012-01-06 11:37:27 UTC (rev 3538)
@@ -18,6 +18,9 @@
// OCEL
alg.type = "ocel"
+// ELTL
+// alg.type = "eltl"
+
// learning problem
lp.type = "posNegStandard"
lp.positiveExamples = {
Modified: trunk/test/family-benchmark/Father.conf
===================================================================
--- trunk/test/family-benchmark/Father.conf 2012-01-06 10:56:39 UTC (rev 3537)
+++ trunk/test/family-benchmark/Father.conf 2012-01-06 11:37:27 UTC (rev 3538)
@@ -18,6 +18,9 @@
// OCEL
alg.type = "ocel"
+// ELTL
+// alg.type = "eltl"
+
// learning problem
lp.type = "posNegStandard"
lp.positiveExamples = {
Deleted: trunk/test/family-benchmark/Female.conf
===================================================================
--- trunk/test/family-benchmark/Female.conf 2012-01-06 10:56:39 UTC (rev 3537)
+++ trunk/test/family-benchmark/Female.conf 2012-01-06 11:37:27 UTC (rev 3538)
@@ -1,223 +0,0 @@
-// declare some prefixes to use as abbreviations
-prefixes = [ ("ex","http://www.benchmark.org/family#") ]
-
-// knowledge source definition
-ks.type = "OWL File"
-ks.fileName = "family-benchmark.owl"
-
-// reasoner
-reasoner.type = "fast instance checker"
-reasoner.sources = { ks }
-
-// CELOE
-/*
-alg.type = "celoe"
-alg.terminateOnNoiseReached = true
-*/
-
-// OCEL
-alg.type = "ocel"
-
-// learning problem
-lp.type = "posNegStandard"
-lp.positiveExamples = {
-"ex:F1F5"
-,"ex:F1F7"
-,"ex:F1F3"
-,"ex:F1F2"
-,"ex:F2F14"
-,"ex:F2F17"
-,"ex:F2F15"
-,"ex:F2F12"
-,"ex:F2F24"
-,"ex:F2F22"
-,"ex:F2F19"
-,"ex:F2F26"
-,"ex:F2F33"
-,"ex:F2F30"
-,"ex:F2F28"
-,"ex:F2F38"
-,"ex:F2F36"
-,"ex:F2F10"
-,"ex:F3F49"
-,"ex:F3F52"
-,"ex:F3F48"
-,"ex:F3F46"
-,"ex:F3F53"
-,"ex:F3F42"
-,"ex:F3F41"
-,"ex:F4F58"
-,"ex:F4F56"
-,"ex:F4F55"
-,"ex:F5F62"
-,"ex:F5F67"
-,"ex:F5F65"
-,"ex:F5F61"
-,"ex:F6F76"
-,"ex:F6F74"
-,"ex:F6F72"
-,"ex:F6F79"
-,"ex:F6F83"
-,"ex:F6F82"
-,"ex:F6F77"
-,"ex:F6F86"
-,"ex:F6F89"
-,"ex:F6F87"
-,"ex:F6F91"
-,"ex:F6F84"
-,"ex:F6F96"
-,"ex:F6F97"
-,"ex:F6F94"
-,"ex:F6F101"
-,"ex:F6F93"
-,"ex:F6F70"
-,"ex:F7F111"
-,"ex:F7F108"
-,"ex:F7F114"
-,"ex:F7F106"
-,"ex:F7F118"
-,"ex:F7F116"
-,"ex:F7F119"
-,"ex:F7F126"
-,"ex:F7F129"
-,"ex:F7F127"
-,"ex:F7F124"
-,"ex:F7F121"
-,"ex:F7F105"
-,"ex:F7F103"
-,"ex:F8F137"
-,"ex:F8F135"
-,"ex:F8F133"
-,"ex:F9F145"
-,"ex:F9F148"
-,"ex:F9F150"
-,"ex:F9F143"
-,"ex:F9F152"
-,"ex:F9F156"
-,"ex:F9F154"
-,"ex:F9F141"
-,"ex:F9F160"
-,"ex:F9F164"
-,"ex:F9F163"
-,"ex:F9F158"
-,"ex:F9F169"
-,"ex:F9F168"
-,"ex:F9F140"
-,"ex:F10F175"
-,"ex:F10F177"
-,"ex:F10F174"
-,"ex:F10F179"
-,"ex:F10F185"
-,"ex:F10F181"
-,"ex:F10F191"
-,"ex:F10F189"
-,"ex:F10F192"
-,"ex:F10F193"
-,"ex:F10F186"
-,"ex:F10F200"
-,"ex:F10F201"
-,"ex:F10F198"
-,"ex:F10F195"
-,"ex:F10F172"
-}
-
-lp.negativeExamples = {
-"ex:F10M183"
-,"ex:F3M43"
-,"ex:F10M199"
-,"ex:F2M16"
-,"ex:F7M110"
-,"ex:F4M54"
-,"ex:F7M113"
-,"ex:F7M107"
-,"ex:F9M146"
-,"ex:F2M20"
-,"ex:F8M136"
-,"ex:F6M75"
-,"ex:F10M190"
-,"ex:F9M157"
-,"ex:F2M25"
-,"ex:F1M8"
-,"ex:F6M92"
-,"ex:F3M47"
-,"ex:F2M18"
-,"ex:F5M64"
-,"ex:F9M155"
-,"ex:F8M138"
-,"ex:F7M130"
-,"ex:F9M170"
-,"ex:F10M188"
-,"ex:F3M45"
-,"ex:F6M78"
-,"ex:F7M102"
-,"ex:F7M120"
-,"ex:F10M180"
-,"ex:F5M66"
-,"ex:F3M50"
-,"ex:F8M134"
-,"ex:F5M60"
-,"ex:F10M182"
-,"ex:F7M122"
-,"ex:F6M69"
-,"ex:F2M21"
-,"ex:F1M1"
-,"ex:F6M81"
-,"ex:F9M162"
-,"ex:F6M71"
-,"ex:F1M4"
-,"ex:F10M176"
-,"ex:F2M23"
-,"ex:F10M171"
-,"ex:F9M159"
-,"ex:F4M59"
-,"ex:F9M153"
-,"ex:F9M167"
-,"ex:F7M123"
-,"ex:F2M32"
-,"ex:F7M112"
-,"ex:F7M125"
-,"ex:F2M13"
-,"ex:F9M147"
-,"ex:F7M115"
-,"ex:F7M128"
-,"ex:F2M37"
-,"ex:F10M194"
-,"ex:F3M44"
-,"ex:F2M29"
-,"ex:F5M68"
-,"ex:F6M90"
-,"ex:F1M6"
-,"ex:F2M9"
-,"ex:F3M51"
-,"ex:F10M196"
-,"ex:F10M178"
-,"ex:F9M139"
-,"ex:F7M104"
-,"ex:F9M149"
-,"ex:F2M34"
-,"ex:F10M173"
-,"ex:F8M132"
-,"ex:F7M131"
-,"ex:F2M11"
-,"ex:F6M85"
-,"ex:F6M88"
-,"ex:F10M184"
-,"ex:F2M31"
-,"ex:F2M27"
-,"ex:F5M63"
-,"ex:F10M187"
-,"ex:F9M161"
-,"ex:F10M202"
-,"ex:F7M109"
-,"ex:F4M57"
-,"ex:F2M39"
-,"ex:F10M197"
-,"ex:F9M165"
-,"ex:F7M117"
-,"ex:F6M80"
-,"ex:F9M142"
-,"ex:F6M73"
-,"ex:F6M100"
-,"ex:F6M95"
-,"ex:F6M98"
-}
\ No newline at end of file
Modified: trunk/test/family-benchmark/Granddaughter.conf
===================================================================
--- trunk/test/family-benchmark/Granddaughter.conf 2012-01-06 10:56:39 UTC (rev 3537)
+++ trunk/test/family-benchmark/Granddaughter.conf 2012-01-06 11:37:27 UTC (rev 3538)
@@ -18,6 +18,9 @@
// OCEL
alg.type = "ocel"
+// ELTL
+// alg.type = "eltl"
+
// learning problem
lp.type = "posNegStandard"
lp.positiveExamples = {
Modified: trunk/test/family-benchmark/Grandfather.conf
===================================================================
--- trunk/test/family-benchmark/Grandfather.conf 2012-01-06 10:56:39 UTC (rev 3537)
+++ trunk/test/family-benchmark/Grandfather.conf 2012-01-06 11:37:27 UTC (rev 3538)
@@ -18,6 +18,9 @@
// OCEL
alg.type = "ocel"
+// ELTL
+// alg.type = "eltl"
+
// learning problem
lp.type = "posNegStandard"
lp.positiveExamples = {
Modified: trunk/test/family-benchmark/Grandgranddaughter.conf
===================================================================
--- trunk/test/family-benchmark/Grandgranddaughter.conf 2012-01-06 10:56:39 UTC (rev 3537)
+++ trunk/test/family-benchmark/Grandgranddaughter.conf 2012-01-06 11:37:27 UTC (rev 3538)
@@ -18,6 +18,9 @@
// OCEL
alg.type = "ocel"
+// ELTL
+// alg.type = "eltl"
+
// learning problem
lp.type = "posNegStandard"
lp.positiveExamples = {
Modified: trunk/test/family-benchmark/Grandgrandfather.conf
===================================================================
--- trunk/test/family-benchmark/Grandgrandfather.conf 2012-01-06 10:56:39 UTC (rev 3537)
+++ trunk/test/family-benchmark/Grandgrandfather.conf 2012-01-06 11:37:27 UTC (rev 3538)
@@ -18,6 +18,9 @@
// OCEL
alg.type = "ocel"
+// ELTL
+// alg.type = "eltl"
+
// learning problem
lp.type = "posNegStandard"
lp.positiveExamples = {
Modified: trunk/test/family-benchmark/Grandgrandmother.conf
===================================================================
--- trunk/test/family-benchmark/Grandgrandmother.conf 2012-01-06 10:56:39 UTC (rev 3537)
+++ trunk/test/family-benchmark/Grandgrandmother.conf 2012-01-06 11:37:27 UTC (rev 3538)
@@ -18,6 +18,9 @@
// OCEL
alg.type = "ocel"
+// ELTL
+// alg.type = "eltl"
+
// learning problem
lp.type = "posNegStandard"
lp.positiveExamples = {
Modified: trunk/test/family-benchmark/Grandgrandson.conf
===================================================================
--- trunk/test/family-benchmark/Grandgrandson.conf 2012-01-06 10:56:39 UTC (rev 3537)
+++ trunk/test/family-benchmark/Grandgrandson.conf 2012-01-06 11:37:27 UTC (rev 3538)
@@ -18,6 +18,9 @@
// OCEL
alg.type = "ocel"
+// ELTL
+// alg.type = "eltl"
+
// learning problem
lp.type = "posNegStandard"
lp.positiveExamples = {
Modified: trunk/test/family-benchmark/Grandmother.conf
===================================================================
--- trunk/test/family-benchmark/Grandmother.conf 2012-01-06 10:56:39 UTC (rev 3537)
+++ trunk/test/family-benchmark/Grandmother.conf 2012-01-06 11:37:27 UTC (rev 3538)
@@ -18,6 +18,9 @@
// OCEL
alg.type = "ocel"
+// ELTL
+// alg.type = "eltl"
+
// learning problem
lp.type = "posNegStandard"
lp.positiveExamples = {
Modified: trunk/test/family-benchmark/Grandson.conf
===================================================================
--- trunk/test/family-benchmark/Grandson.conf 2012-01-06 10:56:39 UTC (rev 3537)
+++ trunk/test/family-benchmark/Grandson.conf 2012-01-06 11:37:27 UTC (rev 3538)
@@ -18,6 +18,9 @@
// OCEL
alg.type = "ocel"
+// ELTL
+// alg.type = "eltl"
+
// learning problem
lp.type = "posNegStandard"
lp.positiveExamples = {
Deleted: trunk/test/family-benchmark/Male.conf
===================================================================
--- trunk/test/family-benchmark/Male.conf 2012-01-06 10:56:39 UTC (rev 3537)
+++ trunk/test/family-benchmark/Male.conf 2012-01-06 11:37:27 UTC (rev 3538)
@@ -1,228 +0,0 @@
-// declare some prefixes to use as abbreviations
-prefixes = [ ("ex","http://www.benchmark.org/family#") ]
-
-// knowledge source definition
-ks.type = "OWL File"
-ks.fileName = "family-benchmark.owl"
-
-// reasoner
-reasoner.type = "fast instance checker"
-reasoner.sources = { ks }
-
-// CELOE
-/*
-alg.type = "celoe"
-alg.terminateOnNoiseReached = true
-*/
-
-// OCEL
-alg.type = "ocel"
-
-// learning problem
-lp.type = "posNegStandard"
-lp.positiveExamples = { "ex:F1M6"
-,"ex:F1M8"
-,"ex:F1M4"
-,"ex:F1M1"
-,"ex:F2M13"
-,"ex:F2M18"
-,"ex:F2M16"
-,"ex:F2M11"
-,"ex:F2M25"
-,"ex:F2M23"
-,"ex:F2M21"
-,"ex:F2M20"
-,"ex:F2M27"
-,"ex:F2M32"
-,"ex:F2M35"
-,"ex:F2M34"
-,"ex:F2M31"
-,"ex:F2M29"
-,"ex:F2M39"
-,"ex:F2M37"
-,"ex:F2M9"
-,"ex:F3M44"
-,"ex:F3M51"
-,"ex:F3M50"
-,"ex:F3M47"
-,"ex:F3M45"
-,"ex:F3M43"
-,"ex:F3M40"
-,"ex:F4M59"
-,"ex:F4M57"
-,"ex:F4M54"
-,"ex:F5M63"
-,"ex:F5M68"
-,"ex:F5M66"
-,"ex:F5M64"
-,"ex:F5M60"
-,"ex:F6M75"
-,"ex:F6M73"
-,"ex:F6M71"
-,"ex:F6M80"
-,"ex:F6M81"
-,"ex:F6M78"
-,"ex:F6M88"
-,"ex:F6M90"
-,"ex:F6M85"
-,"ex:F6M99"
-,"ex:F6M98"
-,"ex:F6M95"
-,"ex:F6M100"
-,"ex:F6M92"
-,"ex:F6M69"
-,"ex:F7M112"
-,"ex:F7M110"
-,"ex:F7M109"
-,"ex:F7M113"
-,"ex:F7M107"
-,"ex:F7M117"
-,"ex:F7M115"
-,"ex:F7M120"
-,"ex:F7M125"
-,"ex:F7M130"
-,"ex:F7M128"
-,"ex:F7M123"
-,"ex:F7M131"
-,"ex:F7M122"
-,"ex:F7M104"
-,"ex:F7M102"
-,"ex:F8M138"
-,"ex:F8M136"
-,"ex:F8M134"
-,"ex:F8M132"
-,"ex:F9M147"
-,"ex:F9M146"
-,"ex:F9M149"
-,"ex:F9M144"
-,"ex:F9M151"
-,"ex:F9M155"
-,"ex:F9M153"
-,"ex:F9M142"
-,"ex:F9M161"
-,"ex:F9M159"
-,"ex:F9M165"
-,"ex:F9M166"
-,"ex:F9M162"
-,"ex:F9M157"
-,"ex:F9M170"
-,"ex:F9M167"
-,"ex:F9M139"
-,"ex:F10M176"
-,"ex:F10M178"
-,"ex:F10M173"
-,"ex:F10M180"
-,"ex:F10M183"
-,"ex:F10M184"
-,"ex:F10M182"
-,"ex:F10M190"
-,"ex:F10M188"
-,"ex:F10M194"
-,"ex:F10M187"
-,"ex:F10M199"
-,"ex:F10M202"
-,"ex:F10M197"
-,"ex:F10M196"
-,"ex:F10M171"
-}
-
-lp.negativeExamples = {
-"ex:F1F5"
-,"ex:F1F7"
-,"ex:F1F3"
-,"ex:F1F2"
-,"ex:F2F14"
-,"ex:F2F17"
-,"ex:F2F15"
-,"ex:F2F12"
-,"ex:F2F24"
-,"ex:F2F22"
-,"ex:F2F19"
-,"ex:F2F26"
-,"ex:F2F33"
-,"ex:F2F30"
-,"ex:F2F28"
-,"ex:F2F38"
-,"ex:F2F36"
-,"ex:F2F10"
-,"ex:F3F49"
-,"ex:F3F52"
-,"ex:F3F48"
-,"ex:F3F46"
-,"ex:F3F53"
-,"ex:F3F42"
-,"ex:F3F41"
-,"ex:F4F58"
-,"ex:F4F56"
-,"ex:F4F55"
-,"ex:F5F62"
-,"ex:F5F67"
-,"ex:F5F65"
-,"ex:F5F61"
-,"ex:F6F76"
-,"ex:F6F74"
-,"ex:F6F72"
-,"ex:F6F79"
-,"ex:F6F83"
-,"ex:F6F82"
-,"ex:F6F77"
-,"ex:F6F86"
-,"ex:F6F89"
-,"ex:F6F87"
-,"ex:F6F91"
-,"ex:F6F84"
-,"ex:F6F96"
-,"ex:F6F97"
-,"ex:F6F94"
-,"ex:F6F101"
-,"ex:F6F93"
-,"ex:F6F70"
-,"ex:F7F111"
-,"ex:F7F108"
-,"ex:F7F114"
-,"ex:F7F106"
-,"ex:F7F118"
-,"ex:F7F116"
-,"ex:F7F119"
-,"ex:F7F126"
-,"ex:F7F129"
-,"ex:F7F127"
-,"ex:F7F124"
-,"ex:F7F121"
-,"ex:F7F105"
-,"ex:F7F103"
-,"ex:F8F137"
-,"ex:F8F135"
-,"ex:F8F133"
-,"ex:F9F145"
-,"ex:F9F148"
-,"ex:F9F150"
-,"ex:F9F143"
-,"ex:F9F152"
-,"ex:F9F156"
-,"ex:F9F154"
-,"ex:F9F141"
-,"ex:F9F160"
-,"ex:F9F164"
-,"ex:F9F163"
-,"ex:F9F158"
-,"ex:F9F169"
-,"ex:F9F168"
-,"ex:F9F140"
-,"ex:F10F175"
-,"ex:F10F177"
-,"ex:F10F174"
-,"ex:F10F179"
-,"ex:F10F185"
-,"ex:F10F181"
-,"ex:F10F191"
-,"ex:F10F189"
-,"ex:F10F192"
-,"ex:F10F193"
-,"ex:F10F186"
-,"ex:F10F200"
-,"ex:F10F201"
-,"ex:F10F198"
-,"ex:F10F195"
-,"ex:F10F172"
-}
\ No newline at end of file
Modified: trunk/test/family-benchmark/Mother.conf
===================================================================
--- trunk/test/family-benchmark/Mother.conf 2012-01-06 10:56:39 UTC (rev 3537)
+++ trunk/test/family-benchmark/Mother.conf 2012-01-06 11:37:27 UTC (rev 3538)
@@ -18,6 +18,9 @@
// OCEL
alg.type = "ocel"
+// ELTL
+// alg.type = "eltl"
+
// learning problem
lp.type = "posNegStandard"
lp.positiveExamples = { "ex:F1F3"
Modified: trunk/test/family-benchmark/PersonWithASibling.conf
===================================================================
--- trunk/test/family-benchmark/PersonWithASibling.conf 2012-01-06 10:56:39 UTC (rev 3537)
+++ trunk/test/family-benchmark/PersonWithASibling.conf 2012-01-06 11:37:27 UTC (rev 3538)
@@ -18,6 +18,9 @@
// OCEL
alg.type = "ocel"
+// ELTL
+// alg.type = "eltl"
+
// learning problem
lp.type = "posNegStandard"
lp.positiveExamples = { "ex:F1F5"
Modified: trunk/test/family-benchmark/Sister.conf
===================================================================
--- trunk/test/family-benchmark/Sister.conf 2012-01-06 10:56:39 UTC (rev 3537)
+++ trunk/test/family-benchmark/Sister.conf 2012-01-06 11:37:27 UTC (rev 3538)
@@ -18,6 +18,9 @@
// OCEL
alg.type = "ocel"
+// ELTL
+// alg.type = "eltl"
+
// learning problem
lp.type = "posNegStandard"
lp.positiveExamples = { "ex:F1F5"
Modified: trunk/test/family-benchmark/Son.conf
===================================================================
--- trunk/test/family-benchmark/Son.conf 2012-01-06 10:56:39 UTC (rev 3537)
+++ trunk/test/family-benchmark/Son.conf 2012-01-06 11:37:27 UTC (rev 3538)
@@ -18,6 +18,9 @@
// OCEL
alg.type = "ocel"
+// ELTL
+// alg.type = "eltl"
+
// learning problem
lp.type = "posNegStandard"
lp.positiveExamples = { "ex:F2M13"
Modified: trunk/test/family-benchmark/Uncle.conf
===================================================================
--- trunk/test/family-benchmark/Uncle.conf 2012-01-06 10:56:39 UTC (rev 3537)
+++ trunk/test/family-benchmark/Uncle.conf 2012-01-06 11:37:27 UTC (rev 3538)
@@ -14,17 +14,19 @@
// op.useAllConstructor = false
// CELOE cofiguration
+/*
h.type ="celoe_heuristic"
h.expansionPenaltyFactor = 0.02
alg.type = "celoe"
alg.maxExecutionTimeInSeconds = 200
alg.terminateOnNoiseReached = true
+*/
// OCEL configuration
-// alg.type = "ocel"
+alg.type = "ocel"
-// alg.writeSearchTree = true
-// alg.replaceSearchTree = true
+// Disjunctive ELTL
+// alg.type = "deltl"
// learning problem
lp.type = "posNegStandard"
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lor...@us...> - 2012-01-06 10:56:46
|
Revision: 3537
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3537&view=rev
Author: lorenz_b
Date: 2012-01-06 10:56:39 +0000 (Fri, 06 Jan 2012)
Log Message:
-----------
Added more output.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/PCELOE.java
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/PCELOE.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/PCELOE.java 2012-01-06 10:51:20 UTC (rev 3536)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/PCELOE.java 2012-01-06 10:56:39 UTC (rev 3537)
@@ -499,21 +499,21 @@
}
- private OENode getNextNodeToExpand() {
+ synchronized private OENode getNextNodeToExpand() {
// we expand the best node of those, which have not achieved 100% accuracy
// already and have a horizontal expansion equal to their length
// (rationale: further extension is likely to add irrelevant syntactical constructs)
- synchronized (nodes) {logger.info("in 1.lock");
+ synchronized (nodes) {logger.info("in 1.lock of getNextNodeToExpand method");
Iterator<OENode> it = nodes.descendingIterator();//logger.info(nodes.size());
logger.info("search tree size: " + nodes.size());
while(it.hasNext()) {
OENode node = it.next();
- logger.info("checking node " + node);
+ logger.info("Checking node " + node + "...");
if(!currentlyProcessedNodes.contains(node) && (node.getAccuracy() < 1.0 || node.getHorizontalExpansion() < node.getDescription().getLength())) {
currentlyProcessedNodes.add(node);
return node;
}
- logger.info("Checked.");
+ logger.info("...checked.");
}
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lor...@us...> - 2012-01-06 10:51:27
|
Revision: 3536
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3536&view=rev
Author: lorenz_b
Date: 2012-01-06 10:51:20 +0000 (Fri, 06 Jan 2012)
Log Message:
-----------
Added more output.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/PCELOE.java
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/PCELOE.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/PCELOE.java 2012-01-06 10:19:04 UTC (rev 3535)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/PCELOE.java 2012-01-06 10:51:20 UTC (rev 3536)
@@ -21,6 +21,7 @@
import java.io.File;
import java.text.DecimalFormat;
+import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
@@ -38,7 +39,10 @@
import java.util.concurrent.ThreadPoolExecutor;
import java.util.concurrent.TimeUnit;
+import org.apache.log4j.FileAppender;
import org.apache.log4j.Logger;
+import org.apache.log4j.PatternLayout;
+import org.apache.log4j.SimpleLayout;
import org.dllearner.core.AbstractCELA;
import org.dllearner.core.AbstractKnowledgeSource;
import org.dllearner.core.AbstractLearningProblem;
@@ -86,7 +90,6 @@
@ComponentAnn(name="PCELOE", shortName="pceloe", version=1.0, description="CELOE is an adapted and extended version of the OCEL algorithm applied for the ontology engineering use case. See http://jens-lehmann.org/files/2011/celoe.pdf for reference.")
public class PCELOE extends AbstractCELA {
- Map<Thread, RefinementOperator> ops = new HashMap<Thread, RefinementOperator>();
//parameters for thread pool
//Parallel running Threads(Executor) on System
private static int corePoolSize = 5;
@@ -441,101 +444,31 @@
addNode(startClass, null);
int nrOfThreads = Runtime.getRuntime().availableProcessors();
+ nrOfThreads = 8;//only for tests TODO make number of threads configurable
ExecutorService service = Executors.newFixedThreadPool(nrOfThreads);
- for(int i = 0; i < 2; i++){
- service.submit(new Runnable() {
-
-
-
- @Override
- public void run() {
- // we use a default operator and inject the class hierarchy for now
- RefinementOperator operator = new RhoDRDown();
- ((RhoDRDown)operator).setStartClass(startClass);
- ((RhoDRDown)operator).setReasoner(reasoner);
- try {
- ((RhoDRDown)operator).init();
- } catch (ComponentInitException e) {
- e.printStackTrace();
- }
- // TODO: find a better solution as this is quite difficult to debug
- ((RhoDRDown)operator).setSubHierarchy(reasoner.getClassHierarchy().clone());
- ((RhoDRDown)operator).setObjectPropertyHierarchy(reasoner.getObjectPropertyHierarchy());
- ((RhoDRDown)operator).setDataPropertyHierarchy(reasoner.getDatatypePropertyHierarchy());
-
- ops.put(Thread.currentThread(), operator);
-
- OENode nextNode;
- double highestAccuracy = 0.0;
- int loop = 0;
- while (!terminationCriteriaSatisfied()) {
-
-
- if(!singleSuggestionMode && bestEvaluatedDescriptions.getBestAccuracy() > highestAccuracy) {
- highestAccuracy = bestEvaluatedDescriptions.getBestAccuracy();
- logger.info("more accurate (" + dfPercent.format(highestAccuracy) + ") class expression found: " + descriptionToString(bestEvaluatedDescriptions.getBest().getDescription()));
- }
-
- // chose best node according to heuristics
- logger.info("Get next node to expand...");
- nextNode = getNextNodeToExpand();
- logger.info("...done");
- try {
- Thread.sleep(10);
- } catch (InterruptedException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- logger.info("next Node: " + nextNode);
- if(nextNode != null){
- int horizExp = nextNode.getHorizontalExpansion();
-
- // apply operator
- Monitor mon = MonitorFactory.start("refineNode");
- logger.info("Refine node...");
- TreeSet<Description> refinements = refineNode(nextNode);
- mon.stop();
- logger.info("...done");
-
- while(refinements.size() != 0) {
- // pick element from set
- Description refinement = refinements.pollFirst();
- int length = refinement.getLength();
-
- // we ignore all refinements with lower length and too high depth
- // (this also avoids duplicate node children)
- if(length > horizExp && refinement.getDepth() <= maxDepth) {
-
-// System.out.println("potentially adding " + refinement + " to search tree as child of " + nextNode + " " + new Date());
- Monitor mon2 = MonitorFactory.start("addNode");
- logger.info("Add node...");
- addNode(refinement, nextNode);
- mon2.stop();
- logger.info("...done");
- // adding nodes is potentially computationally expensive, so we have
- // to check whether max time is exceeded
- if(terminationCriteriaSatisfied()) {
- break;
- }
-// System.out.println("addNode finished" + " " + new Date());
- }
-
-// System.out.println(" refinement queue length: " + refinements.size());
- }
-
-// updateMinMaxHorizExp(nextNode);
-
- loop++;
- currentlyProcessedNodes.remove(nextNode);
- }
-
- }
-
- }
- });
+ List<Runnable> tasks = new ArrayList<Runnable>();
+
+ for(int i = 0; i < nrOfThreads; i++){
+ RhoDRDown operator = new RhoDRDown();
+ operator.setStartClass(startClass);
+ operator.setReasoner(reasoner);
+ try {
+ operator.init();
+ } catch (ComponentInitException e) {
+ e.printStackTrace();
+ }
+ operator.setSubHierarchy(reasoner.getClassHierarchy().clone());
+ operator.setObjectPropertyHierarchy(reasoner.getObjectPropertyHierarchy());
+ operator.setDataPropertyHierarchy(reasoner.getDatatypePropertyHierarchy());
+
+ tasks.add(new Worker(operator));
}
+ for(Runnable task : tasks){
+ service.submit(task);
+ }
+
try {
service.awaitTermination(maxExecutionTimeInSeconds, TimeUnit.SECONDS);
} catch (InterruptedException e) {
@@ -554,12 +487,14 @@
}
// print solution(s)
+
+// System.out.println("isRunning: " + isRunning);
+
logger.info("solutions:\n" + getSolutionString());
// System.out.println(startNode.toTreeString(baseURI));
isRunning = false;
-// System.out.println("isRunning: " + isRunning);
service.shutdown();
}
@@ -568,34 +503,45 @@
// we expand the best node of those, which have not achieved 100% accuracy
// already and have a horizontal expansion equal to their length
// (rationale: further extension is likely to add irrelevant syntactical constructs)
+ synchronized (nodes) {logger.info("in 1.lock");
Iterator<OENode> it = nodes.descendingIterator();//logger.info(nodes.size());
- while(it.hasNext()) {
- OENode node = it.next();
- if(!currentlyProcessedNodes.contains(node) && (node.getAccuracy() < 1.0 || node.getHorizontalExpansion() < node.getDescription().getLength())) {
- currentlyProcessedNodes.add(node);
- return node;
+ logger.info("search tree size: " + nodes.size());
+ while(it.hasNext()) {
+ OENode node = it.next();
+ logger.info("checking node " + node);
+ if(!currentlyProcessedNodes.contains(node) && (node.getAccuracy() < 1.0 || node.getHorizontalExpansion() < node.getDescription().getLength())) {
+ currentlyProcessedNodes.add(node);
+ return node;
+ }
+ logger.info("Checked.");
}
}
+
// this should practically never be called, since for any reasonable learning
// task, we will always have at least one node with less than 100% accuracy
return null;
}
// expand node horizontically
- private TreeSet<Description> refineNode(OENode node) {
+ private TreeSet<Description> refineNode(OENode node, RhoDRDown operator) {
// we have to remove and add the node since its heuristic evaluation changes through the expansion
// (you *must not* include any criteria in the heuristic which are modified outside of this method,
// otherwise you may see rarely occurring but critical false ordering in the nodes set)
- nodes.remove(node);
+ synchronized (nodes) {
+ nodes.remove(node);
+ }
+
// System.out.println("refining: " + node);
int horizExp = node.getHorizontalExpansion();
// TreeSet<Description> refinements = (TreeSet<Description>) operator.refine(node.getDescription(), horizExp+1);
- RefinementOperator operator = ops.get(Thread.currentThread()); //logger.info("Got operator");
TreeSet<Description> refinements = (TreeSet<Description>) operator.refine(node.getDescription(), horizExp+1);
node.incHorizontalExpansion();
node.setRefinementCount(refinements.size());
- nodes.add(node);
+ synchronized (refinements) {
+ nodes.add(node);
+ }
+
return refinements;
}
@@ -688,13 +634,16 @@
// A is not a candidate; on the other hand this suppresses many meaningless extensions of A
boolean shorterDescriptionExists = false;
if(forceMutualDifference) {
- for(EvaluatedDescription ed : bestEvaluatedDescriptions.getSet()) {
- if(Math.abs(ed.getAccuracy()-accuracy) <= 0.00001 && ConceptTransformation.isSubdescription(niceDescription, ed.getDescription())) {
-// System.out.println("shorter: " + ed.getDescription());
- shorterDescriptionExists = true;
- break;
- }
- }
+ synchronized (bestEvaluatedDescriptions) {
+ for(EvaluatedDescription ed : bestEvaluatedDescriptions.getSet()) {
+ if(Math.abs(ed.getAccuracy()-accuracy) <= 0.00001 && ConceptTransformation.isSubdescription(niceDescription, ed.getDescription())) {
+// System.out.println("shorter: " + ed.getDescription());
+ shorterDescriptionExists = true;
+ break;
+ }
+ }
+ }
+
}
logger.info("Point 2");
@@ -822,11 +771,13 @@
}
private boolean terminationCriteriaSatisfied() {
- return
- stop ||
- (maxClassDescriptionTests != 0 && (expressionTests >= maxClassDescriptionTests)) ||
- (maxExecutionTimeInSeconds != 0 && ((System.nanoTime() - nanoStartTime) >= (maxExecutionTimeInSeconds*1000000000l))) ||
- (terminateOnNoiseReached && (100*getCurrentlyBestAccuracy()>=100-noisePercentage));
+ boolean ret = stop ||
+ (maxClassDescriptionTests != 0 && (expressionTests >= maxClassDescriptionTests)) ||
+ (maxExecutionTimeInSeconds != 0 && ((System.nanoTime() - nanoStartTime) >= (maxExecutionTimeInSeconds*1000000000l))) ||
+ (terminateOnNoiseReached && (100*getCurrentlyBestAccuracy()>=100-noisePercentage));
+ logger.info("terminate: " + ret);
+ return ret;
+
}
private void reset() {
@@ -1062,6 +1013,8 @@
public static void main(String[] args) throws Exception{
+ Logger.getLogger(PCELOE.class).addAppender(new FileAppender(new PatternLayout( "[%t] %c: %m%n" ), "log/parallel_run.txt", false));
+
AbstractKnowledgeSource ks = new OWLFile("../examples/family/father_oe.owl");
ks.init();
@@ -1070,15 +1023,98 @@
ClassLearningProblem lp = new ClassLearningProblem(rc);
lp.setClassToDescribe(new NamedClass("http://example.com/father#father"));
+ lp.setCheckConsistency(false);
lp.init();
PCELOE alg = new PCELOE(lp, rc);
alg.setMaxExecutionTimeInSeconds(10);
- alg.setMaxClassDescriptionTests(100);
+// alg.setMaxClassDescriptionTests(200);
alg.init();
alg.start();
}
+ class Worker implements Runnable{
+
+ private RhoDRDown operator;
+
+ public Worker(RhoDRDown operator) {
+ this.operator = operator;
+ }
+
+ @Override
+ public void run() {
+ logger.info("Started thread...");
+
+ OENode nextNode;
+ double highestAccuracy = 0.0;
+ int loop = 0;
+ while (!terminationCriteriaSatisfied()) {
+
+
+ if(!singleSuggestionMode && bestEvaluatedDescriptions.getBestAccuracy() > highestAccuracy) {
+ highestAccuracy = bestEvaluatedDescriptions.getBestAccuracy();
+ logger.info("more accurate (" + dfPercent.format(highestAccuracy) + ") class expression found: " + descriptionToString(bestEvaluatedDescriptions.getBest().getDescription()));
+ }
+
+ // chose best node according to heuristics
+ logger.info("Get next node to expand...");
+ nextNode = getNextNodeToExpand();
+ logger.info("...done");
+ try {
+ Thread.sleep(10);
+ } catch (InterruptedException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ logger.info("next Node: " + nextNode);
+ if(nextNode != null){
+ int horizExp = nextNode.getHorizontalExpansion();
+
+ // apply operator
+ Monitor mon = MonitorFactory.start("refineNode");
+ logger.info("Refine node...");
+ TreeSet<Description> refinements = refineNode(nextNode, operator);
+ mon.stop();
+ logger.info("...done");
+
+ while(refinements.size() != 0) {
+ // pick element from set
+ Description refinement = refinements.pollFirst();
+ int length = refinement.getLength();
+
+ // we ignore all refinements with lower length and too high depth
+ // (this also avoids duplicate node children)
+ if(length > horizExp && refinement.getDepth() <= maxDepth) {
+
+// System.out.println("potentially adding " + refinement + " to search tree as child of " + nextNode + " " + new Date());
+ Monitor mon2 = MonitorFactory.start("addNode");
+ logger.info("Add node...");
+ addNode(refinement, nextNode);
+ mon2.stop();
+ logger.info("...done");
+ // adding nodes is potentially computationally expensive, so we have
+ // to check whether max time is exceeded
+ if(terminationCriteriaSatisfied()) {
+ break;
+ }
+// System.out.println("addNode finished" + " " + new Date());
+ }
+
+// System.out.println(" refinement queue length: " + refinements.size());
+ }
+
+// updateMinMaxHorizExp(nextNode);
+
+ loop++;
+ currentlyProcessedNodes.remove(nextNode);
+ }
+
+ }
+
+ }
+
+ }
+
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <jen...@us...> - 2012-01-06 10:19:10
|
Revision: 3535
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3535&view=rev
Author: jenslehmann
Date: 2012-01-06 10:19:04 +0000 (Fri, 06 Jan 2012)
Log Message:
-----------
CELOE heuristic improvements
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/CELOE.java
trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/OEHeuristicRuntime.java
trunk/components-core/src/main/java/org/dllearner/core/AnnComponentManager.java
trunk/components-core/src/main/java/org/dllearner/core/ComponentAnn.java
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/CELOE.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/CELOE.java 2012-01-06 10:18:12 UTC (rev 3534)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/CELOE.java 2012-01-06 10:19:04 UTC (rev 3535)
@@ -219,7 +219,7 @@
@Override
public void init() throws ComponentInitException {
- if(maxExecutionTimeInSeconds != 0) {
+ if(maxExecutionTimeInSeconds != 0 && maxExecutionTimeInSecondsAfterImprovement != 0) {
maxExecutionTimeInSeconds = Math.min(maxExecutionTimeInSeconds, maxExecutionTimeInSecondsAfterImprovement);
}
@@ -514,7 +514,7 @@
if (stop) {
logger.info("Algorithm stopped ("+expressionTests+" descriptions tested). " + nodes.size() + " nodes in the search tree.\n");
} else {
- logger.info("Algorithm terminated successfully ("+expressionTests+" descriptions tested). " + nodes.size() + " nodes in the search tree.\n");
+ logger.info("Algorithm terminated successfully (time: " + Helper.prettyPrintNanoSeconds(System.nanoTime()-nanoStartTime) + ", "+expressionTests+" descriptions tested, " + nodes.size() + " nodes in the search tree).\n");
logger.info(reasoner.toString());
}
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/OEHeuristicRuntime.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/OEHeuristicRuntime.java 2012-01-06 10:18:12 UTC (rev 3534)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/OEHeuristicRuntime.java 2012-01-06 10:19:04 UTC (rev 3535)
@@ -21,7 +21,11 @@
import java.util.Comparator;
+import org.dllearner.core.Component;
import org.dllearner.core.ComponentAnn;
+import org.dllearner.core.ComponentInitException;
+import org.dllearner.core.config.ConfigOption;
+import org.dllearner.core.config.DoubleEditor;
import org.dllearner.utilities.owl.ConceptComparator;
/**
@@ -32,8 +36,8 @@
* @author Jens Lehmann
*
*/
-@ComponentAnn(name = "OEHeuristicRuntime", shortName = "OEHeuristicRuntime", version = 0.5)
-public class OEHeuristicRuntime implements Comparator<OENode>{
+@ComponentAnn(name = "OEHeuristicRuntime", shortName = "celoe_heuristic", version = 0.5)
+public class OEHeuristicRuntime implements Component, Comparator<OENode>{
// strong penalty for long descriptions
private double expansionPenaltyFactor = 0.1;
@@ -45,11 +49,19 @@
// syntactic comparison as final comparison criterion
private ConceptComparator conceptComparator = new ConceptComparator();
+ @ConfigOption(name = "startNodeBonus", defaultValue="0.1")
+ private double startNodeBonus = 0.1;
+
public OEHeuristicRuntime() {
}
@Override
+ public void init() throws ComponentInitException {
+
+ }
+
+ @Override
public int compare(OENode node1, OENode node2) {
// System.out.println("node1 " + node1);
// System.out.println("score: " + getNodeScore(node1));
@@ -74,6 +86,9 @@
if(!node.isRoot()) {
double parentAccuracy = node.getParent().getAccuracy();
score += (parentAccuracy - score) * gainBonusFactor;
+ // the root node also gets a bonus to possibly spawn useful disjunctions
+ } else {
+ score += startNodeBonus;
}
// penalty for horizontal expansion
score -= node.getHorizontalExpansion() * expansionPenaltyFactor;
@@ -104,5 +119,15 @@
public void setExpansionPenaltyFactor(double expansionPenaltyFactor) {
this.expansionPenaltyFactor = expansionPenaltyFactor;
- }
+ }
+
+ public double getStartNodeBonus() {
+ return startNodeBonus;
+ }
+
+ public void setStartNodeBonus(double startNodeBonus) {
+ this.startNodeBonus = startNodeBonus;
+ }
+
+
}
Modified: trunk/components-core/src/main/java/org/dllearner/core/AnnComponentManager.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/AnnComponentManager.java 2012-01-06 10:18:12 UTC (rev 3534)
+++ trunk/components-core/src/main/java/org/dllearner/core/AnnComponentManager.java 2012-01-06 10:19:04 UTC (rev 3535)
@@ -85,6 +85,7 @@
"org.dllearner.reasoning.fuzzydll.FuzzyOWLAPIReasoner",
"org.dllearner.algorithms.ocel.OCEL",
"org.dllearner.algorithms.ocel.MultiHeuristic",
+ "org.dllearner.algorithms.celoe.OEHeuristicRuntime",
"org.dllearner.refinementoperators.RhoDRDown",
} ));
private static Collection<Class<? extends Component>> components;
Modified: trunk/components-core/src/main/java/org/dllearner/core/ComponentAnn.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/ComponentAnn.java 2012-01-06 10:18:12 UTC (rev 3534)
+++ trunk/components-core/src/main/java/org/dllearner/core/ComponentAnn.java 2012-01-06 10:19:04 UTC (rev 3535)
@@ -42,7 +42,7 @@
/**
* The short name of this component, which should exclusively consist of
- * lower case ASCII symbols without whitespace.
+ * lower case ASCII symbols and "_" without whitespace.
* @return The short name of this component.
*/
String shortName();
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From: <lor...@us...> - 2012-01-06 10:10:14
|
Revision: 3533
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3533&view=rev
Author: lorenz_b
Date: 2012-01-06 10:10:08 +0000 (Fri, 06 Jan 2012)
Log Message:
-----------
Extended tests for CELOE.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/refinementoperators/RhoDRDown.java
Modified: trunk/components-core/src/main/java/org/dllearner/refinementoperators/RhoDRDown.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/refinementoperators/RhoDRDown.java 2012-01-06 03:59:49 UTC (rev 3532)
+++ trunk/components-core/src/main/java/org/dllearner/refinementoperators/RhoDRDown.java 2012-01-06 10:10:08 UTC (rev 3533)
@@ -1458,7 +1458,7 @@
result = isDisjointInstanceBased(d1,d2);
} else {
Description d = new Intersection(d1, d2);
- result = reasoner.isSuperClassOf(new Nothing(), d);
+ result = reasoner.isSuperClassOf(new Nothing(), d); System.out.println("TEST");
}
// add the result to the cache (we add it twice such that
// the order of access does not matter)
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