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[DL-Learner SVN] SF.net SVN: dl-learner: [349] trunk
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From: <jen...@us...> - 2008-01-07 16:23:00
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Revision: 349
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=349&view=rev
Author: jenslehmann
Date: 2008-01-07 08:22:54 -0800 (Mon, 07 Jan 2008)
Log Message:
-----------
- OWL API reasoner implemented but not recommended yet
* Pellet 1.5.1 working but no performance improvement - maybe due to a lot System out calls (one for each instance check)
* FaCT++ 1.10 buggy; wrote a sample case for wrong behaviour in FaCTBugDemo and send it to FaCT developer Dmitry Tsarkov
- CLI adapted such that new reasoner interface can be used
- various smaller fixes in code and examples
Modified Paths:
--------------
trunk/examples/father2.conf
trunk/src/dl-learner/org/dllearner/cli/Start.java
trunk/src/dl-learner/org/dllearner/learningproblems/PosNegDefinitionLP.java
trunk/src/dl-learner/org/dllearner/learningproblems/PosNegInclusionLP.java
trunk/src/dl-learner/org/dllearner/learningproblems/PosNegLP.java
trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java
Added Paths:
-----------
trunk/examples/uncle.owl
trunk/src/dl-learner/org/dllearner/reasoning/FaCTBugDemo.java
Modified: trunk/examples/father2.conf
===================================================================
--- trunk/examples/father2.conf 2008-01-07 16:12:15 UTC (rev 348)
+++ trunk/examples/father2.conf 2008-01-07 16:22:54 UTC (rev 349)
@@ -8,7 +8,6 @@
*/
reasoner = dig;
-digReasonerURL = "http://localhost:8081";
import("father.owl");
// do not display http://example.com/father# in concepts
@@ -19,9 +18,9 @@
digProtocolFile = "log/father2_dig.txt";
/** examples **/
-+father("http://example.com/father#stefan").
-+father("http://example.com/father#markus").
-+father("http://example.com/father#martin").
--father("http://example.com/father#heinz").
--father("http://example.com/father#anna").
--father("http://example.com/father#michelle").
++"http://example.com/father#stefan"
++"http://example.com/father#markus"
++"http://example.com/father#martin"
+-"http://example.com/father#heinz"
+-"http://example.com/father#anna"
+-"http://example.com/father#michelle"
Added: trunk/examples/uncle.owl
===================================================================
--- trunk/examples/uncle.owl (rev 0)
+++ trunk/examples/uncle.owl 2008-01-07 16:22:54 UTC (rev 349)
@@ -0,0 +1,104 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<!DOCTYPE rdf:RDF [
+ <!ENTITY owl 'http://www.w3.org/2002/07/owl#'>
+]>
+
+<rdf:RDF
+ xml:base="http://localhost/foo"
+ xmlns:a="http://localhost/foo#"
+ xmlns:owl="http://www.w3.org/2002/07/owl#"
+ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
+
+<owl:Ontology rdf:about=""/>
+
+<owl:Class rdf:about="&owl;Nothing">
+ <owl:equivalentClass>
+ <owl:Class>
+ <owl:intersectionOf rdf:parseType="Collection">
+ <owl:Class rdf:about="#male"/>
+ <owl:Class rdf:about="#female"/>
+ </owl:intersectionOf>
+ </owl:Class>
+ </owl:equivalentClass>
+</owl:Class>
+
+<owl:ObjectProperty rdf:ID="hasSibling">
+ <rdf:type rdf:resource="&owl;SymmetricProperty"/>
+</owl:ObjectProperty>
+
+<owl:ObjectProperty rdf:ID="married">
+ <rdf:type rdf:resource="&owl;SymmetricProperty"/>
+ <rdf:type rdf:resource="&owl;FunctionalProperty"/>
+</owl:ObjectProperty>
+
+<a:male rdf:ID="alex"/>
+
+<a:male rdf:ID="alfred">
+ <a:hasChild rdf:resource="#hans"/>
+ <a:hasSibling rdf:resource="#heinz"/>
+ <a:hasSibling rdf:resource="#maria"/>
+ <a:married rdf:resource="#katrin"/>
+</a:male>
+
+<a:female rdf:ID="anna">
+ <a:hasChild rdf:resource="#alfred"/>
+ <a:hasChild rdf:resource="#heinz"/>
+ <a:hasChild rdf:resource="#maria"/>
+ <a:married rdf:resource="#jan"/>
+</a:female>
+
+<a:female rdf:ID="hanna">
+ <a:hasChild rdf:resource="#jan"/>
+ <a:hasSibling rdf:resource="#alex"/>
+</a:female>
+
+<a:male rdf:ID="hans">
+ <a:married rdf:resource="#johanna"/>
+</a:male>
+
+<a:male rdf:ID="heinrich">
+ <a:married rdf:resource="#susi"/>
+</a:male>
+
+<a:male rdf:ID="heinz">
+ <a:hasSibling rdf:resource="#maria"/>
+</a:male>
+
+<a:male rdf:ID="jan">
+ <a:hasChild rdf:resource="#alfred"/>
+ <a:hasChild rdf:resource="#heinz"/>
+ <a:hasChild rdf:resource="#maria"/>
+</a:male>
+
+<a:female rdf:ID="johanna">
+ <a:hasSibling rdf:resource="#mandy"/>
+</a:female>
+
+<a:female rdf:ID="katrin">
+ <a:hasChild rdf:resource="#hans"/>
+</a:female>
+
+<a:female rdf:ID="mandy">
+ <a:hasChild rdf:resource="#miriam"/>
+</a:female>
+
+<a:female rdf:ID="maria">
+ <a:hasChild rdf:resource="#markus"/>
+</a:female>
+
+<a:male rdf:ID="markus"/>
+
+<a:female rdf:ID="miriam"/>
+
+<a:female rdf:ID="susi">
+ <a:hasSibling rdf:resource="#anna"/>
+</a:female>
+
+<owl:Class rdf:ID="female"/>
+
+<owl:Class rdf:ID="male"/>
+
+<owl:ObjectProperty rdf:ID="hasChild"/>
+
+</rdf:RDF>
Modified: trunk/src/dl-learner/org/dllearner/cli/Start.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/cli/Start.java 2008-01-07 16:12:15 UTC (rev 348)
+++ trunk/src/dl-learner/org/dllearner/cli/Start.java 2008-01-07 16:22:54 UTC (rev 349)
@@ -70,6 +70,7 @@
import org.dllearner.parser.ParseException;
import org.dllearner.parser.TokenMgrError;
import org.dllearner.reasoning.DIGReasoner;
+import org.dllearner.reasoning.OWLAPIReasoner;
import org.dllearner.utilities.ConceptComparator;
import org.dllearner.utilities.Datastructures;
import org.dllearner.utilities.Helper;
@@ -132,6 +133,8 @@
// default value
if (reasonerOption == null || reasonerOption.getStringValue().equals("dig"))
reasonerClass = DIGReasoner.class;
+ else if(reasonerOption.getStringValue().equals("owlAPI"))
+ reasonerClass = OWLAPIReasoner.class;
else {
handleError("Unknown value " + reasonerOption.getStringValue()
+ "for option \"reasoner\".");
@@ -160,6 +163,7 @@
cm.applyConfigEntry(lp, "positiveExamples", posExamples);
if(lpClass != PosOnlyDefinitionLP.class)
cm.applyConfigEntry(lp, "negativeExamples", negExamples);
+ configureComponent(cm, lp, componentPrefixMapping, parser);
initComponent(cm, lp);
// step 4: detect learning algorithm
@@ -230,7 +234,9 @@
componentPrefixMapping.put(SparqlEndpointRestructured.class, "sparql2");
// reasoners
componentPrefixMapping.put(DIGReasoner.class, "digReasoner");
+ componentPrefixMapping.put(OWLAPIReasoner.class, "owlAPIReasoner");
// learning problems - configured via + and - flags for examples
+ componentPrefixMapping.put(PosNegDefinitionLP.class, "posNegDefinitionLP");
// learning algorithms
componentPrefixMapping.put(ROLearner.class, "refinement");
componentPrefixMapping.put(GP.class, "gp");
Modified: trunk/src/dl-learner/org/dllearner/learningproblems/PosNegDefinitionLP.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/learningproblems/PosNegDefinitionLP.java 2008-01-07 16:12:15 UTC (rev 348)
+++ trunk/src/dl-learner/org/dllearner/learningproblems/PosNegDefinitionLP.java 2008-01-07 16:22:54 UTC (rev 349)
@@ -99,9 +99,9 @@
else
return negAsPos.size();
} else {
- if (useDIGMultiInstanceChecks != UseMultiInstanceChecks.NEVER) {
+ if (useMultiInstanceChecks != UseMultiInstanceChecks.NEVER) {
// two checks
- if (useDIGMultiInstanceChecks == UseMultiInstanceChecks.TWOCHECKS) {
+ if (useMultiInstanceChecks == UseMultiInstanceChecks.TWOCHECKS) {
Set<Individual> s = reasoningService.instanceCheck(concept, positiveExamples);
// if the concept is too weak, then do not query negative
// examples
@@ -172,13 +172,13 @@
}
return new ScoreTwoValued(concept.getLength(), percentPerLengthUnit, posAsPos, posAsNeg, negAsPos, negAsNeg);
// instance checks for classification
- } else {
+ } else {
SortedSet<Individual> posAsPos = new TreeSet<Individual>();
SortedSet<Individual> posAsNeg = new TreeSet<Individual>();
SortedSet<Individual> negAsPos = new TreeSet<Individual>();
SortedSet<Individual> negAsNeg = new TreeSet<Individual>();
-
- if (useDIGMultiInstanceChecks != UseMultiInstanceChecks.NEVER) {
+
+ if (useMultiInstanceChecks != UseMultiInstanceChecks.NEVER) {
SortedSet<Individual> posClassified = reasoningService.instanceCheck(concept,
allExamples);
SortedSet<Individual> negClassified = Helper.difference(allExamples,
@@ -187,15 +187,20 @@
posAsNeg = Helper.intersection(positiveExamples, negClassified);
negAsPos = Helper.intersection(negativeExamples, posClassified);
negAsNeg = Helper.intersection(negativeExamples, negClassified);
+
+ // System.out.println("pos classified: " + posClassified);
+
return new ScoreTwoValued(concept.getLength(), percentPerLengthUnit, posAsPos, posAsNeg, negAsPos,
negAsNeg);
} else {
-
+ System.out.println("TEST");
+
for (Individual example : positiveExamples) {
- if (reasoningService.instanceCheck(concept, example))
+ if (reasoningService.instanceCheck(concept, example)) {
posAsPos.add(example);
- else
- posAsNeg.add(example);
+ } else {
+ posAsNeg.add(example); System.out.println(concept + " " + example);
+ }
}
for (Individual example : negativeExamples) {
if (reasoningService.instanceCheck(concept, example))
Modified: trunk/src/dl-learner/org/dllearner/learningproblems/PosNegInclusionLP.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/learningproblems/PosNegInclusionLP.java 2008-01-07 16:12:15 UTC (rev 348)
+++ trunk/src/dl-learner/org/dllearner/learningproblems/PosNegInclusionLP.java 2008-01-07 16:22:54 UTC (rev 349)
@@ -124,9 +124,9 @@
SortedSet<Individual> negExInNegatedConcept = Helper.intersection(negativeExamples, inNegatedConcept);
return (negativeExamples.size() - negExInNegatedConcept.size());
} else {
- if (useDIGMultiInstanceChecks != UseMultiInstanceChecks.NEVER) {
+ if (useMultiInstanceChecks != UseMultiInstanceChecks.NEVER) {
// two checks
- if (useDIGMultiInstanceChecks == UseMultiInstanceChecks.TWOCHECKS) {
+ if (useMultiInstanceChecks == UseMultiInstanceChecks.TWOCHECKS) {
Set<Individual> posExInNegatedConcept = reasoningService.instanceCheck(new Negation(concept), positiveExamples);
if(posExInNegatedConcept.size()>0) {
Modified: trunk/src/dl-learner/org/dllearner/learningproblems/PosNegLP.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/learningproblems/PosNegLP.java 2008-01-07 16:12:15 UTC (rev 348)
+++ trunk/src/dl-learner/org/dllearner/learningproblems/PosNegLP.java 2008-01-07 16:22:54 UTC (rev 349)
@@ -32,6 +32,7 @@
import org.dllearner.core.config.ConfigEntry;
import org.dllearner.core.config.ConfigOption;
import org.dllearner.core.config.InvalidConfigOptionValueException;
+import org.dllearner.core.config.StringConfigOption;
import org.dllearner.core.config.StringSetConfigOption;
import org.dllearner.core.dl.Concept;
import org.dllearner.core.dl.Individual;
@@ -48,7 +49,7 @@
protected SortedSet<Individual> allExamples;
protected boolean useRetrievalForClassification = false;
- protected UseMultiInstanceChecks useDIGMultiInstanceChecks = UseMultiInstanceChecks.TWOCHECKS;
+ protected UseMultiInstanceChecks useMultiInstanceChecks = UseMultiInstanceChecks.TWOCHECKS;
protected double percentPerLengthUnit = 0.05;
/**
@@ -90,6 +91,9 @@
options.add(new BooleanConfigOption("useRetrievalForClassficiation",
"Specifies whether to use retrieval or instance checks for testing a concept."));
options.add(CommonConfigOptions.getPercentPerLenghtUnitOption(0.05));
+ StringConfigOption multiInstanceChecks = new StringConfigOption("useMultiInstanceChecks", "See UseMultiInstanceChecks enum.");
+ multiInstanceChecks.setAllowedValues(new String[] {"never", "twoChecks", "oneCheck"});
+ options.add(multiInstanceChecks);
return options;
}
@@ -112,6 +116,15 @@
useRetrievalForClassification = (Boolean) entry.getValue();
else if (name.equals("percentPerLengthUnit"))
percentPerLengthUnit = (Double) entry.getValue();
+ else if (name.equals("useMultiInstanceChecks")) {
+ String value = (String) entry.getValue();
+ if(value.equals("oneCheck"))
+ useMultiInstanceChecks = UseMultiInstanceChecks.ONECHECK;
+ else if(value.equals("twoChecks"))
+ useMultiInstanceChecks = UseMultiInstanceChecks.TWOCHECKS;
+ else
+ useMultiInstanceChecks = UseMultiInstanceChecks.NEVER;
+ }
}
/*
Added: trunk/src/dl-learner/org/dllearner/reasoning/FaCTBugDemo.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/reasoning/FaCTBugDemo.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/reasoning/FaCTBugDemo.java 2008-01-07 16:22:54 UTC (rev 349)
@@ -0,0 +1,65 @@
+package org.dllearner.reasoning;
+
+import org.semanticweb.owl.model.*;
+import org.semanticweb.owl.apibinding.OWLManager;
+import org.semanticweb.owl.inference.OWLReasoner;
+import org.semanticweb.owl.inference.OWLReasonerException;
+
+import java.net.URI;
+import java.util.HashSet;
+import java.util.Set;
+import java.io.File;
+
+public class FaCTBugDemo {
+
+ public static void main(String[] args) {
+
+ try {
+ URI uri = new File("examples/father.owl").toURI();
+
+ // Create our ontology manager in the usual way.
+ OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
+
+ // Load a copy of the pizza ontology. We'll load the ontology from the web.
+ OWLOntology ont = manager.loadOntologyFromPhysicalURI(uri);
+
+ OWLReasoner reasoner = new uk.ac.manchester.cs.factplusplus.owlapi.Reasoner(manager);
+ // OWLReasoner reasoner = new org.mindswap.pellet.owlapi.Reasoner(manager);
+
+ // seems to be needed for some reason although no ontology is imported
+ Set<OWLOntology> importsClosure = manager.getImportsClosure(ont);
+ reasoner.loadOntologies(importsClosure);
+
+ reasoner.classify();
+ reasoner.realise();
+
+ OWLDataFactory factory = manager.getOWLDataFactory();
+
+ OWLClass male = factory.getOWLClass(URI.create("http://example.com/father#male"));
+ OWLObjectProperty hasChild = factory.getOWLObjectProperty(URI.create("http://example.com/father#hasChild"));
+ OWLObjectSomeRestriction hasSomeChild = factory.getOWLObjectSomeRestriction(hasChild, factory.getOWLThing());
+ Set<OWLDescription> set = new HashSet<OWLDescription>();
+ set.add(male);
+ set.add(hasSomeChild);
+ OWLDescription father = factory.getOWLObjectIntersectionOf(set);
+ OWLIndividual martin = factory.getOWLIndividual(URI.create("http://example.com/father#martin"));
+
+ if(reasoner.hasType(martin, father, false))
+ System.out.println("positive result"); // Pellet 1.5.1 (correct)
+ else
+ System.out.println("negative result"); // FaCT++ 1.10
+
+ }
+ catch(UnsupportedOperationException exception) {
+ System.out.println("Unsupported reasoner operation.");
+ }
+ catch(OWLReasonerException ex) {
+ System.out.println("Reasoner error: " + ex.getMessage());
+ }
+ catch (OWLOntologyCreationException e) {
+ System.out.println("Could not load the pizza ontology: " + e.getMessage());
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+ }
+}
Modified: trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java 2008-01-07 16:12:15 UTC (rev 348)
+++ trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java 2008-01-07 16:22:54 UTC (rev 349)
@@ -19,6 +19,7 @@
*/
package org.dllearner.reasoning;
+import java.net.MalformedURLException;
import java.net.URI;
import java.net.URISyntaxException;
import java.net.URL;
@@ -80,7 +81,7 @@
*/
public class OWLAPIReasoner extends ReasonerComponent {
- private String reasonerType = "FaCT++";
+ private String reasonerType = "fact";
private Set<KnowledgeSource> sources;
private OWLReasoner reasoner;
@@ -109,7 +110,7 @@
public static Collection<ConfigOption<?>> createConfigOptions() {
Collection<ConfigOption<?>> options = new LinkedList<ConfigOption<?>>();
StringConfigOption type = new StringConfigOption("reasonerType", "FaCT++ or Pellet", "FaCT++");
- type.setAllowedValues(new String[] {"FaCT++", "Pellet"});
+ type.setAllowedValues(new String[] {"fact", "pellet"});
// closure-Option? siehe:
// http://owlapi.svn.sourceforge.net/viewvc/owlapi/owl1_1/trunk/tutorial/src/main/java/uk/ac/manchester/owl/tutorial/examples/ClosureAxiomsExample.java?view=markup
options.add(type);
@@ -143,15 +144,29 @@
Set<OWLObjectProperty> properties = new TreeSet<OWLObjectProperty>(namedObjectComparator);
Set<OWLIndividual> owlIndividuals = new TreeSet<OWLIndividual>(namedObjectComparator);
+ Set<OWLOntology> allImports = new HashSet<OWLOntology>();
+
for(KnowledgeSource source : sources) {
if(!(source instanceof OWLFile)) {
System.out.println("Currently, only OWL files are supported. Ignoring knowledge source " + source + ".");
} else {
URL url = ((OWLFile)source).getURL();
+ /*
try {
+ url = new URL("http://www.co-ode.org/ontologies/pizza/2007/02/12/pizza.owl");
+ } catch (MalformedURLException e1) {
+ // TODO Auto-generated catch block
+ e1.printStackTrace();
+ }
+ */
+ try {
OWLOntology ontology = manager.loadOntologyFromPhysicalURI(url.toURI());
+ allImports.addAll(manager.getImportsClosure(ontology));
classes.addAll(ontology.getReferencedClasses());
properties.addAll(ontology.getReferencedObjectProperties());
+ // does not seem to work => workaround: query all instances of Top
+ // maybe one can also query for instances of OWLObjectProperty,
+ // OWLClass, OWLIndividual
owlIndividuals.addAll(ontology.getReferencedIndividuals());
} catch (OWLOntologyCreationException e) {
e.printStackTrace();
@@ -162,7 +177,7 @@
}
// create actual reasoner
- if(reasonerType.equals("FaCT++")) {
+ if(reasonerType.equals("fact")) {
try {
reasoner = new uk.ac.manchester.cs.factplusplus.owlapi.Reasoner(manager);
} catch (Exception e) {
@@ -173,9 +188,24 @@
reasoner = new org.mindswap.pellet.owlapi.Reasoner(manager);
}
+ /*
+ Set<OWLOntology> importsClosure = manager.getImportsClosure(ontology);
+ System.out.println("imports closure : " + importsClosure);
+ try {
+ reasoner.loadOntologies(importsClosure);
+ } catch (OWLReasonerException e1) {
+ // TODO Auto-generated catch block
+ e1.printStackTrace();
+ }*/
+
+ System.out.println(classes);
+ System.out.println(properties);
+ System.out.println(individuals);
+
// compute class hierarchy and types of individuals
// (done here to speed up later reasoner calls)
try {
+ reasoner.loadOntologies(allImports);
reasoner.classify();
reasoner.realise();
} catch (OWLReasonerException e) {
@@ -184,6 +214,18 @@
factory = manager.getOWLDataFactory();
+
+
+ try {
+ if(reasoner.isDefined(factory.getOWLIndividual(URI.create("http://example.com/father#female"))))
+ System.out.println("DEFINED.");
+ else
+ System.out.println("NOT DEFINED.");
+ } catch (OWLReasonerException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+
// read in primitives
atomicConcepts = new TreeSet<AtomicConcept>(conceptComparator);
for(OWLClass owlClass : classes)
@@ -370,17 +412,20 @@
}
}
- // TODO
@Override
public SortedSet<Individual> retrieval(Concept concept) {
OWLDescription d = getOWLAPIDescription(concept);
+ Set<OWLIndividual> individuals = null;
try {
- reasoner.getIndividuals(d, false);
+ individuals = reasoner.getIndividuals(d, false);
} catch (OWLReasonerException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
- return null;
+ SortedSet<Individual> inds = new TreeSet<Individual>();
+ for(OWLIndividual ind : individuals)
+ inds.add(new Individual(ind.getURI().toString()));
+ return inds;
}
@Override
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