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[DL-Learner SVN] SF.net SVN: dl-learner: [632] trunk/src/dl-learner/org/dllearner
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From: <jen...@us...> - 2008-02-23 21:13:15
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Revision: 632
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=632&view=rev
Author: jenslehmann
Date: 2008-02-23 13:13:06 -0800 (Sat, 23 Feb 2008)
Log Message:
-----------
- added support for two axiom types: different individuals and disjoint classes
- detected bug in OWL API different individuals export
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/core/owl/AssertionalAxiomVisitor.java
trunk/src/dl-learner/org/dllearner/core/owl/TerminologicalAxiomVisitor.java
trunk/src/dl-learner/org/dllearner/examples/Carcinogenesis.java
trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIAxiomConvertVisitor.java
Added Paths:
-----------
trunk/src/dl-learner/org/dllearner/core/owl/DifferentIndividualsAxiom.java
trunk/src/dl-learner/org/dllearner/core/owl/DisjointClassesAxiom.java
trunk/src/dl-learner/org/dllearner/test/OWLAPIBugDemo.java
Modified: trunk/src/dl-learner/org/dllearner/core/owl/AssertionalAxiomVisitor.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/AssertionalAxiomVisitor.java 2008-02-23 09:10:40 UTC (rev 631)
+++ trunk/src/dl-learner/org/dllearner/core/owl/AssertionalAxiomVisitor.java 2008-02-23 21:13:06 UTC (rev 632)
@@ -35,4 +35,6 @@
public void visit(BooleanDatatypePropertyAssertion axiom);
+ public void visit(DifferentIndividualsAxiom axiom);
+
}
Added: trunk/src/dl-learner/org/dllearner/core/owl/DifferentIndividualsAxiom.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/DifferentIndividualsAxiom.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/core/owl/DifferentIndividualsAxiom.java 2008-02-23 21:13:06 UTC (rev 632)
@@ -0,0 +1,65 @@
+/**
+ * Copyright (C) 2007-2008, Jens Lehmann
+ *
+ * This file is part of DL-Learner.
+ *
+ * DL-Learner is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * DL-Learner is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+package org.dllearner.core.owl;
+
+import java.util.Map;
+import java.util.Set;
+
+/**
+ * @author Jens Lehmann
+ *
+ */
+public class DifferentIndividualsAxiom extends AssertionalAxiom {
+
+ private Set<Individual> individuals;
+
+ public DifferentIndividualsAxiom(Set<Individual> individuals) {
+ this.individuals = individuals;
+ }
+
+ /* (non-Javadoc)
+ * @see org.dllearner.core.owl.KBElement#getLength()
+ */
+ public int getLength() {
+ return individuals.size() + 1;
+ }
+
+ /* (non-Javadoc)
+ * @see org.dllearner.core.owl.KBElement#toString(java.lang.String, java.util.Map)
+ */
+ public String toString(String baseURI, Map<String, String> prefixes) {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ public Set<Individual> getIndividuals() {
+ return individuals;
+ }
+
+ @Override
+ public void accept(AxiomVisitor visitor) {
+ visitor.visit(this);
+ }
+
+ public void accept(KBElementVisitor visitor) {
+ visitor.visit(this);
+ }
+
+}
Added: trunk/src/dl-learner/org/dllearner/core/owl/DisjointClassesAxiom.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/DisjointClassesAxiom.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/core/owl/DisjointClassesAxiom.java 2008-02-23 21:13:06 UTC (rev 632)
@@ -0,0 +1,71 @@
+/**
+ * Copyright (C) 2007-2008, Jens Lehmann
+ *
+ * This file is part of DL-Learner.
+ *
+ * DL-Learner is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * DL-Learner is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+package org.dllearner.core.owl;
+
+import java.util.Map;
+import java.util.Set;
+
+/**
+ * @author Jens Lehmann
+ *
+ */
+public class DisjointClassesAxiom extends TerminologicalAxiom {
+
+ private Set<Description> descriptions;
+
+ public DisjointClassesAxiom(Set<Description> descriptions) {
+ this.descriptions = descriptions;
+ }
+
+ /* (non-Javadoc)
+ * @see org.dllearner.core.owl.KBElement#getLength()
+ */
+ public int getLength() {
+ int length = 1;
+ for(Description d : descriptions)
+ length += d.getLength();
+ return length;
+ }
+
+ /* (non-Javadoc)
+ * @see org.dllearner.core.owl.KBElement#toString(java.lang.String, java.util.Map)
+ */
+ public String toString(String baseURI, Map<String, String> prefixes) {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public void accept(AxiomVisitor visitor) {
+ visitor.visit(this);
+ }
+
+ public void accept(KBElementVisitor visitor) {
+ visitor.visit(this);
+ }
+
+ /**
+ * @return the descriptions
+ */
+ public Set<Description> getDescriptions() {
+ return descriptions;
+ }
+
+}
Modified: trunk/src/dl-learner/org/dllearner/core/owl/TerminologicalAxiomVisitor.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/TerminologicalAxiomVisitor.java 2008-02-23 09:10:40 UTC (rev 631)
+++ trunk/src/dl-learner/org/dllearner/core/owl/TerminologicalAxiomVisitor.java 2008-02-23 21:13:06 UTC (rev 632)
@@ -29,4 +29,5 @@
public void visit(SubClassAxiom axiom);
+ public void visit(DisjointClassesAxiom axiom);
}
Modified: trunk/src/dl-learner/org/dllearner/examples/Carcinogenesis.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/examples/Carcinogenesis.java 2008-02-23 09:10:40 UTC (rev 631)
+++ trunk/src/dl-learner/org/dllearner/examples/Carcinogenesis.java 2008-02-23 21:13:06 UTC (rev 632)
@@ -26,6 +26,7 @@
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
+import java.util.HashSet;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
@@ -33,6 +34,9 @@
import java.util.TreeSet;
import org.dllearner.core.owl.BooleanDatatypePropertyAssertion;
+import org.dllearner.core.owl.Description;
+import org.dllearner.core.owl.DifferentIndividualsAxiom;
+import org.dllearner.core.owl.DisjointClassesAxiom;
import org.dllearner.core.owl.NamedClass;
import org.dllearner.core.owl.Axiom;
import org.dllearner.core.owl.ClassAssertionAxiom;
@@ -96,10 +100,14 @@
private static int bondNr = 0;
private static int structureNr = 0;
+ // list of all individuals in the knowlege base
+// private static Set<String> individuals = new TreeSet<String>();
// list of all compounds
private static Set<String> compounds = new TreeSet<String>();
// compounds with positive ames test
private static Set<String> compoundsAmes = new TreeSet<String>();
+ // list of all bonds
+ private static Set<String> bonds = new TreeSet<String>();
// list of all "hasProperty" test
private static Set<String> tests = new TreeSet<String>();
@@ -187,9 +195,17 @@
}
}
- // TODO: disjoint classes axioms
- // TODO: all different axiom (UNA)
+ // disjoint classes axioms
+ DisjointClassesAxiom disjointAtomTypes = getDisjointClassesAxiom(atomTypes);
+ kb.addAxiom(disjointAtomTypes);
+ // all different axiom (UNA)
+ // exporting differentIndividuals axioms is broken in OWL API
+// individuals.addAll(compounds);
+// individuals.addAll(bonds);
+// DifferentIndividualsAxiom una = getDifferentIndividualsAxiom(individuals);
+// kb.addAxiom(una);
+
duration = System.nanoTime() - startTime;
time = Helper.prettyPrintNanoSeconds(duration, false, false);
System.out.println("OK (" + time + ").");
@@ -294,6 +310,7 @@
String bondType = head.getArgument(3).toPLString();
String bondClass = "Bond-" + bondType;
String bondInstance = "bond" + bondNr;
+ bonds.add(bondInstance);
ObjectPropertyAssertion op = getRoleAssertion("hasBond", compoundName, "bond" + bondNr);
axioms.add(op);
// make Bond-X subclass of Bond if that hasn't been done already
@@ -426,6 +443,21 @@
return new DoubleDatatypePropertyAssertion(dp, ind, value);
}
+ private static DisjointClassesAxiom getDisjointClassesAxiom(Set<String> classes) {
+ Set<Description> descriptions = new HashSet<Description>();
+ for(String namedClass : classes)
+ descriptions.add(new NamedClass(namedClass));
+ return new DisjointClassesAxiom(descriptions);
+ }
+
+ @SuppressWarnings({"unused"})
+ private static DifferentIndividualsAxiom getDifferentIndividualsAxiom(Set<String> individuals) {
+ Set<Individual> inds = new HashSet<Individual>();
+ for(String i : individuals)
+ inds.add(new Individual(i));
+ return new DifferentIndividualsAxiom(inds);
+ }
+
private static Individual getIndividual(String name) {
return new Individual(ontologyURI + "#" + name);
}
Modified: trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIAxiomConvertVisitor.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIAxiomConvertVisitor.java 2008-02-23 09:10:40 UTC (rev 631)
+++ trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIAxiomConvertVisitor.java 2008-02-23 21:13:06 UTC (rev 632)
@@ -31,9 +31,13 @@
import org.dllearner.core.owl.Datatype;
import org.dllearner.core.owl.DatatypePropertyDomainAxiom;
import org.dllearner.core.owl.DatatypePropertyRangeAxiom;
+import org.dllearner.core.owl.Description;
+import org.dllearner.core.owl.DifferentIndividualsAxiom;
+import org.dllearner.core.owl.DisjointClassesAxiom;
import org.dllearner.core.owl.DoubleDatatypePropertyAssertion;
import org.dllearner.core.owl.EquivalentClassesAxiom;
import org.dllearner.core.owl.FunctionalObjectPropertyAxiom;
+import org.dllearner.core.owl.Individual;
import org.dllearner.core.owl.InverseObjectPropertyAxiom;
import org.dllearner.core.owl.KB;
import org.dllearner.core.owl.ObjectPropertyAssertion;
@@ -294,4 +298,28 @@
addAxiom(axiomOWLAPI);
}
+ /* (non-Javadoc)
+ * @see org.dllearner.core.owl.AssertionalAxiomVisitor#visit(org.dllearner.core.owl.DifferentIndividualsAxiom)
+ */
+ public void visit(DifferentIndividualsAxiom axiom) {
+ Set<Individual> individuals = axiom.getIndividuals();
+ Set<OWLIndividual> owlAPIIndividuals = new HashSet<OWLIndividual>();
+ for(Individual individual : individuals)
+ owlAPIIndividuals.add(factory.getOWLIndividual(URI.create(individual.getName())));
+ OWLAxiom axiomOWLAPI = factory.getOWLDifferentIndividualsAxiom(owlAPIIndividuals);
+ addAxiom(axiomOWLAPI);
+ }
+
+ /* (non-Javadoc)
+ * @see org.dllearner.core.owl.TerminologicalAxiomVisitor#visit(org.dllearner.core.owl.DisjointClassesAxiom)
+ */
+ public void visit(DisjointClassesAxiom axiom) {
+ Set<Description> descriptions = axiom.getDescriptions();
+ Set<OWLDescription> owlAPIDescriptions = new HashSet<OWLDescription>();
+ for(Description description : descriptions)
+ owlAPIDescriptions.add(getOWLDescription(description));
+ OWLAxiom axiomOWLAPI = factory.getOWLDisjointClassesAxiom(owlAPIDescriptions);
+ addAxiom(axiomOWLAPI);
+ }
+
}
Added: trunk/src/dl-learner/org/dllearner/test/OWLAPIBugDemo.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/test/OWLAPIBugDemo.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/test/OWLAPIBugDemo.java 2008-02-23 21:13:06 UTC (rev 632)
@@ -0,0 +1,42 @@
+package org.dllearner.test;
+
+import org.semanticweb.owl.apibinding.OWLManager;
+import org.semanticweb.owl.model.*;
+import org.semanticweb.owl.util.SimpleURIMapper;
+
+import java.io.File;
+import java.net.URI;
+import java.util.HashSet;
+import java.util.Set;
+
+public class OWLAPIBugDemo {
+
+ public static void main(String[] args) {
+ try {
+
+ OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
+ URI ontologyURI = URI.create("http://www.examples.com/test");
+ File f = new File("test.owl");
+ URI physicalURI = f.toURI();
+ SimpleURIMapper mapper = new SimpleURIMapper(ontologyURI, physicalURI);
+ manager.addURIMapper(mapper);
+
+ OWLOntology ontology = manager.createOntology(ontologyURI);
+ OWLDataFactory factory = manager.getOWLDataFactory();
+
+ OWLIndividual a = factory.getOWLIndividual(URI.create(ontologyURI + "#a"));
+ OWLIndividual b = factory.getOWLIndividual(URI.create(ontologyURI + "#b"));
+ Set<OWLIndividual> inds = new HashSet<OWLIndividual>();
+ inds.add(a);
+ inds.add(b);
+
+ OWLAxiom axiom = factory.getOWLDifferentIndividualsAxiom(inds);
+ AddAxiom addAxiom = new AddAxiom(ontology, axiom);
+ manager.applyChange(addAxiom);
+ manager.saveOntology(ontology);
+ }
+ catch (OWLException e) {
+ e.printStackTrace();
+ }
+ }
+}
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