From: <ku...@us...> - 2011-04-05 10:19:07
|
Revision: 2755 http://dl-learner.svn.sourceforge.net/dl-learner/?rev=2755&view=rev Author: kurzum Date: 2011-04-05 10:18:56 +0000 (Tue, 05 Apr 2011) Log Message: ----------- Modified Paths: -------------- trunk/scripts/src/main/java/org/dllearner/scripts/improveWikipedia/DBpediaClassLearnerCELOE.java Added Paths: ----------- trunk/scripts/src/main/resources/ trunk/scripts/src/main/resources/allClasses.vm trunk/scripts/src/main/resources/directClassesOfInstance.vm trunk/scripts/src/main/resources/instancesOfClass.vm Removed Paths: ------------- trunk/scripts/src/main/java/org/dllearner/scripts/improveWikipedia/InstanceFinderSPARQL.java Modified: trunk/scripts/src/main/java/org/dllearner/scripts/improveWikipedia/DBpediaClassLearnerCELOE.java =================================================================== --- trunk/scripts/src/main/java/org/dllearner/scripts/improveWikipedia/DBpediaClassLearnerCELOE.java 2011-04-05 09:53:35 UTC (rev 2754) +++ trunk/scripts/src/main/java/org/dllearner/scripts/improveWikipedia/DBpediaClassLearnerCELOE.java 2011-04-05 10:18:56 UTC (rev 2755) @@ -25,7 +25,6 @@ import org.aksw.commons.sparql.core.decorator.CachingSparqlEndpoint; import org.aksw.commons.sparql.core.impl.HttpSparqlEndpoint; import org.apache.velocity.VelocityContext; -import org.apache.velocity.app.Velocity; import org.dllearner.algorithms.celoe.CELOE; import org.dllearner.core.ComponentManager; import org.dllearner.core.LearningProblemUnsupportedException; @@ -44,10 +43,8 @@ import java.io.File; import java.io.IOException; -import java.util.Arrays; -import java.util.HashSet; -import java.util.Set; -import java.util.SortedSet; +import java.util.*; +import java.util.logging.Logger; /** * A script, which learns definitions / super classes of classes in the DBpedia ontology. @@ -55,6 +52,8 @@ * @author Jens Lehmann */ public class DBpediaClassLearnerCELOE { + private static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(DBpediaClassLearnerCELOE.class); + SparqlEndpoint sparqlEndpoint = new CachingSparqlEndpoint(new HttpSparqlEndpoint("http://dbpedia.org/sparql", "http://dbpedia.org"), "cache/"); public DBpediaClassLearnerCELOE() { @@ -62,48 +61,29 @@ // parameters to the constructure e.g. YAGO_ } - public KB learnAllClasses(Set<String> classesToLearn) throws LearningProblemUnsupportedException, IOException { + public KB learnAllClasses(Set<String> classesToLearn) { KB kb = new KB(); for (String classToLearn : classesToLearn) { + try{ Description d = learnClass(classToLearn); if (d == null) { continue; } kb.addAxiom(new EquivalentClassesAxiom(new NamedClass(classToLearn), d)); + }catch (Exception e) { + logger.warn("", e); + } } return kb; } - public Description learnClass(String classToLearn) throws LearningProblemUnsupportedException, IOException { + public Description learnClass(String classToLearn) throws Exception { Set<String> posEx = getPosEx(classToLearn); if (posEx.isEmpty()) { return null; } - Set<String> classes = new HashSet<String>(); + Set<String> negEx = getNegEx(classToLearn, posEx); - for (String pos : posEx) { - SparqlTemplate st = new SparqlTemplate(0); - st.addFilter(sparqlEndpoint.like("classes", new HashSet<String>(Arrays.asList(new String[]{"http://dbpedia.org/ontology/"})))); - VelocityContext vc = new VelocityContext(); - vc.put("instance", pos ); - String query = st.getQuery("sparqltemplates/directClassesOfInstance.vm", vc); - classes.addAll(ResultSetRenderer.asStringSet(sparqlEndpoint.executeSelect(query))); - classes.remove(classToLearn); - } - System.out.println(classes.size()); - System.exit(0); - - Set<String> negEx = new HashSet<String>(); - for (String oneClass : classes) { - /* st = new SparqlTemplate(0); - st.addFilter(sparqlEndpoint.like("classes", new HashSet<String>(Arrays.asList(new String[]{"http://dbpedia.org/ontology/"})))); - query = st.getQuery("sparqltemplates/classesOfInstance.vm", new VelocityContext()); - classes.addAll(ResultSetRenderer.asStringSet(sparqlEndpoint.executeSelect(query))); - classes.remove(classToLearn);*/ - } - //System.out.println(posEx); - System.exit(0); - //Set<String> negEx = InstanceFinderSPARQL.findInstancesWithSimilarClasses(posEx, -1, sparqlEndpoint); SortedSet<Individual> posExamples = Helper.getIndividualSet(posEx); SortedSet<Individual> negExamples = Helper.getIndividualSet(negEx); SortedSetTuple<Individual> examples = new SortedSetTuple<Individual>(posExamples, negExamples); @@ -144,26 +124,72 @@ public static void main(String args[]) throws LearningProblemUnsupportedException, IOException { DBpediaClassLearnerCELOE dcl = new DBpediaClassLearnerCELOE(); - SparqlTemplate st = new SparqlTemplate(0); - st.addFilter(dcl.sparqlEndpoint.like("classes", new HashSet<String>(Arrays.asList(new String[]{"http://dbpedia.org/ontology/"})))); + Set<String> classesToLearn = dcl.getClasses(); + System.out.println(classesToLearn); + System.exit(0); - String query = st.getQuery("sparqltemplates/allClasses.vm", new VelocityContext()); - //System.out.println(query); - Set<String> classesToLearn = ResultSetRenderer.asStringSet(dcl.sparqlEndpoint.executeSelect(query)); - //System.out.println(classesToLearn); - KB kb = dcl.learnAllClasses(classesToLearn); System.exit(0); kb.export(new File("/dev/null"), OntologyFormat.RDF_XML); // TODO: pick appropriate place to save ontology } + public Set<String> getClasses(){ + SparqlTemplate st = new SparqlTemplate("allClasses.vm"); + st.setLimit(0); + st.addFilter(sparqlEndpoint.like("classes", new HashSet<String>(Arrays.asList(new String[]{"http://dbpedia.org/ontology/"})))); + VelocityContext vc = st.getVelocityContext(); + String query = st.getQuery(); + return ResultSetRenderer.asStringSet(sparqlEndpoint.executeSelect(query)); + } public Set<String> getPosEx(String clazz) { - VelocityContext vc = new VelocityContext(); + SparqlTemplate st = new SparqlTemplate("instancesOfClass.vm"); + st.setLimit(0); + VelocityContext vc = st.getVelocityContext(); vc.put("class", clazz); - vc.put("limit", 0); - String query = SparqlTemplate.instancesOfClass(vc); + String query = st.getQuery(); return ResultSetRenderer.asStringSet(sparqlEndpoint.executeSelect(query)); } + public Set<String> getNegEx(String clazz, Set<String> posEx) { + Map<String, Integer> m = new HashMap<String, Integer>(); + + for (String pos : posEx) { + SparqlTemplate st = new SparqlTemplate("directClassesOfInstance.vm"); + st.setLimit(0); + st.addFilter(sparqlEndpoint.like("classes", new HashSet<String>(Arrays.asList(new String[]{"http://dbpedia.org/ontology/"})))); + VelocityContext vc = st.getVelocityContext(); + vc.put("instance", pos); + String query = st.getQuery(); + Set<String> classes = ResultSetRenderer.asStringSet(sparqlEndpoint.executeSelect(query)); + classes.remove(clazz); + for (String s : classes) { + if (m.get(s) == null) { + m.put(s, 0); + } + m.put(s, m.get(s).intValue() + 1); + } + } + + int max = 0; + String maxClass = ""; + for (String key : m.keySet()) { + if (m.get(key).intValue() > max) { + maxClass = key; + } + } + + + SparqlTemplate st = new SparqlTemplate("instancesOfClass.vm"); + st.setLimit(0); + VelocityContext vc = st.getVelocityContext(); + vc.put("class", clazz); + String query = st.getQuery(); + Set<String> negEx = ResultSetRenderer.asStringSet(sparqlEndpoint.executeSelect(query)); + negEx.removeAll(posEx); + return negEx; + + + } + } Deleted: trunk/scripts/src/main/java/org/dllearner/scripts/improveWikipedia/InstanceFinderSPARQL.java =================================================================== --- trunk/scripts/src/main/java/org/dllearner/scripts/improveWikipedia/InstanceFinderSPARQL.java 2011-04-05 09:53:35 UTC (rev 2754) +++ trunk/scripts/src/main/java/org/dllearner/scripts/improveWikipedia/InstanceFinderSPARQL.java 2011-04-05 10:18:56 UTC (rev 2755) @@ -1,325 +0,0 @@ -/** - * Copyright (C) 2007, 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.scripts.improveWikipedia; - -import com.hp.hpl.jena.query.ResultSet; -import com.hp.hpl.jena.vocabulary.OWL; -import com.hp.hpl.jena.vocabulary.RDF; -import org.aksw.commons.sparql.core.ResultSetRenderer; -import org.aksw.commons.sparql.core.SparqlEndpoint; -import org.aksw.commons.sparql.core.SparqlTemplate; -import org.apache.log4j.Logger; -import org.apache.velocity.VelocityContext; -import org.dllearner.algorithm.tbsl.learning.SPARQLTemplateBasedLearner; -import org.dllearner.kb.sparql.SPARQLTasks; -import org.dllearner.utilities.datastructures.SetManipulation; - -import java.util.*; - -public class InstanceFinderSPARQL { - - // LOGGER: ComponentManager - private static Logger logger = Logger.getLogger(InstanceFinderSPARQL.class); - - /** - * query is SELECT ?subject { ?subject rdf:type owl:Thing } LIMIT 100 - * - * @param blacklist instances removed from the returned set - * @param sparqlEndpoint - * @param limit if <= 0, 100 will be used - * @return a set of uris - */ - public static Set<String> arbitraryInstances(Set<String> blacklist, SparqlEndpoint sparqlEndpoint, int limit) { - String query = "SELECT ?subject { ?subject <" + RDF.type + "> <" + OWL.Thing + "> } " + ((limit > 0) ? "LIMIT " + limit : " LIMIT 100"); - ResultSet r = sparqlEndpoint.executeSelect(query); - Set<String> s = ResultSetRenderer.asStringSet(r); - s.removeAll(blacklist); - logger.debug("retrieving " + s.size() + " random instances "); - return s; - } - - - /** - * TODO refactor - * makes neg ex from related instances, that take part in a role R(pos,neg) - * filters all objects, that don't use the given namespace - * - * @param instances - */ - public static void relatedInstances(Set<String> instances, Set<String> blacklist, Set<String> allowedProperties, SparqlEndpoint sparqlEndpoint) { - /*public void makeNegativeExamplesFromRelatedInstances(SortedSet<String> instances, - String objectNamespace) { - logger.debug("making examples from related instances"); - for (String oneInstance : instances) { - //makeNegativeExamplesFromRelatedInstances(oneInstance, objectNamespace); - } - logger.debug("|-negExample size from related: " + fromRelated.size()); - } */ - /*String query = "SELECT * { " + "<" + oneInstance + "> " + "?p ?object.}" - + "FILTER (REGEX(str(?object), '" + objectnamespace + "')).\n" + "}"; - // SortedSet<String> result = new TreeSet<String>(); - - String SPARQLquery = "SELECT * WHERE { \n" + "<" + oneInstance + "> " + "?p ?object. \n" - + "FILTER (REGEX(str(?object), '" + objectnamespace + "')).\n" + "}"; - - fromRelated.addAll(sparqltasks.queryAsSet(SPARQLquery, "object")); - fromRelated.removeAll(fullPositiveSet); - */ - } - - - /** - * TODO document - * @param instances this will serve as a blacklist also - */ - public static Set<String> findInstancesWithSimilarClasses(Set<String> instances, - int limit, SparqlEndpoint sparqlEndpoint) { - Set<String> classes = new HashSet<String>(); - Set<String> ret = new HashSet<String>(); - for (String instance : instances) { - try { - SparqlTemplate st = new SparqlTemplate(0); - //st.addFilter(sparqlEndpoint.like()); - VelocityContext vc = new VelocityContext(); - vc.put("instance", instance); - vc.put("limit", limit); - String query = SparqlTemplate.classesOfInstance(vc); - classes.addAll(ResultSetRenderer.asStringSet(sparqlEndpoint.executeSelect(query))); - } catch (Exception e) { - logger.warn("ignoring SPARQLQuery failure geClasses for " + instance); - } - - } - System.out.println(classes); - System.exit(0); - - logger.debug("retrieved " + classes.size() + " classes"); - - - for (String oneClass : classes) { - logger.debug(oneClass); - try { - VelocityContext vc = new VelocityContext(); - vc.put("class", oneClass); - vc.put("limit", limit); - String query = SparqlTemplate.classesOfInstance(vc); - ret.addAll(ResultSetRenderer.asStringSet(sparqlEndpoint.executeSelect(query))); - } catch (Exception e) { - logger.warn("ignoring SPARQLQuery failure classesOfInstance for " + oneClass); - } - } - - ret.removeAll(instances); - return ret; - - // superClasses.add(concept.replace("\"", "")); - // logger.debug("before"+superClasses); - // superClasses = dbpediaGetSuperClasses( superClasses, 4); - // logger.debug("getting negExamples from "+superClasses.size()+" - // superclasses"); - - /*for (String oneClass : classes) { - logger.debug(oneClass); - // rsc = new - // JenaResultSetConvenience(queryConcept("\""+oneClass+"\"",limit)); - try { - this.fromParallelClasses.addAll(sparqltasks.retrieveInstancesForClassDescription("\"" + oneClass - + "\"", sparqlResultLimit)); - } catch (Exception e) { - logger.warn("ignoring SPARQLQuery failure, see log/sparql.txt"); - } - } - - for (String instance : positiveSet) { - try { - classes.addAll(sparqltasks.getClassesForInstance(instance, sparqlResultLimit)); - - } - logger.debug("getting negExamples from " + classes.size() + " parallel classes"); - - - fromParallelClasses.removeAll(fullPositiveSet); - logger.debug("|-neg Example size from parallelclass: " + fromParallelClasses.size()); - */ - } - - - - - - /** - * aggregates all collected neg examples - * CAVE: it is necessary to call one of the make functions before calling this - * OTHERWISE it will choose random examples - * - * @param neglimit size of negative Example set, 0 means all, which can be quite large several thousands - * @param stable decides whether neg Examples are randomly picked, default false, faster for developing, since the cache can be used - */ - /*public SortedSet<String> getNegativeExamples - ( - int neglimit, - boolean stable) { - SortedSet<String> negatives = new TreeSet<String>(); - negatives.addAll(fromNearbyClasses); - negatives.addAll(fromParallelClasses); - negatives.addAll(fromRelated); - negatives.addAll(fromSuperclasses); - if (negatives.isEmpty()) { - negatives.addAll(fromRandom); - } - if (neglimit <= 0) { - logger.debug("neg Example size NO shrinking: " + negatives.size()); - return negatives; - } - - logger.debug("neg Example size before shrinking: " + negatives.size()); - if (stable) { - negatives = SetManipulation.stableShrink(negatives, neglimit); - } else { - negatives = SetManipulation.fuzzyShrink(negatives, neglimit); - } - logger.debug("neg Example size after shrinking: " + negatives.size()); - return negatives; - } */ - - - // keep a while may still be needed - /*public void dbpediaMakeNegativeExamplesFromRelatedInstances(String subject) { - // SortedSet<String> result = new TreeSet<String>(); - - String SPARQLquery = "SELECT * WHERE { \n" + "<" + subject + "> " + "?p ?o. \n" - + "FILTER (REGEX(str(?o), 'http://dbpedia.org/resource/')).\n" - + "FILTER (!REGEX(str(?p), 'http://www.w3.org/2004/02/skos'))\n" + "}"; - - this.fromRelated.addAll(sparqltasks.queryAsSet(SPARQLquery, "o")); - - }*/ - - /* - public void makeNegativeExamplesFromNearbyClasses(SortedSet<String> positiveSet, int sparqlResultLimit) { - SortedSet<String> classes = new TreeSet<String>(); - Iterator<String> instanceIter = positiveSet.iterator(); - while (classes.isEmpty() && instanceIter.hasNext()) { - classes.addAll(sparqltasks.getClassesForInstance(instanceIter.next(), 100)); - } - String concept = classes.first(); - if (filterClasses != null && filterClasses.size() > 0) { - boolean br = false; - for (String oneClass : classes) { - Iterator<String> iter = filterClasses.iterator(); - while (iter.hasNext()) { - if (oneClass.startsWith(iter.next())) { - break; - } else { - concept = oneClass; - br = true; - break; - } - } - if (br) break; - } - } - concept = concept.replaceAll("\"", ""); - SortedSet<String> superClasses = sparqltasks.getSuperClasses(concept, 1); - - classes = new TreeSet<String>(); - for (String oneSuperClass : superClasses) { - classes.addAll(sparqltasks.getSubClasses(oneSuperClass, 1)); - } - classes.remove(concept); - for (String oneClass : classes) { - try { - fromNearbyClasses.addAll(sparqltasks.retrieveInstancesForClassDescription("\"" - + oneClass + "\"", sparqlResultLimit)); - } catch (Exception e) { - } - } - - this.fromNearbyClasses.removeAll(fullPositiveSet); - } - - */ - - /** - * it gets the first class of an arbitrary instance and queries the superclasses of it, - * could be more elaborate. - * It is better to use makeNegativeExamplesFromSuperClasses - * - * @param positiveSet - * @param sparqlResultSetLimit - */ - /* public void makeNegativeExamplesFromSuperClassesOfInstances(SortedSet<String> positiveSet, - int sparqlResultSetLimit) { - SortedSet<String> classes = new TreeSet<String>(); - Iterator<String> instanceIter = positiveSet.iterator(); - while (classes.isEmpty() && instanceIter.hasNext()) { - classes.addAll(sparqltasks.getClassesForInstance(instanceIter.next(), sparqlResultSetLimit)); - - } - makeNegativeExamplesFromSuperClasses(classes.first(), sparqlResultSetLimit); - } - - - public void makeNegativeExamplesFromSuperClasses(String concept, int sparqlResultSetLimit) { - makeNegativeExamplesFromSuperClasses(concept, sparqlResultSetLimit, 2); - } - */ - /** - * if pos ex derive from one class, then neg ex are taken from a superclass - * - * @param concept - * @param sparqlResultSetLimit - */ - /* - public void makeNegativeExamplesFromSuperClasses(String concept, int sparqlResultSetLimit, int depth) { - - concept = concept.replaceAll("\"", ""); - // superClasses.add(concept.replace("\"", "")); - // logger.debug("before"+superClasses); - SortedSet<String> superClasses = sparqltasks.getSuperClasses(concept, depth); - logger.debug("making neg Examples from " + superClasses.size() + " superclasses"); - - for (String oneSuperClass : superClasses) { - logger.debug(oneSuperClass); - fromSuperclasses.addAll(sparqltasks.retrieveInstancesForClassDescription("\"" - + oneSuperClass + "\"", sparqlResultSetLimit)); - - } - this.fromSuperclasses.removeAll(fullPositiveSet); - logger.debug("|-neg Example from superclass: " + fromSuperclasses.size()); - } - - @SuppressWarnings("unused") - private void makeNegativeExamplesFromDomain(String role, int sparqlResultSetLimit) { - logger.debug("making Negative Examples from Domain of : " + role); - fromDomain.addAll(sparqltasks.getDomainInstances(role, sparqlResultSetLimit)); - fromDomain.removeAll(fullPositiveSet); - logger.debug("|-neg Example size from Domain: " + this.fromDomain.size()); - } - - @SuppressWarnings("unused") - private void makeNegativeExamplesFromRange(String role, int sparqlResultSetLimit) { - logger.debug("making Negative Examples from Range of : " + role); - fromRange.addAll(sparqltasks.getRangeInstances(role, sparqlResultSetLimit)); - fromRange.removeAll(fullPositiveSet); - logger.debug("|-neg Example size from Range: " + fromRange.size()); - } - */ -} Added: trunk/scripts/src/main/resources/allClasses.vm =================================================================== --- trunk/scripts/src/main/resources/allClasses.vm (rev 0) +++ trunk/scripts/src/main/resources/allClasses.vm 2011-04-05 10:18:56 UTC (rev 2755) @@ -0,0 +1,2 @@ +#parse("org/aksw/commons/sparqltemplates/prefix.vm") +SELECT ?classes #parse("org/aksw/commons/sparqltemplates/from.vm") { ?classes rdf:type owl:Class. #parse("org/aksw/commons/sparqltemplates/filter.vm") } #parse("org/aksw/commons/sparqltemplates/limit.vm") \ No newline at end of file Added: trunk/scripts/src/main/resources/directClassesOfInstance.vm =================================================================== --- trunk/scripts/src/main/resources/directClassesOfInstance.vm (rev 0) +++ trunk/scripts/src/main/resources/directClassesOfInstance.vm 2011-04-05 10:18:56 UTC (rev 2755) @@ -0,0 +1,7 @@ +#parse("org/aksw/commons/sparqltemplates/prefix.vm") +SELECT ?classes #parse("org/aksw/commons/sparqltemplates/from.vm") { + <$instance> rdf:type ?classes . + Optional{ ?sub rdfs:subClassOf ?classes } + Filter (!bound(?sub)). + #parse("org/aksw/commons/sparqltemplates/filter.vm") +} #parse("org/aksw/commons/sparqltemplates/limit.vm") \ No newline at end of file Added: trunk/scripts/src/main/resources/instancesOfClass.vm =================================================================== --- trunk/scripts/src/main/resources/instancesOfClass.vm (rev 0) +++ trunk/scripts/src/main/resources/instancesOfClass.vm 2011-04-05 10:18:56 UTC (rev 2755) @@ -0,0 +1,4 @@ +#parse("org/aksw/commons/sparqltemplates/prefix.vm") +SELECT ?instances #parse("org/aksw/commons/sparqltemplates/from.vm") { + { ?instances rdf:type <$class> } +} #parse("org/aksw/commons/sparqltemplates/limit.vm") \ No newline at end of file This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ku...@us...> - 2011-04-05 17:03:30
|
Revision: 2757 http://dl-learner.svn.sourceforge.net/dl-learner/?rev=2757&view=rev Author: kurzum Date: 2011-04-05 17:03:24 +0000 (Tue, 05 Apr 2011) Log Message: ----------- script finished Modified Paths: -------------- trunk/scripts/src/main/java/org/dllearner/scripts/improveWikipedia/DBpediaClassLearnerCELOE.java Added Paths: ----------- trunk/scripts/src/main/resources/parallelClass.vm trunk/scripts/src/main/resources/someInstances.vm Modified: trunk/scripts/src/main/java/org/dllearner/scripts/improveWikipedia/DBpediaClassLearnerCELOE.java =================================================================== --- trunk/scripts/src/main/java/org/dllearner/scripts/improveWikipedia/DBpediaClassLearnerCELOE.java 2011-04-05 12:44:33 UTC (rev 2756) +++ trunk/scripts/src/main/java/org/dllearner/scripts/improveWikipedia/DBpediaClassLearnerCELOE.java 2011-04-05 17:03:24 UTC (rev 2757) @@ -39,12 +39,13 @@ import org.dllearner.reasoning.FastInstanceChecker; import org.dllearner.utilities.Helper; import org.dllearner.utilities.datastructures.Datastructures; +import org.dllearner.utilities.datastructures.SetManipulation; import org.dllearner.utilities.datastructures.SortedSetTuple; import java.io.File; import java.io.IOException; +import java.net.URL; import java.util.*; -import java.util.logging.Logger; /** * A script, which learns definitions / super classes of classes in the DBpedia ontology. @@ -52,72 +53,100 @@ * @author Jens Lehmann */ public class DBpediaClassLearnerCELOE { - private static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(DBpediaClassLearnerCELOE.class); - SparqlEndpoint sparqlEndpoint = new CachingSparqlEndpoint(new HttpSparqlEndpoint("http://dbpedia.org/sparql", "http://dbpedia.org"), "cache/"); + public static String endpointurl = "http://139.18.2.96:8910/sparql"; + private static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(DBpediaClassLearnerCELOE.class); + + SparqlEndpoint sparqlEndpoint = new CachingSparqlEndpoint(new HttpSparqlEndpoint(endpointurl, "http://dbpedia.org"), "cache/"); + public DBpediaClassLearnerCELOE() { // OPTIONAL: if you want to do some case distinctions in the learnClass method, you could add // parameters to the constructure e.g. YAGO_ } - public KB learnAllClasses(Set<String> classesToLearn) { + public KB learnAllClasses(Set<String> classesToLearn) { KB kb = new KB(); for (String classToLearn : classesToLearn) { - try{ - Description d = learnClass(classToLearn); - if (d == null) { - continue; + try { + Description d = learnClass(classToLearn); + if (d == null) { + continue; + } + kb.addAxiom(new EquivalentClassesAxiom(new NamedClass(classToLearn), d)); + System.out.println(d); + } catch (Exception e) { + logger.warn("", e); } - kb.addAxiom(new EquivalentClassesAxiom(new NamedClass(classToLearn), d)); - }catch (Exception e) { - logger.warn("", e); - } } + return kb; } public Description learnClass(String classToLearn) throws Exception { - Set<String> posEx = getPosEx(classToLearn); + SortedSet<String> posEx = new TreeSet<String> (getPosEx(classToLearn)); + logger.info("Found " + posEx.size() + " positive examples"); if (posEx.isEmpty()) { return null; } - Set<String> negEx = getNegEx(classToLearn, posEx); + SortedSet<String> negEx = new TreeSet<String> (getNegEx(classToLearn, posEx)); + posEx = SetManipulation.fuzzyShrink(posEx, 100); + negEx = SetManipulation.fuzzyShrink(negEx, 100); + SortedSet<Individual> posExamples = Helper.getIndividualSet(posEx); SortedSet<Individual> negExamples = Helper.getIndividualSet(negEx); SortedSetTuple<Individual> examples = new SortedSetTuple<Individual>(posExamples, negExamples); - System.out.println(posEx.size()); - System.out.println(negEx.size()); - System.exit(0); + ComponentManager cm = ComponentManager.getInstance(); SparqlKnowledgeSource ks = cm.knowledgeSource(SparqlKnowledgeSource.class); ks.getConfigurator().setInstances(Datastructures.individualSetToStringSet(examples.getCompleteSet())); - ks.getConfigurator().setPredefinedEndpoint("DBPEDIA"); // TODO: probably the official endpoint is too slow? + //ks.getConfigurator().setPredefinedEndpoint("DBPEDIA"); // TODO: probably the official endpoint is too slow? + ks.getConfigurator().setUrl(new URL(endpointurl)); + ks.getConfigurator().setUseLits(false); + ks.getConfigurator().setUseCacheDatabase(true); + ks.getConfigurator().setRecursionDepth(2); + ks.getConfigurator().setSaveExtractedFragment(true); + ks.getConfigurator().setPredList( new HashSet<String> (Arrays.asList(new String[]{ + "http://dbpedia.org/property/wikiPageUsesTemplate", + "http://dbpedia.org/ontology/wikiPageExternalLink", + "http://dbpedia.org/property/wordnet_type", + "http://www.w3.org/2002/07/owl#sameAs"}))); + + ks.getConfigurator().setObjList(new HashSet<String> (Arrays.asList(new String[]{"http://dbpedia.org/class/yago/","http://dbpedia.org/resource/Category:"}))); + + + + + ks.init(); - + ReasonerComponent rc = cm.reasoner(FastInstanceChecker.class, ks); rc.init(); - + PosNegLPStandard lp = cm.learningProblem(PosNegLPStandard.class, rc); lp.getConfigurator().setAccuracyMethod("fMeasure"); lp.getConfigurator().setUseApproximations(false); lp.init(); - + CELOE la = cm.learningAlgorithm(CELOE.class, lp, rc); CELOEConfigurator cc = la.getConfigurator(); cc.setMaxExecutionTimeInSeconds(100); + cc.setUseNegation(false); + cc.setUseAllConstructor(false); + cc.setUseCardinalityRestrictions(false); + cc.setUseHasValueConstructor(true); cc.setNoisePercentage(20); - // TODO: set more options as needed la.init(); - + // to write the above configuration in a conf file (optional) Config cf = new Config(cm, ks, rc, lp, la); new ConfigSave(cf).saveFile(new File("/dev/null")); la.start(); + return la.getCurrentlyBestDescription(); } @@ -125,33 +154,32 @@ DBpediaClassLearnerCELOE dcl = new DBpediaClassLearnerCELOE(); Set<String> classesToLearn = dcl.getClasses(); - System.out.println(classesToLearn); - System.exit(0); KB kb = dcl.learnAllClasses(classesToLearn); - System.exit(0); - kb.export(new File("/dev/null"), OntologyFormat.RDF_XML); // TODO: pick appropriate place to save ontology + kb.export(new File("result.owl"), OntologyFormat.RDF_XML); } - public Set<String> getClasses(){ + public Set<String> getClasses() { SparqlTemplate st = new SparqlTemplate("allClasses.vm"); st.setLimit(0); st.addFilter(sparqlEndpoint.like("classes", new HashSet<String>(Arrays.asList(new String[]{"http://dbpedia.org/ontology/"})))); VelocityContext vc = st.getVelocityContext(); String query = st.getQuery(); - return ResultSetRenderer.asStringSet(sparqlEndpoint.executeSelect(query)); + return new HashSet<String>(ResultSetRenderer.asStringSet(sparqlEndpoint.executeSelect(query))); } public Set<String> getPosEx(String clazz) { SparqlTemplate st = new SparqlTemplate("instancesOfClass.vm"); st.setLimit(0); VelocityContext vc = st.getVelocityContext(); + System.out.println(clazz); vc.put("class", clazz); String query = st.getQuery(); - return ResultSetRenderer.asStringSet(sparqlEndpoint.executeSelect(query)); + return new HashSet<String>(ResultSetRenderer.asStringSet(sparqlEndpoint.executeSelect(query))); } - public Set<String> getNegEx(String clazz, Set<String> posEx) { + + public String selectClass(String clazz, Set<String> posEx) { Map<String, Integer> m = new HashMap<String, Integer>(); for (String pos : posEx) { @@ -161,7 +189,7 @@ VelocityContext vc = st.getVelocityContext(); vc.put("instance", pos); String query = st.getQuery(); - Set<String> classes = ResultSetRenderer.asStringSet(sparqlEndpoint.executeSelect(query)); + Set<String> classes = new HashSet<String>(ResultSetRenderer.asStringSet(sparqlEndpoint.executeSelect(query))); classes.remove(clazz); for (String s : classes) { if (m.get(s) == null) { @@ -171,6 +199,7 @@ } } + int max = 0; String maxClass = ""; for (String key : m.keySet()) { @@ -178,18 +207,47 @@ maxClass = key; } } + return maxClass; + } + public Set<String> getNegEx(String clazz, Set<String> posEx) { + Set<String> negEx = new HashSet<String>(); + String targetClass = getParallelClass(clazz); + if (targetClass != null) { - SparqlTemplate st = new SparqlTemplate("instancesOfClass.vm"); - st.setLimit(0); - VelocityContext vc = st.getVelocityContext(); - vc.put("class", clazz); - String query = st.getQuery(); - Set<String> negEx = ResultSetRenderer.asStringSet(sparqlEndpoint.executeSelect(query)); + SparqlTemplate st = new SparqlTemplate("instancesOfClass.vm"); + st.setLimit(0); + VelocityContext vc = st.getVelocityContext(); + vc.put("class", targetClass); + st.addFilter(sparqlEndpoint.like("class", new HashSet<String>(Arrays.asList(new String[]{"http://dbpedia.org/ontology/"})))); + String query = st.getQuery(); + negEx.addAll(new HashSet<String>(ResultSetRenderer.asStringSet(sparqlEndpoint.executeSelect(query)))); + } else { + + SparqlTemplate st = new SparqlTemplate("someInstances.vm"); + st.setLimit(posEx.size() + 100); + VelocityContext vc = st.getVelocityContext(); + String query = st.getQuery(); + negEx.addAll(new HashSet<String>(ResultSetRenderer.asStringSet(sparqlEndpoint.executeSelect(query)))); + } negEx.removeAll(posEx); return negEx; } + + public String getParallelClass(String clazz) { + SparqlTemplate st = new SparqlTemplate("parallelClass.vm"); + st.setLimit(0); + VelocityContext vc = st.getVelocityContext(); + vc.put("class", clazz); + String query = st.getQuery(); + Set<String> negEx = new HashSet<String>(ResultSetRenderer.asStringSet(sparqlEndpoint.executeSelect(query))); + for (String s : negEx) { + return s; + } + return null; + } + } Copied: trunk/scripts/src/main/resources/parallelClass.vm (from rev 2755, trunk/scripts/src/main/resources/directClassesOfInstance.vm) =================================================================== --- trunk/scripts/src/main/resources/parallelClass.vm (rev 0) +++ trunk/scripts/src/main/resources/parallelClass.vm 2011-04-05 17:03:24 UTC (rev 2757) @@ -0,0 +1,7 @@ +#parse("org/aksw/commons/sparqltemplates/prefix.vm") +SELECT ?sub #parse("org/aksw/commons/sparqltemplates/from.vm") { + <$class> rdfs:subClassOf ?super . + ?sub rdfs:subClassOf ?super . + Filter (?sub != <$class>) . + #parse("org/aksw/commons/sparqltemplates/filter.vm") +} #parse("org/aksw/commons/sparqltemplates/limit.vm") \ No newline at end of file Added: trunk/scripts/src/main/resources/someInstances.vm =================================================================== --- trunk/scripts/src/main/resources/someInstances.vm (rev 0) +++ trunk/scripts/src/main/resources/someInstances.vm 2011-04-05 17:03:24 UTC (rev 2757) @@ -0,0 +1,5 @@ +#parse("org/aksw/commons/sparqltemplates/prefix.vm") +SELECT ?instances #parse("org/aksw/commons/sparqltemplates/from.vm") { + ?instances rdf:type owl:Thing . + #parse("org/aksw/commons/sparqltemplates/filter.vm") +} #parse("org/aksw/commons/sparqltemplates/limit.vm") \ No newline at end of file This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ku...@us...> - 2011-04-15 07:26:46
|
Revision: 2770 http://dl-learner.svn.sourceforge.net/dl-learner/?rev=2770&view=rev Author: kurzum Date: 2011-04-15 07:26:40 +0000 (Fri, 15 Apr 2011) Log Message: ----------- minor fix in script Modified Paths: -------------- trunk/scripts/src/main/java/org/dllearner/scripts/improveWikipedia/DBpediaClassLearnerCELOE.java trunk/scripts/src/main/resources/directClassesOfInstance.vm Modified: trunk/scripts/src/main/java/org/dllearner/scripts/improveWikipedia/DBpediaClassLearnerCELOE.java =================================================================== --- trunk/scripts/src/main/java/org/dllearner/scripts/improveWikipedia/DBpediaClassLearnerCELOE.java 2011-04-14 06:29:57 UTC (rev 2769) +++ trunk/scripts/src/main/java/org/dllearner/scripts/improveWikipedia/DBpediaClassLearnerCELOE.java 2011-04-15 07:26:40 UTC (rev 2770) @@ -81,13 +81,13 @@ for (String classToLearn : classesToLearn) { try { Description d = learnClass(classToLearn); - if (d == null) { - logger.error("Description was null, continueing"); - //continue; + if (d == null || d.toKBSyntaxString().equals(new Thing().toKBSyntaxString()) ) { + logger.error("Description was "+d+", continueing"); + continue; } kb.addAxiom(new EquivalentClassesAxiom(new NamedClass(classToLearn), d)); kb.export(new File("result_partial.owl"), OntologyFormat.RDF_XML); - System.out.println(d); + System.out.println("DESCRIPTION: "+d); } catch (Exception e) { logger.warn("", e); } @@ -203,7 +203,7 @@ for (String pos : posEx) { SparqlTemplate st = SparqlTemplate.getInstance("directClassesOfInstance.vm"); st.setLimit(0); - st.addFilter(sparqlEndpoint.like("classes", new HashSet<String>(Arrays.asList(new String[]{"http://dbpedia.org/ontology/"})))); + st.addFilter(sparqlEndpoint.like("direct", new HashSet<String>(Arrays.asList(new String[]{"http://dbpedia.org/ontology/"})))); VelocityContext vc = st.getVelocityContext(); vc.put("instance", pos); String query = st.getQuery(); @@ -271,8 +271,8 @@ VelocityContext vc = st.getVelocityContext(); vc.put("class", clazz); String query = st.getQuery(); - Set<String> negEx = new HashSet<String>(ResultSetRenderer.asStringSet(sparqlEndpoint.executeSelect(query))); - for (String s : negEx) { + Set<String> parClasses = new HashSet<String>(ResultSetRenderer.asStringSet(sparqlEndpoint.executeSelect(query))); + for (String s : parClasses) { return s; } return null; Modified: trunk/scripts/src/main/resources/directClassesOfInstance.vm =================================================================== --- trunk/scripts/src/main/resources/directClassesOfInstance.vm 2011-04-14 06:29:57 UTC (rev 2769) +++ trunk/scripts/src/main/resources/directClassesOfInstance.vm 2011-04-15 07:26:40 UTC (rev 2770) @@ -1,7 +1,12 @@ #parse("org/aksw/commons/sparqltemplates/prefix.vm") SELECT ?classes #parse("org/aksw/commons/sparqltemplates/from.vm") { - <$instance> rdf:type ?classes . - Optional{ ?sub rdfs:subClassOf ?classes } - Filter (!bound(?sub)). + <$instance> rdf:type ?direct . + + Optional{ + <$instance> rdf:type ?super . + Filter (?super != ?direct) . + ?direct rdfs:subClassOf ?super . + } + Filter (!bound(?super)). #parse("org/aksw/commons/sparqltemplates/filter.vm") } #parse("org/aksw/commons/sparqltemplates/limit.vm") \ No newline at end of file This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <lor...@us...> - 2011-11-10 14:58:36
|
Revision: 3394 http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3394&view=rev Author: lorenz_b Date: 2011-11-10 14:58:27 +0000 (Thu, 10 Nov 2011) Log Message: ----------- Started script which picks some random resources from endpoint, and retrieves their surrounding up to a specific level and uses this data together with a generated DBpedia ontology for debugging tests. Added Paths: ----------- trunk/scripts/src/main/java/org/dllearner/scripts/SPARQLSampleDebugging.java trunk/scripts/src/main/resources/dbpedia_0.75.owl Added: trunk/scripts/src/main/java/org/dllearner/scripts/SPARQLSampleDebugging.java =================================================================== --- trunk/scripts/src/main/java/org/dllearner/scripts/SPARQLSampleDebugging.java (rev 0) +++ trunk/scripts/src/main/java/org/dllearner/scripts/SPARQLSampleDebugging.java 2011-11-10 14:58:27 UTC (rev 3394) @@ -0,0 +1,129 @@ +package org.dllearner.scripts; + +import java.io.ByteArrayInputStream; +import java.io.ByteArrayOutputStream; +import java.net.URL; +import java.util.Collections; +import java.util.HashSet; +import java.util.Set; + +import org.apache.log4j.Level; +import org.apache.log4j.Logger; +import org.dllearner.algorithm.qtl.util.ModelGenerator; +import org.dllearner.algorithm.qtl.util.ModelGenerator.Strategy; +import org.dllearner.kb.sparql.ExtractionDBCache; +import org.dllearner.kb.sparql.SparqlEndpoint; +import org.dllearner.kb.sparql.SparqlQuery; +import org.semanticweb.owlapi.apibinding.OWLManager; +import org.semanticweb.owlapi.model.IRI; +import org.semanticweb.owlapi.model.OWLOntology; +import org.semanticweb.owlapi.model.OWLOntologyCreationException; +import org.semanticweb.owlapi.model.OWLOntologyManager; +import org.semanticweb.owlapi.reasoner.OWLReasoner; + +import com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory; +import com.hp.hpl.jena.query.ResultSet; +import com.hp.hpl.jena.rdf.model.Model; +import com.hp.hpl.jena.rdf.model.ModelFactory; + +public class SPARQLSampleDebugging { + + private SparqlEndpoint endpoint; + private ExtractionDBCache cache = new ExtractionDBCache("cache"); + + private int sampleSize = 1000; + private int depth = 3; + + private Logger logger = Logger.getLogger(SPARQLSampleDebugging.class); + + public SPARQLSampleDebugging(SparqlEndpoint endpoint) { + this.endpoint = endpoint; + } + + private Set<String> extractSampleResources(int offset){ + logger.info("Extracting " + sampleSize + "sample resources..."); + long startTime = System.currentTimeMillis(); + Set<String> resources = new HashSet<String>(); + String query = String.format("SELECT DISTINCT ?s WHERE {?s a ?type} LIMIT %d OFFSET %d", sampleSize, offset); + + ResultSet rs = SparqlQuery.convertJSONtoResultSet(cache.executeSelectQuery(endpoint, query)); + + while(rs.hasNext()){ + resources.add(rs.next().getResource("s").getURI()); + } + logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms."); + return resources; + } + + private OWLOntology extractSampleModule(Set<String> resources){ + logger.info("Extracting sample module..."); + long startTime = System.currentTimeMillis(); + ModelGenerator modelGen = new ModelGenerator(endpoint, cache); + Model model = ModelFactory.createDefaultModel(); + for(String resource : resources){ + model.add(modelGen.createModel(resource, Strategy.CHUNKS, depth)); + } + logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms."); + return convert(model); + + } + + private OWLOntology loadReferenceOntology() throws OWLOntologyCreationException{ + OWLOntology ontology = OWLManager.createOWLOntologyManager().loadOntologyFromOntologyDocument( + getClass().getClassLoader().getResourceAsStream("dbpedia_0.75.owl")); + return ontology; + } + + private OWLOntology convert(Model model) { + ByteArrayOutputStream baos = new ByteArrayOutputStream(); + model.write(baos, "N-TRIPLE"); + ByteArrayInputStream bais = new ByteArrayInputStream(baos.toByteArray()); + OWLOntologyManager manager = OWLManager.createOWLOntologyManager(); + OWLOntology retOnt = null; + try { + retOnt = manager.loadOntologyFromOntologyDocument(bais); + } catch (OWLOntologyCreationException e) { + + } + return retOnt; + } + + public void run() throws OWLOntologyCreationException{ + OWLOntology reference = loadReferenceOntology(); + + OWLOntology sample; + OWLOntology merged; + OWLReasoner reasoner; + for(int i = 0; i < 10; i++){ + Set<String> resources = extractSampleResources(i * sampleSize); + sample = extractSampleModule(resources); + + Set<OWLOntology> ontologies = new HashSet<OWLOntology>(); + ontologies.add(sample); + ontologies.add(reference); + + merged = OWLManager.createOWLOntologyManager().createOntology(IRI.create("http://merged.en"), ontologies); + + reasoner = PelletReasonerFactory.getInstance().createNonBufferingReasoner(merged); + boolean isConsistent = reasoner.isConsistent(); + logger.info("Consistent: " + isConsistent); + System.out.println(isConsistent); + reasoner.dispose(); + } + + } + + /** + * @param args + * @throws Exception + */ + public static void main(String[] args) throws Exception { + Logger.getRootLogger().setLevel(Level.INFO); + Logger.getLogger(SPARQLSampleDebugging.class).setLevel(Level.INFO); + SparqlEndpoint endpoint = new SparqlEndpoint(new URL("http://dbpedia.aksw.org:8902/sparql"), + Collections.singletonList("http://dbpedia.org"), Collections.<String>emptyList()); + new SPARQLSampleDebugging(endpoint).run(); + + } + +} Property changes on: trunk/scripts/src/main/java/org/dllearner/scripts/SPARQLSampleDebugging.java ___________________________________________________________________ Added: svn:mime-type + text/plain Added: trunk/scripts/src/main/resources/dbpedia_0.75.owl =================================================================== --- trunk/scripts/src/main/resources/dbpedia_0.75.owl (rev 0) +++ trunk/scripts/src/main/resources/dbpedia_0.75.owl 2011-11-10 14:58:27 UTC (rev 3394) @@ -0,0 +1,32812 @@ +<?xml version="1.0"?> +<rdf:RDF xmlns="owlapi:ontology:ont1#" + xml:base="owlapi:ontology:ont1" + xmlns:Software="http://dbpedia.org/ontology/Software/" + xmlns:Astronaut="http://dbpedia.org/ontology/Astronaut/" + xmlns:SpaceStation="http://dbpedia.org/ontology/SpaceStation/" + xmlns:Building="http://dbpedia.org/ontology/Building/" + xmlns:Work="http://dbpedia.org/ontology/Work/" + xmlns:GrandPrix="http://dbpedia.org/ontology/GrandPrix/" + xmlns:Spacecraft="http://dbpedia.org/ontology/Spacecraft/" + xmlns:Infrastructure="http://dbpedia.org/ontology/Infrastructure/" + xmlns:MeanOfTransportation="http://dbpedia.org/ontology/MeanOfTransportation/" + xmlns:schema="http://schema.org/" + xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" + xmlns:PopulatedPlace="http://dbpedia.org/ontology/PopulatedPlace/" + xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" + xmlns:SpaceShuttle="http://dbpedia.org/ontology/SpaceShuttle/" + xmlns:Lake="http://dbpedia.org/ontology/Lake/" + xmlns:LunarCrater="http://dbpedia.org/ontology/LunarCrater/" + xmlns:School="http://dbpedia.org/ontology/School/" + xmlns:Rocket="http://dbpedia.org/ontology/Rocket/" + xmlns:foaf="http://xmlns.com/foaf/0.1/" + xmlns:AutomobileEngine="http://dbpedia.org/ontology/AutomobileEngine/" + xmlns:Automobile="http://dbpedia.org/ontology/Automobile/" + xmlns:ontology="http://dbpedia.org/ontology/" + xmlns:Canal="http://dbpedia.org/ontology/Canal/" + xmlns:SpaceMission="http://dbpedia.org/ontology/SpaceMission/" + xmlns:Planet="http://dbpedia.org/ontology/Planet/" + xmlns:Stream="http://dbpedia.org/ontology/Stream/" + xmlns:Weapon="http://dbpedia.org/ontology/Weapon/" + xmlns:xsd="http://www.w3.org/2001/XMLSchema#" + xmlns:owl="http://www.w3.org/2002/07/owl#" + xmlns:gml="http://www.opengis.net/gml/" + xmlns:Person="http://dbpedia.org/ontology/Person/"> + <owl:Ontology rdf:about="owlapi:ontology:ont1"/> + + + + <!-- + /////////////////////////////////////////////////////////////////////////////////////// + // + // Datatypes + // + /////////////////////////////////////////////////////////////////////////////////////// + --> + + + + + <!-- http://dbpedia.org/datatype/centimetre --> + + <rdfs:Datatype rdf:about="http://dbpedia.org/datatype/centimetre"/> + + + + <!-- http://dbpedia.org/datatype/cubicCentimetre --> + + <rdfs:Datatype rdf:about="http://dbpedia.org/datatype/cubicCentimetre"/> + + + + <!-- http://dbpedia.org/datatype/cubicKilometre --> + + <rdfs:Datatype rdf:about="http://dbpedia.org/datatype/cubicKilometre"/> + + + + <!-- http://dbpedia.org/datatype/cubicMetre --> + + <rdfs:Datatype rdf:about="http://dbpedia.org/datatype/cubicMetre"/> + + + + <!-- http://dbpedia.org/datatype/cubicMetrePerSecond --> + + <rdfs:Datatype rdf:about="http://dbpedia.org/datatype/cubicMetrePerSecond"/> + + + + <!-- http://dbpedia.org/datatype/day --> + + <rdfs:Datatype rdf:about="http://dbpedia.org/datatype/day"/> + + + + <!-- http://dbpedia.org/datatype/engineConfiguration --> + + <rdfs:Datatype rdf:about="http://dbpedia.org/datatype/engineConfiguration"/> + + + + <!-- http://dbpedia.org/datatype/euro --> + + <rdfs:Datatype rdf:about="http://dbpedia.org/datatype/euro"/> + + + + <!-- http://dbpedia.org/datatype/fuelType --> + + <rdfs:Datatype rdf:about="http://dbpedia.org/datatype/fuelType"/> + + + + <!-- http://dbpedia.org/datatype/hour --> + + <rdfs:Datatype rdf:about="http://dbpedia.org/datatype/hour"/> + + + + <!-- http://dbpedia.org/datatype/inhabitantsPerSquareKilometre --> + + <rdfs:Datatype rdf:about="http://dbpedia.org/datatype/inhabitantsPerSquareKilometre"/> + + + + <!-- http://dbpedia.org/datatype/kelvin --> + + <rdfs:Datatype rdf:about="http://dbpedia.org/datatype/kelvin"/> + + + + <!-- http://dbpedia.org/datatype/kilogram --> + + <rdfs:Datatype rdf:about="http://dbpedia.org/datatype/kilogram"/> + + + + <!-- http://dbpedia.org/datatype/kilogramPerCubicMetre --> + + <rdfs:Datatype rdf:about="http://dbpedia.org/datatype/kilogramPerCubicMetre"/> + + + + <!-- http://dbpedia.org/datatype/kilometre --> + + <rdfs:Datatype rdf:about="http://dbpedia.org/datatype/kilometre"/> + + + + <!-- http://dbpedia.org/datatype/kilometrePerSecond --> + + <rdfs:Datatype rdf:about="http://dbpedia.org/datatype/kilometrePerSecond"/> + + + + <!-- http://dbpedia.org/datatype/kilowatt --> + + <rdfs:Datatype rdf:about="http://dbpedia.org/datatype/kilowatt"/> + + + + <!-- http://dbpedia.org/datatype/litre --> + + <rdfs:Datatype rdf:about="http://dbpedia.org/datatype/litre"/> + + + + <!-- http://dbpedia.org/datatype/megabyte --> + + <rdfs:Datatype rdf:about="http://dbpedia.org/datatype/megabyte"/> + + + + <!-- http://dbpedia.org/datatype/metre --> + + <rdfs:Datatype rdf:about="http://dbpedia.org/datatype/metre"/> + + + + <!-- http://dbpedia.org/datatype/millimetre --> + + <rdfs:Datatype rdf:about="http://dbpedia.org/datatype/millimetre"/> + + + + <!-- http://dbpedia.org/datatype/minute --> + + <rdfs:Datatype rdf:about="http://dbpedia.org/datatype/minute"/> + + + + <!-- http://dbpedia.org/datatype/newtonMetre --> + + <rdfs:Datatype rdf:about="http://dbpedia.org/datatype/newtonMetre"/> + + + + <!-- http://dbpedia.org/datatype/poundSterling --> + + <rdfs:Datatype rdf:about="http://dbpedia.org/datatype/poundSterling"/> + + + + <!-- http://dbpedia.org/datatype/squareKilometre --> + + <rdfs:Datatype rdf:about="http://dbpedia.org/datatype/squareKilometre"/> + + + + <!-- http://dbpedia.org/datatype/squareMetre --> + + <rdfs:Datatype rdf:about="http://dbpedia.org/datatype/squareMetre"/> + + + + <!-- http://dbpedia.org/datatype/usDollar --> + + <rdfs:Datatype rdf:about="http://dbpedia.org/datatype/usDollar"/> + + + + <!-- http://dbpedia.org/datatype/valvetrain --> + + <rdfs:Datatype rdf:about="http://dbpedia.org/datatype/valvetrain"/> + + + + <!-- http://www.w3.org/2001/XMLSchema#date --> + + <rdfs:Datatype rdf:about="http://www.w3.org/2001/XMLSchema#date"/> + + + + <!-- http://www.w3.org/2001/XMLSchema#gYear --> + + <rdfs:Datatype rdf:about="http://www.w3.org/2001/XMLSchema#gYear"/> + + + + <!-- http://www.w3.org/2001/XMLSchema#gYearMonth --> + + <rdfs:Datatype rdf:about="http://www.w3.org/2001/XMLSchema#gYearMonth"/> + + + + <!-- + /////////////////////////////////////////////////////////////////////////////////////// + // + // Object Properties + // + /////////////////////////////////////////////////////////////////////////////////////// + --> + + + + + <!-- http://dbpedia.org/ontology/academicAdvisor --> + + <owl:ObjectProperty rdf:about="http://dbpedia.org/ontology/academicAdvisor"> + <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#InverseFunctionalProperty"/> + <rdfs:domain rdf:resource="http://dbpedia.org/ontology/Person"/> + <rdfs:domain rdf:resource="http://dbpedia.org/ontology/Scientist"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/actScore"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/addressInRoad"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/administrativeCollectivity"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/administrativeDistrict"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/affiliation"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/aircraftAttack"/> + 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<owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/regionServed"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/regionalLanguage"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/related"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/relatedMeanOfTransportation"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/relation"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/relative"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/religion"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/religiousHead"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/religiousHeadLabel"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/residence"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/resolution"/> + <owl:propertyDisjointWith 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<owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/routeEnd"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/routeEndLocation"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/routeJunctio... [truncated message content] |
From: <lor...@us...> - 2011-12-06 15:14:45
|
Revision: 3479 http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3479&view=rev Author: lorenz_b Date: 2011-12-06 15:14:33 +0000 (Tue, 06 Dec 2011) Log Message: ----------- Added example. Modified Paths: -------------- trunk/scripts/src/main/java/org/dllearner/scripts/ApproximateDebugging.java Added Paths: ----------- trunk/scripts/src/main/resources/dbpedia_0.75_no_datapropaxioms.owl Modified: trunk/scripts/src/main/java/org/dllearner/scripts/ApproximateDebugging.java =================================================================== --- trunk/scripts/src/main/java/org/dllearner/scripts/ApproximateDebugging.java 2011-12-06 15:01:09 UTC (rev 3478) +++ trunk/scripts/src/main/java/org/dllearner/scripts/ApproximateDebugging.java 2011-12-06 15:14:33 UTC (rev 3479) @@ -484,11 +484,11 @@ ConciseBoundedDescriptionGenerator cbdGen = new ConciseBoundedDescriptionGeneratorImpl(endpoint, new ExtractionDBCache("cache")); // ConciseBoundedDescriptionGenerator cbdGen = new SymmetricConciseBoundedDescriptionGeneratorImpl(endpoint, new ExtractionDBCache("cache")); - Model model = cbdGen.getConciseBoundedDescription(resource, 4); + Model model = cbdGen.getConciseBoundedDescription(resource, 3); OWLOntology data = convert(model); OWLOntologyManager man = OWLManager.createOWLOntologyManager(); - OWLOntology schema = man.loadOntologyFromOntologyDocument(new File("/home/lorenz/arbeit/dbpedia_0.75_no_datapropaxioms.owl")); + OWLOntology schema = man.loadOntologyFromOntologyDocument(new File("src/main/resources/dbpedia_0.75_no_datapropaxioms.owl")); ApproximateDebugging debug = new ApproximateDebugging(schema, data); Set<Set<OWLAxiom>> explanations1 = debug.computeInconsistencyExplanations(); Added: trunk/scripts/src/main/resources/dbpedia_0.75_no_datapropaxioms.owl =================================================================== --- trunk/scripts/src/main/resources/dbpedia_0.75_no_datapropaxioms.owl (rev 0) +++ trunk/scripts/src/main/resources/dbpedia_0.75_no_datapropaxioms.owl 2011-12-06 15:14:33 UTC (rev 3479) @@ -0,0 +1,234448 @@ +<?xml version="1.0"?> +<rdf:RDF xmlns="owlapi:ontology:ont1#" + xml:base="owlapi:ontology:ont1" + xmlns:schema="http://schema.org/" + xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" + xmlns:foaf="http://xmlns.com/foaf/0.1/" + 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:gml="http://www.opengis.net/gml/" + xmlns:ontology="http://dbpedia.org/ontology/" + xmlns:skos="http://www.w3.org/2004/02/skos/core#"> + <owl:Ontology rdf:about="owlapi:ontology:ont1"/> + + + + <!-- + /////////////////////////////////////////////////////////////////////////////////////// + // + // Object Properties + // + /////////////////////////////////////////////////////////////////////////////////////// + --> + + + + + <!-- http://dbpedia.org/ontology/academicAdvisor --> + + <owl:ObjectProperty rdf:about="http://dbpedia.org/ontology/academicAdvisor"> + <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#AsymmetricProperty"/> + <rdf:type 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rdf:resource="http://dbpedia.org/ontology/aircraftBomber"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/aircraftElectronic"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/aircraftFighter"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/aircraftHelicopter"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/aircraftHelicopterAttack"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/aircraftHelicopterCargo"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/aircraftHelicopterMultirole"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/aircraftHelicopterObservation"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/aircraftHelicopterTransport"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/aircraftHelicopterUtility"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/aircraftInterceptor"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/aircraftPatrol"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/aircraftRecon"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/aircraftTrainer"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/aircraftTransport"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/album"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/alliance"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/almaMater"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/alumni"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/animal"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/anthem"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/appointer"/> + 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rdf:resource="http://dbpedia.org/ontology/associatedBand"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/associatedMusicalArtist"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/associatedRocket"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/associationOfLocalGovernment"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/athletics"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/author"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/authority"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/automobilePlatform"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/availableSmartCard"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/award"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/bandMember"/> + <owl:propertyDisjointWith 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<owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/college"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/colour"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/commandStructure"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/commander"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/committeeInLegislature"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/company"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/comparable"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/compiler"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/component"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/composer"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/computingInput"/> + <owl:propertyDisjointWith 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<owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/education"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/educationSystem"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/emmyAward"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/employer"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/endPoint"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/endingTheme"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/engine"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/engineType"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/engineer"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/equipment"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/era"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/ethnicGroup"/> + 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rdf:resource="http://dbpedia.org/ontology/river"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/riverBranch"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/riverBranchOf"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/riverMouth"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/rocket"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/rocketFunction"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/routeEnd"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/routeEndLocation"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/routeJunction"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/routeStart"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/routeStartLocation"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/royalAnthem"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/runningMate"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/ruralMunicipality"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/saint"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/satScore"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/school"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/schoolBoard"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/schoolPatron"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/secondCommander"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/secondDriver"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/secondDriverCountry"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/secondLeader"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/secondPopularVote"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/secondTeam"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/secretaryGeneral"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/selection"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/series"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/service"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/servingRailwayLine"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/sheading"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/showJudge"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/significantBuilding"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/significantDesign"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/significantProject"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/similar"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/sisterCollege"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/sisterNewspaper"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/sisterStation"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/source"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/sourceConfluence"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/sourceConfluenceMountain"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/sourceConfluencePlace"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/sourceConfluencePosition"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/sourceConfluenceRegion"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/sourceConfluenceState"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/sourceCountry"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/sourceMountain"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/sourcePlace"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/sourcePosition"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/sourceRegion"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/spacecraft"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/species"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/splitFromParty"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/spokenIn"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/spokesperson"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/sport"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/sportCountry"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/sportGoverningBody"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/spouse"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/spurOf"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/starring"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/startPoint"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/state"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/stateDelegate"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/stateOfOrigin"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/statisticLabel"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/storyEditor"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/structuralSystem"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/stylisticOrigin"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/subregion"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/subsequentInfrastructure"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/subsequentWork"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/subsidiary"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/successor"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/summerAppearances"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/superintendent"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/supplies"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/targetAirport"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/targetSpaceStation"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/teachingStaff"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/team"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/tenant"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/territory"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/thirdCommander"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/thirdDriver"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/thirdDriverCountry"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/thirdTeam"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/timeZone"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/torchBearer"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/trainer"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/training"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/translator"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/trustee"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/twinCity"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/twinCountry"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/type"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/typeOfElectrification"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/unitaryAuthority"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/university"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/usedInWar"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/usingCountry"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/variantOf"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/varietals"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/vehicle"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/vein"/> + <owl:propertyDisjointWith rdf:resource="http://dbpedia.org/ontology/veneratedIn"/> + <owl:propertyDisjointWith rdf:resource="http... [truncated message content] |
From: <lor...@us...> - 2014-05-07 11:25:58
|
Revision: 4261 http://sourceforge.net/p/dl-learner/code/4261 Author: lorenz_b Date: 2014-05-07 11:25:54 +0000 (Wed, 07 May 2014) Log Message: ----------- Added eprocurement eval script. Added Paths: ----------- trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomsHTMLWriter.java trunk/scripts/src/main/java/org/dllearner/scripts/RAChallenge.java trunk/scripts/src/main/java/org/dllearner/scripts/evaluation/EProcurementUseCase.java trunk/scripts/src/main/java/org/dllearner/scripts/evaluation/QTLEvaluation.java trunk/scripts/src/main/java/org/dllearner/scripts/pattern/FixPointDetection.java trunk/scripts/src/main/java/org/dllearner/scripts/pattern/UserEvaluation.java trunk/scripts/src/main/resources/db_settings.ini Added: trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomsHTMLWriter.java =================================================================== --- trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomsHTMLWriter.java (rev 0) +++ trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomsHTMLWriter.java 2014-05-07 11:25:54 UTC (rev 4261) @@ -0,0 +1,91 @@ +package org.dllearner.scripts; + +import java.io.File; +import java.io.FileOutputStream; +import java.text.DecimalFormat; +import java.util.HashMap; +import java.util.List; +import java.util.Map; +import java.util.Map.Entry; +import java.util.SortedMap; +import java.util.TreeMap; + +import org.dllearner.utilities.MapUtils; +import org.semanticweb.owlapi.apibinding.OWLManager; +import org.semanticweb.owlapi.io.ToStringRenderer; +import org.semanticweb.owlapi.model.AxiomType; +import org.semanticweb.owlapi.model.IRI; +import org.semanticweb.owlapi.model.OWLAnnotationProperty; +import org.semanticweb.owlapi.model.OWLClass; +import org.semanticweb.owlapi.model.OWLClassExpression; +import org.semanticweb.owlapi.model.OWLDataFactory; +import org.semanticweb.owlapi.model.OWLEquivalentClassesAxiom; +import org.semanticweb.owlapi.model.OWLLiteral; +import org.semanticweb.owlapi.model.OWLOntology; +import org.semanticweb.owlapi.model.OWLOntologyManager; + +import uk.ac.manchester.cs.owl.owlapi.mansyntaxrenderer.ManchesterOWLSyntaxOWLObjectRendererImpl; + +public class OWLAxiomsHTMLWriter { + + public static void main(String[] args) throws Exception{ + if(args.length != 2){ + System.out.println("Usage: OWLAxiomsHTMLWriter <ontology> <targetFile>"); + } + ToStringRenderer.getInstance().setRenderer(new ManchesterOWLSyntaxOWLObjectRendererImpl()); + + String ontologyURL = args[0]; + OWLOntologyManager man = OWLManager.createOWLOntologyManager(); + OWLDataFactory dataFactory = man.getOWLDataFactory(); + OWLOntology ontology = man.loadOntologyFromOntologyDocument(new File(ontologyURL)); + OWLAnnotationProperty anProp = dataFactory.getOWLAnnotationProperty(IRI.create("http://www.dl-learner.org/ontologies/enrichment.owl#confidence")); + + StringBuilder sb = new StringBuilder(); + DecimalFormat dfPercent = new DecimalFormat("0.00%"); + sb.append("<html>\n"); + sb.append("<table border=\"3\">\n"); + sb.append("<thead><tr><th>Source Class</th><th>Equivalent Class Expression</th><th>Accuracy</th></tr></thead>\n"); + sb.append("<tbody>\n"); + + SortedMap<OWLClass, Map<OWLClassExpression, Double>> map = new TreeMap<OWLClass, Map<OWLClassExpression,Double>>(); + for (OWLEquivalentClassesAxiom axiom : ontology.getAxioms(AxiomType.EQUIVALENT_CLASSES)) { + List<OWLClassExpression> classExpressionsAsList = axiom.getClassExpressionsAsList(); + OWLClass left = classExpressionsAsList.get(0).asOWLClass(); + if(!left.toStringID().startsWith("http://dbpedia.org/ontology/"))continue;//skip not DBpedia + OWLClassExpression right = classExpressionsAsList.get(1); + OWLLiteral lit = (OWLLiteral) axiom.getAnnotations(anProp).iterator().next().getValue(); + double accuracy = lit.parseDouble(); + Map<OWLClassExpression, Double> equivalentClasses = map.get(left); + if(equivalentClasses == null){ + equivalentClasses = new HashMap<OWLClassExpression, Double>(); + map.put(left, equivalentClasses); + } + equivalentClasses.put(right, accuracy); + } + + for (Entry<OWLClass, Map<OWLClassExpression, Double>> entry : map.entrySet()) { + OWLClass cls = entry.getKey(); + Map<OWLClassExpression, Double> equivalentClasses = entry.getValue(); + List<Entry<OWLClassExpression, Double>> sorted = MapUtils.sortByValues(equivalentClasses); + sb.append("<tr><th rowspan=\"" + (sorted.size()+1) + "\">" + cls.toString() + "</th>\n"); + for (Entry<OWLClassExpression, Double> expr : sorted) { + OWLClassExpression classExpression = expr.getKey(); + Double value = expr.getValue(); + sb.append("<tr>"); + sb.append("<td>" + classExpression.toString() + "</td>"); + sb.append("<td>" + dfPercent.format(value.doubleValue()) + "</td>"); + sb.append("</tr>\n"); + } + + } + + sb.append("</tbody>\n"); + sb.append("</table>\n"); + sb.append("</html>\n"); + + FileOutputStream fos = new FileOutputStream(new File(args[1])); + fos.write(sb.toString().getBytes()); + fos.close(); + } + +} Added: trunk/scripts/src/main/java/org/dllearner/scripts/RAChallenge.java =================================================================== --- trunk/scripts/src/main/java/org/dllearner/scripts/RAChallenge.java (rev 0) +++ trunk/scripts/src/main/java/org/dllearner/scripts/RAChallenge.java 2014-05-07 11:25:54 UTC (rev 4261) @@ -0,0 +1,299 @@ +/** + * + */ +package org.dllearner.scripts; + +import java.io.ByteArrayInputStream; +import java.io.ByteArrayOutputStream; +import java.io.File; +import java.io.FileInputStream; +import java.io.FileNotFoundException; +import java.io.FileOutputStream; +import java.io.FilenameFilter; +import java.net.MalformedURLException; +import java.net.URL; +import java.util.ArrayList; +import java.util.HashMap; +import java.util.List; +import java.util.Map; +import java.util.Map.Entry; +import java.util.SortedSet; +import java.util.TreeSet; + +import org.dllearner.algorithms.celoe.CELOE; +import org.dllearner.algorithms.celoe.OEHeuristicRuntime; +import org.dllearner.algorithms.elcopy.ELLearningAlgorithm; +import org.dllearner.algorithms.qtl.QueryTreeFactory; +import org.dllearner.algorithms.qtl.datastructures.QueryTree; +import org.dllearner.algorithms.qtl.datastructures.impl.QueryTreeImpl; +import org.dllearner.algorithms.qtl.impl.QueryTreeFactoryImpl; +import org.dllearner.algorithms.qtl.operations.lgg.LGGGenerator; +import org.dllearner.algorithms.qtl.operations.lgg.LGGGeneratorImpl; +import org.dllearner.core.AbstractCELA; +import org.dllearner.core.KnowledgeSource; +import org.dllearner.core.owl.Individual; +import org.dllearner.core.owl.NamedClass; +import org.dllearner.kb.OWLAPIOntology; +import org.dllearner.kb.sparql.ConciseBoundedDescriptionGenerator; +import org.dllearner.kb.sparql.ConciseBoundedDescriptionGeneratorImpl; +import org.dllearner.kb.sparql.SparqlEndpoint; +import org.dllearner.learningproblems.PosNegLPStandard; +import org.dllearner.reasoning.FastInstanceChecker; +import org.dllearner.reasoning.OWLAPIReasoner; +import org.dllearner.refinementoperators.RhoDRDown; +import org.semanticweb.owlapi.apibinding.OWLManager; +import org.semanticweb.owlapi.io.ToStringRenderer; +import org.semanticweb.owlapi.model.OWLClassExpression; +import org.semanticweb.owlapi.model.OWLOntology; +import org.semanticweb.owlapi.model.OWLOntologyManager; +import org.semanticweb.owlapi.util.SimpleShortFormProvider; + +import uk.ac.manchester.cs.owl.owlapi.mansyntaxrenderer.ManchesterOWLSyntaxOWLObjectRendererImpl; + +import com.hp.hpl.jena.query.QueryExecution; +import com.hp.hpl.jena.query.QueryExecutionFactory; +import com.hp.hpl.jena.query.QuerySolution; +import com.hp.hpl.jena.query.ResultSet; +import com.hp.hpl.jena.query.ResultSetFormatter; +import com.hp.hpl.jena.rdf.model.Model; +import com.hp.hpl.jena.rdf.model.ModelFactory; +import com.hp.hpl.jena.rdf.model.RDFNode; +import com.hp.hpl.jena.rdf.model.Statement; +import com.hp.hpl.jena.rdf.model.StmtIterator; +import com.hp.hpl.jena.vocabulary.OWL; +import com.hp.hpl.jena.vocabulary.RDF; + +/** + * @author Lorenz Buehmann + * + */ +public class RAChallenge { + + + private static boolean useEL = false; + + static Map<String, String> prefixes = new HashMap<>(); + + private static String baseURI = "http://bio2rdf.org/ra.challenge:"; + + static { + +// prefixes.put("ra", "http://bio2rdf.org/ra.challenge:"); + prefixes.put("ra-voc", "http://bio2rdf.org/ra.challenge_vocabulary:"); + prefixes.put("dbsnp", "http://bio2rdf.org/dbsnp:"); + prefixes.put("xsd", "http://www.w3.org/2001/XMLSchema#"); + prefixes.put("foaf", "http://xmlns.com/foaf/0.1/"); + prefixes.put("rdfs", "http://www.w3.org/2000/01/rdf-schema#"); + prefixes.put("rdf", "http://www.w3.org/1999/02/22-rdf-syntax-ns#"); + prefixes.put("drug-voc", "http://bio2rdf.org/drugbank_vocabulary:"); + + + } + + public static void main(String[] args) throws Exception{ + //load the data + File dataDir = new File(args[0]); + File[] files = dataDir.listFiles(new FilenameFilter() { + @Override + public boolean accept(File dir, String name) { + return name.endsWith(".nt") || name.endsWith(".ttl") || name.endsWith(".rdf") || name.endsWith(".owl"); + } + }); + System.out.println("loading data..."); + Model model = ModelFactory.createDefaultModel(); + for (File file : files) { + model.read(new FileInputStream(file), null, "TURTLE"); + } + + analyzeData(model); + + //get the positive and negative examples via SPARQL + //<http://bio2rdf.org/ra.challenge:1877000> <http://bio2rdf.org/ra.challenge_vocabulary:non-responder> "true"^^<http://www.w3.org/2001/XMLSchema#boolean> . + System.out.println("extracting pos/neg examples..."); + SortedSet<Individual> posExamples = new TreeSet<Individual>(); + SortedSet<Individual> negExamples = new TreeSet<Individual>(); + String query = "SELECT ?s WHERE {?s <http://bio2rdf.org/ra.challenge_vocabulary:non-responder> \"true\"^^<http://www.w3.org/2001/XMLSchema#boolean>} limit 400"; + QueryExecution qe = QueryExecutionFactory.create(query, model); + ResultSet rs = qe.execSelect(); + QuerySolution qs; + while(rs.hasNext()){ + qs = rs.next(); + posExamples.add(new Individual(qs.getResource("s").getURI())); + } + query = "SELECT ?s WHERE {?s <http://bio2rdf.org/ra.challenge_vocabulary:non-responder> \"false\"^^<http://www.w3.org/2001/XMLSchema#boolean>} limit 400"; + qe = QueryExecutionFactory.create(query, model); + rs = qe.execSelect(); + while(rs.hasNext()){ + qs = rs.next(); + negExamples.add(new Individual(qs.getResource("s").getURI())); + } + qe.close(); + System.out.println("#pos examples: " + posExamples.size()); + System.out.println("#neg examples: " + negExamples.size()); + + //remove triples with property non-responder + model.remove(model.listStatements(null, model.createProperty("http://bio2rdf.org/ra.challenge_vocabulary:non-responder"), (RDFNode)null)); + + //enrich with additional data + enrich(model); + + //check the LGG +// computeLGG(model, posExamples); + + //convert JENA model to OWL API ontology + ByteArrayOutputStream baos = new ByteArrayOutputStream(); + model.write(baos , "N-TRIPLES"); + OWLOntologyManager man = OWLManager.createOWLOntologyManager(); + OWLOntology ontology = man.loadOntologyFromOntologyDocument(new ByteArrayInputStream(baos.toByteArray())); + + //init knowledge source + KnowledgeSource ks = new OWLAPIOntology(ontology); + + //init reasoner + System.out.println("initializing reasoner..."); + OWLAPIReasoner baseReasoner = new OWLAPIReasoner(ks); +// baseReasoner.setReasonerTypeString("elk"); + baseReasoner.init(); + FastInstanceChecker rc = new FastInstanceChecker(ks); + rc.setReasonerComponent(baseReasoner); + rc.setBaseURI(baseURI); + rc.setPrefixes(prefixes); + rc.init(); + + //init learning problem + System.out.println("initializing learning problem..."); + PosNegLPStandard lp = new PosNegLPStandard(rc, posExamples, negExamples); + lp.setUseApproximations(true); + lp.init(); + + //init learning algorithm + System.out.println("initializing learning algorithm..."); + AbstractCELA la; + if(useEL){ + la = new ELLearningAlgorithm(lp, rc); + ((ELLearningAlgorithm) la).setNoisePercentage(30); + ((ELLearningAlgorithm) la).setMaxNrOfResults(50); + ((ELLearningAlgorithm) la).setTreeSearchTimeSeconds(10); + } else { + OEHeuristicRuntime heuristic = new OEHeuristicRuntime(); + heuristic.setExpansionPenaltyFactor(0.1); + la = new CELOE(lp, rc); + ((CELOE) la).setHeuristic(heuristic); + ((CELOE) la).setMaxExecutionTimeInSeconds(100); + ((CELOE) la).setNoisePercentage(50); + ((CELOE) la).setMaxNrOfResults(50); + ((CELOE) la).setWriteSearchTree(true); + ((CELOE) la).setReplaceSearchTree(true); + ((CELOE) la).setStartClass(new NamedClass("http://xmlns.com/foaf/0.1/Person")); + RhoDRDown op = new RhoDRDown(); + op.setUseHasValueConstructor(true); + op.setUseObjectValueNegation(true); + op.setReasoner(rc); + op.init(); +// ((CELOE) la).setOperator(op); + } + la.init(); + + la.start(); + } + + /** + * Do some statistical queries. + * @param model + */ + private static void analyzeData(Model model){ + String query = "SELECT (COUNT(DISTINCT ?s)AS ?cnt) WHERE {?s <http://bio2rdf.org/ra.challenge_vocabulary:has-two> ?o.} "; + QueryExecution qe = QueryExecutionFactory.create(query, model); + ResultSet rs = qe.execSelect(); + System.out.println(ResultSetFormatter.asText(rs)); + + query = "SELECT ?o (COUNT(?s) AS ?cnt) WHERE {?s <http://bio2rdf.org/ra.challenge_vocabulary:has-two> ?o." +// + "OPTIONAL{?s_res <http://bio2rdf.org/ra.challenge_vocabulary:non-responder> \"true\"^^<http://www.w3.org/2001/XMLSchema#boolean>.FILTER(?s=s_res)} " +// + "?s_non_res <http://bio2rdf.org/ra.challenge_vocabulary:non-responder> \"false\"^^<http://www.w3.org/2001/XMLSchema#boolean>" + + "}" + + " GROUP BY ?o ORDER BY DESC(?cnt)"; + qe = QueryExecutionFactory.create(query, model); + rs = qe.execSelect(); + System.out.println(ResultSetFormatter.asText(rs)); + + query = "SELECT ?o (COUNT(?s) AS ?cnt) WHERE {" + + "?s <http://bio2rdf.org/ra.challenge_vocabulary:has-two> ?o." + + "?s <http://bio2rdf.org/ra.challenge_vocabulary:non-responder> \"true\"^^<http://www.w3.org/2001/XMLSchema#boolean>." + + "}" + + " GROUP BY ?o ORDER BY DESC(?cnt)"; + qe = QueryExecutionFactory.create(query, model); + rs = qe.execSelect(); + System.out.println(ResultSetFormatter.asText(rs)); + + query = "SELECT ?o (COUNT(?s) AS ?total) (Min(?cnt_res) as ?responder) (Min(?cnt_non_res) as ?non_responder) WHERE {" + + "?s <http://bio2rdf.org/ra.challenge_vocabulary:has-two> ?o." + + "{SELECT ?o (COUNT(?s) AS ?cnt_res) WHERE {" + + "?s <http://bio2rdf.org/ra.challenge_vocabulary:has-two> ?o." + + "?s <http://bio2rdf.org/ra.challenge_vocabulary:non-responder> \"true\"^^<http://www.w3.org/2001/XMLSchema#boolean>." + + "} GROUP BY ?o}" + + "{SELECT ?o (COUNT(?s) AS ?cnt_non_res) WHERE {" + + "?s <http://bio2rdf.org/ra.challenge_vocabulary:has-two> ?o." + + "?s <http://bio2rdf.org/ra.challenge_vocabulary:non-responder> \"false\"^^<http://www.w3.org/2001/XMLSchema#boolean>." + + "}" + + " GROUP BY ?o}} GROUP BY ?o ORDER BY DESC(?total)"; + qe = QueryExecutionFactory.create(query, model); + rs = qe.execSelect(); + System.out.println(ResultSetFormatter.asText(rs)); + } + + private static void computeLGG(Model model, SortedSet<Individual> posExamples){ + QueryTreeFactory<String> queryTreeFactory = new QueryTreeFactoryImpl(); + + List<QueryTree<String>> posExampleTrees = new ArrayList<QueryTree<String>>(); + for (Individual ex : posExamples) { + QueryTreeImpl<String> tree = queryTreeFactory.getQueryTree(ex.getName(), model); + posExampleTrees.add(tree); + } + + LGGGenerator<String> lggGenerator = new LGGGeneratorImpl<String>(); + QueryTree<String> lgg = lggGenerator.getLGG(posExampleTrees); + String lggString = lgg.getStringRepresentation(true); + lggString = lggString.replace(baseURI, ""); + for (Entry<String, String> entry : prefixes.entrySet()) { + String key = entry.getKey(); + String value = entry.getValue(); + lggString = lggString.replace(value, key + ":"); + } + System.out.println(lggString); + + OWLClassExpression classExpression = lgg.asOWLClassExpression(); + ToStringRenderer.getInstance().setRenderer(new ManchesterOWLSyntaxOWLObjectRendererImpl()); + ToStringRenderer.getInstance().setShortFormProvider(new SimpleShortFormProvider()); + System.out.println(classExpression); + } + + private static void enrich(Model model) throws MalformedURLException, FileNotFoundException{ + System.out.println("enriching data..."); + SparqlEndpoint endpoint = new SparqlEndpoint(new URL("http://cu.drugbank.bio2rdf.org/sparql")); + +// StmtIterator stmtIterator = model.listStatements(null, RDF.type, (RDFNode)null); +// Model classes = ModelFactory.createDefaultModel(); +// while(stmtIterator.hasNext()){ +// Statement st = stmtIterator.next(); +// classes.add(classes.createStatement(st.getObject().asResource(), RDF.type, OWL.Class)); +// } +// classes.write(new FileOutputStream("classes.nt"), "TURTLE"); + + ConciseBoundedDescriptionGenerator cbdGen = new ConciseBoundedDescriptionGeneratorImpl(endpoint, "cache/drugbank"); + List<RDFNode> drugs = model.listObjectsOfProperty(model.getProperty("http://bio2rdf.org/ra.challenge_vocabulary:drug")).toList(); + Model drugbankData = ModelFactory.createDefaultModel(); + Model cbd; + for (RDFNode drug : drugs) { + cbd = cbdGen.getConciseBoundedDescription(drug.asResource().getURI(), 0, true); + drugbankData.add(cbd); + } + drugbankData.setNsPrefix("drug-voc", "http://bio2rdf.org/drugbank_vocabulary:"); + drugbankData.setNsPrefix("drug-res", "http://bio2rdf.org/drugbank_resource:"); + drugbankData.setNsPrefix("drug", "http://bio2rdf.org/drugbank:"); + + drugbankData.write(new FileOutputStream("drugbank.ttl"), "TURTLE", null); + model.add(drugbankData); + + + } +} Added: trunk/scripts/src/main/java/org/dllearner/scripts/evaluation/EProcurementUseCase.java =================================================================== --- trunk/scripts/src/main/java/org/dllearner/scripts/evaluation/EProcurementUseCase.java (rev 0) +++ trunk/scripts/src/main/java/org/dllearner/scripts/evaluation/EProcurementUseCase.java 2014-05-07 11:25:54 UTC (rev 4261) @@ -0,0 +1,290 @@ +/** + * + */ +package org.dllearner.scripts.evaluation; + +import static org.dllearner.utilities.examples.AutomaticNegativeExampleFinderSPARQL2.Strategy.SIBLING; +import static org.dllearner.utilities.examples.AutomaticNegativeExampleFinderSPARQL2.Strategy.SUPERCLASS; + +import java.io.ByteArrayInputStream; +import java.io.ByteArrayOutputStream; +import java.io.File; +import java.io.FileInputStream; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Collection; +import java.util.Collections; +import java.util.HashMap; +import java.util.List; +import java.util.Map; +import java.util.Map.Entry; +import java.util.Set; +import java.util.SortedSet; + +import org.apache.log4j.Logger; +import org.dllearner.algorithms.celoe.CELOE; +import org.dllearner.algorithms.elcopy.ELLearningAlgorithm; +import org.dllearner.algorithms.qtl.QueryTreeFactory; +import org.dllearner.algorithms.qtl.datastructures.QueryTree; +import org.dllearner.algorithms.qtl.datastructures.impl.QueryTreeImpl; +import org.dllearner.algorithms.qtl.impl.QueryTreeFactoryImpl; +import org.dllearner.algorithms.qtl.operations.lgg.LGGGenerator; +import org.dllearner.algorithms.qtl.operations.lgg.LGGGeneratorImpl; +import org.dllearner.core.AbstractCELA; +import org.dllearner.core.AbstractKnowledgeSource; +import org.dllearner.core.AbstractLearningProblem; +import org.dllearner.core.AbstractReasonerComponent; +import org.dllearner.core.owl.Individual; +import org.dllearner.core.owl.NamedClass; +import org.dllearner.kb.LocalModelBasedSparqlEndpointKS; +import org.dllearner.kb.OWLAPIOntology; +import org.dllearner.kb.sparql.ConciseBoundedDescriptionGenerator; +import org.dllearner.kb.sparql.ConciseBoundedDescriptionGeneratorImpl; +import org.dllearner.learningproblems.PosNegLPStandard; +import org.dllearner.reasoning.FastInstanceChecker; +import org.dllearner.reasoning.SPARQLReasoner; +import org.dllearner.refinementoperators.RhoDRDown; +import org.dllearner.utilities.examples.AutomaticNegativeExampleFinderSPARQL2; +import org.dllearner.utilities.owl.OWLEntityTypeAdder; +import org.semanticweb.owlapi.apibinding.OWLManager; +import org.semanticweb.owlapi.model.OWLOntology; + +import com.google.common.collect.Sets; +import com.hp.hpl.jena.rdf.model.Model; +import com.hp.hpl.jena.rdf.model.ModelFactory; +import com.hp.hpl.jena.vocabulary.OWL; +import com.hp.hpl.jena.vocabulary.RDFS; + +/** + * @author Lorenz Buehmann + * + */ +public class EProcurementUseCase { + + + private static final Logger logger = Logger.getLogger(EProcurementUseCase.class.getName()); + static final int maxNrOfPositiveExamples = 100; + static final int maxNrOfNegativeExamples = 200; + static boolean posOnly = false; + static int maxCBDDepth = 2; + static int maxNrOfResults = 100; + static int maxExecutionTimeInSeconds = 200; + static double noiseInPercentage = 50; + static boolean useNegation = false; + static boolean useAllConstructor = false; + static String testFolder = "logs/eprocurement"; + + static boolean useEL = false; + private static int maxClassExpressionDepth = 2; + + static Map<String, String> prefixes = new HashMap<String, String>();; + static { + prefixes.put("pc", "http://purl.org/procurement/public-contracts#"); + prefixes.put("rdfs", "http://www.w3.org/2000/01/rdf-schema#"); + prefixes.put("skos", "http://www.w3.org/2004/02/skos/core#"); + prefixes.put("dcterms", "http://purl.org/dc/terms/"); + prefixes.put("rdf", "http://www.w3.org/1999/02/22-rdf-syntax-ns#"); + prefixes.put("activities", "http://purl.org/procurement/public-contracts-activities#"); + prefixes.put("gr", "http://purl.org/goodrelations/v1#"); + prefixes.put("schema", "http://schema.org/"); + + + } + + /** + * @param args + */ + public static void main(String[] args) throws Exception{ + NamedClass posClass = new NamedClass("http://purl.org/procurement/public-contracts#SuccessfulTender"); + NamedClass negClass = new NamedClass("http://purl.org/procurement/public-contracts#UnsuccessfulTender"); + + //1. setup the knowledge base + Model model = ModelFactory.createDefaultModel(); + //the data + model.read(new FileInputStream("../test/eprocurement/dl-learner-sample-with-classes-pco.rdf"), null); + //the schema + Model schema = ModelFactory.createDefaultModel(); + schema.read(new FileInputStream("../test/eprocurement/pco.rdf"), null); + schema.add(schema.getResource("http://purl.org/procurement/public-contracts#SuccessfulTender"), + OWL.disjointWith, + schema.getResource("http://purl.org/procurement/public-contracts#UnsuccessfulTender")); + schema.add(schema.getResource("http://purl.org/procurement/public-contracts#SuccessfulTender"), + RDFS.subClassOf, + schema.getResource("http://purl.org/procurement/public-contracts#Tender")); + schema.add(schema.getResource("http://purl.org/procurement/public-contracts#UnsuccessfulTender"), + RDFS.subClassOf, + schema.getResource("http://purl.org/procurement/public-contracts#Tender")); +// schema.read(new URL("http://opendata.cz/pco/public-contracts.ttl").openStream(), null, "TURTLE"); + model.add(schema); + // get positive examples + SortedSet<Individual> positiveExamples = getExamples(model, posClass); + // get negative examples +// SortedSet<Individual> negativeExamples = getNegativeExamples(model, cls, positiveExamples); + SortedSet<Individual> negativeExamples = getExamples(model, negClass); + //get the lgg of the pos. examples +// showLGG(model, positiveExamples); + // build a sample of the kb + model = getSample(model, Sets.union(positiveExamples, negativeExamples)); + //add inferred entity types + OWLEntityTypeAdder.addEntityTypes(model); + //the ontology + model.add(schema); + //convert all into DL-Learner kb object + ByteArrayOutputStream baos = new ByteArrayOutputStream(); + model.write(baos, "TURTLE"); + OWLOntology ontology = OWLManager.createOWLOntologyManager().loadOntologyFromOntologyDocument(new ByteArrayInputStream(baos.toByteArray())); + AbstractKnowledgeSource ks = new OWLAPIOntology(ontology); + ks.init(); + + + + //2. setup the reasoner + AbstractReasonerComponent rc = new FastInstanceChecker(ks); + rc.init(); + + //3. setup the learning problem + AbstractLearningProblem lp; +// lp = new ClassLearningProblem(rc); +// ((ClassLearningProblem)lp).setClassToDescribe(cls); +// ((ClassLearningProblem)lp).setEquivalence(true); + lp = new PosNegLPStandard(rc, positiveExamples, negativeExamples); + lp.init(); + + //4. setup the learning algorithm + AbstractCELA la; + if(useEL){ + la = new ELLearningAlgorithm(lp, rc); + ((ELLearningAlgorithm)la).setNoisePercentage(noiseInPercentage); +// ((ELLearningAlgorithm)la).setStartClass(startClass); + ((ELLearningAlgorithm)la).setIgnoredConcepts(Sets.newHashSet(posClass)); + ((ELLearningAlgorithm)la).setClassToDescribe(posClass); + ((ELLearningAlgorithm)la).setTreeSearchTimeSeconds(maxExecutionTimeInSeconds); + ((ELLearningAlgorithm)la).setMaxNrOfResults(maxNrOfResults); + ((ELLearningAlgorithm)la).setMaxClassExpressionDepth(maxClassExpressionDepth ); +// la = new ELLearningAlgorithmDisjunctive(lp, reasoner); + } else { + //set up the refinement operator and the allowed OWL constructs + RhoDRDown rop = new RhoDRDown(); + rop.setReasoner(rc); + rop.setUseNegation(useNegation); + rop.setUseAllConstructor(useAllConstructor); + rop.init(); + //build CELOE la + CELOE laTmp = new CELOE(lp, rc); + laTmp.setMaxNrOfResults(maxNrOfResults); + laTmp.setOperator(rop); + laTmp.setMaxExecutionTimeInSeconds(maxExecutionTimeInSeconds); +// laTmp.setStartClass(startClass); + laTmp.setNoisePercentage(noiseInPercentage); + new File(testFolder).mkdirs(); + laTmp.setSearchTreeFile(testFolder + "searchTree.txt"); + laTmp.setWriteSearchTree(true); +// isle.setTerminateOnNoiseReached(true); + laTmp.setIgnoredConcepts(Collections.singleton(posClass)); + laTmp.setReplaceSearchTree(true); + laTmp.setMaxExecutionTimeInSeconds(maxExecutionTimeInSeconds); + laTmp.setExpandAccuracy100Nodes(true); + la = laTmp; + } + la.init(); + + //5. run + la.start(); + + + } + + private static void showLGG(Model model, SortedSet<Individual> positiveExamples){ + LGGGenerator<String> lggGen = new LGGGeneratorImpl<String>(); + QueryTree<String> lgg = lggGen.getLGG(buildTrees(model, positiveExamples)); + String s = lgg.getStringRepresentation(); + for (Entry<String, String> entry : prefixes.entrySet()) { + s = s.replace(entry.getValue(), entry.getKey() + ":"); + } + System.out.println(s); + ((QueryTreeImpl<String>) lgg).asGraph(); + } + + private static SortedSet<Individual> getExamples(Model model, NamedClass cls){ + logger.info("Generating examples..."); + SortedSet<Individual> individuals = new SPARQLReasoner(new LocalModelBasedSparqlEndpointKS(model)).getIndividuals(cls, 1000); + List<Individual> individualsList = new ArrayList<>(individuals); +// Collections.shuffle(individualsList, new Random(1234)); + individuals.clear(); + individuals.addAll(individualsList.subList(0, Math.min(maxNrOfPositiveExamples, individualsList.size()))); + logger.info("Done. Got " + individuals.size() + ": " + individuals); + return individuals; + } + + private static SortedSet<Individual> getPositiveExamples(Model model, NamedClass cls){ + logger.info("Generating positive examples..."); + SortedSet<Individual> individuals = new SPARQLReasoner(new LocalModelBasedSparqlEndpointKS(model)).getIndividuals(cls, 1000); + List<Individual> individualsList = new ArrayList<>(individuals); +// Collections.shuffle(individualsList, new Random(1234)); + individuals.clear(); + individuals.addAll(individualsList.subList(0, Math.min(maxNrOfPositiveExamples, individualsList.size()))); + logger.info("Done. Got " + individuals.size() + ": " + individuals); + return individuals; + } + + private static SortedSet<Individual> getNegativeExamples(Model model, NamedClass classToDescribe, Set<Individual> positiveExamples){ + logger.info("Generating positive examples..."); + SortedSet<Individual> individuals = new AutomaticNegativeExampleFinderSPARQL2(new SPARQLReasoner(new LocalModelBasedSparqlEndpointKS(model))).getNegativeExamples(classToDescribe, positiveExamples, Arrays.asList(SIBLING, SUPERCLASS), maxNrOfNegativeExamples); + logger.info("Done. Got " + individuals.size() + ": " + individuals); + return individuals; + } + + private static Model getSample(Model model, Individual individual){ + logger.info("Generating sample..."); + ConciseBoundedDescriptionGenerator cbdGen = new ConciseBoundedDescriptionGeneratorImpl(model, maxCBDDepth); + Model sample = cbdGen.getConciseBoundedDescription(individual.getName(), maxCBDDepth, true); + logger.info("Done. Got " + sample.size() + " triples."); + return sample; + } + + private static Model getSample(Model model, Set<Individual> individuals){ + logger.info("Generating sample..."); + ConciseBoundedDescriptionGenerator cbdGen = new ConciseBoundedDescriptionGeneratorImpl(model, maxCBDDepth); + Model sample = ModelFactory.createDefaultModel(); + Model cbd; + for (Individual individual : individuals) { +// System.out.println("##########################"); +// System.out.println(individual); + try { + cbd = cbdGen.getConciseBoundedDescription(individual.getName(), maxCBDDepth, true); +// showTree(individual, model); + sample.add(cbd); + } catch (Exception e) { + e.printStackTrace(); + } + } + logger.info("Done. Got " + sample.size() + " triples."); + return sample; + } + + private static QueryTree<String> buildTree(Individual ind, Model model){ + QueryTreeFactory<String> qf = new QueryTreeFactoryImpl(); + QueryTreeImpl<String> queryTree = qf.getQueryTree(ind.getName(), model); + return queryTree; + } + + private static List<QueryTree<String>> buildTrees(Model model, Collection<Individual> individuals){ + List<QueryTree<String>> trees = new ArrayList<QueryTree<String>>(); + for (Individual individual : individuals) { + trees.add(buildTree(individual, getSample(model, individual))); + } + return trees; + } + + private static void showTree(Individual ind, Model model){ + QueryTree<String> tree = buildTree(ind, model); + String s = tree.getStringRepresentation(); + + for (Entry<String, String> entry : prefixes.entrySet()) { + s = s.replace(entry.getValue(), entry.getKey() + ":"); + } + System.out.println(s); + } + + +} Added: trunk/scripts/src/main/java/org/dllearner/scripts/evaluation/QTLEvaluation.java =================================================================== --- trunk/scripts/src/main/java/org/dllearner/scripts/evaluation/QTLEvaluation.java (rev 0) +++ trunk/scripts/src/main/java/org/dllearner/scripts/evaluation/QTLEvaluation.java 2014-05-07 11:25:54 UTC (rev 4261) @@ -0,0 +1,516 @@ +/** + * + */ +package org.dllearner.scripts.evaluation; + +import java.io.File; +import java.io.FileInputStream; +import java.io.FileNotFoundException; +import java.util.ArrayList; +import java.util.Collections; +import java.util.LinkedList; +import java.util.List; +import java.util.Random; +import java.util.SortedSet; +import java.util.TreeSet; + +import org.dllearner.algorithms.qtl.QTL2; +import org.dllearner.algorithms.qtl.QTL2Disjunctive; +import org.dllearner.algorithms.qtl.QueryTreeFactory; +import org.dllearner.algorithms.qtl.datastructures.QueryTree; +import org.dllearner.algorithms.qtl.datastructures.impl.QueryTreeImpl; +import org.dllearner.algorithms.qtl.impl.QueryTreeFactoryImpl; +import org.dllearner.cli.CrossValidation; +import org.dllearner.cli.SPARQLCrossValidation; +import org.dllearner.core.ComponentInitException; +import org.dllearner.core.LearningProblemUnsupportedException; +import org.dllearner.core.owl.Individual; +import org.dllearner.kb.LocalModelBasedSparqlEndpointKS; +import org.dllearner.kb.OWLAPIOntology; +import org.dllearner.learningproblems.PosNegLP; +import org.dllearner.learningproblems.PosNegLPStandard; +import org.dllearner.reasoning.FastInstanceChecker; +import org.dllearner.reasoning.SPARQLReasoner; +import org.semanticweb.owlapi.apibinding.OWLManager; +import org.semanticweb.owlapi.model.IRI; +import org.semanticweb.owlapi.model.OWLDataFactory; +import org.semanticweb.owlapi.model.OWLOntology; +import org.semanticweb.owlapi.model.OWLOntologyChange; +import org.semanticweb.owlapi.model.OWLOntologyCreationException; +import org.semanticweb.owlapi.model.OWLOntologyManager; +import org.semanticweb.owlapi.reasoner.OWLReasoner; +import org.semanticweb.owlapi.reasoner.OWLReasonerFactory; + +import com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory; +import com.google.common.collect.Lists; +import com.hp.hpl.jena.rdf.model.Model; +import com.hp.hpl.jena.rdf.model.ModelFactory; + +/** + * @author Lorenz Buehmann + * + */ +public class QTLEvaluation { + + int nrOfFolds = 10; + private int nrOfPosExamples = 100; + private int nrOfNegExamples = 100; + + List<String> posExamples = Lists.newArrayList( + "http://dl-learner.org/carcinogenesis#d1", + "http://dl-learner.org/carcinogenesis#d10", + "http://dl-learner.org/carcinogenesis#d101", + "http://dl-learner.org/carcinogenesis#d102", + "http://dl-learner.org/carcinogenesis#d103", + "http://dl-learner.org/carcinogenesis#d106", + "http://dl-learner.org/carcinogenesis#d107", + "http://dl-learner.org/carcinogenesis#d108", + "http://dl-learner.org/carcinogenesis#d11", + "http://dl-learner.org/carcinogenesis#d12", + "http://dl-learner.org/carcinogenesis#d13", + "http://dl-learner.org/carcinogenesis#d134", + "http://dl-learner.org/carcinogenesis#d135", + "http://dl-learner.org/carcinogenesis#d136", + "http://dl-learner.org/carcinogenesis#d138", + "http://dl-learner.org/carcinogenesis#d140", + "http://dl-learner.org/carcinogenesis#d141", + "http://dl-learner.org/carcinogenesis#d144", + "http://dl-learner.org/carcinogenesis#d145", + "http://dl-learner.org/carcinogenesis#d146", + "http://dl-learner.org/carcinogenesis#d147", + "http://dl-learner.org/carcinogenesis#d15", + "http://dl-learner.org/carcinogenesis#d17", + "http://dl-learner.org/carcinogenesis#d19", + "http://dl-learner.org/carcinogenesis#d192", + "http://dl-learner.org/carcinogenesis#d193", + "http://dl-learner.org/carcinogenesis#d195", + "http://dl-learner.org/carcinogenesis#d196", + "http://dl-learner.org/carcinogenesis#d197", + "http://dl-learner.org/carcinogenesis#d198", + "http://dl-learner.org/carcinogenesis#d199", + "http://dl-learner.org/carcinogenesis#d2", + "http://dl-learner.org/carcinogenesis#d20", + "http://dl-learner.org/carcinogenesis#d200", + "http://dl-learner.org/carcinogenesis#d201", + "http://dl-learner.org/carcinogenesis#d202", + "http://dl-learner.org/carcinogenesis#d203", + "http://dl-learner.org/carcinogenesis#d204", + "http://dl-learner.org/carcinogenesis#d205", + "http://dl-learner.org/carcinogenesis#d21", + "http://dl-learner.org/carcinogenesis#d22", + "http://dl-learner.org/carcinogenesis#d226", + "http://dl-learner.org/carcinogenesis#d227", + "http://dl-learner.org/carcinogenesis#d228", + "http://dl-learner.org/carcinogenesis#d229", + "http://dl-learner.org/carcinogenesis#d231", + "http://dl-learner.org/carcinogenesis#d232", + "http://dl-learner.org/carcinogenesis#d234", + "http://dl-learner.org/carcinogenesis#d236", + "http://dl-learner.org/carcinogenesis#d239", + "http://dl-learner.org/carcinogenesis#d23_2", + "http://dl-learner.org/carcinogenesis#d242", + "http://dl-learner.org/carcinogenesis#d245", + "http://dl-learner.org/carcinogenesis#d247", + "http://dl-learner.org/carcinogenesis#d249", + "http://dl-learner.org/carcinogenesis#d25", + "http://dl-learner.org/carcinogenesis#d252", + "http://dl-learner.org/carcinogenesis#d253", + "http://dl-learner.org/carcinogenesis#d254", + "http://dl-learner.org/carcinogenesis#d255", + "http://dl-learner.org/carcinogenesis#d26", + "http://dl-learner.org/carcinogenesis#d272", + "http://dl-learner.org/carcinogenesis#d275", + "http://dl-learner.org/carcinogenesis#d277", + "http://dl-learner.org/carcinogenesis#d279", + "http://dl-learner.org/carcinogenesis#d28", + "http://dl-learner.org/carcinogenesis#d281", + "http://dl-learner.org/carcinogenesis#d283", + "http://dl-learner.org/carcinogenesis#d284", + "http://dl-learner.org/carcinogenesis#d288", + "http://dl-learner.org/carcinogenesis#d29", + "http://dl-learner.org/carcinogenesis#d290", + "http://dl-learner.org/carcinogenesis#d291", + "http://dl-learner.org/carcinogenesis#d292", + "http://dl-learner.org/carcinogenesis#d30", + "http://dl-learner.org/carcinogenesis#d31", + "http://dl-learner.org/carcinogenesis#d32", + "http://dl-learner.org/carcinogenesis#d33", + "http://dl-learner.org/carcinogenesis#d34", + "http://dl-learner.org/carcinogenesis#d35", + "http://dl-learner.org/carcinogenesis#d36", + "http://dl-learner.org/carcinogenesis#d37", + "http://dl-learner.org/carcinogenesis#d38", + "http://dl-learner.org/carcinogenesis#d42", + "http://dl-learner.org/carcinogenesis#d43", + "http://dl-learner.org/carcinogenesis#d44", + "http://dl-learner.org/carcinogenesis#d45", + "http://dl-learner.org/carcinogenesis#d46", + "http://dl-learner.org/carcinogenesis#d47", + "http://dl-learner.org/carcinogenesis#d48", + "http://dl-learner.org/carcinogenesis#d49", + "http://dl-learner.org/carcinogenesis#d5", + "http://dl-learner.org/carcinogenesis#d51", + "http://dl-learner.org/carcinogenesis#d52", + "http://dl-learner.org/carcinogenesis#d53", + "http://dl-learner.org/carcinogenesis#d55", + "http://dl-learner.org/carcinogenesis#d58", + "http://dl-learner.org/carcinogenesis#d6", + "http://dl-learner.org/carcinogenesis#d7", + "http://dl-learner.org/carcinogenesis#d84", + "http://dl-learner.org/carcinogenesis#d85_2", + "http://dl-learner.org/carcinogenesis#d86", + "http://dl-learner.org/carcinogenesis#d87", + "http://dl-learner.org/carcinogenesis#d88", + "http://dl-learner.org/carcinogenesis#d89", + "http://dl-learner.org/carcinogenesis#d9", + "http://dl-learner.org/carcinogenesis#d91", + "http://dl-learner.org/carcinogenesis#d92", + "http://dl-learner.org/carcinogenesis#d93", + "http://dl-learner.org/carcinogenesis#d95", + "http://dl-learner.org/carcinogenesis#d96", + "http://dl-learner.org/carcinogenesis#d98", + "http://dl-learner.org/carcinogenesis#d99", + "http://dl-learner.org/carcinogenesis#d100", + "http://dl-learner.org/carcinogenesis#d104", + "http://dl-learner.org/carcinogenesis#d105", + "http://dl-learner.org/carcinogenesis#d109", + "http://dl-learner.org/carcinogenesis#d137", + "http://dl-learner.org/carcinogenesis#d139", + "http://dl-learner.org/carcinogenesis#d14", + "http://dl-learner.org/carcinogenesis#d142", + "http://dl-learner.org/carcinogenesis#d143", + "http://dl-learner.org/carcinogenesis#d148", + "http://dl-learner.org/carcinogenesis#d16", + "http://dl-learner.org/carcinogenesis#d18", + "http://dl-learner.org/carcinogenesis#d191", + "http://dl-learner.org/carcinogenesis#d206", + "http://dl-learner.org/carcinogenesis#d230", + "http://dl-learner.org/carcinogenesis#d233", + "http://dl-learner.org/carcinogenesis#d235", + "http://dl-learner.org/carcinogenesis#d237", + "http://dl-learner.org/carcinogenesis#d238", + "http://dl-learner.org/carcinogenesis#d23_1", + "http://dl-learner.org/carcinogenesis#d24", + "http://dl-learner.org/carcinogenesis#d240", + "http://dl-learner.org/carcinogenesis#d241", + "http://dl-learner.org/carcinogenesis#d243", + "http://dl-learner.org/carcinogenesis#d244", + "http://dl-learner.org/carcinogenesis#d246", + "http://dl-learner.org/carcinogenesis#d248", + "http://dl-learner.org/carcinogenesis#d250", + "http://dl-learner.org/carcinogenesis#d251", + "http://dl-learner.org/carcinogenesis#d27", + "http://dl-learner.org/carcinogenesis#d273", + "http://dl-learner.org/carcinogenesis#d274", + "http://dl-learner.org/carcinogenesis#d278", + "http://dl-learner.org/carcinogenesis#d286", + "http://dl-learner.org/carcinogenesis#d289", + "http://dl-learner.org/carcinogenesis#d3", + "http://dl-learner.org/carcinogenesis#d39", + "http://dl-learner.org/carcinogenesis#d4", + "http://dl-learner.org/carcinogenesis#d40", + "http://dl-learner.org/carcinogenesis#d41", + "http://dl-learner.org/carcinogenesis#d50", + "http://dl-learner.org/carcinogenesis#d54", + "http://dl-learner.org/carcinogenesis#d56", + "http://dl-learner.org/carcinogenesis#d57", + "http://dl-learner.org/carcinogenesis#d8", + "http://dl-learner.org/carcinogenesis#d85_1", + "http://dl-learner.org/carcinogenesis#d90", + "http://dl-learner.org/carcinogenesis#d94", + "http://dl-learner.org/carcinogenesis#d97", + "http://dl-learner.org/carcinogenesis#d296", + "http://dl-learner.org/carcinogenesis#d305", + "http://dl-learner.org/carcinogenesis#d306", + "http://dl-learner.org/carcinogenesis#d307", + "http://dl-learner.org/carcinogenesis#d308", + "http://dl-learner.org/carcinogenesis#d311", + "http://dl-learner.org/carcinogenesis#d314", + "http://dl-learner.org/carcinogenesis#d315", + "http://dl-learner.org/carcinogenesis#d316", + "http://dl-learner.org/carcinogenesis#d320", + "http://dl-learner.org/carcinogenesis#d322", + "http://dl-learner.org/carcinogenesis#d323", + "http://dl-learner.org/carcinogenesis#d325", + "http://dl-learner.org/carcinogenesis#d329", + "http://dl-learner.org/carcinogenesis#d330", + "http://dl-learner.org/carcinogenesis#d331", + "http://dl-learner.org/carcinogenesis#d332", + "http://dl-learner.org/carcinogenesis#d333", + "http://dl-learner.org/carcinogenesis#d336", + "http://dl-learner.org/carcinogenesis#d337" + ); + + List<String> negExamples = Lists.newArrayList( + "http://dl-learner.org/carcinogenesis#d110", + "http://dl-learner.org/carcinogenesis#d111", + "http://dl-learner.org/carcinogenesis#d114", + "http://dl-learner.org/carcinogenesis#d116", + "http://dl-learner.org/carcinogenesis#d117", + "http://dl-learner.org/carcinogenesis#d119", + "http://dl-learner.org/carcinogenesis#d121", + "http://dl-learner.org/carcinogenesis#d123", + "http://dl-learner.org/carcinogenesis#d124", + "http://dl-learner.org/carcinogenesis#d125", + "http://dl-learner.org/carcinogenesis#d127", + "http://dl-learner.org/carcinogenesis#d128", + "http://dl-learner.org/carcinogenesis#d130", + "http://dl-learner.org/carcinogenesis#d133", + "http://dl-learner.org/carcinogenesis#d150", + "http://dl-learner.org/carcinogenesis#d151", + "http://dl-learner.org/carcinogenesis#d154", + "http://dl-learner.org/carcinogenesis#d155", + "http://dl-learner.org/carcinogenesis#d156", + "http://dl-learner.org/carcinogenesis#d159", + "http://dl-learner.org/carcinogenesis#d160", + "http://dl-learner.org/carcinogenesis#d161", + "http://dl-learner.org/carcinogenesis#d162", + "http://dl-learner.org/carcinogenesis#d163", + "http://dl-learner.org/carcinogenesis#d164", + "http://dl-learner.org/carcinogenesis#d165", + "http://dl-learner.org/carcinogenesis#d166", + "http://dl-learner.org/carcinogenesis#d169", + "http://dl-learner.org/carcinogenesis#d170", + "http://dl-learner.org/carcinogenesis#d171", + "http://dl-learner.org/carcinogenesis#d172", + "http://dl-learner.org/carcinogenesis#d173", + "http://dl-learner.org/carcinogenesis#d174", + "http://dl-learner.org/carcinogenesis#d178", + "http://dl-learner.org/carcinogenesis#d179", + "http://dl-learner.org/carcinogenesis#d180", + "http://dl-learner.org/carcinogenesis#d181", + "http://dl-learner.org/carcinogenesis#d183", + "http://dl-learner.org/carcinogenesis#d184", + "http://dl-learner.org/carcinogenesis#d185", + "http://dl-learner.org/carcinogenesis#d186", + "http://dl-learner.org/carcinogenesis#d188", + "http://dl-learner.org/carcinogenesis#d190", + "http://dl-learner.org/carcinogenesis#d194", + "http://dl-learner.org/carcinogenesis#d207", + "http://dl-learner.org/carcinogenesis#d208_1", + "http://dl-learner.org/carcinogenesis#d209", + "http://dl-learner.org/carcinogenesis#d210", + "http://dl-learner.org/carcinogenesis#d211", + "http://dl-learner.org/carcinogenesis#d212", + "http://dl-learner.org/carcinogenesis#d213", + "http://dl-learner.org/carcinogenesis#d214", + "http://dl-learner.org/carcinogenesis#d215", + "http://dl-learner.org/carcinogenesis#d217", + "http://dl-learner.org/carcinogenesis#d218", + "http://dl-learner.org/carcinogenesis#d219", + "http://dl-learner.org/carcinogenesis#d220", + "http://dl-learner.org/carcinogenesis#d224", + "http://dl-learner.org/carcinogenesis#d256", + "http://dl-learner.org/carcinogenesis#d257", + "http://dl-learner.org/carcinogenesis#d258", + "http://dl-learner.org/carcinogenesis#d261", + "http://dl-learner.org/carcinogenesis#d262", + "http://dl-learner.org/carcinogenesis#d263", + "http://dl-learner.org/carcinogenesis#d264", + "http://dl-learner.org/carcinogenesis#d265", + "http://dl-learner.org/carcinogenesis#d266", + "http://dl-learner.org/carcinogenesis#d267", + "http://dl-learner.org/carcinogenesis#d269", + "http://dl-learner.org/carcinogenesis#d271", + "http://dl-learner.org/carcinogenesis#d276", + "http://dl-learner.org/carcinogenesis#d280", + "http://dl-learner.org/carcinogenesis#d285", + "http://dl-learner.org/carcinogenesis#d287", + "http://dl-learner.org/carcinogenesis#d293", + "http://dl-learner.org/carcinogenesis#d294", + "http://dl-learner.org/carcinogenesis#d59", + "http://dl-learner.org/carcinogenesis#d60", + "http://dl-learner.org/carcinogenesis#d61", + "http://dl-learner.org/carcinogenesis#d63", + "http://dl-learner.org/carcinogenesis#d64", + "http://dl-learner.org/carcinogenesis#d65", + "http://dl-learner.org/carcinogenesis#d69", + "http://dl-learner.org/carcinogenesis#d70", + "http://dl-learner.org/carcinogenesis#d71", + "http://dl-learner.org/carcinogenesis#d72", + "http://dl-learner.org/carcinogenesis#d73", + "http://dl-learner.org/carcinogenesis#d74", + "http://dl-learner.org/carcinogenesis#d75", + "http://dl-learner.org/carcinogenesis#d76", + "http://dl-learner.org/carcinogenesis#d77", + "http://dl-learner.org/carcinogenesis#d78", + "http://dl-learner.org/carcinogenesis#d79", + "http://dl-learner.org/carcinogenesis#d80", + "http://dl-learner.org/carcinogenesis#d81", + "http://dl-learner.org/carcinogenesis#d82", + "http://dl-learner.org/carcinogenesis#d112", + "http://dl-learner.org/carcinogenesis#d113", + "http://dl-learner.org/carcinogenesis#d115", + "http://dl-learner.org/carcinogenesis#d118", + "http://dl-learner.org/carcinogenesis#d120", + "http://dl-learner.org/carcinogenesis#d122", + "http://dl-learner.org/carcinogenesis#d126", + "http://dl-learner.org/carcinogenesis#d129", + "http://dl-learner.org/carcinogenesis#d131", + "http://dl-learner.org/carcinogenesis#d132", + "http://dl-learner.org/carcinogenesis#d149", + "http://dl-learner.org/carcinogenesis#d152", + "http://dl-learner.org/carcinogenesis#d153", + "http://dl-learner.org/carcinogenesis#d157", + "http://dl-learner.org/carcinogenesis#d158", + "http://dl-learner.org/carcinogenesis#d167", + "http://dl-learner.org/carcinogenesis#d168", + "http://dl-learner.org/carcinogenesis#d175", + "http://dl-learner.org/carcinogenesis#d176", + "http://dl-learner.org/carcinogenesis#d177", + "http://dl-learner.org/carcinogenesis#d182", + "http://dl-learner.org/carcinogenesis#d187", + "http://dl-learner.org/carcinogenesis#d189", + "http://dl-learner.org/carcinogenesis#d208_2", + "http://dl-learner.org/carcinogenesis#d216", + "http://dl-learner.org/carcinogenesis#d221", + "http://dl-learner.org/carcinogenesis#d222", + "http://dl-learner.org/carcinogenesis#d223", + "http://dl-learner.org/carcinogenesis#d225", + "http://dl-learner.org/carcinogenesis#d259", + "http://dl-learner.org/carcinogenesis#d260", + "http://dl-learner.org/carcinogenesis#d268", + "http://dl-learner.org/carcinogenesis#d270", + "http://dl-learner.org/carcinogenesis#d282", + "http://dl-learner.org/carcinogenesis#d295", + "http://dl-learner.org/carcinogenesis#d62", + "http://dl-learner.org/carcinogenesis#d66", + "http://dl-learner.org/carcinogenesis#d67", + "http://dl-learner.org/carcinogenesis#d68", + "http://dl-learner.org/carcinogenesis#d83", + "http://dl-learner.org/carcinogenesis#d297", + "http://dl-learner.org/carcinogenesis#d298", + "http://dl-learner.org/carcinogenesis#d299", + "http://dl-learner.org/carcinogenesis#d300", + "http://dl-learner.org/carcinogenesis#d302", + "http://dl-learner.org/carcinogenesis#d303", + "http://dl-learner.org/carcinogenesis#d304", + "http://dl-learner.org/carcinogenesis#d309", + "http://dl-learner.org/carcinogenesis#d312", + "http://dl-learner.org/carcinogenesis#d313", + "http://dl-learner.org/carcinogenesis#d317", + "http://dl-learner.org/carcinogenesis#d318", + "http://dl-learner.org/carcinogenesis#d319", + "http://dl-learner.org/carcinogenesis#d324", + "http://dl-learner.org/carcinogenesis#d326", + "http://dl-learner.org/carcinogenesis#d327", + "http://dl-learner.org/carcinogenesis#d328", + "http://dl-learner.org/carcinogenesis#d334", + "http://dl-learner.org/carcinogenesis#d335" + ); + + private Model model; + private OWLOntology ontology; + private QueryTreeFactory<String> queryTreeFactory; + private List<QueryTree<String>> posExampleTrees; + private List<QueryTree<String>> negExampleTrees; + private PosNegLP lp; + + + + public QTLEvaluation() throws ComponentInitException { + queryTreeFactory = new QueryTreeFactoryImpl(); + queryTreeFactory.setMaxDepth(3); + + loadDataset(); + + loadExamples(); + } + + private void loadDataset(){ + File file = new File("../examples/carcinogenesis/carcinogenesis.owl"); + model = ModelFactory.createDefaultModel(); + try { + model.read(new FileInputStream(file), null, "RDF/XML"); + } catch (FileNotFoundException e) { + e.printStackTrace(); + } + + OWLOntologyManager man = OWLManager.createOWLOntologyManager(); + try { + ontology = man.loadOntologyFromOntologyDocument(file); + } catch (OWLOntologyCreationException e) { + e.printStackTrace(); + } + } + + private void loadExamples() throws ComponentInitException{ + + Collections.shuffle(posExamples, new Random(1)); + Collections.shuffle(negExamples, new Random(2)); + posExamples = posExamples.subList(0, Math.min(posExamples.size(), nrOfPosExamples)); + negExamples = negExamples.subList(0, Math.min(negExamples.size(), nrOfNegExamples)); + +// posExamples.clear(); +// String string = "http://dl-learner.org/carcinogenesis#d101, http://dl-learner.org/carcinogenesis#d103, http://dl-learner.org/carcinogenesis#d107, http://dl-learner.org/carcinogenesis#d108, http://dl-learner.org/carcinogenesis#d135, http://dl-learner.org/carcinogenesis#d139, http://dl-learner.org/carcinogenesis#d14, http://dl-learner.org/carcinogenesis#d141, http://dl-learner.org/carcinogenesis#d143, http://dl-learner.org/carcinogenesis#d147, http://dl-learner.org/carcinogenesis#d17, http://dl-learner.org/carcinogenesis#d19, http://dl-learner.org/carcinogenesis#d193, http://dl-learner.org/carcinogenesis#d198, http://dl-learner.org/carcinogenesis#d228, http://dl-learner.org/carcinogenesis#d236, http://dl-learner.org/carcinogenesis#d242, http://dl-learner.org/carcinogenesis#d244, http://dl-learner.org/carcinogenesis#d273, http://dl-learner.org/carcinogenesis#d275, http://dl-learner.org/carcinogenesis#d28, http://dl-learner.org/carcinogenesis#d283, http://dl-learner.org/carcinogenesis#d286, http://dl-learner.org/carcinogenesis#d291, http://dl-learner.org/carcinogenesis#d292, http://dl-learner.org/carcinogenesis#d307, http://dl-learner.org/carcinogenesis#d31, http://dl-learner.org/carcinogenesis#d325, http://dl-learner.org/carcinogenesis#d33, http://dl-learner.org/carcinogenesis#d333, http://dl-learner.org/carcinogenesis#d34, http://dl-learner.org/carcinogenesis#d36, http://dl-learner.org/carcinogenesis#d38, http://dl-learner.org/carcinogenesis#d4, http://dl-learner.org/carcinogenesis#d40, http://dl-learner.org/carcinogenesis#d44, http://dl-learner.org/carcinogenesis#d51, http://dl-learner.org/carcinogenesis#d85_2, http://dl-learner.org/carcinogenesis#d98, http://dl-learner.org/carcinogenesis#d99"; +// String[] split = string.split(","); +// for (String s : split) { +// posExamples.add(s.trim()); +// } +// negExamples.clear(); +// string = "http://dl-learner.org/carcinogenesis#d112, http://dl-learner.org/carcinogenesis#d116, http://dl-learner.org/carcinogenesis#d117, http://dl-learner.org/carcinogenesis#d119, http://dl-learner.org/carcinogenesis#d157, http://dl-learner.org/carcinogenesis#d160, http://dl-learner.org/carcinogenesis#d161, http://dl-learner.org/carcinogenesis#d162, http://dl-learner.org/carcinogenesis#d163, http://dl-learner.org/carcinogenesis#d167, http://dl-learner.org/carcinogenesis#d169, http://dl-learner.org/carcinogenesis#d175, http://dl-learner.org/carcinogenesis#d177, http://dl-learner.org/carcinogenesis#d184, http://dl-learner.org/carcinogenesis#d194, http://dl-learner.org/carcinogenesis#d208_2, http://dl-learner.org/carcinogenesis#d209, http://dl-learner.org/carcinogenesis#d217, http://dl-learner.org/carcinogenesis#d256, http://dl-learner.org/carcinogenesis#d257, http://dl-learner.org/carcinogenesis#d260, http://dl-learner.org/carcinogenesis#d271, http://dl-learner.org/carcinogenesis#d276, http://dl-learner.org/carcinogenesis#d282, http://dl-learner.org/carcinogenesis#d287, http://dl-learner.org/carcinogenesis#d294, http://dl-learner.org/carcinogenesis#d298, http://dl-learner.org/carcinogenesis#d300, http://dl-learner.org/carcinogenesis#d309, http://dl-learner.org/carcinogenesis#d319, http://dl-learner.org/carcinogenesis#d326, http://dl-learner.org/carcinogenesis#d328, http://dl-learner.org/carcinogenesis#d334, http://dl-learner.org/carcinogenesis#d60, http://dl-learner.org/carcinogenesis#d61, http://dl-learner.org/carcinogenesis#d66, http://dl-learner.org/carcinogenesis#d75, http://dl-learner.org/carcinogenesis#d79, http://dl-learner.org/carcinogenesis#d80, http://dl-learner.org/carcinogenesis#d83"; +// split = string.split(","); +// for (String s : split) { +// negExamples.add(s.trim()); +// } + + posExampleTrees = new ArrayList<QueryTree<String>>(); + for (String ex : posExamples) { + QueryTreeImpl<String> tree = queryTreeFactory.getQueryTree(ex, model); + posExampleTrees.add(tree); + } + + negExampleTrees = new ArrayList<QueryTree<String>>(); + for (String ex : negExamples) { + QueryTreeImpl<String> tree = queryTreeFactory.getQueryTree(ex, model); + negExampleTrees.add(tree); + } + + int cnt = 1; + for(QueryTree<String> tree : posExampleTrees){ +// System.out.println("TREE " + cnt); +// tree.dump(); +// +// System.out.println("-----------------------------"); + cnt++; +// System.out.println(((QueryTreeImpl<String>)tree).toQuery()); + } + + SortedSet<Individual> pos = new TreeSet<Individual>(); + for (String ex : posExamples) { + pos.add(new Individual(ex)); + } + SortedSet<Individual> neg = new TreeSet<Individual>(); + for (String ex : negExamples) { + neg.add(new Individual(ex)); + } + lp = new PosNegLPStandard(); + lp.setPositiveExamples(pos); + lp.setNegativeExamples(neg); + } + + public void run(boolean multiThreaded) throws ComponentInitException, LearningProblemUnsupportedException{ + long startTime = System.currentTimeMillis(); + FastInstanceChecker reasoner = new FastInstanceChecker(new OWLAPIOntology(ontology)); + reasoner.init(); + lp.setReasoner(reasoner); + lp.init(); + QTL2Disjunctive la = new QTL2Disjunctive(lp, reasoner); + la.init(); + la.start(); + +// CrossValidation.outputFile = new File("log/qtl-cv.log"); +// CrossValidation.writeToFile = true; +// CrossValidation.multiThreaded = multiThreaded; +// CrossValidation cv = new CrossValidation(la, lp, reasoner, nrOfFolds, false); + long endTime = System.currentTimeMillis(); + System.err.println((endTime - startTime) + "ms"); + } + + + public static void main(String[] args) throws Exception { + boolean multiThreaded = Boolean.valueOf(args[0]); + new QTLEvaluation().run(multiThreaded); + } + +} Added: trunk/scripts/src/main/java/org/dllearner/scripts/pattern/FixPointDetection.java =================================================================== --- trunk/scripts/src/main/java/org/dllearner/scripts/pattern/FixPointDetection.java (rev 0) +++ trunk/scripts/src/main/java/org/dllearner/scripts/pattern/FixPointDetection.java 2014-05-07 11:25:54 UTC (rev 4261) @@ -0,0 +1,281 @@ +/** + * + */ +package org.dllearner.scripts.pattern; + +import java.io.File; +import java.io.FileNotFoundException; +import java.io.IOException; +import java.io.InputStream; +import java.io.StringWriter; +import java.sql.Connection; +import java.sql.DriverManager; +import java.sql.PreparedStatement; +import java.sql.ResultSet; +import java.sql.SQLException; +import java.util.ArrayList; +import java.util.Collection; +import java.util.Collections; +import java.util.HashSet; +import java.util.List; +import java.util.Map; +import java.util.Map.Entry; +import java.util.Random; +import java.util.Set; +import java.util.TreeMap; +import java.util.prefs.Preferences; + +import org.ini4j.IniPreferences; +import org.ini4j.InvalidFileFormatException; +import org.semanticweb.owlapi.apibinding.OWLManager; +import org.semanticweb.owlapi.io.OWLObjectRenderer; +import org.semanticweb.owlapi.model.OWLAxiom; +import org.semanticweb.owlapi.model.OWLOntology; +import org.semanticweb.owlapi.model.OWLOntologyCreationException; +import org.semanticweb.owlapi.model.OWLOntologyManager; + +import uk.ac.manchester.cs.owl.owlapi.mansyntaxrenderer.ManchesterOWLSyntaxOWLObjectRendererImpl; + +import com.google.common.base.Charsets; +import com.google.common.base.Joiner; +import com.google.common.collect.LinkedListMultimap; +import com.google.common.collect.Multimap; +import com.google.common.io.Files; + +/** + * @author Lorenz Buehmann + * + */ +public class FixPointDetection { + + private OWLObjectRenderer axiomRenderer = new ManchesterOWLSyntaxOWLObjectRendererImpl(); + + public FixPointDetection() { + initDBConnection(); + + File dir = new File("pattern-fixpoint"); + dir.mkdir(); + } + + private Connection conn; + private PreparedStatement ps; + + private void initDBConnection() { + try { + InputStream is = this.getClass().getClassLoader().getResourceAsStream("db_settings.ini"); + Preferences prefs = new IniPreferences(is); + String dbServer = prefs.node("database").get("server", null); + String dbName = prefs.node("database").get("name", null); + String dbUser = prefs.node("database").get("user", null); + String dbPass = prefs.node("database").get("pass", null); + + Class.forName("com.mysql.jdbc.Driver"); + String url = "jdbc:mysql://" + dbServer + "/" + dbName; + conn = DriverManager.getConnection(url, dbUser, dbPass); + } catch (ClassNotFoundException e) { + e.printStackTrace(); + } catch (SQLException e) { + e.printStackTrace(); + } catch (InvalidFileFormatException e) { + e.printStackTrace(); + } catch (FileNotFoundException e) { + e.printStackTrace(); + } catch (IOException e) { + e.printStackTrace(); + } + + try { + ps = conn.prepareStatement("SELECT occurrences FROM Ontology_Pattern WHERE pattern_id=? AND ontology_id=?"); + } catch (SQLException e) { + e.printStackTrace(); + } + } + + + private List<Integer> getProcessedOntologies() throws SQLException{ + List<Integer> ids = new ArrayList<Integer>(); + ResultSet rs = conn.createStatement().executeQuery("SELECT DISTINCT id FROM Ontology"); + while(rs.next()){ + int id = rs.getInt(1); + ... [truncated message content] |