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From: <lor...@us...> - 2013-06-06 13:32:33
|
Revision: 3985
http://sourceforge.net/p/dl-learner/code/3985
Author: lorenz_b
Date: 2013-06-06 13:32:30 +0000 (Thu, 06 Jun 2013)
Log Message:
-----------
Updated LGG.
Modified Paths:
--------------
trunk/components-core/pom.xml
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/QueryTree.java
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/impl/QueryTreeImpl.java
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/operations/lgg/LGGGeneratorImpl.java
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/operations/lgg/NoiseSensitiveLGG.java
trunk/components-core/src/main/java/org/dllearner/kb/sparql/ConciseBoundedDescriptionGeneratorImpl.java
trunk/components-core/src/main/java/org/dllearner/kb/sparql/ExtractionDBCache.java
trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
trunk/components-core/src/main/java/org/dllearner/utilities/examples/AutomaticNegativeExampleFinderSPARQL2.java
trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLClassExpressionToSPARQLConverter.java
trunk/components-core/src/main/resources/prefixes.csv
Modified: trunk/components-core/pom.xml
===================================================================
--- trunk/components-core/pom.xml 2013-05-24 09:16:41 UTC (rev 3984)
+++ trunk/components-core/pom.xml 2013-06-06 13:32:30 UTC (rev 3985)
@@ -320,6 +320,11 @@
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
</dependency>
+ <dependency>
+ <groupId>org.aksw.jena-sparql-api</groupId>
+ <artifactId>jena-sparql-api-core</artifactId>
+ <version>2.10.0-3</version>
+ </dependency>
</dependencies>
<dependencyManagement>
<dependencies>
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/QueryTree.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/QueryTree.java 2013-05-24 09:16:41 UTC (rev 3984)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/QueryTree.java 2013-06-06 13:32:30 UTC (rev 3985)
@@ -55,6 +55,8 @@
QueryTree<N> getNodeById(int nodeId);
+ boolean sameType(QueryTree<N> tree);
+
boolean isLiteralNode();
void setLiteralNode(boolean isLiteralNode);
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/impl/QueryTreeImpl.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/impl/QueryTreeImpl.java 2013-05-24 09:16:41 UTC (rev 3984)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/impl/QueryTreeImpl.java 2013-06-06 13:32:30 UTC (rev 3985)
@@ -124,6 +124,12 @@
addChild(subTree, tree.getEdge(child));
}
}
+
+ public boolean sameType(QueryTree<N> tree){
+ return (isResourceNode && tree.isResourceNode()) ||
+ (isVarNode() && tree.isVarNode()) ||
+ (isLiteralNode && tree.isLiteralNode());
+ }
public N getUserObject() {
return userObject;
@@ -327,6 +333,9 @@
@Override
public boolean isSubsumedBy(QueryTree<N> tree) {
+// if(!sameType(tree)){
+// return false;
+// }
if(!(tree.getUserObject().equals("?") || tree.getUserObject().equals(this.userObject))){
return false;
}
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/operations/lgg/LGGGeneratorImpl.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/operations/lgg/LGGGeneratorImpl.java 2013-05-24 09:16:41 UTC (rev 3984)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/operations/lgg/LGGGeneratorImpl.java 2013-06-06 13:32:30 UTC (rev 3985)
@@ -145,7 +145,7 @@
// }
// }
// }
- if(!lgg.getUserObject().equals(tree2.getUserObject())){
+ if(!lgg.sameType(tree2) || !lgg.getUserObject().equals(tree2.getUserObject())){
lgg.setUserObject((N)"?");
lgg.setLiteralNode(false);
lgg.setResourceNode(false);
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/operations/lgg/NoiseSensitiveLGG.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/operations/lgg/NoiseSensitiveLGG.java 2013-05-24 09:16:41 UTC (rev 3984)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/operations/lgg/NoiseSensitiveLGG.java 2013-06-06 13:32:30 UTC (rev 3985)
@@ -2,7 +2,6 @@
import java.util.ArrayList;
import java.util.Collection;
-import java.util.HashSet;
import java.util.List;
import java.util.PriorityQueue;
import java.util.Queue;
@@ -11,6 +10,9 @@
import org.dllearner.algorithms.qtl.datastructures.QueryTree;
+import com.jamonapi.Monitor;
+import com.jamonapi.MonitorFactory;
+
public class NoiseSensitiveLGG<N> {
private LGGGenerator<N> lggGenerator = new LGGGeneratorImpl<N>();
@@ -22,19 +24,25 @@
}
public List<EvaluatedQueryTree<N>> computeLGG(List<QueryTree<N>> trees){
+ Monitor subMon = MonitorFactory.getTimeMonitor("subsumption-mon");
+ Monitor lggMon = MonitorFactory.getTimeMonitor("lgg-mon");
init(trees);
EvaluatedQueryTree<N> currentElement;
- do{
+ do{System.out.println("TODO list size: " + todoList.size());
//pick best element from todo list
currentElement = todoList.poll();
for (QueryTree<N> example : currentElement.getUncoveredExamples()) {
QueryTree<N> tree = currentElement.getTree();
//compute the LGG
+ lggMon.start();
QueryTree<N> lgg = lggGenerator.getLGG(tree, example);
+ lggMon.stop();
//compute examples which are not covered by LGG
- Collection<QueryTree<N>> uncoveredExamples = new HashSet<QueryTree<N>>();
+ Collection<QueryTree<N>> uncoveredExamples = new ArrayList<QueryTree<N>>();
for (QueryTree<N> queryTree : trees) {
+ subMon.start();
boolean subsumed = queryTree.isSubsumedBy(lgg);
+ subMon.stop();
if(!subsumed){
uncoveredExamples.add(queryTree);
}
@@ -45,6 +53,12 @@
EvaluatedQueryTree<N> solution = new EvaluatedQueryTree<N>(lgg, uncoveredExamples, score);
todo(solution);
}
+ System.out.println("LGG time: " + lggMon.getTotal() + "ms");
+ System.out.println("Avg. LGG time: " + lggMon.getAvg() + "ms");
+ System.out.println("#LGG computations: " + lggMon.getHits());
+ System.out.println("Subsumption test time: " + subMon.getTotal() + "ms");
+ System.out.println("Avg. subsumption test time: " + subMon.getAvg() + "ms");
+ System.out.println("#Subsumption tests: " + subMon.getHits());
solutions.add(currentElement);
// todoList.remove(currentElement);
} while(!terminationCriteriaSatisfied());
@@ -57,8 +71,8 @@
// EvaluatedQueryTree<N> dummy = new EvaluatedQueryTree<N>(new QueryTreeImpl<N>((N)"TOP"), trees, 0d);
// todoList.add(dummy);
//compute distinct trees
- Collection<QueryTree<N>> distinctTrees = new HashSet<QueryTree<N>>();
- for (QueryTree<N> queryTree : trees) {
+ Collection<QueryTree<N>> distinctTrees = new ArrayList<QueryTree<N>>();
+ for (QueryTree<N> queryTree : trees) {//System.out.println(queryTree.getStringRepresentation());
boolean distinct = true;
for (QueryTree<N> otherTree : distinctTrees) {
if(queryTree.isSubsumedBy(otherTree)){
@@ -71,7 +85,7 @@
}
}
for (QueryTree<N> queryTree : distinctTrees) {
- Collection<QueryTree<N>> uncoveredExamples = new HashSet<QueryTree<N>>(distinctTrees);
+ Collection<QueryTree<N>> uncoveredExamples = new ArrayList<QueryTree<N>>(distinctTrees);
uncoveredExamples.remove(queryTree);
double score = (trees.size() - uncoveredExamples.size()) / (double)trees.size();
todoList.add(new EvaluatedQueryTree<N>(queryTree, uncoveredExamples, score));
Modified: trunk/components-core/src/main/java/org/dllearner/kb/sparql/ConciseBoundedDescriptionGeneratorImpl.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/kb/sparql/ConciseBoundedDescriptionGeneratorImpl.java 2013-05-24 09:16:41 UTC (rev 3984)
+++ trunk/components-core/src/main/java/org/dllearner/kb/sparql/ConciseBoundedDescriptionGeneratorImpl.java 2013-06-06 13:32:30 UTC (rev 3985)
@@ -1,16 +1,24 @@
package org.dllearner.kb.sparql;
-import java.io.UnsupportedEncodingException;
import java.sql.SQLException;
import java.util.Iterator;
import java.util.List;
+import java.util.concurrent.TimeUnit;
+import org.aksw.jena_sparql_api.cache.core.QueryExecutionFactoryCacheEx;
+import org.aksw.jena_sparql_api.cache.extra.CacheCoreEx;
+import org.aksw.jena_sparql_api.cache.extra.CacheCoreH2;
+import org.aksw.jena_sparql_api.cache.extra.CacheEx;
+import org.aksw.jena_sparql_api.cache.extra.CacheExImpl;
+import org.aksw.jena_sparql_api.core.QueryExecutionFactory;
+import org.aksw.jena_sparql_api.http.QueryExecutionFactoryHttp;
+import org.aksw.jena_sparql_api.model.QueryExecutionFactoryModel;
+import org.aksw.jena_sparql_api.pagination.core.QueryExecutionFactoryPaginated;
import org.apache.log4j.Level;
import org.apache.log4j.Logger;
-import com.hp.hpl.jena.query.QueryExecutionFactory;
+import com.hp.hpl.jena.query.QueryExecution;
import com.hp.hpl.jena.rdf.model.Model;
-import com.hp.hpl.jena.rdf.model.ModelFactory;
//import com.hp.hpl.jena.sparql.engine.http.QueryEngineHTTP;
public class ConciseBoundedDescriptionGeneratorImpl implements ConciseBoundedDescriptionGenerator{
@@ -25,6 +33,7 @@
private List<String> namespaces;
private int maxRecursionDepth = 1;
+ private String cacheDir;
public ConciseBoundedDescriptionGeneratorImpl(SparqlEndpoint endpoint, ExtractionDBCache cache) {
this.endpoint = endpoint;
@@ -37,8 +46,19 @@
this.maxRecursionDepth = maxRecursionDepth;
}
+ public ConciseBoundedDescriptionGeneratorImpl(SparqlEndpoint endpoint, String cacheDir, int maxRecursionDepth) {
+ this.endpoint = endpoint;
+ this.cacheDir = cacheDir;
+ this.maxRecursionDepth = maxRecursionDepth;
+ }
+
+ public ConciseBoundedDescriptionGeneratorImpl(SparqlEndpoint endpoint, String cacheDir) {
+ this.endpoint = endpoint;
+ this.cacheDir = cacheDir;
+ }
+
public ConciseBoundedDescriptionGeneratorImpl(SparqlEndpoint endpoint) {
- this(endpoint, null);
+ this(endpoint, (String)null);
}
public ConciseBoundedDescriptionGeneratorImpl(Model model) {
@@ -59,34 +79,28 @@
private Model getModelChunked(String resource, int depth){
String query = makeConstructQueryOptional(resource, chunkSize, 0, depth);
- Model all = ModelFactory.createDefaultModel();
- try {
- Model model;
- if(cache == null){
- model = getModel(query);
- } else {
- model = cache.executeConstructQuery(endpoint, query);
+ QueryExecutionFactory qef;
+ if(endpoint != null){
+ qef = new QueryExecutionFactoryHttp(endpoint.getURL().toString(), endpoint.getDefaultGraphURIs());
+ if(cacheDir != null){
+ try {
+ long timeToLive = TimeUnit.DAYS.toMillis(30);
+ CacheCoreEx cacheBackend = CacheCoreH2.create(cacheDir, timeToLive, true);
+ CacheEx cacheFrontend = new CacheExImpl(cacheBackend);
+ qef = new QueryExecutionFactoryCacheEx(qef, cacheFrontend);
+ } catch (ClassNotFoundException e) {
+ e.printStackTrace();
+ } catch (SQLException e) {
+ e.printStackTrace();
+ }
}
- all.add(model);
- int i = 1;
- do{
-// while(model.size() == CHUNK_SIZE){
- query = makeConstructQueryOptional(resource, chunkSize, i * chunkSize, depth);
- if(cache == null){
- model = getModel(query);
- } else {
- model = cache.executeConstructQuery(endpoint, query);
- }
- all.add(model);
- i++;
- } while(chunkSize > 0 && model.size() != 0);
- } catch (UnsupportedEncodingException e) {
- logger.error(e);
- } catch (SQLException e) {
- logger.error(e);
+ qef = new QueryExecutionFactoryPaginated(qef, 10000);
+ } else {
+ qef = new QueryExecutionFactoryModel(baseModel);
}
-
- return all;
+ QueryExecution qe = qef.createQueryExecution(query);
+ Model model = qe.execConstruct();
+ return model;
}
@Override
@@ -151,36 +165,6 @@
return filter;
}
- private Model getModel(String query) throws UnsupportedEncodingException, SQLException{
- if(logger.isDebugEnabled()){
- logger.debug("Sending SPARQL query ...");
- logger.debug("Query:\n" + query.toString());
- }
-
- Model model;
- if(baseModel == null){
- if(cache == null){
- QueryEngineHTTP queryExecution = new QueryEngineHTTP(endpoint.getURL().toString(), query);
- for (String dgu : endpoint.getDefaultGraphURIs()) {
- queryExecution.addDefaultGraph(dgu);
- }
- for (String ngu : endpoint.getNamedGraphURIs()) {
- queryExecution.addNamedGraph(ngu);
- }
- model = queryExecution.execConstruct();
- } else {
- model = cache.executeConstructQuery(endpoint, query);
- }
- } else {
- model = QueryExecutionFactory.create(query, baseModel).execConstruct();
- }
-
- if(logger.isDebugEnabled()){
- logger.debug("Got " + model.size() + " new triples in.");
- }
- return model;
- }
-
public static void main(String[] args) {
Logger.getRootLogger().setLevel(Level.DEBUG);
ConciseBoundedDescriptionGenerator cbdGen = new ConciseBoundedDescriptionGeneratorImpl(SparqlEndpoint.getEndpointDBpedia());
Modified: trunk/components-core/src/main/java/org/dllearner/kb/sparql/ExtractionDBCache.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/kb/sparql/ExtractionDBCache.java 2013-05-24 09:16:41 UTC (rev 3984)
+++ trunk/components-core/src/main/java/org/dllearner/kb/sparql/ExtractionDBCache.java 2013-06-06 13:32:30 UTC (rev 3985)
@@ -78,6 +78,10 @@
Statement stmt = conn.createStatement();
stmt.execute("CREATE TABLE IF NOT EXISTS QUERY_CACHE(QUERYHASH BINARY PRIMARY KEY,QUERY VARCHAR(20000), TRIPLES CLOB, STORE_TIME TIMESTAMP)");
}
+
+ public String getCacheDirectory() {
+ return databaseDirectory;
+ }
public ExtractionDBCache(String cacheDir) {
databaseDirectory = cacheDir;
Modified: trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java 2013-05-24 09:16:41 UTC (rev 3984)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java 2013-06-06 13:32:30 UTC (rev 3985)
@@ -73,6 +73,7 @@
import com.hp.hpl.jena.query.QueryExecution;
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.Resource;
@@ -494,7 +495,7 @@
Set<NamedClass> siblings = new HashSet<NamedClass>();
String query = "SELECT ?sub WHERE { <" + cls.getName() + "> <http://www.w3.org/2000/01/rdf-schema#subClassOf> ?super .";
query += "?sub <http://www.w3.org/2000/01/rdf-schema#subClassOf> ?super .";
- query += "FILTER( !SAMETERM(?sub, <" + cls.getName() + ">)) . }";
+ query += "FILTER( !SAMETERM(?sub, <" + cls.getName() + ">)) . }";System.out.println(query);
ResultSet rs = executeSelectQuery(query);
QuerySolution qs;
while(rs.hasNext()){
@@ -590,7 +591,6 @@
* @author sherif
*/
public SortedSet<Individual> getIndividualsExcluding(Description wantedClass, Description excludeClass, int limit) {
-
if(!(wantedClass instanceof NamedClass)){
throw new UnsupportedOperationException("Only named classes are supported.");
}
@@ -598,7 +598,7 @@
String query =
"SELECT DISTINCT ?ind WHERE {" +
"?ind a <"+((NamedClass)wantedClass).getName() + "> . " +
- "FILTER(NOT EXISTS { ?ind a <" + ((NamedClass)excludeClass).getName() + "> } )}";
+ "FILTER NOT EXISTS { ?ind a <" + ((NamedClass)excludeClass).getName() + "> } }";
if(limit != 0) {
query += " LIMIT " + limit;
}
Modified: trunk/components-core/src/main/java/org/dllearner/utilities/examples/AutomaticNegativeExampleFinderSPARQL2.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/examples/AutomaticNegativeExampleFinderSPARQL2.java 2013-05-24 09:16:41 UTC (rev 3984)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/examples/AutomaticNegativeExampleFinderSPARQL2.java 2013-06-06 13:32:30 UTC (rev 3985)
@@ -19,10 +19,22 @@
package org.dllearner.utilities.examples;
+import static org.dllearner.utilities.examples.AutomaticNegativeExampleFinderSPARQL2.Strategy.RANDOM;
+import static org.dllearner.utilities.examples.AutomaticNegativeExampleFinderSPARQL2.Strategy.SIBLING;
+import static org.dllearner.utilities.examples.AutomaticNegativeExampleFinderSPARQL2.Strategy.SUPERCLASS;
+
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Map.Entry;
import java.util.Set;
import java.util.SortedSet;
import java.util.TreeSet;
+import org.dllearner.core.owl.ClassHierarchy;
+import org.dllearner.core.owl.Description;
+import org.dllearner.core.owl.Individual;
import org.dllearner.core.owl.NamedClass;
import org.dllearner.kb.SparqlEndpointKS;
import org.dllearner.kb.sparql.SPARQLTasks;
@@ -30,6 +42,10 @@
import org.dllearner.reasoning.SPARQLReasoner;
import org.dllearner.utilities.datastructures.Datastructures;
+import com.google.common.base.Predicate;
+import com.google.common.collect.HashMultiset;
+import com.google.common.collect.Multiset;
+import com.google.common.collect.Multisets;
/**
*
* Utility class for automatically retrieving negative examples from a
@@ -40,12 +56,18 @@
*
*/
public class AutomaticNegativeExampleFinderSPARQL2 {
+
+ public enum Strategy{
+ SUPERCLASS, SIBLING, RANDOM;
+ }
private SparqlEndpoint se;
// for re-using existing queries
private SPARQLReasoner sr;
private SPARQLTasks st;
+
+ private String namespace;
public AutomaticNegativeExampleFinderSPARQL2(SparqlEndpoint se) {
this.se = se;
@@ -54,6 +76,15 @@
st = new SPARQLTasks(se);
}
+ public AutomaticNegativeExampleFinderSPARQL2(SPARQLReasoner reasoner, String namespace) {
+ this.sr = reasoner;
+ this.namespace = namespace;
+ }
+
+ public AutomaticNegativeExampleFinderSPARQL2(SPARQLReasoner reasoner) {
+ this.sr = reasoner;
+ }
+
/**
* Get negative examples when learning the description of a class, i.e.
* all positives are from some known class.
@@ -82,4 +113,92 @@
return negEx;
}
+ public SortedSet<Individual> getNegativeExamples(Set<Individual> positiveExamples, int limit) {
+ return getNegativeExamples(positiveExamples, Arrays.asList(SUPERCLASS, SIBLING, RANDOM), limit);
+ }
+
+ public SortedSet<Individual> getNegativeExamples(Set<Individual> positiveExamples, Collection<Strategy> strategies, int limit) {
+ Map<Strategy, Double> strategiesWithWeight = new HashMap<Strategy, Double>();
+ double weight = 1d/strategies.size();
+ for (Strategy strategy : strategies) {
+ strategiesWithWeight.put(strategy, weight);
+ }
+ return getNegativeExamples(positiveExamples, strategiesWithWeight, limit);
+ }
+
+ public SortedSet<Individual> getNegativeExamples(Set<Individual> positiveExamples, Map<Strategy, Double> strategiesWithWeight, int maxNrOfReturnedInstances) {
+ SortedSet<Individual> negEx = new TreeSet<Individual>();
+
+ //get the types for each instance
+ Multiset<NamedClass> types = HashMultiset.create();
+ for (Individual ex : positiveExamples) {
+ types.addAll(sr.getTypes(ex));
+ }
+
+ //remove types that do not have the given namespace
+ if(namespace != null){
+ types = Multisets.filter(types, new Predicate<NamedClass>() {
+ public boolean apply(NamedClass input){
+ return input.getName().startsWith(namespace);
+ }
+ });
+ }
+
+ //keep the most specific types
+ keepMostSpecificClasses(types);
+
+ for (Entry<Strategy, Double> entry : strategiesWithWeight.entrySet()) {
+ Strategy strategy = entry.getKey();
+ Double weight = entry.getValue();
+ //the max number of instances returned by the current strategy
+ int limit = (int)(weight * maxNrOfReturnedInstances);
+ //the highest frequency value
+ int maxFrequency = types.entrySet().iterator().next().getCount();
+ if(strategy == SIBLING){
+ System.out.println("Sibling Classes Strategy");
+ for (NamedClass nc : types.elementSet()) {
+ int frequency = types.count(nc);
+ //get sibling classes
+ Set<NamedClass> siblingClasses = sr.getSiblingClasses(nc);
+ int nrOfSiblings = siblingClasses.size();
+ int v = (int)Math.ceil(((double)frequency / types.size()) / nrOfSiblings * limit); System.out.println(nc + ": " + v);
+ for (NamedClass siblingClass : siblingClasses) {
+ negEx.addAll(sr.getIndividualsExcluding(siblingClass, nc, v));
+ }
+
+ }
+ } else if(strategy == SUPERCLASS){
+ System.out.println("Super Classes Strategy");
+ for (NamedClass nc : types.elementSet()) {
+ int frequency = types.count(nc);
+ //get sibling classes
+ Set<Description> superClasses = sr.getSuperClasses(nc);System.out.println(superClasses);
+ int nrOfSuperClasses = superClasses.size();
+ int v = (int)Math.ceil(((double)frequency / types.size()) / nrOfSuperClasses * limit); System.out.println(nc + ": " + v);
+ for (Description superClass : superClasses) {
+ negEx.addAll(sr.getIndividualsExcluding(superClass, nc, v));
+ }
+ }
+ } else if(strategy == RANDOM){
+
+ }
+ }
+ return negEx;
+ }
+
+ private void keepMostSpecificClasses(Multiset<NamedClass> classes){
+ HashMultiset<NamedClass> copy = HashMultiset.create(classes);
+ final ClassHierarchy hierarchy = sr.getClassHierarchy();
+ for (NamedClass nc1 : copy.elementSet()) {
+ for (NamedClass nc2 : copy.elementSet()) {
+ if(!nc1.equals(nc2)){
+ //remove class nc1 if it is superclass of another class nc2
+ if(hierarchy.isSubclassOf(nc2, nc1)){
+ classes.remove(nc1, classes.count(nc1));
+ break;
+ }
+ }
+ }
+ }
+ }
}
Modified: trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLClassExpressionToSPARQLConverter.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLClassExpressionToSPARQLConverter.java 2013-05-24 09:16:41 UTC (rev 3984)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLClassExpressionToSPARQLConverter.java 2013-06-06 13:32:30 UTC (rev 3985)
@@ -73,12 +73,7 @@
private String sparql = "";
private Stack<String> variables = new Stack<String>();
- private Map<OWLEntity, String> variablesMapping = new HashMap<OWLEntity, String>();
- private int classCnt = 0;
- private int propCnt = 0;
- private int indCnt = 0;
-
private OWLDataFactory df = new OWLDataFactoryImpl();
private Multimap<Integer, OWLEntity> properties = HashMultimap.create();
@@ -86,8 +81,19 @@
private Map<Integer, Boolean> intersection;
private Set<? extends OWLEntity> variableEntities = new HashSet<OWLEntity>();
+ private VariablesMapping mapping;
+
+ public OWLClassExpressionToSPARQLConverter(VariablesMapping mapping) {
+ this.mapping = mapping;
+ }
+
public OWLClassExpressionToSPARQLConverter() {
+ mapping = new VariablesMapping();
}
+
+ public VariablesMapping getVariablesMapping() {
+ return mapping;
+ }
public String convert(String rootVariable, OWLClassExpression expr){
reset();
@@ -132,7 +138,7 @@
queryString += rootVariable + " WHERE {";
} else {
for (OWLEntity owlEntity : variableEntities) {
- String var = variablesMapping.get(owlEntity);
+ String var = mapping.get(owlEntity);
queryString += var + " ";
}
if(count){
@@ -149,7 +155,7 @@
if(count){
queryString += "GROUP BY ";
for (OWLEntity owlEntity : variableEntities) {
- String var = variablesMapping.get(owlEntity);
+ String var = mapping.get(owlEntity);
queryString += var;
}
queryString += " ORDER BY DESC(?cnt)";
@@ -158,40 +164,14 @@
return QueryFactory.create(queryString, Syntax.syntaxARQ);
}
- public Map<OWLEntity, String> getVariablesMapping() {
- return variablesMapping;
- }
-
private void reset(){
- variablesMapping.clear();
variables.clear();
properties.clear();
- classCnt = 0;
- propCnt = 0;
- indCnt = 0;
sparql = "";
intersection = new HashMap<Integer, Boolean>();
+ mapping.reset();
}
- private String getVariable(OWLEntity entity){
- String var = variablesMapping.get(entity);
- if(var == null){
- if(entity.isOWLClass()){
- var = "?cls" + classCnt++;
- } else if(entity.isOWLObjectProperty() || entity.isOWLDataProperty()){
- var = "?p" + propCnt++;
- } else if(entity.isOWLNamedIndividual()){
- var = buildIndividualVariable();
- }
- variablesMapping.put(entity, var);
- }
- return var;
- }
-
- private String buildIndividualVariable(){
- return "?s" + indCnt++;
- }
-
private int modalDepth(){
return variables.size();
}
@@ -253,7 +233,7 @@
private String render(OWLEntity entity){
String s;
if(variableEntities.contains(entity)){
- s = getVariable(entity);
+ s = mapping.getVariable(entity);
} else {
s = "<" + entity.toStringID() + ">";
}
@@ -295,8 +275,8 @@
if(props.size() > 1){
Collection<String> vars = new TreeSet<String>();
for (OWLEntity p : props) {
- if(variablesMapping.containsKey(p)){
- vars.add(variablesMapping.get(p));
+ if(mapping.containsKey(p)){
+ vars.add(mapping.get(p));
}
}
if(vars.size() == 2){
@@ -334,7 +314,7 @@
@Override
public void visit(OWLObjectSomeValuesFrom ce) {
- String objectVariable = buildIndividualVariable();
+ String objectVariable = mapping.newIndividualVariable();
OWLObjectPropertyExpression propertyExpression = ce.getProperty();
if(propertyExpression.isAnonymous()){
//property expression is inverse of a property
@@ -356,7 +336,7 @@
@Override
public void visit(OWLObjectAllValuesFrom ce) {
String subject = variables.peek();
- String objectVariable = buildIndividualVariable();
+ String objectVariable = mapping.newIndividualVariable();
OWLObjectPropertyExpression propertyExpression = ce.getProperty();
OWLObjectProperty predicate = propertyExpression.getNamedProperty();
OWLClassExpression filler = ce.getFiller();
@@ -367,7 +347,7 @@
sparql += triple(variables.peek(), predicate, objectVariable);
}
- String var = buildIndividualVariable();
+ String var = mapping.newIndividualVariable();
sparql += "{SELECT " + subject + " (COUNT(" + var + ") AS ?cnt1) WHERE {";
sparql += triple(subject, predicate, var);
variables.push(var);
@@ -375,7 +355,7 @@
variables.pop();
sparql += "} GROUP BY " + subject + "}";
- var = buildIndividualVariable();
+ var = mapping.newIndividualVariable();
sparql += "{SELECT " + subject + " (COUNT(" + var + ") AS ?cnt2) WHERE {";
sparql += triple(subject, predicate, var);
sparql += "} GROUP BY " + subject + "}";
@@ -399,7 +379,7 @@
@Override
public void visit(OWLObjectMinCardinality ce) {
String subjectVariable = variables.peek();
- String objectVariable = buildIndividualVariable();
+ String objectVariable = mapping.newIndividualVariable();
OWLObjectPropertyExpression propertyExpression = ce.getProperty();
int cardinality = ce.getCardinality();
sparql += "{SELECT " + subjectVariable + " WHERE {";
@@ -411,7 +391,7 @@
}
OWLClassExpression filler = ce.getFiller();
if(filler.isAnonymous()){
- String var = buildIndividualVariable();
+ String var = mapping.newIndividualVariable();
variables.push(var);
sparql += triple(objectVariable, "a", var);
filler.accept(this);
@@ -427,7 +407,7 @@
@Override
public void visit(OWLObjectExactCardinality ce) {
String subjectVariable = variables.peek();
- String objectVariable = buildIndividualVariable();
+ String objectVariable = mapping.newIndividualVariable();
OWLObjectPropertyExpression propertyExpression = ce.getProperty();
int cardinality = ce.getCardinality();
sparql += "{SELECT " + subjectVariable + " WHERE {";
@@ -439,7 +419,7 @@
}
OWLClassExpression filler = ce.getFiller();
if(filler.isAnonymous()){
- String var = buildIndividualVariable();
+ String var = mapping.newIndividualVariable();
variables.push(var);
sparql += triple(objectVariable, "a", var);
filler.accept(this);
@@ -454,7 +434,7 @@
@Override
public void visit(OWLObjectMaxCardinality ce) {
String subjectVariable = variables.peek();
- String objectVariable = buildIndividualVariable();
+ String objectVariable = mapping.newIndividualVariable();
OWLObjectPropertyExpression propertyExpression = ce.getProperty();
int cardinality = ce.getCardinality();
sparql += "{SELECT " + subjectVariable + " WHERE {";
@@ -466,7 +446,7 @@
}
OWLClassExpression filler = ce.getFiller();
if(filler.isAnonymous()){
- String var = buildIndividualVariable();
+ String var = mapping.newIndividualVariable();
variables.push(var);
sparql += triple(objectVariable, "a", var);
filler.accept(this);
@@ -506,7 +486,7 @@
@Override
public void visit(OWLDataSomeValuesFrom ce) {
- String objectVariable = buildIndividualVariable();
+ String objectVariable = mapping.newIndividualVariable();
OWLDataPropertyExpression propertyExpression = ce.getProperty();
sparql += triple(variables.peek(), propertyExpression.asOWLDataProperty(), objectVariable);
OWLDataRange filler = ce.getFiller();
@@ -518,13 +498,13 @@
@Override
public void visit(OWLDataAllValuesFrom ce) {
String subject = variables.peek();
- String objectVariable = buildIndividualVariable();
+ String objectVariable = mapping.newIndividualVariable();
OWLDataPropertyExpression propertyExpression = ce.getProperty();
String predicate = propertyExpression.asOWLDataProperty().toStringID();
OWLDataRange filler = ce.getFiller();
sparql += triple(variables.peek(), predicate, objectVariable);
- String var = buildIndividualVariable();
+ String var = mapping.newIndividualVariable();
sparql += "{SELECT " + subject + " (COUNT(" + var + ") AS ?cnt1) WHERE {";
sparql += triple(subject, predicate, var);
variables.push(var);
@@ -532,7 +512,7 @@
variables.pop();
sparql += "} GROUP BY " + subject + "}";
- var = buildIndividualVariable();
+ var = mapping.newIndividualVariable();
sparql += "{SELECT " + subject + " (COUNT(" + var + ") AS ?cnt2) WHERE {";
sparql += triple(subject, predicate, var);
sparql += "} GROUP BY " + subject + "}";
@@ -550,7 +530,7 @@
@Override
public void visit(OWLDataMinCardinality ce) {
String subjectVariable = variables.peek();
- String objectVariable = buildIndividualVariable();
+ String objectVariable = mapping.newIndividualVariable();
OWLDataPropertyExpression propertyExpression = ce.getProperty();
int cardinality = ce.getCardinality();
sparql += "{SELECT " + subjectVariable + " WHERE {";
@@ -566,7 +546,7 @@
@Override
public void visit(OWLDataExactCardinality ce) {
String subjectVariable = variables.peek();
- String objectVariable = buildIndividualVariable();
+ String objectVariable = mapping.newIndividualVariable();
OWLDataPropertyExpression propertyExpression = ce.getProperty();
int cardinality = ce.getCardinality();
sparql += "{SELECT " + subjectVariable + " WHERE {";
@@ -582,7 +562,7 @@
@Override
public void visit(OWLDataMaxCardinality ce) {
String subjectVariable = variables.peek();
- String objectVariable = buildIndividualVariable();
+ String objectVariable = mapping.newIndividualVariable();
OWLDataPropertyExpression propertyExpression = ce.getProperty();
int cardinality = ce.getCardinality();
sparql += "{SELECT " + subjectVariable + " WHERE {";
@@ -774,7 +754,4 @@
System.out.println(expr + "\n" + query);
}
-
-
-
}
\ No newline at end of file
Modified: trunk/components-core/src/main/resources/prefixes.csv
===================================================================
--- trunk/components-core/src/main/resources/prefixes.csv 2013-05-24 09:16:41 UTC (rev 3984)
+++ trunk/components-core/src/main/resources/prefixes.csv 2013-06-06 13:32:30 UTC (rev 3985)
@@ -4,609 +4,963 @@
dbp,http://dbpedia.org/property/
owl,http://www.w3.org/2002/07/owl#
dc,http://purl.org/dc/elements/1.1/
+rdfs,http://www.w3.org/2000/01/rdf-schema#
dbo,http://dbpedia.org/ontology/
-rdfs,http://www.w3.org/2000/01/rdf-schema#
-sc,http://umbel.org/umbel/sc/
rss,http://purl.org/rss/1.0/
+sc,http://purl.org/science/owl/sciencecommons/
+skos,http://www.w3.org/2004/02/skos/core#
fb,http://rdf.freebase.com/ns/
geonames,http://www.geonames.org/ontology#
-skos,http://www.w3.org/2004/02/skos/core#
-cyc,http://sw.opencyc.org/concept/
geo,http://www.w3.org/2003/01/geo/wgs84_pos#
sioc,http://rdfs.org/sioc/ns#
+gr,http://purl.org/goodrelations/v1#
+gldp,http://www.w3.org/ns/people#
+cyc,http://sw.opencyc.org/concept/
akt,http://www.aktors.org/ontology/portal#
+xsd,http://www.w3.org/2001/XMLSchema#
dbpedia,http://dbpedia.org/resource/
+dcterms,http://purl.org/dc/terms/
+swrc,http://swrc.ontoware.org/ontology#
+commerce,http://search.yahoo.com/searchmonkey/commerce/
admin,http://webns.net/mvcb/
-gr,http://purl.org/goodrelations/v1#
-swrc,http://swrc.ontoware.org/ontology#
-xsd,http://www.w3.org/2001/XMLSchema#
-xhtml,http://www.w3.org/1999/xhtml/vocab#
+content,http://purl.org/rss/1.0/modules/content/
doap,http://usefulinc.com/ns/doap#
+void,http://rdfs.org/ns/void#
+xhtml,http://www.w3.org/1999/xhtml#
+bibo,http://purl.org/ontology/bibo/
+org,http://www.w3.org/ns/org#
vcard,http://www.w3.org/2006/vcard/ns#
-content,http://purl.org/rss/1.0/modules/content/
+gen,http://www.w3.org/2006/gen/ont#
bill,http://www.rdfabout.com/rdf/schema/usbill/
-dcterms,http://purl.org/dc/terms/
-mo,http://purl.org/ontology/mo/
+aiiso,http://purl.org/vocab/aiiso/schema#
wot,http://xmlns.com/wot/0.1/
-wn20schema,http://www.w3.org/2006/03/wn/wn20/schema/
-d2rq,http://www.wiwiss.fu-berlin.de/suhl/bizer/D2RQ/0.1#
-gen,http://www.w3.org/2006/gen/ont#
+qb,http://purl.org/linked-data/cube#
nie,http://www.semanticdesktop.org/ontologies/2007/01/19/nie#
-void,http://rdfs.org/ns/void#
test2,http://this.invalid/test2#
-org,http://www.w3.org/ns/org#
-movie,http://data.linkedmdb.org/resource/movie/
-ex,http://example.com/
+d2rq,http://www.wiwiss.fu-berlin.de/suhl/bizer/D2RQ/0.1#
rel,http://purl.org/vocab/relationship/
-bio,http://purl.org/vocab/bio/0.1/
+dcmit,http://purl.org/dc/dcmitype/
http,http://www.w3.org/2006/http#
-dcmit,http://purl.org/dc/dcmitype/
-reco,http://purl.org/reco#
cc,http://creativecommons.org/ns#
-nfo,http://www.semanticdesktop.org/ontologies/2007/03/22/nfo#
-ac,http://umbel.org/umbel/ac/
-xfn,http://vocab.sindice.com/xfn#
+og,http://opengraphprotocol.org/schema/
+factbook,http://www4.wiwiss.fu-berlin.de/factbook/ns#
+vann,http://purl.org/vocab/vann/
+ex,http://example.com/
+bio,http://purl.org/vocab/bio/0.1/
+mo,http://purl.org/ontology/mo/
+ad,http://schemas.talis.com/2005/address/schema#
+media,http://purl.org/microformat/hmedia/
+event,http://purl.org/NET/c4dm/event.owl#
earl,http://www.w3.org/ns/earl#
-og,http://opengraphprotocol.org/schema/
+book,http://purl.org/NET/book/vocab#
+cv,http://purl.org/captsolo/resume-rdf/0.2/cv#
+ical,http://www.w3.org/2002/12/cal/ical#
+botany,http://purl.org/NET/biol/botany#
air,http://dig.csail.mit.edu/TAMI/2007/amord/air#
-ical,http://www.w3.org/2002/12/cal/ical#
-media,http://purl.org/media#
-rev,http://purl.org/stuff/rev#
-cv,http://rdfs.org/resume-rdf/
tag,http://www.holygoat.co.uk/owl/redwood/0.1/tags/
+dv,http://rdf.data-vocabulary.org/#
+cld,http://purl.org/cld/terms/
swc,http://data.semanticweb.org/ns/swc/ontology#
-botany,http://purl.org/NET/biol/botany#
-bibo,http://purl.org/ontology/bibo/
-xf,http://www.w3.org/2002/xforms/
-factbook,http://www4.wiwiss.fu-berlin.de/factbook/ns#
+drugbank,http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugbank/
+musim,http://purl.org/ontology/similarity/
+dir,http://schemas.talis.com/2005/dir/schema#
+reco,http://purl.org/reco#
+rev,http://purl.org/stuff/rev#
+biblio,http://purl.org/net/biblio#
+ctag,http://commontag.org/ns#
+af,http://purl.org/ontology/af/
days,http://ontologi.es/days#
-cfp,http://sw.deri.org/2005/08/conf/cfp.owl#
-sism,http://purl.oclc.org/NET/sism/0.1/
-vann,http://purl.org/vocab/vann/
+log,http://www.w3.org/2000/10/swap/log#
+cs,http://purl.org/vocab/changeset/schema#
+sd,http://www.w3.org/ns/sparql-service-description#
osag,http://www.ordnancesurvey.co.uk/ontology/AdministrativeGeography/v2.0/AdministrativeGeography.rdf#
-owlim,http://www.ontotext.com/trree/owlim#
-dir,http://schemas.talis.com/2005/dir/schema#
-cld,http://purl.org/cld/terms/
-afn,http://jena.hpl.hp.com/ARQ/function#
-book,http://purl.org/NET/book/vocab#
+xhv,http://www.w3.org/1999/xhtml/vocab#
+rdfg,http://www.w3.org/2004/03/trix/rdfg-1/
+co,http://purl.org/ontology/co/core#
fn,http://www.w3.org/2005/xpath-functions#
-musim,http://purl.org/ontology/similarity/
-akts,http://www.aktors.org/ontology/support#
-cs,http://purl.org/vocab/changeset/schema#
-aiiso,http://purl.org/vocab/aiiso/schema#
-ad,http://schemas.talis.com/2005/address/schema#
+sism,http://purl.oclc.org/NET/sism/0.1/
mu,http://www.kanzaki.com/ns/music#
-sd,http://www.w3.org/ns/sparql-service-description#
-po,http://purl.org/ontology/po/
-biblio,http://purl.org/net/biblio#
-event,http://purl.org/NET/c4dm/event.owl#
-dv,http://rdf.data-vocabulary.org/#
-drugbank,http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugbank/
-uniprot,http://purl.uniprot.org/core/
memo,http://ontologies.smile.deri.ie/2009/02/27/memo#
-dcn,http://www.w3.org/2007/uwa/context/deliverycontext.owl#
-rdfg,http://www.w3.org/2004/03/trix/rdfg-1/
-log,http://www.w3.org/2000/10/swap/log#
-co,http://purl.org/ontology/co/core#
-qb,http://purl.org/linked-data/cube#
ome,http://purl.org/ontomedia/core/expression#
-af,http://purl.org/ontology/af/
+daia,http://purl.org/ontology/daia/
+cmp,http://www.ontologydesignpatterns.org/cp/owl/componency.owl#
+owlim,http://www.ontotext.com/trree/owlim#
+cfp,http://sw.deri.org/2005/08/conf/cfp.owl#
+xfn,http://vocab.sindice.com/xfn#
+afn,http://jena.hpl.hp.com/ARQ/function#
+ok,http://okkam.org/terms#
giving,http://ontologi.es/giving#
+ir,http://www.ontologydesignpatterns.org/cp/owl/informationrealization.owl#
+xf,http://www.w3.org/2002/xforms/
+dcn,http://www.w3.org/2007/uwa/context/deliverycontext.owl#
swanq,http://purl.org/swan/1.2/qualifiers/
-cmp,http://www.ontologydesignpatterns.org/cp/owl/componency.owl#
lomvoc,http://ltsc.ieee.org/rdf/lomv1p0/vocabulary#
+math,http://www.w3.org/2000/10/swap/math#
+swande,http://purl.org/swan/1.2/discourse-elements/
rif,http://www.w3.org/2007/rif#
-ir,http://www.ontologydesignpatterns.org/cp/owl/informationrealization.owl#
-ctag,http://commontag.org/ns#
-ok,http://okkam.org/terms#
-swande,http://purl.org/swan/1.2/discourse-elements/
-math,http://www.w3.org/2000/10/swap/math#
-daia,http://purl.org/ontology/daia/
-sioct,http://rdfs.org/sioc/types#
+sr,http://www.openrdf.org/config/repository/sail#
jdbc,http://d2rq.org/terms/jdbc/
+tzont,http://www.w3.org/2006/timezone#
myspace,http://purl.org/ontology/myspace#
-sr,http://www.openrdf.org/config/repository/sail#
-tzont,http://www.w3.org/2006/timezone#
+con,http://www.w3.org/2000/10/swap/pim/contact#
+sider,http://www4.wiwiss.fu-berlin.de/sider/resource/sider/
+wn20schema,http://www.w3.org/2006/03/wn/wn20/schema/
+cert,http://www.w3.org/ns/auth/cert#
+pto,http://www.productontology.org/id/
+movie,http://data.linkedmdb.org/resource/movie/
+oo,http://purl.org/openorg/
+nfo,http://www.semanticdesktop.org/ontologies/nfo/#
+ac,http://umbel.org/umbel/ac/
+po,http://purl.org/ontology/po/
+akts,http://www.aktors.org/ontology/support#
+frbr,http://purl.org/vocab/frbr/core#
+uniprot,http://purl.uniprot.org/core/
+dcat,http://www.w3.org/ns/dcat#
+rsa,http://www.w3.org/ns/auth/rsa#
+ov,http://open.vocab.org/terms/
+sioct,http://rdfs.org/sioc/types#
+prv,http://purl.org/net/provenance/ns#
+prov,http://www.w3.org/ns/prov#
+granatum,http://chem.deri.ie/granatum/
+wo,http://purl.org/ontology/wo/
daml,http://www.daml.org/2001/03/daml+oil#
-wo,http://purl.org/ontology/wo/
-politico,http://www.rdfabout.com/rdf/schema/politico/
+spacerel,http://data.ordnancesurvey.co.uk/ontology/spatialrelations/
+pc,http://purl.org/procurement/public-contracts#
pmlj,http://inference-web.org/2.0/pml-justification.owl#
+vs,http://www.w3.org/2003/06/sw-vocab-status/ns#
usgov,http://www.rdfabout.com/rdf/schema/usgovt/
+acm,http://www.rkbexplorer.com/ontologies/acm#
taxo,http://purl.org/rss/1.0/modules/taxonomy/
-lfm,http://purl.org/ontology/last-fm/
-vote,http://www.rdfabout.com/rdf/schema/vote/
-frbr,http://purl.org/vocab/frbr/core#
-doac,http://ramonantonio.net/doac/0.1/#
wn,http://xmlns.com/wordnet/1.6/
-affy,http://www.affymetrix.com/community/publications/affymetrix/tmsplice#
-con,http://www.w3.org/2000/10/swap/pim/contact#
-prv,http://purl.org/net/provenance/ns#
-scot,http://scot-project.org/scot/ns#
-irrl,http://www.ontologydesignpatterns.org/cp/owl/informationobjectsandrepresentationlanguages.owl#
+wdrs,http://www.w3.org/2007/05/powder-s#
scovo,http://purl.org/NET/scovo#
-nco,http://www.semanticdesktop.org/ontologies/2007/03/22/nco#
+oauth,http://demiblog.org/vocab/oauth#
+politico,http://www.rdfabout.com/rdf/schema/politico/
lgd,http://linkedgeodata.org/ontology/
-wordmap,http://purl.org/net/ns/wordmap#
+lode,http://linkedevents.org/ontology/
+acl,http://www.w3.org/ns/auth/acl#
+ore,http://www.openarchives.org/ore/terms/
+abc,http://www.metadata.net/harmony/ABCSchemaV5Commented.rdf#
omt,http://purl.org/ontomedia/ext/common/trait#
-sider,http://www4.wiwiss.fu-berlin.de/sider/resource/sider/
+nao,http://www.semanticdesktop.org/ontologies/2007/08/15/nao#
+omb,http://purl.org/ontomedia/ext/common/being#
+loc,http://www.w3.org/2007/uwa/context/location.owl#
+mit,http://purl.org/ontology/mo/mit#
+skosxl,http://www.w3.org/2008/05/skos-xl#
+spc,http://purl.org/ontomedia/core/space#
+vote,http://www.rdfabout.com/rdf/schema/vote/
+lfm,http://purl.org/ontology/last-fm/
+irrl,http://www.ontologydesignpatterns.org/cp/owl/informationobjectsandrepresentationlanguages.owl#
+rep,http://www.openrdf.org/config/repository#
+chord,http://purl.org/ontology/chord/
+dcam,http://purl.org/dc/dcam/
user,http://schemas.talis.com/2005/user/schema#
-ore,http://www.openarchives.org/ore/terms/
-lode,http://linkedevents.org/ontology/
-ecs,http://rdf.ecs.soton.ac.uk/ontology/ecs#
-rep,http://www.openrdf.org/config/repository#
-nao,http://www.semanticdesktop.org/ontologies/2007/08/15/nao#
-spin,http://spinrdf.org/spin#
+resex,http://resex.rkbexplorer.com/ontologies/resex#
swrl,http://www.w3.org/2003/11/swrl#
-lx,http://purl.org/NET/lx#
+music,http://musicontology.com/
+doac,http://ramonantonio.net/doac/0.1/#
+scot,http://scot-project.org/scot/ns#
+irw,http://www.ontologydesignpatterns.org/ont/web/irw.owl#
ti,http://www.ontologydesignpatterns.org/cp/owl/timeinterval.owl#
-unit,http://qudt.org/vocab/unit#
-spc,http://purl.org/ontomedia/core/space#
-es,http://eulersharp.sourceforge.net/2003/03swap/log-rules#
-zoology,http://purl.org/NET/biol/zoology#
-swrlb,http://www.w3.org/2003/11/swrlb#
+affy,http://www.affymetrix.com/community/publications/affymetrix/tmsplice#
+lingvoj,http://www.lingvoj.org/ontology#
+courseware,http://courseware.rkbexplorer.com/ontologies/courseware#
+link,http://www.w3.org/2006/link#
+video,http://purl.org/media/video#
+tl,http://purl.org/NET/c4dm/timeline.owl#
+nco,http://www.semanticdesktop.org/ontologies/2007/03/22/nco#
fec,http://www.rdfabout.com/rdf/schema/usfec/
-lang,http://ontologi.es/lang/core#
-coref,http://www.rkbexplorer.com/ontologies/coref#
-doc,http://www.w3.org/2000/10/swap/pim/doc#
-os,http://www.w3.org/2000/10/swap/os#
-atomix,http://buzzword.org.uk/rdf/atomix#
-ne,http://umbel.org/umbel/ne/
-omb,http://purl.org/ontomedia/ext/common/being#
money,http://purl.org/net/rdf-money/
-hard,http://www.w3.org/2007/uwa/context/hardware.owl#
-ov,http://open.vocab.org/terms/
-java,http://www.w3.org/2007/uwa/context/java.owl#
-eztag,http://ontologies.ezweb.morfeo-project.org/eztag/ns#
-abc,http://www.metadata.net/harmony/ABCSchemaV5Commented.rdf#
-tmo,http://www.semanticdesktop.org/ontologies/2008/05/20/tmo#
-vs,http://www.w3.org/2003/06/sw-vocab-status/ns#
sede,http://eventography.org/sede/0.1/
+rec,http://purl.org/ontology/rec/core#
+atom,http://www.w3.org/2005/Atom/
+atomix,http://buzzword.org.uk/rdf/atomix#
+sit,http://www.ontologydesignpatterns.org/cp/owl/situation.owl#
+powder,http://www.w3.org/2007/05/powder#
+fresnel,http://www.w3.org/2004/09/fresnel#
+rei,http://www.w3.org/2004/06/rei#
+doc,http://www.w3.org/2000/10/swap/pim/doc#
+coref,http://www.rkbexplorer.com/ontologies/coref#
nrl,http://www.semanticdesktop.org/ontologies/2007/08/15/nrl#
-ibis,http://purl.org/ibis#
+spin,http://spinrdf.org/spin#
+umbel,http://umbel.org/umbel#
code,http://telegraphis.net/ontology/measurement/code#
-omp,http://purl.org/ontomedia/ext/common/profession#
-dcam,http://purl.org/dc/dcam/
+zoology,http://purl.org/NET/biol/zoology#
+wordmap,http://purl.org/net/ns/wordmap#
+lotico,http://www.lotico.com/resource/
+audio,http://purl.org/media/audio#
+meta,http://www.openrdf.org/rdf/2009/metadata#
+protege,http://protege.stanford.edu/system#
+time,http://www.w3.org/2006/time#
+sv,http://schemas.talis.com/2005/service/schema#
+ya,http://blogs.yandex.ru/schema/foaf/
+bio2rdf,http://bio2rdf.org/
+biol,http://purl.org/NET/biol/ns#
imm,http://schemas.microsoft.com/imm/
-xhe,http://buzzword.org.uk/rdf/xhtml-elements#
+sp,http://spinrdf.org/sp#
+exif,http://www.w3.org/2003/12/exif/ns#
+swrlb,http://www.w3.org/2003/11/swrlb#
+iswc,http://annotation.semanticweb.org/2004/iswc#
+ecs,http://rdf.ecs.soton.ac.uk/ontology/ecs#
+p3p,http://www.w3.org/2002/01/p3prdfv1#
kwijibo,http://kwijibo.talis.com/
-sv,http://schemas.talis.com/2005/service/schema#
-h5,http://buzzword.org.uk/rdf/h5#
-space,http://purl.org/net/schemas/space/
-wdrs,http://www.w3.org/2007/05/powder-s#
-video,http://purl.org/media/video#
-wnschema,http://www.cogsci.princeton.edu/~wn/schema/
+eztag,http://ontologies.ezweb.morfeo-project.org/eztag/ns#
+so,http://purl.org/ontology/symbolic-music/
+lang,http://ontologi.es/lang/core#
+tmo,http://www.semanticdesktop.org/ontologies/2008/05/20/tmo#
+airport,http://www.daml.org/2001/10/html/airport-ont#
+java,http://www.w3.org/2007/uwa/context/java.owl#
+acc,http://purl.org/NET/acc#
+os,http://www.w3.org/2000/10/swap/os#
+ne,http://umbel.org/umbel/ne/
+omp,http://purl.org/ontomedia/ext/common/profession#
+lx,http://purl.org/NET/lx#
+doclist,http://www.junkwork.net/xml/DocumentList#
+lifecycle,http://purl.org/vocab/lifecycle/schema#
+omc,http://purl.org/ontomedia/ext/common/bestiary#
+dailymed,http://www4.wiwiss.fu-berlin.de/dailymed/resource/dailymed/
+ibis,http://purl.org/ibis#
sail,http://www.openrdf.org/config/sail#
-custom,http://www.openrdf.org/config/sail/custom#
-acc,http://purl.org/NET/acc#
-rsa,http://www.w3.org/ns/auth/rsa#
-sit,http://www.ontologydesignpatterns.org/cp/owl/situation.owl#
-wdr,http://www.w3.org/2007/05/powder#
-airport,http://www.daml.org/2001/10/html/airport-ont#
-rei,http://www.w3.org/2004/06/rei#
-mit,http://purl.org/ontology/mo/mit#
-phss,http://ns.poundhill.com/phss/1.0/
-ncal,http://www.semanticdesktop.org/ontologies/2007/04/02/ncal#
osoc,http://web-semantics.org/ns/opensocial#
+hard,http://www.w3.org/2007/uwa/context/hardware.owl#
+grddl,http://www.w3.org/2003/g/data-view#
ptr,http://www.w3.org/2009/pointers#
-protege,http://protege.stanford.edu/system#
-irw,http://www.ontologydesignpatterns.org/ont/web/irw.owl#
-omc,http://purl.org/ontomedia/ext/common/bestiary#
-tdb,http://jena.hpl.hp.com/2008/tdb#
-meta,http://www.openrdf.org/rdf/2009/metadata#
-iswc,http://annotation.semanticweb.org/2004/iswc#
-lingvoj,http://www.lingvoj.org/ontology#
-resex,http://resex.rkbexplorer.com/ontologies/resex#
-chord,http://purl.org/ontology/chord/
-p3p,http://www.w3.org/2002/01/p3prdfv1#
-oauth,http://demiblog.org/vocab/oauth#
-acl,http://www.w3.org/ns/auth/acl#
-tl,http://purl.org/NET/c4dm/timeline.owl#
-xen,http://buzzword.org.uk/rdf/xen#
-acm,http://www.rkbexplorer.com/ontologies/acm#
-link,http://www.w3.org/2006/link#
-umbel,http://umbel.org/umbel#
-swh,http://plugin.org.uk/swh-plugins/
+spl,http://spinrdf.org/spl#
+wnschema,http://www.cogsci.princeton.edu/~wn/schema/
+es,http://eulersharp.sourceforge.net/2003/03swap/log-rules#
+unit,http://qudt.org/vocab/unit#
+label,http://purl.org/net/vocab/2004/03/label#
+moat,http://moat-project.org/ns#
+hlisting,http://sindice.com/hlisting/0.1/
+test,http://test2.example.com/
lom,http://ltsc.ieee.org/rdf/lomv1p0/lom#
-common,http://www.w3.org/2007/uwa/context/common.owl#
-ya,http://blogs.yandex.ru/schema/foaf/
-frbre,http://purl.org/vocab/frbr/extended#
+osgb,http://data.ordnancesurvey.co.uk/id/
+custom,http://www.openrdf.org/config/sail/custom#
prj,http://purl.org/stuff/project/
+resist,http://www.rkbexplorer.com/ontologies/resist#
+pmlp,http://inference-web.org/2.0/pml-provenance.owl#
+smiley,http://www.smileyontology.com/ns#
+formats,http://www.w3.org/ns/formats/
+h5,http://buzzword.org.uk/rdf/h5#
+sdl,http://purl.org/vocab/riro/sdl#
+space,http://purl.org/net/schemas/space/
+wv,http://vocab.org/waiver/terms/
+ncal,http://www.semanticdesktop.org/ontologies/2007/04/02/ncal#
+ping,http://purl.org/net/pingback/
+list,http://www.w3.org/2000/10/swap/list#
+sml,http://topbraid.org/sparqlmotionlib#
+phss,http://ns.poundhill.com/phss/1.0/
+omm,http://purl.org/ontomedia/core/media#
+meetup,http://www.lotico.com/meetup/
net,http://www.w3.org/2007/uwa/context/network.owl#
-hlisting,http://sindice.com/hlisting/0.1/
-sdl,http://purl.org/vocab/riro/sdl#
-trackback,http://madskills.com/public/xml/rss/module/trackback/
+qdoslf,http://foaf.qdos.com/lastfm/schema/
+xen,http://buzzword.org.uk/rdf/xen#
+tdb,http://jena.hpl.hp.com/2008/tdb#
+gold,http://purl.org/linguistics/gold/
nmo,http://www.semanticdesktop.org/ontologies/2007/03/22/nmo#
-cert,http://www.w3.org/ns/auth/cert#
-spl,http://spinrdf.org/spl#
-sp,http://spinrdf.org/sp#
-dailymed,http://www4.wiwiss.fu-berlin.de/dailymed/resource/dailymed/
-resist,http://www.rkbexplorer.com/ontologies/resist#
+xhe,http://buzzword.org.uk/rdf/xhtml-elements#
swp,http://www.w3.org/2004/03/trix/swp-2/
-fresnel,http://www.w3.org/2004/09/fresnel#
-lt,http://diplomski.nelakolundzija.org/LTontology.rdf#
-wv,http://vocab.org/waiver/terms/
product,http://purl.org/commerce/product#
-test,http://test2.example.com/
-gold,http://purl.org/linguistics/gold/
-smiley,http://www.smileyontology.com/ns#
+lfn,http://www.dotnetrdf.org/leviathan#
+whois,http://www.kanzaki.com/ns/whois#
+pr,http://ontologi.es/profiling#
+biocore,http://bio2rdf.org/core#
+cnt,http://www.w3.org/2008/content#
swandr,http://purl.org/swan/1.2/discourse-relationships/
-ddc,http://purl.org/NET/decimalised#
-soft,http://www.w3.org/2007/uwa/context/software.owl#
+frbre,http://purl.org/vocab/frbr/extended#
nexif,http://www.semanticdesktop.org/ontologies/2007/05/10/nexif#
-skosxl,http://www.w3.org/2008/05/skos-xl#
+sm,http://topbraid.org/sparqlmotion#
+fed,http://www.openrdf.org/config/sail/federation#
+oat,http://openlinksw.com/schemas/oat/
+c4n,http://vocab.deri.ie/c4n#
+smf,http://topbraid.org/sparqlmotionfunctions#
+trackback,http://madskills.com/public/xml/rss/module/trackback/
ire,http://www.ontologydesignpatterns.org/cpont/ire.owl#
-fed,http://www.openrdf.org/config/sail/federation#
-courseware,http://courseware.rkbexplorer.com/ontologies/courseware#
-biol,http://purl.org/NET/biol/ns#
+opm,http://openprovenance.org/ontology#
+common,http://www.w3.org/2007/uwa/context/common.owl#
gpt,http://purl.org/vocab/riro/gpt#
+soft,http://www.w3.org/2007/uwa/context/software.owl#
+bibtex,http://purl.oclc.org/NET/nknouf/ns/bibtex#
+climb,http://climb.dataincubator.org/vocabs/climb/
+wisski,http://wiss-ki.eu/
+pmt,http://tipsy.googlecode.com/svn/trunk/vocab/pmt#
+opensearch,http://a9.com/-/spec/opensearch/1.1/
+bsbm,http://www4.wiwiss.fu-berlin.de/bizer/bsbm/v01/vocabulary/
sesame,http://www.openrdf.org/schema/sesame#
-time,http://www.w3.org/2006/time#
-atom,http://www.w3.org/2005/Atom/
-omm,http://purl.org/ontomedia/core/media#
-lotico,http://www.lotico.com/resource/
+swh,http://plugin.org.uk/swh-plugins/
+mysql,http://web-semantics.org/ns/mysql/
+nid3,http://www.semanticdesktop.org/ontologies/2007/05/10/nid3#
+lt,http://diplomski.nelakolundzija.org/LTontology.rdf#
web,http://www.w3.org/2007/uwa/context/web.owl#
-sm,http://topbraid.org/sparqlmotion#
+like,http://ontologi.es/like#
states,http://www.w3.org/2005/07/aaa#
-moat,http://moat-project.org/ns#
-pimo,http://www.semanticdesktop.org/ontologies/2007/11/01/pimo#
-push,http://www.w3.org/2007/uwa/context/push.owl#
-bio2rdf,http://bio2rdf.org/
-bsbm,http://www4.wiwiss.fu-berlin.de/bizer/bsbm/v01/vocabulary/
-bibtex,http://purl.oclc.org/NET/nknouf/ns/bibtex#
-music,http://musicontology.com/
+ddc,http://purl.org/NET/decimalised#
+imreg,http://www.w3.org/2004/02/image-regions#
+ddl,http://purl.org/vocab/riro/ddl#
+cycann,http://sw.cyc.com/CycAnnotations_v1#
dummy,http://hello.com/
-am,http://vocab.deri.ie/am#
-wairole,http://www.w3.org/2005/01/wai-rdf/GUIRoleTaxonomy#
-pmt,http://tipsy.googlecode.com/svn/trunk/vocab/pmt#
-loc,http://www.w3.org/2007/uwa/context/location.owl#
-doclist,http://www.junkwork.net/xml/DocumentList#
-pmlr,http://inference-web.org/2.0/pml-relation.owl#
-ddl,http://purl.org/vocab/riro/ddl#
-audio,http://purl.org/media/audio#
-qdoslf,http://foaf.qdos.com/lastfm/schema/
-uri,http://purl.org/NET/uri#
+obj,http://www.openrdf.org/rdf/2009/object#
+resource,http://purl.org/vocab/resourcelist/schema#
+compass,http://purl.org/net/compass#
+swanag,http://purl.org/swan/1.2/agents/
crypto,http://www.w3.org/2000/10/swap/crypto#
-like,http://ontologi.es/like#
-lfn,http://www.dotnetrdf.org/leviathan#
+push,http://www.w3.org/2007/uwa/context/push.owl#
+puc,http://purl.org/NET/puc#
+rdfa,http://www.w3.org/ns/rdfa#
xl,http://langegger.at/xlwrap/vocab#
+xhtmlvocab,http://www.w3.org/1999/xhtml/vocab/
dady,http://purl.org/NET/dady#
-sl,http://www.semanlink.net/2001/00/semanlink-schema#
-wisski,http://wiss-ki.eu/
-pr,http://ontologi.es/profiling#
-climb,http://climb.dataincubator.org/vocabs/climb/
+pmlr,http://inference-web.org/2.0/pml-relation.owl#
+psych,http://purl.org/vocab/psychometric-profile/
+pimo,http://www.semanticdesktop.org/ontologies/2007/11/01/pimo#
+string,http://www.w3.org/2000/10/swap/string#
+urn,http://fliqz.com/
+coin,http://purl.org/court/def/2009/coin#
+plink,http://buzzword.org.uk/rdf/personal-link-types#
conserv,http://conserv.deri.ie/ontology#
-sml,http://topbraid.org/sparqlmotionlib#
-dcat,http://www.w3.org/ns/dcat#
-formats,http://www.w3.org/ns/formats/
-label,http://purl.org/net/vocab/2004/03/label#
-puc,http://purl.org/NET/puc#
-list,http://www.w3.org/2000/10/swap/list#
-lifecycle,http://purl.org/vocab/lifecycle/schema#
-swanpav,http://purl.org/swan/1.2/pav/
-smf,http://topbraid.org/sparqlmotionfunctions#
-grddl,http://www.w3.org/2003/g/data-view#
-pmlp,http://inference-web.org/2.0/pml-provenance.owl#
-opm,http://openprovenance.org/ontology#
-cycann,http://sw.cyc.com/CycAnnotations_v1#
-obj,http://www.openrdf.org/rdf/2009/object#
-urn,http://fliqz.com/
+rooms,http://vocab.deri.ie/rooms#
+cco,http://purl.org/ontology/cco/core#
+xesam,http://freedesktop.org/standards/xesam/1.0/core#
+am,http://vocab.deri.ie/am#
play,http://uriplay.org/spec/ontology/#
-ping,http://purl.org/net/pingback/
-c4n,http://vocab.deri.ie/c4n#
-mysql,http://web-semantics.org/ns/mysql/
-rdfa,http://www.w3.org/ns/rdfa#
-osgb,http://data.ordnancesurvey.co.uk/id/
-resource,http://purl.org/vocab/resourcelist/schema#
-xesam,http://freedesktop.org/standards/xesam/1.0/core#
-plink,http://buzzword.org.uk/rdf/personal-link-types#
-so,http://purl.org/ontology/symbolic-music/
-commerce,http://purl.org/commerce#
-opensearch,http://a9.com/-/spec/opensearch/1.1/
-exif,http://www.w3.org/2003/12/exif/ns#
-psych,http://purl.org/vocab/psychometric-profile/
evset,http://dsnotify.org/vocab/eventset/0.1/
+mf,http://poshrdf.org/ns/mf#
+geographis,http://telegraphis.net/ontology/geography/geography#
sysont,http://ns.ontowiki.net/SysOnt/
-ldap,http://purl.org/net/ldap/
-string,http://www.w3.org/2000/10/swap/string#
-swanag,http://purl.org/swan/1.2/agents/
-nid3,http://www.semanticdesktop.org/ontologies/2007/05/10/nid3#
+sl,http://www.semanlink.net/2001/00/semanlink-schema#
+uri,http://purl.org/NET/uri#
+wairole,http://www.w3.org/2005/01/wai-rdf/GUIRoleTaxonomy#
ttl,http://www.w3.org/2008/turtle#
+swanpav,http://purl.org/swan/1.2/pav/
+bib,http://zeitkunst.org/bibtex/0.1/bibtex.owl#
+tripfs,http://purl.org/tripfs/2010/02#
swanco,http://purl.org/swan/1.2/swan-commons/
-tripfs,http://purl.org/tripfs/2010/02#
-imreg,http://www.w3.org/2004/02/image-regions#
-swanci,http://purl.org/swan/1.2/citations/
-meetup,http://www.lotico.com/meetup/
-cnt,http://www.w3.org/2008/content#
+opo,http://online-presence.net/opo/ns#
okkam,http://models.okkam.org/ENS-core-vocabulary#
-mf,http://poshrdf.org/ns/mf#
-rec,http://purl.org/ontology/rec/core#
-xhtmlvocab,http://www.w3.org/1999/xhtml/vocab/
-coin,http://purl.org/court/def/2009/coin#
-geographis,http://telegraphis.net/ontology/geography/geography#
-opo,http://online-presence.net/opo/ns#
+game,http://data.totl.net/game/
swivt,http://semantic-mediawiki.org/swivt/1.0#
-rooms,http://vocab.deri.ie/rooms#
-oat,http://openlinksw.com/schemas/oat/
-bib,http://zeitkunst.org/bibtex/0.1/bibtex.owl#
+status,http://ontologi.es/status#
+swanci,http://purl.org/swan/1.2/citations/
+olo,http://purl.org/ontology/olo/core#
+txn,http://lod.taxonconcept.org/ontology/txn.owl#
oc,http://opencoinage.org/rdf/
-status,http://ontologi.es/status#
ezcontext,http://ontologies.ezweb.morfeo-project.org/ezcontext/ns#
-swid,http://semanticweb.org/id/
-pmlt,http://inference-web.org/2.0/pml-trust.owl#
+geoes,http://geo.linkeddata.es/ontology/
+xtypes,http://purl.org/xtypes/
+meteo,http://purl.org/ns/meteo#
sparql,http://www.openrdf.org/config/repository/sparql#
-txn,http://lod.taxonconcept.org/ontology/txn.owl#
-oo,http://purl.org/openorg/
-ct,http://data.linkedct.org/resource/linkedct/
-wlp,http://weblab-project.org/core/model/property/processing/
-ufmedia,http://purl.org/microformat/hmedia/
-sioca,http://rdfs.org/sioc/actions#
awol,http://bblfish.net/work/atom-owl/2006-06-06/#
-pdo,http://ontologies.smile.deri.ie/pdo#
-pto,http://www.productontology.org/id/
+evopat,http://ns.aksw.org/Evolution/
+sdmx,http://purl.org/linked-data/sdmx#
+ldap,http://purl.org/net/ldap/
+isq,http://purl.org/ontology/is/quality/
+lark1,http://users.utcluj.ro/~raluca/ontology/Ontology1279614123500.owl#
aifb,http://www.aifb.kit.edu/id/
-prot,http://www.proteinontology.info/po.owl#
-evopat,http://ns.aksw.org/Evolution/
-meteo,http://purl.org/ns/meteo#
+isi,http://purl.org/ontology/is/inst/
+ao,http://purl.org/ontology/ao/core#
+wlp,http://weblab-project.org/core/model/property/processing/
+ct,http://data.linkedct.org/resource/linkedct/
tarot,http://data.totl.net/tarot/card/
+anca,http://users.utcluj.ro/~raluca/rdf_ontologies_ralu/ralu_modified_ontology_pizzas2_0#
+kb,http://deductions.sf.net/ontology/knowledge_base.owl#
+opmv,http://purl.org/net/opmv/ns#
+pmlt,http://inference-web.org/2.0/pml-trust.owl#
+xbrli,http://www.xbrl.org/2003/instance#
ist,http://purl.org/ontology/is/types/
-anca,http://users.utcluj.ro/~raluca/rdf_ontologies_ralu/ralu_modified_ontology_pizzas2_0#
-whois,http://www.kanzaki.com/ns/whois#
+xro,http://purl.org/xro/ns#
+postcode,http://data.ordnancesurvey.co.uk/id/postcodeunit/
+dayta,http://dayta.me/resource#
+swid,http://semanticweb.org/id/
+prot,http://www.proteinontology.info/po.owl#
+opus,http://lsdis.cs.uga.edu/projects/semdis/opus#
+core,http://vivoweb.org/ontology/core#
+geospecies,http://rdf.geospecies.org/ont/geospecies#
+go,http://www.geneontology.org/go#
sawsdl,http://www.w3.org/ns/sawsdl#
+pdo,http://ontologies.smil...
[truncated message content] |
|
From: <lor...@us...> - 2013-05-24 09:16:44
|
Revision: 3984
http://sourceforge.net/p/dl-learner/code/3984
Author: lorenz_b
Date: 2013-05-24 09:16:41 +0000 (Fri, 24 May 2013)
Log Message:
-----------
Prepare reasoner only once.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
Modified: trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java 2013-05-24 07:56:26 UTC (rev 3983)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java 2013-05-24 09:16:41 UTC (rev 3984)
@@ -101,6 +101,8 @@
private Map<NamedClass, Integer> classPopularityMap;
private Map<ObjectProperty, Integer> objectPropertyPopularityMap;
private Map<DatatypeProperty, Integer> dataPropertyPopularityMap;
+
+ private boolean prepared = false;
public SPARQLReasoner(SparqlEndpointKS ks) {
@@ -247,54 +249,57 @@
}
public final ClassHierarchy prepareSubsumptionHierarchy() {
- logger.info("Preparing subsumption hierarchy ...");
- long startTime = System.currentTimeMillis();
- ConceptComparator conceptComparator = new ConceptComparator();
- TreeMap<Description, SortedSet<Description>> subsumptionHierarchyUp = new TreeMap<Description, SortedSet<Description>>(
- conceptComparator);
- TreeMap<Description, SortedSet<Description>> subsumptionHierarchyDown = new TreeMap<Description, SortedSet<Description>>(
- conceptComparator);
+ if(!prepared){
+ logger.info("Preparing subsumption hierarchy ...");
+ long startTime = System.currentTimeMillis();
+ ConceptComparator conceptComparator = new ConceptComparator();
+ TreeMap<Description, SortedSet<Description>> subsumptionHierarchyUp = new TreeMap<Description, SortedSet<Description>>(
+ conceptComparator);
+ TreeMap<Description, SortedSet<Description>> subsumptionHierarchyDown = new TreeMap<Description, SortedSet<Description>>(
+ conceptComparator);
- // parents/children of top ...
- SortedSet<Description> tmp = getSubClasses(Thing.instance);
- subsumptionHierarchyUp.put(Thing.instance, new TreeSet<Description>(conceptComparator));
- subsumptionHierarchyDown.put(Thing.instance, tmp);
+ // parents/children of top ...
+ SortedSet<Description> tmp = getSubClasses(Thing.instance);
+ subsumptionHierarchyUp.put(Thing.instance, new TreeSet<Description>(conceptComparator));
+ subsumptionHierarchyDown.put(Thing.instance, tmp);
- // ... bottom ...
- tmp = getSuperClasses(Nothing.instance);
- subsumptionHierarchyUp.put(Nothing.instance, tmp);
- subsumptionHierarchyDown.put(Nothing.instance, new TreeSet<Description>(conceptComparator));
+ // ... bottom ...
+ tmp = getSuperClasses(Nothing.instance);
+ subsumptionHierarchyUp.put(Nothing.instance, tmp);
+ subsumptionHierarchyDown.put(Nothing.instance, new TreeSet<Description>(conceptComparator));
- // ... and named classes
- Set<NamedClass> atomicConcepts;
- if(ks.isRemote()){
- atomicConcepts = new SPARQLTasks(ks.getEndpoint()).getAllClasses();
- } else {
- atomicConcepts = new TreeSet<NamedClass>();
- for(OntClass cls : ((LocalModelBasedSparqlEndpointKS)ks).getModel().listClasses().toList()){
- if(!cls.isAnon()){
- atomicConcepts.add(new NamedClass(cls.getURI()));
+ // ... and named classes
+ Set<NamedClass> atomicConcepts;
+ if(ks.isRemote()){
+ atomicConcepts = new SPARQLTasks(ks.getEndpoint()).getAllClasses();
+ } else {
+ atomicConcepts = new TreeSet<NamedClass>();
+ for(OntClass cls : ((LocalModelBasedSparqlEndpointKS)ks).getModel().listClasses().toList()){
+ if(!cls.isAnon()){
+ atomicConcepts.add(new NamedClass(cls.getURI()));
+ }
}
}
- }
- for (NamedClass atom : atomicConcepts) {
- tmp = getSubClasses(atom);
- // quality control: we explicitly check that no reasoner implementation returns null here
- if(tmp == null) {
- logger.error("Class hierarchy: getSubClasses returned null instead of empty set.");
- }
- subsumptionHierarchyDown.put(atom, tmp);
+ for (NamedClass atom : atomicConcepts) {
+ tmp = getSubClasses(atom);
+ // quality control: we explicitly check that no reasoner implementation returns null here
+ if(tmp == null) {
+ logger.error("Class hierarchy: getSubClasses returned null instead of empty set.");
+ }
+ subsumptionHierarchyDown.put(atom, tmp);
- tmp = getSuperClasses(atom);
- // quality control: we explicitly check that no reasoner implementation returns null here
- if(tmp == null) {
- logger.error("Class hierarchy: getSuperClasses returned null instead of empty set.");
- }
- subsumptionHierarchyUp.put(atom, tmp);
- }
- logger.info("... done in {}ms", (System.currentTimeMillis()-startTime));
- hierarchy = new ClassHierarchy(subsumptionHierarchyUp, subsumptionHierarchyDown);
+ tmp = getSuperClasses(atom);
+ // quality control: we explicitly check that no reasoner implementation returns null here
+ if(tmp == null) {
+ logger.error("Class hierarchy: getSuperClasses returned null instead of empty set.");
+ }
+ subsumptionHierarchyUp.put(atom, tmp);
+ }
+ logger.info("... done in {}ms", (System.currentTimeMillis()-startTime));
+ hierarchy = new ClassHierarchy(subsumptionHierarchyUp, subsumptionHierarchyDown);
+ prepared = true;
+ }
return hierarchy;
}
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|
|
From: <lor...@us...> - 2013-05-24 07:56:31
|
Revision: 3983
http://sourceforge.net/p/dl-learner/code/3983
Author: lorenz_b
Date: 2013-05-24 07:56:26 +0000 (Fri, 24 May 2013)
Log Message:
-----------
Avoid NPE.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/algorithms/properties/FunctionalObjectPropertyAxiomLearner.java
trunk/components-core/src/main/java/org/dllearner/core/owl/ClassHierarchy.java
trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLEntityTypeAdder.java
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/properties/FunctionalObjectPropertyAxiomLearner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/properties/FunctionalObjectPropertyAxiomLearner.java 2013-05-22 15:35:39 UTC (rev 3982)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/properties/FunctionalObjectPropertyAxiomLearner.java 2013-05-24 07:56:26 UTC (rev 3983)
@@ -164,7 +164,7 @@
public static void main(String[] args) throws Exception{
FunctionalObjectPropertyAxiomLearner l = new FunctionalObjectPropertyAxiomLearner(new SparqlEndpointKS(SparqlEndpoint.getEndpointDBpedia()));
- l.setPropertyToDescribe(new ObjectProperty("http://dbpedia.org/ontology/currency"));
+ l.setPropertyToDescribe(new ObjectProperty("http://dbpedia.org/property/father"));
l.setMaxExecutionTimeInSeconds(20);
l.setForceSPARQL_1_0_Mode(true);
l.init();
Modified: trunk/components-core/src/main/java/org/dllearner/core/owl/ClassHierarchy.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/owl/ClassHierarchy.java 2013-05-22 15:35:39 UTC (rev 3982)
+++ trunk/components-core/src/main/java/org/dllearner/core/owl/ClassHierarchy.java 2013-05-24 07:56:26 UTC (rev 3983)
@@ -203,18 +203,21 @@
if (subClass.equals(superClass)) {
return true;
} else {
- for (Description moreGeneralClass : subsumptionHierarchyUp.get(subClass)) {
-
- // search the upper classes of the subclass
- if (moreGeneralClass instanceof NamedClass) {
- if (isSubclassOf((NamedClass) moreGeneralClass, superClass)) {
- return true;
+ SortedSet<Description> superClasses = subsumptionHierarchyUp.get(subClass);
+ if(superClasses != null){
+ for (Description moreGeneralClass : subsumptionHierarchyUp.get(subClass)) {
+
+ // search the upper classes of the subclass
+ if (moreGeneralClass instanceof NamedClass) {
+ if (isSubclassOf((NamedClass) moreGeneralClass, superClass)) {
+ return true;
+ }
+ // we reached top, so we can return false (if top is a
+ // direct upper
+ // class, then no other upper classes can exist)
+ } else {
+ return false;
}
- // we reached top, so we can return false (if top is a
- // direct upper
- // class, then no other upper classes can exist)
- } else {
- return false;
}
}
// we cannot reach the class via any of the upper classes,
Modified: trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java 2013-05-22 15:35:39 UTC (rev 3982)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java 2013-05-24 07:56:26 UTC (rev 3983)
@@ -651,7 +651,7 @@
String query =
" SELECT DISTINCT ?ind WHERE {"+
- "?ind ?p ?o ."+
+ "?ind a ?o .?o <http://www.w3.org/2000/01/rdf-schema#subClassOf> <http://www.w3.org/2002/07/owl#Class>"+
filterStr+ " }";
if(limit != 0) {
query += " LIMIT " + limit;
Modified: trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLEntityTypeAdder.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLEntityTypeAdder.java 2013-05-22 15:35:39 UTC (rev 3982)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLEntityTypeAdder.java 2013-05-24 07:56:26 UTC (rev 3983)
@@ -3,7 +3,6 @@
import java.util.HashSet;
import java.util.Set;
-import com.google.common.collect.Sets;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.Property;
import com.hp.hpl.jena.rdf.model.RDFNode;
@@ -28,7 +27,8 @@
while(iterator.hasNext()){
Statement st = iterator.next();
Property predicate = st.getPredicate();
- if(!predicate.getURI().startsWith(RDF.getURI()) && !predicate.getURI().startsWith(RDFS.getURI())){
+ if(!predicate.getURI().startsWith(RDF.getURI()) && !predicate.getURI().startsWith(RDFS.getURI())
+ && !predicate.getURI().startsWith(OWL.getURI())){
RDFNode object = st.getObject();
if(object.isLiteral()){
dataPropertyPredicates.add(predicate);
@@ -38,13 +38,6 @@
}
}
iterator.close();
-
- for (Property property : Sets.difference(objectPropertyPredicates, dataPropertyPredicates)) {
- model.add(property, RDF.type, OWL.ObjectProperty);
- }
- for (Property property : Sets.difference(dataPropertyPredicates, objectPropertyPredicates)) {
- model.add(property, RDF.type, OWL.DatatypeProperty);
- }
}
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <moa...@us...> - 2013-05-22 15:35:42
|
Revision: 3982
http://sourceforge.net/p/dl-learner/code/3982
Author: moahmedsherif
Date: 2013-05-22 15:35:39 +0000 (Wed, 22 May 2013)
Log Message:
-----------
add getRandomIndividuals()
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
Modified: trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java 2013-05-17 15:47:53 UTC (rev 3981)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java 2013-05-22 15:35:39 UTC (rev 3982)
@@ -22,6 +22,7 @@
import java.net.SocketTimeoutException;
import java.net.URL;
import java.util.ArrayList;
+import java.util.Collection;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
@@ -576,6 +577,37 @@
return individuals;
}
+ /**
+ * @param wantedClass
+ * @param excludeClass
+ * @param limit
+ * @return get individual of class wantedClass excluding all individual of type excludeClass
+ * @author sherif
+ */
+ public SortedSet<Individual> getIndividualsExcluding(Description wantedClass, Description excludeClass, int limit) {
+
+ if(!(wantedClass instanceof NamedClass)){
+ throw new UnsupportedOperationException("Only named classes are supported.");
+ }
+ SortedSet<Individual> individuals = new TreeSet<Individual>();
+ String query =
+ "SELECT DISTINCT ?ind WHERE {" +
+ "?ind a <"+((NamedClass)wantedClass).getName() + "> . " +
+ "FILTER(NOT EXISTS { ?ind a <" + ((NamedClass)excludeClass).getName() + "> } )}";
+ if(limit != 0) {
+ query += " LIMIT " + limit;
+ }
+ System.out.println("query: "+query);
+ ResultSet rs = executeSelectQuery(query);
+ QuerySolution qs;
+ while(rs.hasNext()){
+ qs = rs.next();
+ if(qs.get("ind").isURIResource()){
+ individuals.add(new Individual(qs.getResource("ind").getURI()));
+ }
+ }
+ return individuals;
+ }
/**
* @param cls
@@ -602,6 +634,40 @@
}
return individuals;
}
+
+ /**
+ * @param cls
+ * @param limit
+ * @return Random Individuals not including any of the input classes individuals
+ * @author sherif
+ */
+ public SortedSet<Individual> getRandomIndividuals(Set<NamedClass> cls, int limit) {
+ SortedSet<Individual> individuals = new TreeSet<Individual>();
+
+ String filterStr="";
+ for(NamedClass nc : cls){
+ filterStr = filterStr.concat("FILTER(NOT EXISTS { ?ind a <").concat(nc.getName()).concat("> } ) ");
+ }
+
+ String query =
+ " SELECT DISTINCT ?ind WHERE {"+
+ "?ind ?p ?o ."+
+ filterStr+ " }";
+ if(limit != 0) {
+ query += " LIMIT " + limit;
+ }
+
+ System.out.println("!!!!!!!!!!!!!!!!!!!! "+query);
+ ResultSet rs = executeSelectQuery(query);
+ QuerySolution qs;
+ while(rs.hasNext()){
+ qs = rs.next();
+ if(qs.get("ind").isURIResource()){
+ individuals.add(new Individual(qs.getResource("ind").getURI()));
+ }
+ }
+ return individuals;
+ }
/**
* @param cls
@@ -618,9 +684,14 @@
" SELECT DISTINCT ?ind WHERE { "+
"?ind a <" + parentClass.getName() + "> ."+
"FILTER(NOT EXISTS { ?ind a <" + cls.getName() + "> } ) }";
+
+
if(limit != 0) {
query += " LIMIT " + limit/parentClasses.size();
}
+
+ System.out.println("---------------------------------------------- "+query);
+
ResultSet rs = executeSelectQuery(query);
QuerySolution qs;
while(rs.hasNext()){
@@ -629,7 +700,10 @@
individuals.add(new Individual(qs.getResource("ind").getURI()));
}
}
+ System.out.println(individuals.size());
+ System.out.println(individuals);
}
+
return individuals;
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <moa...@us...> - 2013-05-17 15:47:57
|
Revision: 3981
http://sourceforge.net/p/dl-learner/code/3981
Author: moahmedsherif
Date: 2013-05-17 15:47:53 +0000 (Fri, 17 May 2013)
Log Message:
-----------
fix add parent class individuals and random individuals
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
Modified: trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java 2013-05-15 13:09:32 UTC (rev 3980)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java 2013-05-17 15:47:53 UTC (rev 3981)
@@ -85,60 +85,60 @@
@ComponentAnn(name = "SPARQL Reasoner", shortName = "spr", version = 0.1)
public class SPARQLReasoner implements SchemaReasoner, IndividualReasoner {
-
+
private static final Logger logger = LoggerFactory.getLogger(SPARQLReasoner.class);
-
+
@ConfigOption(name = "useCache", description = "Whether to use a DB cache", defaultValue = "true", required = false, propertyEditorClass = BooleanEditor.class)
private boolean useCache = true;
-
+
private ExtractionDBCache cache;
-
+
private SparqlEndpointKS ks;
private ClassHierarchy hierarchy;
private OntModel model;
-
+
private Map<NamedClass, Integer> classPopularityMap;
private Map<ObjectProperty, Integer> objectPropertyPopularityMap;
private Map<DatatypeProperty, Integer> dataPropertyPopularityMap;
-
-
+
+
public SPARQLReasoner(SparqlEndpointKS ks) {
this.ks = ks;
-
+
if(useCache){
cache = new ExtractionDBCache("cache");
}
classPopularityMap = new HashMap<NamedClass, Integer>();
objectPropertyPopularityMap = new HashMap<ObjectProperty, Integer>();
}
-
+
public SPARQLReasoner(SparqlEndpointKS ks, ExtractionDBCache cache) {
this.ks = ks;
this.cache = cache;
-
+
classPopularityMap = new HashMap<NamedClass, Integer>();
objectPropertyPopularityMap = new HashMap<ObjectProperty, Integer>();
}
-
+
public SPARQLReasoner(OntModel model) {
this.model = model;
-
+
classPopularityMap = new HashMap<NamedClass, Integer>();
objectPropertyPopularityMap = new HashMap<ObjectProperty, Integer>();
}
-
+
public void precomputePopularity(){
precomputeClassPopularity();
precomputeDataPropertyPopularity();
precomputeObjectPropertyPopularity();
}
-
+
public void precomputeClassPopularity(){
logger.info("Precomputing class popularity ...");
-
+
Set<NamedClass> classes = new SPARQLTasks(ks.getEndpoint()).getAllClasses();
String queryTemplate = "SELECT (COUNT(*) AS ?cnt) WHERE {?s a <%s>}";
-
+
ResultSet rs;
for(NamedClass nc : classes){
rs = executeSelectQuery(String.format(queryTemplate, nc.getName()));
@@ -146,14 +146,14 @@
classPopularityMap.put(nc, cnt);
}
}
-
+
public void precomputeObjectPropertyPopularity(){
logger.info("Precomputing object property popularity ...");
objectPropertyPopularityMap = new HashMap<ObjectProperty, Integer>();
-
+
Set<ObjectProperty> properties = new SPARQLTasks(ks.getEndpoint()).getAllObjectProperties();
String queryTemplate = "SELECT (COUNT(*) AS ?cnt) WHERE {?s <%s> ?o}";
-
+
ResultSet rs;
for(ObjectProperty op : properties){
rs = executeSelectQuery(String.format(queryTemplate, op.getName()));
@@ -161,14 +161,14 @@
objectPropertyPopularityMap.put(op, cnt);
}
}
-
+
public void precomputeDataPropertyPopularity(){
logger.info("Precomputing data property popularity ...");
dataPropertyPopularityMap = new HashMap<DatatypeProperty, Integer>();
-
+
Set<DatatypeProperty> properties = new SPARQLTasks(ks.getEndpoint()).getAllDataProperties();
String queryTemplate = "SELECT (COUNT(*) AS ?cnt) WHERE {?s <%s> ?o}";
-
+
ResultSet rs;
for(DatatypeProperty dp : properties){
rs = executeSelectQuery(String.format(queryTemplate, dp.getName()));
@@ -176,7 +176,7 @@
dataPropertyPopularityMap.put(dp, cnt);
}
}
-
+
public int getSubjectCountForProperty(Property p, long timeout){
int cnt = -1;
String query = String.format(
@@ -186,10 +186,10 @@
if(rs.hasNext()){
cnt = rs.next().getLiteral("cnt").getInt();
}
-
+
return cnt;
}
-
+
public int getObjectCountForProperty(ObjectProperty p, long timeout){
int cnt = -1;
String query = String.format(
@@ -199,52 +199,52 @@
if(rs.hasNext()){
cnt = rs.next().getLiteral("cnt").getInt();
}
-
+
return cnt;
}
-
+
public int getPopularity(NamedClass nc){
if(classPopularityMap != null && classPopularityMap.containsKey(nc)){
return classPopularityMap.get(nc);
} else {
String queryTemplate = "SELECT (COUNT(*) AS ?cnt) WHERE {?s a <%s>}";
-
+
ResultSet rs = executeSelectQuery(String.format(queryTemplate, nc.getName()));
int cnt = rs.next().getLiteral("cnt").getInt();
classPopularityMap.put(nc, cnt);
return cnt;
}
-
+
}
-
+
public int getPopularity(ObjectProperty op){
if(objectPropertyPopularityMap != null && objectPropertyPopularityMap.containsKey(op)){
return objectPropertyPopularityMap.get(op);
} else {
String queryTemplate = "SELECT (COUNT(*) AS ?cnt) WHERE {?s <%s> ?o}";
-
+
ResultSet rs = executeSelectQuery(String.format(queryTemplate, op.getName()));
int cnt = rs.next().getLiteral("cnt").getInt();
objectPropertyPopularityMap.put(op, cnt);
return cnt;
}
-
+
}
-
+
public int getPopularity(DatatypeProperty dp){
if(dataPropertyPopularityMap.containsKey(dp)){
return dataPropertyPopularityMap.get(dp);
} else {
String queryTemplate = "SELECT (COUNT(*) AS ?cnt) WHERE {?s <%s> ?o}";
-
+
ResultSet rs = executeSelectQuery(String.format(queryTemplate, dp.getName()));
int cnt = rs.next().getLiteral("cnt").getInt();
dataPropertyPopularityMap.put(dp, cnt);
return cnt;
}
-
+
}
-
+
public final ClassHierarchy prepareSubsumptionHierarchy() {
logger.info("Preparing subsumption hierarchy ...");
long startTime = System.currentTimeMillis();
@@ -263,7 +263,7 @@
tmp = getSuperClasses(Nothing.instance);
subsumptionHierarchyUp.put(Nothing.instance, tmp);
subsumptionHierarchyDown.put(Nothing.instance, new TreeSet<Description>(conceptComparator));
-
+
// ... and named classes
Set<NamedClass> atomicConcepts;
if(ks.isRemote()){
@@ -276,7 +276,7 @@
}
}
}
-
+
for (NamedClass atom : atomicConcepts) {
tmp = getSubClasses(atom);
// quality control: we explicitly check that no reasoner implementation returns null here
@@ -296,7 +296,7 @@
hierarchy = new ClassHierarchy(subsumptionHierarchyUp, subsumptionHierarchyDown);
return hierarchy;
}
-
+
public final ClassHierarchy prepareSubsumptionHierarchyFast() {
logger.info("Preparing subsumption hierarchy ...");
long startTime = System.currentTimeMillis();
@@ -305,7 +305,7 @@
conceptComparator);
TreeMap<Description, SortedSet<Description>> subsumptionHierarchyDown = new TreeMap<Description, SortedSet<Description>>(
conceptComparator);
-
+
String queryTemplate = "SELECT * WHERE {?sub <http://www.w3.org/2000/01/rdf-schema#subClassOf> ?sup} LIMIT <%d> OFFSET <%d>";
int limit = 1000;
int offset = 0;
@@ -337,15 +337,15 @@
}
offset += limit;
}
-
+
logger.info("... done in {}ms", (System.currentTimeMillis()-startTime));
hierarchy = new ClassHierarchy(subsumptionHierarchyUp, subsumptionHierarchyDown);
return hierarchy;
}
-
+
public Model loadSchema(){
Model model = ModelFactory.createDefaultModel();
-
+
//load class hierarchy
String query = "CONSTRUCT {?s <http://www.w3.org/2000/01/rdf-schema#subClassOf> ?o} WHERE {?s <http://www.w3.org/2000/01/rdf-schema#subClassOf> ?o.FILTER(!REGEX(STR(?s), 'http://dbpedia.org/class/yago/'))}";
model.add(loadIncrementally(query));
@@ -372,7 +372,7 @@
"WHERE {?s <http://www.w3.org/2000/01/rdf-schema#subPropertyOf> ?o. ?s a <http://www.w3.org/2002/07/owl#ObjectProperty>}";
model.add(loadIncrementally(query));
query = "CONSTRUCT {?s <http://www.w3.org/2000/01/rdf-schema#subPropertyOf> ?o. ?s a <http://www.w3.org/2002/07/owl#DatatypeProperty>} " +
- "WHERE {?s <http://www.w3.org/2000/01/rdf-schema#subPropertyOf> ?o. ?s a <http://www.w3.org/2002/07/owl#DatatypeProperty>}";
+ "WHERE {?s <http://www.w3.org/2000/01/rdf-schema#subPropertyOf> ?o. ?s a <http://www.w3.org/2002/07/owl#DatatypeProperty>}";
model.add(loadIncrementally(query));
query = "CONSTRUCT {?s <http://www.w3.org/2002/07/owl#equivalentProperty> ?o. ?s a <http://www.w3.org/2002/07/owl#ObjectProperty>} " +
"WHERE {?s <http://www.w3.org/2002/07/owl#equivalentProperty> ?o. ?s a <http://www.w3.org/2002/07/owl#ObjectProperty>}";
@@ -391,7 +391,7 @@
model.add(loadIncrementally(query));
//load property characteristics
Set<Resource> propertyCharacteristics = new HashSet<Resource>();
-// propertyCharacteristics.add(OWL.FunctionalProperty);
+ // propertyCharacteristics.add(OWL.FunctionalProperty);
propertyCharacteristics.add(OWL.InverseFunctionalProperty);
propertyCharacteristics.add(OWL.SymmetricProperty);
propertyCharacteristics.add(OWL.TransitiveProperty);
@@ -406,34 +406,34 @@
//for functional properties we have to distinguish between data and object properties,
//i.e. we have to keep the property type information, otherwise conversion to OWLAPI ontology makes something curious
query = "CONSTRUCT {?s a <%s>. ?s a <http://www.w3.org/2002/07/owl#ObjectProperty>} WHERE {?s a <%s>.?s a <http://www.w3.org/2002/07/owl#ObjectProperty>}".
- replaceAll("%s", OWL.FunctionalProperty.getURI());
+ replaceAll("%s", OWL.FunctionalProperty.getURI());
model.add(loadIncrementally(query));
query = "CONSTRUCT {?s a <%s>. ?s a <http://www.w3.org/2002/07/owl#DatatypeProperty>} WHERE {?s a <%s>.?s a <http://www.w3.org/2002/07/owl#DatatypeProperty>}".
- replaceAll("%s", OWL.FunctionalProperty.getURI());
+ replaceAll("%s", OWL.FunctionalProperty.getURI());
model.add(loadIncrementally(query));
-
-
+
+
return model;
}
-
+
private Model loadIncrementally(String query){
System.out.println(StringUtils.md5Hash(query));
-// try {
- QueryExecutionFactory f = new QueryExecutionFactoryHttp(ks.getEndpoint().getURL().toString(), ks.getEndpoint().getDefaultGraphURIs());
-// f = new QueryExecutionFactoryCache(f, new CacheImpl(CacheCoreH2.create("cache", 60 * 24 *5)));
-// System.out.println("SPARQLReasoner.loadIncrementally needs to be rewritten for aksw-commons 0.1");
-// System.exit(0);
- f = new QueryExecutionFactoryPaginated(f, 1000);
- Model model = f.createQueryExecution(query).execConstruct();
- System.out.println(query);
- System.out.println("Got " + model.size() + " triple.");
- return model;
-// } catch (ClassNotFoundException e) {
-// e.printStackTrace();
-// } catch (SQLException e) {
-// e.printStackTrace();
-// }
-// return null;
+ // try {
+ QueryExecutionFactory f = new QueryExecutionFactoryHttp(ks.getEndpoint().getURL().toString(), ks.getEndpoint().getDefaultGraphURIs());
+ // f = new QueryExecutionFactoryCache(f, new CacheImpl(CacheCoreH2.create("cache", 60 * 24 *5)));
+ // System.out.println("SPARQLReasoner.loadIncrementally needs to be rewritten for aksw-commons 0.1");
+ // System.exit(0);
+ f = new QueryExecutionFactoryPaginated(f, 1000);
+ Model model = f.createQueryExecution(query).execConstruct();
+ System.out.println(query);
+ System.out.println("Got " + model.size() + " triple.");
+ return model;
+ // } catch (ClassNotFoundException e) {
+ // e.printStackTrace();
+ // } catch (SQLException e) {
+ // e.printStackTrace();
+ // }
+ // return null;
}
@Override
@@ -448,11 +448,11 @@
}
return types;
}
-
+
public Set<NamedClass> getTypes() {
return getTypes((String)null);
}
-
+
public Set<NamedClass> getTypes(String namespace) {
Set<NamedClass> types = new TreeSet<NamedClass>();
String query = String.format("SELECT DISTINCT ?class WHERE {[] a ?class." + (namespace != null ? ("FILTER(REGEX(?class,'^" + namespace + "'))") : "") + "}");
@@ -464,7 +464,7 @@
}
return types;
}
-
+
public Set<NamedClass> getOWLClasses() {
Set<NamedClass> types = new HashSet<NamedClass>();
String query = String.format("SELECT DISTINCT ?class WHERE {?class a <%s>.}",OWL.Class.getURI());
@@ -476,7 +476,7 @@
}
return types;
}
-
+
/**
* Returns a set of classes which are siblings, i.e. on the same level
* in the class hierarchy.
@@ -516,7 +516,7 @@
}
return parents;
}
-
+
/**
* Returns a set of classes which are children of current class
* in the class hierarchy.
@@ -535,7 +535,7 @@
}
return children;
}
-
+
@Override
public boolean hasType(Description description, Individual individual) {
if(!(description instanceof NamedClass)){
@@ -575,7 +575,64 @@
}
return individuals;
}
+
+ /**
+ * @param cls
+ * @param limit
+ * @return Random Individuals not including any of the input class individuals
+ * @author sherif
+ */
+ public SortedSet<Individual> getRandomIndividuals(NamedClass cls, int limit) {
+ SortedSet<Individual> individuals = new TreeSet<Individual>();
+ String query =
+ " SELECT DISTINCT ?ind WHERE {"+
+ "?ind ?p ?o ."+
+ "FILTER(NOT EXISTS { ?ind a <" + cls.getName() + "> } ) }";
+ if(limit != 0) {
+ query += " LIMIT " + limit;
+ }
+ ResultSet rs = executeSelectQuery(query);
+ QuerySolution qs;
+ while(rs.hasNext()){
+ qs = rs.next();
+ if(qs.get("ind").isURIResource()){
+ individuals.add(new Individual(qs.getResource("ind").getURI()));
+ }
+ }
+ return individuals;
+ }
+
+ /**
+ * @param cls
+ * @param limit
+ * @return Super class of the input class Individuals not including any of the input class individuals
+ * @author sherif
+ */
+ public SortedSet<Individual> getSuperClassIndividuals(NamedClass cls, int limit) {
+ SortedSet<Individual> individuals = new TreeSet<Individual>();
+ Set<NamedClass> parentClasses = getParentClasses(cls);
+
+ for(NamedClass parentClass : parentClasses){
+ String query =
+ " SELECT DISTINCT ?ind WHERE { "+
+ "?ind a <" + parentClass.getName() + "> ."+
+ "FILTER(NOT EXISTS { ?ind a <" + cls.getName() + "> } ) }";
+ if(limit != 0) {
+ query += " LIMIT " + limit/parentClasses.size();
+ }
+ ResultSet rs = executeSelectQuery(query);
+ QuerySolution qs;
+ while(rs.hasNext()){
+ qs = rs.next();
+ if(qs.get("ind").isURIResource()){
+ individuals.add(new Individual(qs.getResource("ind").getURI()));
+ }
+ }
+ }
+ return individuals;
+ }
+
@Override
public SortedSetTuple<Individual> doubleRetrieval(Description description) {
throw new UnsupportedOperationException();
@@ -585,7 +642,7 @@
public Set<Individual> getRelatedIndividuals(Individual individual, ObjectProperty objectProperty) {
Set<Individual> individuals = new HashSet<Individual>();
String query = String.format("SELECT ?ind WHERE {<%s> <%s> ?ind, FILTER(isIRI(?ind))}", individual.getName(), objectProperty.getName());
-
+
ResultSet rs = executeSelectQuery(query);
QuerySolution qs;
while(rs.hasNext()){
@@ -608,7 +665,7 @@
"<%s> ?prop ?ind." +
" FILTER(isIRI(?ind) && ?prop != <%s> && ?prop != <%s>)}",
individual.getName(), RDF.type.getURI(), OWL.sameAs.getURI());
-
+
ResultSet rs = executeSelectQuery(query);
QuerySolution qs;
Set<Individual> individuals;
@@ -624,7 +681,7 @@
prop2individuals.put(property, individuals);
}
individuals.add(ind);
-
+
}
return prop2individuals;
}
@@ -636,7 +693,7 @@
"?s <%s> ?o." +
" FILTER(isIRI(?o))}",
objectProperty.getName());
-
+
ResultSet rs = executeSelectQuery(query);
QuerySolution qs;
Individual sub;
@@ -652,7 +709,7 @@
subject2objects.put(sub, objects);
}
objects.add(obj);
-
+
}
return subject2objects;
}
@@ -670,7 +727,7 @@
"?s <%s> ?o." +
" FILTER(DATATYPE(?o) = <%s>)}",
datatypeProperty.getName(), XSD.DOUBLE.toStringID());
-
+
ResultSet rs = executeSelectQuery(query);
QuerySolution qs;
Individual sub;
@@ -686,7 +743,7 @@
subject2objects.put(sub, objects);
}
objects.add(obj);
-
+
}
return subject2objects;
}
@@ -698,7 +755,7 @@
"?s <%s> ?o." +
" FILTER(DATATYPE(?o) = <%s>)}",
datatypeProperty.getName(), XSD.INT.toStringID());
-
+
ResultSet rs = executeSelectQuery(query);
QuerySolution qs;
Individual sub;
@@ -714,7 +771,7 @@
subject2objects.put(sub, objects);
}
objects.add(obj);
-
+
}
return subject2objects;
}
@@ -726,7 +783,7 @@
"?s <%s> ?o." +
" FILTER(DATATYPE(?o) = <%s>)}",
datatypeProperty.getName(), XSD.BOOLEAN.toStringID());
-
+
ResultSet rs = executeSelectQuery(query);
QuerySolution qs;
Individual sub;
@@ -742,7 +799,7 @@
subject2objects.put(sub, objects);
}
objects.add(obj);
-
+
}
return subject2objects;
}
@@ -755,13 +812,13 @@
" FILTER(isLiteral(?o) && DATATYPE(?o) = <%s> && ?o = %s)}",
datatypeProperty.getName(), XSD.BOOLEAN.toStringID(),
"\"true\"^^<" + XSD.BOOLEAN.toStringID() + ">");
-
+
ResultSet rs = executeSelectQuery(query);
QuerySolution qs;
while(rs.hasNext()){
qs = rs.next();
members.add(new Individual(qs.getResource("ind").getURI()));
-
+
}
return members;
}
@@ -774,13 +831,13 @@
" FILTER(isLiteral(?o) && DATATYPE(?o) = <%s> && ?o = %s)}",
datatypeProperty.getName(), XSD.BOOLEAN.toStringID(),
"\"false\"^^<"+XSD.BOOLEAN.toStringID() + ">");
-
+
ResultSet rs = executeSelectQuery(query);
QuerySolution qs;
while(rs.hasNext()){
qs = rs.next();
members.add(new Individual(qs.getResource("ind").getURI()));
-
+
}
return members;
}
@@ -802,14 +859,14 @@
"<%s> <%s> ?domain. FILTER(isIRI(?domain))" +
"}",
objectProperty.getName(), RDFS.domain.getURI());
-
+
ResultSet rs = executeSelectQuery(query);
QuerySolution qs;
List<Description> domains = new ArrayList<Description>();
while(rs.hasNext()){
qs = rs.next();
domains.add(new NamedClass(qs.getResource("domain").getURI()));
-
+
}
if(domains.size() == 1){
return domains.get(0);
@@ -825,14 +882,14 @@
"<%s> <%s> ?domain. FILTER(isIRI(?domain))" +
"}",
datatypeProperty.getName(), RDFS.domain.getURI());
-
+
ResultSet rs = executeSelectQuery(query);
QuerySolution qs;
List<Description> domains = new ArrayList<Description>();
while(rs.hasNext()){
qs = rs.next();
domains.add(new NamedClass(qs.getResource("domain").getURI()));
-
+
}
if(domains.size() == 1){
return domains.get(0);
@@ -848,14 +905,14 @@
"<%s> <%s> ?range. FILTER(isIRI(?range))" +
"}",
objectProperty.getName(), RDFS.range.getURI());
-
+
ResultSet rs = executeSelectQuery(query);
QuerySolution qs;
List<Description> ranges = new ArrayList<Description>();
while(rs.hasNext()){
qs = rs.next();
ranges.add(new NamedClass(qs.getResource("range").getURI()));
-
+
}
if(ranges.size() == 1){
return ranges.get(0);
@@ -864,13 +921,13 @@
}
return null;
}
-
+
public boolean isObjectProperty(String propertyURI){
String query = String.format("ASK {<%s> a <%s>}", propertyURI, OWL.ObjectProperty.getURI());
boolean isObjectProperty = executeAskQuery(query);
return isObjectProperty;
}
-
+
public boolean isObjectProperty(String propertyURI, boolean analyzeData){
String query = String.format("ASK {<%s> a <%s>}", propertyURI, OWL.ObjectProperty.getURI());
boolean isObjectProperty = executeAskQuery(query);
@@ -880,14 +937,14 @@
}
return isObjectProperty;
}
-
+
public boolean isDataProperty(String propertyURI){
if(propertyURI.equals("http://www.w3.org/2000/01/rdf-schema#label")) return true;
String query = String.format("ASK {<%s> a <%s>}", propertyURI, OWL.DatatypeProperty.getURI());
boolean isDataProperty = executeAskQuery(query);
return isDataProperty;
}
-
+
public boolean isDataProperty(String propertyURI, boolean analyzeData){
if(propertyURI.equals("http://www.w3.org/2000/01/rdf-schema#label")) return true;
String query = String.format("ASK {<%s> a <%s>}", propertyURI, OWL.DatatypeProperty.getURI());
@@ -898,7 +955,7 @@
}
return isDataProperty;
}
-
+
public int getIndividualsCount(NamedClass nc){
String query = String.format("SELECT (COUNT(?s) AS ?cnt) WHERE {" +
"?s a <%s>." +
@@ -907,17 +964,17 @@
ResultSet rs = executeSelectQuery(query);
int cnt = rs.next().get(rs.getResultVars().get(0)).asLiteral().getInt();
return cnt;
-
+
}
-
+
public int getPropertyCount(ObjectProperty property){
String query = String.format("SELECT (COUNT(*) AS ?cnt) WHERE {?s <%s> ?o.}", property.getName());
ResultSet rs = executeSelectQuery(query);
int cnt = rs.next().get(rs.getResultVars().get(0)).asLiteral().getInt();
return cnt;
-
+
}
-
+
public SortedSet<ObjectProperty> getInverseObjectProperties(ObjectProperty property){
SortedSet<ObjectProperty> inverseObjectProperties = new TreeSet<ObjectProperty>();
String query = "SELECT ?p WHERE {" +
@@ -927,7 +984,7 @@
while(rs.hasNext()){
qs = rs.next();
inverseObjectProperties.add(new ObjectProperty(qs.getResource("p").getURI()));
-
+
}
return inverseObjectProperties;
}
@@ -938,14 +995,14 @@
"<%s> <%s> ?range. FILTER(isIRI(?range))" +
"}",
datatypeProperty.getName(), RDFS.range.getURI());
-
+
ResultSet rs = executeSelectQuery(query);
QuerySolution qs;
DataRange range = null;
while(rs.hasNext()){
qs = rs.next();
range = new Datatype(qs.getResource("range").getURI());
-
+
}
return range;
}
@@ -957,8 +1014,8 @@
}
String query = String.format("ASK {<%s> <%s> <%s>.}",
((NamedClass)subClass).getURI().toString(),
- RDFS.subClassOf.getURI(),
- ((NamedClass)superClass).getURI().toString());
+ RDFS.subClassOf.getURI(),
+ ((NamedClass)superClass).getURI().toString());
boolean superClassOf = executeAskQuery(query);
return superClassOf;
}
@@ -970,8 +1027,8 @@
}
String query = String.format("ASK {<%s> <%s> <%s>.}",
((NamedClass)class1).getURI().toString(),
- OWL.equivalentClass.getURI(),
- ((NamedClass)class2).getURI().toString());
+ OWL.equivalentClass.getURI(),
+ ((NamedClass)class2).getURI().toString());
boolean equivalentClass = executeAskQuery(query);
return equivalentClass;
}
@@ -984,7 +1041,7 @@
OWL.equivalentClass.getURI(),
OWL.equivalentClass.getURI(),
namedClass.getURI().toString()
- );
+ );
ResultSet rs = executeSelectQuery(query);
QuerySolution qs;
while(rs.hasNext()){
@@ -1017,7 +1074,7 @@
String query = String.format("SELECT ?sup {<%s> <%s> ?sup. FILTER(isIRI(?sup))}",
((NamedClass)description).getURI().toString(),
RDFS.subClassOf.getURI()
- );
+ );
ResultSet rs = executeSelectQuery(query);
QuerySolution qs;
while(rs.hasNext()){
@@ -1027,7 +1084,7 @@
superClasses.remove(description);
return superClasses;
}
-
+
public SortedSet<Description> getSuperClasses(Description description, boolean direct){
if(!(description instanceof NamedClass)){
throw new IllegalArgumentException("Only named classes are supported.");
@@ -1038,9 +1095,9 @@
"{ SELECT ?x ?y WHERE { ?x rdfs:subClassOf ?y } }" +
"OPTION ( TRANSITIVE, T_DISTINCT, t_in(?x), t_out(?y), t_step('path_id') as ?path, t_step(?x) as ?route, t_step('step_no') AS ?jump, T_DIRECTION 3 )" +
"FILTER ( ?x = <%s> )}", ((NamedClass)description).getURI().toString());
-
-
-
+
+
+
return superClasses;
}
@@ -1048,7 +1105,7 @@
public SortedSet<Description> getSubClasses(Description description) {
return getSubClasses(description, false);
}
-
+
public SortedSet<Description> getSubClasses(Description description, boolean useVirtuoso) {
if(!(description instanceof NamedClass || description instanceof Thing)){
throw new IllegalArgumentException("Only named classes are supported.");
@@ -1064,8 +1121,8 @@
query = String.format("SELECT ?sub {?sub <%s> <%s>. FILTER(isIRI(?sub))}",
RDFS.subClassOf.getURI(),
((NamedClass)description).getURI().toString()
-
- );
+
+ );
}
ResultSet rs = executeSelectQuery(query);
QuerySolution qs;
@@ -1076,13 +1133,13 @@
subClasses.remove(description);
return subClasses;
}
-
+
private String getAllSubClassesVirtuosoQuery(Description description){
String query = String.format(
"SELECT DISTINCT ?sub WHERE {"+
- "{SELECT ?sub ?o where {?sub rdfs:subClassOf ?o.}}"+
- "OPTION ( TRANSITIVE, t_distinct, t_in(?sub), t_out(?o), t_min (1), t_max (8), t_step ('step_no') as ?dist ) ."+
- "FILTER(?o = <%s>)}", description.toString());
+ "{SELECT ?sub ?o where {?sub rdfs:subClassOf ?o.}}"+
+ "OPTION ( TRANSITIVE, t_distinct, t_in(?sub), t_out(?o), t_min (1), t_max (8), t_step ('step_no') as ?dist ) ."+
+ "FILTER(?o = <%s>)}", description.toString());
return query;
}
@@ -1098,7 +1155,7 @@
String query = String.format("SELECT ?sup {<%s> <%s> ?sup. FILTER(isIRI(?sup))}",
objectProperty.getURI().toString(),
RDFS.subPropertyOf.getURI()
- );
+ );
ResultSet rs = executeSelectQuery(query);
QuerySolution qs;
while(rs.hasNext()){
@@ -1114,8 +1171,8 @@
String query = String.format("SELECT ?sub {?sub <%s> <%s>. FILTER(isIRI(?sub))}",
RDFS.subPropertyOf.getURI(),
objectProperty.getURI().toString()
-
- );
+
+ );
ResultSet rs = executeSelectQuery(query);
QuerySolution qs;
while(rs.hasNext()){
@@ -1124,13 +1181,13 @@
}
return subProperties;
}
-
+
public SortedSet<ObjectProperty> getEquivalentProperties(ObjectProperty objectProperty) {
SortedSet<ObjectProperty> superProperties = new TreeSet<ObjectProperty>();
String query = String.format("SELECT ?equ {<%s> <%s> ?equ. FILTER(isIRI(?equ))}",
objectProperty.getURI().toString(),
OWL.equivalentProperty.getURI()
- );
+ );
ResultSet rs = executeSelectQuery(query);
QuerySolution qs;
while(rs.hasNext()){
@@ -1139,13 +1196,13 @@
}
return superProperties;
}
-
+
public SortedSet<DatatypeProperty> getEquivalentProperties(DatatypeProperty objectProperty) {
SortedSet<DatatypeProperty> superProperties = new TreeSet<DatatypeProperty>();
String query = String.format("SELECT ?equ {<%s> <%s> ?equ. FILTER(isIRI(?equ))}",
objectProperty.getURI().toString(),
OWL.equivalentProperty.getURI()
- );
+ );
ResultSet rs = executeSelectQuery(query);
QuerySolution qs;
while(rs.hasNext()){
@@ -1176,7 +1233,7 @@
String query = String.format("SELECT ?sup {<%s> <%s> ?sup. FILTER(isIRI(?sup))}",
dataProperty.getURI().toString(),
RDFS.subPropertyOf.getURI()
- );
+ );
ResultSet rs = executeSelectQuery(query);
QuerySolution qs;
while(rs.hasNext()){
@@ -1192,8 +1249,8 @@
String query = String.format("SELECT ?sub {?sub <%s> <%s>. FILTER(isIRI(?sub))}",
RDFS.subPropertyOf.getURI(),
dataProperty.getURI().toString()
-
- );
+
+ );
ResultSet rs = executeSelectQuery(query);
QuerySolution qs;
while(rs.hasNext()){
@@ -1212,7 +1269,7 @@
public TreeSet<DatatypeProperty> getMostSpecialDatatypeProperties() {
throw new UnsupportedOperationException();
}
-
+
private ResultSet executeSelectQuery(String query){
logger.debug("Sending query \n {}", query);
ResultSet rs = null;
@@ -1232,11 +1289,11 @@
} else {
QueryExecution qExec = com.hp.hpl.jena.query.QueryExecutionFactory.create(query, ((LocalModelBasedSparqlEndpointKS)ks).getModel());
rs = qExec.execSelect();
-
+
}
return rs;
}
-
+
private ResultSet executeSelectQuery(String query, long timeout){
logger.debug("Sending query \n {}", query);
ResultSet rs = null;
@@ -1263,7 +1320,7 @@
}
return rs;
}
-
+
/**
* Returns TRUE if the class hierarchy was computed before.
* @return
@@ -1271,15 +1328,15 @@
public boolean isPrepared(){
return hierarchy != null;
}
-
+
public void setCache(ExtractionDBCache cache) {
this.cache = cache;
}
-
+
public void setUseCache(boolean useCache) {
this.useCache = useCache;
}
-
+
private boolean executeAskQuery(String query){
boolean ret;
if(ks.isRemote()){
@@ -1291,35 +1348,35 @@
queryExecution.addNamedGraph(ngu);
}
ret = queryExecution.execAsk();
-
+
} else {
QueryExecution qExec = com.hp.hpl.jena.query.QueryExecutionFactory.create(query, ((LocalModelBasedSparqlEndpointKS)ks).getModel());
ret = qExec.execAsk();
}
-
+
return ret;
}
-
-
+
+
public static void main(String[] args) throws Exception{
-// QueryEngineHTTP e = new QueryEngineHTTP("http://bibleontology.com/sparql/index.jsp",
-// "SELECT DISTINCT ?type WHERE {?s a ?type) LIMIT 10");
-// e.addParam("type1", "xml");System.out.println(e.toString());
-// e.execSelect();
-
-
+ // QueryEngineHTTP e = new QueryEngineHTTP("http://bibleontology.com/sparql/index.jsp",
+ // "SELECT DISTINCT ?type WHERE {?s a ?type) LIMIT 10");
+ // e.addParam("type1", "xml");System.out.println(e.toString());
+ // e.execSelect();
+
+
SparqlEndpointKS ks = new SparqlEndpointKS(new SparqlEndpoint(new URL("http://live.dbpedia.org/sparql/")));
SPARQLReasoner r = new SPARQLReasoner(ks);
long startTime = System.currentTimeMillis();
ClassHierarchy h = r.prepareSubsumptionHierarchyFast();
System.out.println(h.toString(false));
-// Model schema = r.loadSchema();
-// for(Statement st : schema.listStatements().toList()){
-// System.out.println(st);
-// }
+ // Model schema = r.loadSchema();
+ // for(Statement st : schema.listStatements().toList()){
+ // System.out.println(st);
+ // }
System.out.println(h.getSubClasses(new NamedClass("http://dbpedia.org/ontology/Bridge"), false));
System.out.println("Time needed: " + (System.currentTimeMillis()-startTime) + "ms");
-
+
}
}
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|
|
From: <moa...@us...> - 2013-05-15 13:09:35
|
Revision: 3980
http://sourceforge.net/p/dl-learner/code/3980
Author: moahmedsherif
Date: 2013-05-15 13:09:32 +0000 (Wed, 15 May 2013)
Log Message:
-----------
add getParentClasses() and getChildClasses()
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
Modified: trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java 2013-05-10 21:55:32 UTC (rev 3979)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java 2013-05-15 13:09:32 UTC (rev 3980)
@@ -498,6 +498,44 @@
return siblings;
}
+ /**
+ * Returns a set of classes which are Parent of current class
+ * in the class hierarchy.
+ * @param cls
+ * @param limit
+ * @return
+ */
+ public Set<NamedClass> getParentClasses(NamedClass cls) {
+ Set<NamedClass> parents = new HashSet<NamedClass>();
+ String query = "SELECT DISTINCT ?parentClass WHERE { <" + cls.getName() + "> <http://www.w3.org/2000/01/rdf-schema#subClassOf> ?parentClass }";
+ ResultSet rs = executeSelectQuery(query);
+ QuerySolution qs;
+ while(rs.hasNext()){
+ qs = rs.next();
+ parents.add(new NamedClass(qs.getResource("parentClass").getURI()));
+ }
+ return parents;
+ }
+
+ /**
+ * Returns a set of classes which are children of current class
+ * in the class hierarchy.
+ * @param cls
+ * @param limit
+ * @return
+ */
+ public Set<NamedClass> getChildClasses(NamedClass cls) {
+ Set<NamedClass> children = new HashSet<NamedClass>();
+ String query = "SELECT DISTINCT ?childClass WHERE { ?childClass <http://www.w3.org/2000/01/rdf-schema#subClassOf> <" + cls.getName() + ">}";
+ ResultSet rs = executeSelectQuery(query);
+ QuerySolution qs;
+ while(rs.hasNext()){
+ qs = rs.next();
+ children.add(new NamedClass(qs.getResource("childClass").getURI()));
+ }
+ return children;
+ }
+
@Override
public boolean hasType(Description description, Individual individual) {
if(!(description instanceof NamedClass)){
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|
|
From: <jen...@us...> - 2013-05-10 21:55:35
|
Revision: 3979
http://sourceforge.net/p/dl-learner/code/3979
Author: jenslehmann
Date: 2013-05-10 21:55:32 +0000 (Fri, 10 May 2013)
Log Message:
-----------
bug fix in F-beta
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/learningproblems/Heuristics.java
Modified: trunk/components-core/src/main/java/org/dllearner/learningproblems/Heuristics.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/learningproblems/Heuristics.java 2013-05-10 13:27:03 UTC (rev 3978)
+++ trunk/components-core/src/main/java/org/dllearner/learningproblems/Heuristics.java 2013-05-10 21:55:32 UTC (rev 3979)
@@ -52,10 +52,10 @@
*/
public static double getFScore(double recall, double precision, double beta) {
return (precision + recall == 0) ? 0 :
- ( (1+Math.sqrt(beta)) * (precision * recall)
- / (Math.sqrt(beta) * precision + recall) );
+ ( (1+ beta * beta) * (precision * recall)
+ / (beta * beta * precision + recall) );
}
-
+
/**
* Computes arithmetic mean of precision and recall, which is called "A-Score"
* here (A=arithmetic), but is not an established notion in machine learning.
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|
|
From: <lor...@us...> - 2013-05-10 13:27:06
|
Revision: 3978
http://sourceforge.net/p/dl-learner/code/3978
Author: lorenz_b
Date: 2013-05-10 13:27:03 +0000 (Fri, 10 May 2013)
Log Message:
-----------
Write eval stats to DB.
Modified Paths:
--------------
trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java 2013-05-10 11:48:50 UTC (rev 3977)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java 2013-05-10 13:27:03 UTC (rev 3978)
@@ -1132,25 +1132,33 @@
} else if(axiom.isOfType(AxiomType.SUBCLASS_OF)){
superClass = ((OWLSubClassOfAxiom)axiom).getSuperClass();
}
+ //count subclass+superClass
+ Query query = converter.asQuery("?x", df.getOWLObjectIntersectionOf(cls, superClass), true);System.out.println(query);
+ rs = executeSelectQuery(query);
+ int overlap = rs.next().getLiteral("cnt").getInt();
//count subclass
- Query query = converter.asQuery("?x", cls, true);
+ query = converter.asQuery("?x", cls, true);
if(subClassCnt == -1){
System.out.println(query);
rs = executeSelectQuery(query);
subClassCnt = rs.next().getLiteral("cnt").getInt();
}
+
+ //compute recall
+ double recall = wald(subClassCnt, overlap);
+ //if recall is too low we can skip the computation of the precision
+ if(recall < 0.2){
+ logger.warn("Recall(" + recall + ") too low. Skipping precision computation.");
+ continue;
+ }
//count superClass
query = converter.asQuery("?x", superClass, true);System.out.println(query);
rs = executeSelectQuery(query);
int superClassCnt = rs.next().getLiteral("cnt").getInt();
- //count subclass+superClass
- query = converter.asQuery("?x", df.getOWLObjectIntersectionOf(cls, superClass), true);System.out.println(query);
- rs = executeSelectQuery(query);
- int overlap = rs.next().getLiteral("cnt").getInt();
-
+ //compute precision
double precision = wald(superClassCnt, overlap);
- double recall = wald(subClassCnt, overlap);
+
double fScore = 0;
if(axiom.isOfType(AxiomType.SUBCLASS_OF)){
fScore = Heuristics.getFScore(recall, precision, 3);
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|
|
From: <lor...@us...> - 2013-05-10 11:48:53
|
Revision: 3977
http://sourceforge.net/p/dl-learner/code/3977
Author: lorenz_b
Date: 2013-05-10 11:48:50 +0000 (Fri, 10 May 2013)
Log Message:
-----------
Write eval stats to DB.
Modified Paths:
--------------
trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java 2013-05-10 10:01:19 UTC (rev 3976)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java 2013-05-10 11:48:50 UTC (rev 3977)
@@ -7,11 +7,16 @@
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
+import java.io.InputStream;
+import java.io.StringWriter;
import java.io.UnsupportedEncodingException;
import java.net.MalformedURLException;
import java.net.SocketTimeoutException;
import java.net.URI;
import java.net.URL;
+import java.sql.Connection;
+import java.sql.DriverManager;
+import java.sql.PreparedStatement;
import java.sql.SQLException;
import java.text.DecimalFormat;
import java.util.ArrayList;
@@ -29,6 +34,7 @@
import java.util.Set;
import java.util.TreeSet;
import java.util.concurrent.TimeUnit;
+import java.util.prefs.Preferences;
import joptsimple.OptionException;
import joptsimple.OptionParser;
@@ -51,6 +57,8 @@
import org.dllearner.reasoning.SPARQLReasoner;
import org.dllearner.utilities.owl.DLLearnerDescriptionConvertVisitor;
import org.dllearner.utilities.owl.OWLClassExpressionToSPARQLConverter;
+import org.ini4j.IniPreferences;
+import org.ini4j.InvalidFileFormatException;
import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.io.OWLObjectRenderer;
import org.semanticweb.owlapi.io.ToStringRenderer;
@@ -106,6 +114,8 @@
import com.hp.hpl.jena.sparql.engine.http.QueryEngineHTTP;
import com.hp.hpl.jena.sparql.engine.http.QueryExceptionHTTP;
import com.hp.hpl.jena.vocabulary.RDF;
+import com.jamonapi.Monitor;
+import com.jamonapi.MonitorFactory;
public class OWLAxiomPatternUsageEvaluation {
@@ -139,6 +149,10 @@
private OWLOntology dbpediaOntology;
private String ontologyURL = "http://downloads.dbpedia.org/3.8/dbpedia_3.8.owl.bz2";
private OWLReasoner reasoner;
+
+ private Connection conn;
+
+ private PreparedStatement ps;
public OWLAxiomPatternUsageEvaluation() {
try {
@@ -153,8 +167,49 @@
} catch (IOException e) {
e.printStackTrace();
}
+
+ initDBConnection();
}
+ 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);
+
+ java.sql.Statement st = conn.createStatement();
+ st.execute("CREATE TABLE IF NOT EXISTS Eval_Statistics ("
+ + "id MEDIUMINT NOT NULL AUTO_INCREMENT,"
+ + "pattern TEXT NOT NULL,"
+ + "pattern_pretty TEXT NOT NULL,"
+ + "class TEXT NOT NULL,"
+ + "runtime MEDIUMINT DEFAULT 0,"
+ + "nrOfAxiomsLocal MEDIUMINT DEFAULT 0,"
+ + "nrOfAxiomsGlobal MEDIUMINT DEFAULT 0,"
+ + "PRIMARY KEY(id),"
+ + "INDEX(pattern(8000))) DEFAULT CHARSET=utf8");
+
+ ps = conn.prepareStatement("INSERT INTO Eval_Statistics (pattern, pattern_pretty, class, runtime, nrOfAxiomsLocal, nrOfAxiomsGlobal) VALUES(?,?,?,?,?,?)");
+ } 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();
+ }
+ }
+
public void runUsingFragmentExtraction(SparqlEndpoint endpoint, OWLOntology patternOntology, File outputFile, int maxNrOfTestedClasses){
ks = new SparqlEndpointKS(endpoint, cache);
SPARQLReasoner reasoner = new SPARQLReasoner(ks, cache);
@@ -170,7 +225,7 @@
Collections.shuffle(classesList, new Random(123));
classesList = classesList.subList(0, maxNrOfTestedClasses);
classes = classesList;
-// classes = Collections.singleton(new NamedClass("http://dbpedia.org/ontology/ChristianBishop"));
+ //classes = Collections.singleton(new NamedClass("http://dbpedia.org/ontology/ChristianBishop"));
//get the maximum modal depth in the pattern axioms
int maxModalDepth = maxModalDepth(patterns);
@@ -193,7 +248,10 @@
}
//for each pattern
+ Monitor patternTimeMon = MonitorFactory.getTimeMonitor("pattern-runtime");
for (OWLAxiom pattern : patterns) {
+ Monitor patternClassTimeMon = MonitorFactory.getTimeMonitor("class-pattern-runtime");
+ patternTimeMon.start();
//run if not already exists a result on disk
File file = new File(axiomRenderer.render(pattern).replace(" ", "_") + "-instantiations.ttl");
OWLOntology ontology = null;
@@ -202,6 +260,7 @@
Set<OWLAxiom> learnedAxioms = new HashSet<OWLAxiom>();
// for each class
for (NamedClass cls : classes) {
+ patternClassTimeMon.start();
logger.info("...on class " + cls + "...");
OWLClass owlClass = df.getOWLClass(IRI.create(cls.getName()));
Model fragment = class2Fragment.get(cls);
@@ -209,9 +268,14 @@
Set<OWLAxiom> annotatedAxioms = asAnnotatedAxioms(result);
filterOutTrivialAxioms(annotatedAxioms);
filterOutAxiomsBelowThreshold(annotatedAxioms, threshold);
+ int nrOfAxiomsLocal = annotatedAxioms.size();
annotatedAxioms = computeScoreGlobal(annotatedAxioms, owlClass);
+ filterOutAxiomsBelowThreshold(annotatedAxioms, threshold);
+ int nrOfAxiomsGlobal = annotatedAxioms.size();
learnedAxioms.addAll(annotatedAxioms);
printAxioms(annotatedAxioms, threshold);
+ patternClassTimeMon.stop();
+ write2DB(pattern, owlClass, patternClassTimeMon.getLastValue(), nrOfAxiomsLocal, nrOfAxiomsGlobal);
}
ontology = save(pattern, learnedAxioms, file);
} else {
@@ -222,6 +286,7 @@
e.printStackTrace();
}
}
+ patternTimeMon.stop();
if(sampling){
List<OWLAxiom> sample = createSample(ontology);//, classes);
List<String> lines = new ArrayList<String>();
@@ -789,6 +854,20 @@
return axioms2Score;
}
+ private void write2DB(OWLAxiom pattern, OWLClass cls, double runtime, int nrOfAxiomsLocal, int nrOfAxiomsGlobal){
+ try {
+ ps.setString(1, render(pattern));
+ ps.setString(2, axiomRenderer.render(pattern));
+ ps.setString(3, axiomRenderer.render(cls));
+ ps.setDouble(4, runtime);
+ ps.setInt(5, nrOfAxiomsLocal);
+ ps.setInt(6, nrOfAxiomsGlobal);
+ ps.execute();
+ } catch (SQLException e) {
+ e.printStackTrace();
+ }
+ }
+
private Map<OWLAxiom, Score> applyPattern2(OWLSubClassOfAxiom pattern, OWLClass cls, Model fragment) {
Map<OWLAxiom, Score> axioms2Score = new HashMap<OWLAxiom, Score>();
@@ -950,6 +1029,11 @@
}
}
}
+ try {
+ Thread.sleep(100);
+ } catch (InterruptedException e) {
+ e.printStackTrace();
+ }
} else {
QueryExecution queryExecution = QueryExecutionFactory.create(query, ((LocalModelBasedSparqlEndpointKS)ks).getModel());
@@ -1029,51 +1113,60 @@
private Set<OWLAxiom> computeScoreGlobal(Set<OWLAxiom> axioms, OWLClass cls){
Set<OWLAxiom> newAxioms = new HashSet<OWLAxiom>();
+ int subClassCnt = -1;
+ ResultSet rs;
for (Iterator<OWLAxiom> iter = axioms.iterator(); iter.hasNext();) {
- OWLAxiom axiom = iter.next();
- OWLClassExpression subClass;
- OWLClassExpression superClass = null;
- OWLClassExpressionToSPARQLConverter converter = new OWLClassExpressionToSPARQLConverter();
- if (axiom.isOfType(AxiomType.EQUIVALENT_CLASSES)) {
- Set<OWLSubClassOfAxiom> subClassOfAxioms = ((OWLEquivalentClassesAxiom) axiom).asOWLSubClassOfAxioms();
- for (OWLSubClassOfAxiom subClassOfAxiom : subClassOfAxioms) {
- if (subClassOfAxiom.getSubClass().equals(cls)) {
- superClass = subClassOfAxiom.getSuperClass();
- break;
+ try {
+ OWLAxiom axiom = iter.next();
+ OWLClassExpression subClass;
+ OWLClassExpression superClass = null;
+ OWLClassExpressionToSPARQLConverter converter = new OWLClassExpressionToSPARQLConverter();
+ if (axiom.isOfType(AxiomType.EQUIVALENT_CLASSES)) {
+ Set<OWLSubClassOfAxiom> subClassOfAxioms = ((OWLEquivalentClassesAxiom) axiom).asOWLSubClassOfAxioms();
+ for (OWLSubClassOfAxiom subClassOfAxiom : subClassOfAxioms) {
+ if (subClassOfAxiom.getSubClass().equals(cls)) {
+ superClass = subClassOfAxiom.getSuperClass();
+ break;
+ }
}
+ } else if(axiom.isOfType(AxiomType.SUBCLASS_OF)){
+ superClass = ((OWLSubClassOfAxiom)axiom).getSuperClass();
}
- } else if(axiom.isOfType(AxiomType.SUBCLASS_OF)){
- superClass = ((OWLSubClassOfAxiom)axiom).getSuperClass();
+ //count subclass
+ Query query = converter.asQuery("?x", cls, true);
+ if(subClassCnt == -1){
+ System.out.println(query);
+ rs = executeSelectQuery(query);
+ subClassCnt = rs.next().getLiteral("cnt").getInt();
+ }
+ //count superClass
+ query = converter.asQuery("?x", superClass, true);System.out.println(query);
+ rs = executeSelectQuery(query);
+ int superClassCnt = rs.next().getLiteral("cnt").getInt();
+ //count subclass+superClass
+ query = converter.asQuery("?x", df.getOWLObjectIntersectionOf(cls, superClass), true);System.out.println(query);
+ rs = executeSelectQuery(query);
+ int overlap = rs.next().getLiteral("cnt").getInt();
+
+ double precision = wald(superClassCnt, overlap);
+ double recall = wald(subClassCnt, overlap);
+
+ double fScore = 0;
+ if(axiom.isOfType(AxiomType.SUBCLASS_OF)){
+ fScore = Heuristics.getFScore(recall, precision, 3);
+ } else if(axiom.isOfType(AxiomType.EQUIVALENT_CLASSES)){
+ fScore = Heuristics.getFScore(recall, precision, 1);
+ }
+
+ System.out.println(axiom);
+ System.out.println(subClassCnt + "|" + superClassCnt + "|" + overlap);
+ System.out.println("P=" + precision + "|R=" + recall +"|F=" + fScore);
+
+ newAxioms.add(axiom.getAxiomWithoutAnnotations().getAnnotatedAxiom(
+ Collections.singleton(df.getOWLAnnotation(confidenceProperty, df.getOWLLiteral(fScore)))));
+ } catch (Exception e) {
+ e.printStackTrace();
}
- //count subclass
- Query query = converter.asQuery("?x", cls, true);System.out.println(query);
- ResultSet rs = executeSelectQuery(query);
- int subClassCnt = rs.next().getLiteral("cnt").getInt();
- //count subclass+superClass
- query = converter.asQuery("?x", df.getOWLObjectIntersectionOf(cls, superClass), true);System.out.println(query);
- rs = executeSelectQuery(query);
- int overlap = rs.next().getLiteral("cnt").getInt();
- //count superClass
- query = converter.asQuery("?x", superClass, true);System.out.println(query);
- rs = executeSelectQuery(query);
- int superClassCnt = rs.next().getLiteral("cnt").getInt();
-
- double precision = wald(superClassCnt, overlap);
- double recall = wald(subClassCnt, overlap);
-
- double fScore = 0;
- if(axiom.isOfType(AxiomType.SUBCLASS_OF)){
- fScore = Heuristics.getFScore(recall, precision, 3);
- } else if(axiom.isOfType(AxiomType.EQUIVALENT_CLASSES)){
- fScore = Heuristics.getFScore(recall, precision, 1);
- }
-
- System.out.println(axiom);
- System.out.println(subClassCnt + "|" + superClassCnt + "|" + overlap);
- System.out.println("P=" + precision + "|R=" + recall +"|F=" + fScore);
-
- newAxioms.add(axiom.getAxiomWithoutAnnotations().getAnnotatedAxiom(
- Collections.singleton(df.getOWLAnnotation(confidenceProperty, df.getOWLLiteral(fScore)))));
}
return newAxioms;
@@ -1125,6 +1218,21 @@
return new AxiomScore(accuracy, confidence, total, success, total-success);
}
+ private String render(OWLAxiom axiom){
+ try {
+ OWLOntologyManager man = OWLManager.createOWLOntologyManager();
+ OWLOntology ontology = man.createOntology();
+ man.addAxiom(ontology, axiom);
+ StringWriter sw = new StringWriter();
+ org.coode.owlapi.functionalrenderer.OWLObjectRenderer r = new org.coode.owlapi.functionalrenderer.OWLObjectRenderer(man, ontology, sw);
+ axiom.accept(r);
+ return sw.toString();
+ } catch (OWLOntologyCreationException e) {
+ e.printStackTrace();
+ }
+ return null;
+ }
+
public static void main(String[] args) throws Exception {
ToStringRenderer.getInstance().setRenderer(new DLSyntaxObjectRenderer());
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|
|
From: <lor...@us...> - 2013-05-10 10:01:24
|
Revision: 3976
http://sourceforge.net/p/dl-learner/code/3976
Author: lorenz_b
Date: 2013-05-10 10:01:19 +0000 (Fri, 10 May 2013)
Log Message:
-----------
Changed SPARQL converter.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLClassExpressionToSPARQLConverter.java
Modified: trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLClassExpressionToSPARQLConverter.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLClassExpressionToSPARQLConverter.java 2013-05-10 09:55:47 UTC (rev 3975)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLClassExpressionToSPARQLConverter.java 2013-05-10 10:01:19 UTC (rev 3976)
@@ -108,7 +108,16 @@
}
public Query asQuery(String rootVariable, OWLClassExpression expr, boolean countQuery){
- return asQuery(rootVariable, expr, Collections.<OWLEntity>emptySet());
+ String queryString = "SELECT ";
+ String triplePattern = convert(rootVariable, expr);
+ if(countQuery){
+ queryString += "(COUNT(DISTINCT " + rootVariable + ") AS ?cnt) WHERE {";
+ } else {
+ queryString += "DISTINCT " + rootVariable + " WHERE {";
+ }
+ queryString += triplePattern;
+ queryString += "}";
+ return QueryFactory.create(queryString, Syntax.syntaxARQ);
}
public Query asQuery(String rootVariable, OWLClassExpression expr, Set<? extends OWLEntity> variableEntities){
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|
|
From: <lor...@us...> - 2013-05-10 09:55:51
|
Revision: 3975
http://sourceforge.net/p/dl-learner/code/3975
Author: lorenz_b
Date: 2013-05-10 09:55:47 +0000 (Fri, 10 May 2013)
Log Message:
-----------
Continued filtering of trivial axioms in pattern eval.
Modified Paths:
--------------
trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java 2013-05-10 07:59:48 UTC (rev 3974)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java 2013-05-10 09:55:47 UTC (rev 3975)
@@ -97,6 +97,7 @@
import com.hp.hpl.jena.query.QueryExecutionFactory;
import com.hp.hpl.jena.query.QueryFactory;
import com.hp.hpl.jena.query.QuerySolution;
+import com.hp.hpl.jena.query.ResultSet;
import com.hp.hpl.jena.query.Syntax;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
@@ -131,7 +132,7 @@
private long maxExecutionTime = TimeUnit.SECONDS.toMillis(20);
private int queryLimit = 10000;
private boolean sampling = true;
- private double sampleThreshold = 0.8;
+ private double sampleThreshold = 0.6;
private int sampleSize = 100;
private Set<String> entites2Ignore = Sets.newHashSet("subject", "Concept", "wikiPage");
//DBpedia schema
@@ -169,7 +170,7 @@
Collections.shuffle(classesList, new Random(123));
classesList = classesList.subList(0, maxNrOfTestedClasses);
classes = classesList;
- //classes = Collections.singleton(new NamedClass("http://dbpedia.org/ontology/ChristianBishop"));
+// classes = Collections.singleton(new NamedClass("http://dbpedia.org/ontology/ChristianBishop"));
//get the maximum modal depth in the pattern axioms
int maxModalDepth = maxModalDepth(patterns);
@@ -202,11 +203,13 @@
// for each class
for (NamedClass cls : classes) {
logger.info("...on class " + cls + "...");
+ OWLClass owlClass = df.getOWLClass(IRI.create(cls.getName()));
Model fragment = class2Fragment.get(cls);
- Map<OWLAxiom, Score> result = applyPattern(pattern,
- df.getOWLClass(IRI.create(cls.getName())), fragment);
+ Map<OWLAxiom, Score> result = applyPattern(pattern, owlClass, fragment);
Set<OWLAxiom> annotatedAxioms = asAnnotatedAxioms(result);
filterOutTrivialAxioms(annotatedAxioms);
+ filterOutAxiomsBelowThreshold(annotatedAxioms, threshold);
+ annotatedAxioms = computeScoreGlobal(annotatedAxioms, owlClass);
learnedAxioms.addAll(annotatedAxioms);
printAxioms(annotatedAxioms, threshold);
}
@@ -248,7 +251,7 @@
return annotatedAxioms;
}
- private void printAxioms(Set<OWLAxiom> axioms, double threshold){
+ private void printAxioms(Set<OWLAxiom> axioms, double threshold){OWLClassExpressionToSPARQLConverter c = new OWLClassExpressionToSPARQLConverter();
for (Iterator<OWLAxiom> iter = axioms.iterator(); iter.hasNext();) {
OWLAxiom axiom = iter.next();
double accuracy = getAccuracy(axiom);
@@ -341,6 +344,15 @@
return axiomList.subList(0, Math.min(sampleSize, axiomList.size()));
}
+ private void filterOutAxiomsBelowThreshold(Set<OWLAxiom> axioms, double threshold) {
+ for (Iterator<OWLAxiom> iter = axioms.iterator(); iter.hasNext();) {
+ OWLAxiom axiom = iter.next();
+ if(getAccuracy(axiom) < threshold){
+ iter.remove();
+ }
+ }
+ }
+
private void filterOutTrivialAxioms(Set<OWLAxiom> axioms) {
for (Iterator<OWLAxiom> iter = axioms.iterator(); iter.hasNext();) {
OWLAxiom axiom = iter.next();
@@ -1015,6 +1027,94 @@
}
}
+ private Set<OWLAxiom> computeScoreGlobal(Set<OWLAxiom> axioms, OWLClass cls){
+ Set<OWLAxiom> newAxioms = new HashSet<OWLAxiom>();
+ for (Iterator<OWLAxiom> iter = axioms.iterator(); iter.hasNext();) {
+ OWLAxiom axiom = iter.next();
+ OWLClassExpression subClass;
+ OWLClassExpression superClass = null;
+ OWLClassExpressionToSPARQLConverter converter = new OWLClassExpressionToSPARQLConverter();
+ if (axiom.isOfType(AxiomType.EQUIVALENT_CLASSES)) {
+ Set<OWLSubClassOfAxiom> subClassOfAxioms = ((OWLEquivalentClassesAxiom) axiom).asOWLSubClassOfAxioms();
+ for (OWLSubClassOfAxiom subClassOfAxiom : subClassOfAxioms) {
+ if (subClassOfAxiom.getSubClass().equals(cls)) {
+ superClass = subClassOfAxiom.getSuperClass();
+ break;
+ }
+ }
+ } else if(axiom.isOfType(AxiomType.SUBCLASS_OF)){
+ superClass = ((OWLSubClassOfAxiom)axiom).getSuperClass();
+ }
+ //count subclass
+ Query query = converter.asQuery("?x", cls, true);System.out.println(query);
+ ResultSet rs = executeSelectQuery(query);
+ int subClassCnt = rs.next().getLiteral("cnt").getInt();
+ //count subclass+superClass
+ query = converter.asQuery("?x", df.getOWLObjectIntersectionOf(cls, superClass), true);System.out.println(query);
+ rs = executeSelectQuery(query);
+ int overlap = rs.next().getLiteral("cnt").getInt();
+ //count superClass
+ query = converter.asQuery("?x", superClass, true);System.out.println(query);
+ rs = executeSelectQuery(query);
+ int superClassCnt = rs.next().getLiteral("cnt").getInt();
+
+ double precision = wald(superClassCnt, overlap);
+ double recall = wald(subClassCnt, overlap);
+
+ double fScore = 0;
+ if(axiom.isOfType(AxiomType.SUBCLASS_OF)){
+ fScore = Heuristics.getFScore(recall, precision, 3);
+ } else if(axiom.isOfType(AxiomType.EQUIVALENT_CLASSES)){
+ fScore = Heuristics.getFScore(recall, precision, 1);
+ }
+
+ System.out.println(axiom);
+ System.out.println(subClassCnt + "|" + superClassCnt + "|" + overlap);
+ System.out.println("P=" + precision + "|R=" + recall +"|F=" + fScore);
+
+ newAxioms.add(axiom.getAxiomWithoutAnnotations().getAnnotatedAxiom(
+ Collections.singleton(df.getOWLAnnotation(confidenceProperty, df.getOWLLiteral(fScore)))));
+
+ }
+ return newAxioms;
+ }
+
+ private Score computeScoreGlobal(OWLAxiom axiom, OWLClass cls){
+ OWLClassExpression subClass;
+ OWLClassExpression superClass = null;
+ OWLClassExpressionToSPARQLConverter converter = new OWLClassExpressionToSPARQLConverter();
+ if (axiom.isOfType(AxiomType.EQUIVALENT_CLASSES)) {
+ Set<OWLSubClassOfAxiom> subClassOfAxioms = ((OWLEquivalentClassesAxiom) axiom).asOWLSubClassOfAxioms();
+ for (OWLSubClassOfAxiom subClassOfAxiom : subClassOfAxioms) {
+ if (subClassOfAxiom.getSubClass().equals(cls)) {
+ superClass = subClassOfAxiom.getSuperClass();
+ break;
+ }
+ }
+ } else if(axiom.isOfType(AxiomType.SUBCLASS_OF)){
+ superClass = ((OWLSubClassOfAxiom)axiom).getSuperClass();
+ }
+ //count subclass+superClass
+ Query query = converter.asQuery("?x", df.getOWLObjectIntersectionOf(cls, superClass), true);System.out.println(query);
+ ResultSet rs = executeSelectQuery(query);
+ int subClassCnt = rs.next().getLiteral("cnt").getInt();
+ //count superClass
+ query = converter.asQuery("?x", superClass, true);System.out.println(query);
+ rs = executeSelectQuery(query);
+ int superClassCnt = rs.next().getLiteral("cnt").getInt();
+
+ Score score = computeScore(superClassCnt, subClassCnt);
+ return score;
+ }
+
+ private double wald(int total, int success){
+ double[] confidenceInterval = Heuristics.getConfidenceInterval95Wald(total, success);
+
+ double accuracy = (confidenceInterval[0] + confidenceInterval[1]) / 2;
+
+ return accuracy;
+ }
+
private Score computeScore(int total, int success){
double[] confidenceInterval = Heuristics.getConfidenceInterval95Wald(total, success);
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|
|
From: <lor...@us...> - 2013-05-10 07:59:51
|
Revision: 3974
http://sourceforge.net/p/dl-learner/code/3974
Author: lorenz_b
Date: 2013-05-10 07:59:48 +0000 (Fri, 10 May 2013)
Log Message:
-----------
Continued filtering of trivial axioms in pattern eval.
Modified Paths:
--------------
trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java 2013-05-10 07:14:57 UTC (rev 3973)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java 2013-05-10 07:59:48 UTC (rev 3974)
@@ -8,6 +8,7 @@
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.UnsupportedEncodingException;
+import java.net.MalformedURLException;
import java.net.SocketTimeoutException;
import java.net.URI;
import java.net.URL;
@@ -33,6 +34,7 @@
import joptsimple.OptionParser;
import joptsimple.OptionSet;
+import org.apache.commons.compress.compressors.bzip2.BZip2CompressorInputStream;
import org.apache.log4j.Logger;
import org.coode.owlapi.turtle.TurtleOntologyFormat;
import org.dllearner.core.EvaluatedAxiom;
@@ -70,12 +72,14 @@
import org.semanticweb.owlapi.model.OWLOntologyManager;
import org.semanticweb.owlapi.model.OWLOntologyStorageException;
import org.semanticweb.owlapi.model.OWLSubClassOfAxiom;
+import org.semanticweb.owlapi.reasoner.OWLReasoner;
import org.semanticweb.owlapi.util.OWLObjectDuplicator;
import uk.ac.manchester.cs.owl.owlapi.OWLDataFactoryImpl;
import uk.ac.manchester.cs.owl.owlapi.mansyntaxrenderer.ManchesterOWLSyntaxOWLObjectRendererImpl;
import uk.ac.manchester.cs.owlapi.dlsyntax.DLSyntaxObjectRenderer;
+import com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory;
import com.google.common.base.Charsets;
import com.google.common.base.Joiner;
import com.google.common.collect.HashMultiset;
@@ -130,12 +134,26 @@
private double sampleThreshold = 0.8;
private int sampleSize = 100;
private Set<String> entites2Ignore = Sets.newHashSet("subject", "Concept", "wikiPage");
+ //DBpedia schema
+ private OWLOntology dbpediaOntology;
+ private String ontologyURL = "http://downloads.dbpedia.org/3.8/dbpedia_3.8.owl.bz2";
+ private OWLReasoner reasoner;
public OWLAxiomPatternUsageEvaluation() {
+ try {
+ BZip2CompressorInputStream is = new BZip2CompressorInputStream(new URL(ontologyURL).openStream());
+ OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
+ dbpediaOntology = manager.loadOntologyFromOntologyDocument(is);
+ reasoner = PelletReasonerFactory.getInstance().createNonBufferingReasoner(dbpediaOntology);
+ } catch (MalformedURLException e) {
+ e.printStackTrace();
+ } catch (OWLOntologyCreationException e) {
+ e.printStackTrace();
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
}
-
-
public void runUsingFragmentExtraction(SparqlEndpoint endpoint, OWLOntology patternOntology, File outputFile, int maxNrOfTestedClasses){
ks = new SparqlEndpointKS(endpoint, cache);
SPARQLReasoner reasoner = new SPARQLReasoner(ks, cache);
@@ -151,7 +169,7 @@
Collections.shuffle(classesList, new Random(123));
classesList = classesList.subList(0, maxNrOfTestedClasses);
classes = classesList;
- classes = Collections.singleton(new NamedClass("http://dbpedia.org/ontology/ChristianBishop"));
+ //classes = Collections.singleton(new NamedClass("http://dbpedia.org/ontology/ChristianBishop"));
//get the maximum modal depth in the pattern axioms
int maxModalDepth = maxModalDepth(patterns);
@@ -202,7 +220,7 @@
}
}
if(sampling){
- List<OWLAxiom> sample = createSample(ontology);//createSample(ontology, classes);
+ List<OWLAxiom> sample = createSample(ontology);//, classes);
List<String> lines = new ArrayList<String>();
for (OWLAxiom axiom : sample) {
double accuracy = getAccuracy(axiom);
@@ -283,11 +301,42 @@
NavigableSet<Double> keySet = (NavigableSet<Double>)accuracyWithAxioms.keySet();
Double score = keySet.first();
Collection<OWLAxiom> axiomsWithHighestScore = accuracyWithAxioms.get(score);
- for (OWLAxiom ax : axiomsWithHighestScore) {
- System.out.println(ax + ":" + getAccuracy(ax));
+ Map<OWLAxiom, OWLClassExpression> superClasses = new HashMap<OWLAxiom, OWLClassExpression>();
+ for (OWLAxiom axiom : axiomsWithHighestScore) {
+ if (axiom.isOfType(AxiomType.EQUIVALENT_CLASSES)) {
+ Set<OWLSubClassOfAxiom> subClassOfAxioms = ((OWLEquivalentClassesAxiom) axiom).asOWLSubClassOfAxioms();
+ for (OWLSubClassOfAxiom subClassOfAxiom : subClassOfAxioms) {
+ if (subClassOfAxiom.getSubClass().equals(owlClass)) {
+ superClasses.put(axiom, subClassOfAxiom.getSuperClass());
+ break;
+ }
+ }
+ }
+ if (axiom.isOfType(AxiomType.SUBCLASS_OF)) {
+ superClasses.put(axiom, ((OWLSubClassOfAxiom) axiom).getSuperClass());
+ }
}
+
+ for (Entry<OWLAxiom, OWLClassExpression> entry : superClasses.entrySet()) {
+ OWLAxiom axiom1 = entry.getKey();
+ OWLClassExpression ce1 = entry.getValue();
+ boolean remove = false;
+ for (Entry<OWLAxiom, OWLClassExpression> entry2 : superClasses.entrySet()) {
+ OWLAxiom axiom2 = entry2.getKey();
+ if(!axiom1.equals(axiom2)){
+ OWLClassExpression ce2 = entry2.getValue();
+ if(reasoner.isEntailed(df.getOWLSubClassOfAxiom(ce2, ce1))){
+ remove = true;
+ break;
+ }
+ }
+ }
+ if(remove){
+ axiomsWithHighestScore.remove(axiom1);
+ }
+ }
+ axiomList.addAll(axiomsWithHighestScore);
}
-
Collections.shuffle(axiomList, new Random(123));
return axiomList.subList(0, Math.min(sampleSize, axiomList.size()));
}
@@ -296,6 +345,10 @@
for (Iterator<OWLAxiom> iter = axioms.iterator(); iter.hasNext();) {
OWLAxiom axiom = iter.next();
if (axiom.isOfType(AxiomType.EQUIVALENT_CLASSES)) {
+ if(((OWLEquivalentClassesAxiom) axiom).getClassExpressions().size() == 1){
+ iter.remove();
+ continue;
+ }
Set<OWLSubClassOfAxiom> subClassOfAxioms = ((OWLEquivalentClassesAxiom) axiom).asOWLSubClassOfAxioms();
for (OWLSubClassOfAxiom subClassOfAxiom : subClassOfAxioms) {
if (!subClassOfAxiom.getSubClass().isAnonymous()) {
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lor...@us...> - 2013-05-10 07:15:01
|
Revision: 3973
http://sourceforge.net/p/dl-learner/code/3973
Author: lorenz_b
Date: 2013-05-10 07:14:57 +0000 (Fri, 10 May 2013)
Log Message:
-----------
Added filtering of trivial axioms in pattern eval.
Modified Paths:
--------------
trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java 2013-05-10 06:39:31 UTC (rev 3972)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java 2013-05-10 07:14:57 UTC (rev 3973)
@@ -19,11 +19,11 @@
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
-import java.util.LinkedHashMap;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
+import java.util.NavigableSet;
import java.util.Random;
import java.util.Set;
import java.util.TreeSet;
@@ -79,8 +79,10 @@
import com.google.common.base.Charsets;
import com.google.common.base.Joiner;
import com.google.common.collect.HashMultiset;
+import com.google.common.collect.Multimap;
import com.google.common.collect.Multiset;
import com.google.common.collect.Sets;
+import com.google.common.collect.TreeMultimap;
import com.google.common.hash.HashCode;
import com.google.common.hash.HashFunction;
import com.google.common.hash.Hashing;
@@ -149,7 +151,7 @@
Collections.shuffle(classesList, new Random(123));
classesList = classesList.subList(0, maxNrOfTestedClasses);
classes = classesList;
-// classes = Collections.singleton(new NamedClass("http://dbpedia.org/ontology/ChristianBishop"));
+ classes = Collections.singleton(new NamedClass("http://dbpedia.org/ontology/ChristianBishop"));
//get the maximum modal depth in the pattern axioms
int maxModalDepth = maxModalDepth(patterns);
@@ -187,6 +189,7 @@
df.getOWLClass(IRI.create(cls.getName())), fragment);
Set<OWLAxiom> annotatedAxioms = asAnnotatedAxioms(result);
filterOutTrivialAxioms(annotatedAxioms);
+ learnedAxioms.addAll(annotatedAxioms);
printAxioms(annotatedAxioms, threshold);
}
ontology = save(pattern, learnedAxioms, file);
@@ -199,7 +202,7 @@
}
}
if(sampling){
- List<OWLAxiom> sample = createSample(ontology);
+ List<OWLAxiom> sample = createSample(ontology);//createSample(ontology, classes);
List<String> lines = new ArrayList<String>();
for (OWLAxiom axiom : sample) {
double accuracy = getAccuracy(axiom);
@@ -264,6 +267,31 @@
return axiomList.subList(0, Math.min(sampleSize, axiomList.size()));
}
+ private List<OWLAxiom> createSample(OWLOntology ontology, Collection<NamedClass> classes){
+ List<OWLAxiom> axiomList = new ArrayList<OWLAxiom>();
+ for (NamedClass cls : classes) {
+ OWLClass owlClass = df.getOWLClass(IRI.create(cls.getName()));
+ Set<OWLAxiom> referencingAxioms = ontology.getReferencingAxioms(owlClass);
+ Multimap<Double, OWLAxiom> accuracyWithAxioms = TreeMultimap.create();
+ for (OWLAxiom axiom : referencingAxioms) {
+ double accuracy = getAccuracy(axiom);
+ if(accuracy >= sampleThreshold){
+ accuracyWithAxioms.put(accuracy, axiom);
+ }
+ }
+ //pick the set of axioms with highest score
+ NavigableSet<Double> keySet = (NavigableSet<Double>)accuracyWithAxioms.keySet();
+ Double score = keySet.first();
+ Collection<OWLAxiom> axiomsWithHighestScore = accuracyWithAxioms.get(score);
+ for (OWLAxiom ax : axiomsWithHighestScore) {
+ System.out.println(ax + ":" + getAccuracy(ax));
+ }
+ }
+
+ Collections.shuffle(axiomList, new Random(123));
+ return axiomList.subList(0, Math.min(sampleSize, axiomList.size()));
+ }
+
private void filterOutTrivialAxioms(Set<OWLAxiom> axioms) {
for (Iterator<OWLAxiom> iter = axioms.iterator(); iter.hasNext();) {
OWLAxiom axiom = iter.next();
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lor...@us...> - 2013-05-10 06:39:35
|
Revision: 3972
http://sourceforge.net/p/dl-learner/code/3972
Author: lorenz_b
Date: 2013-05-10 06:39:31 +0000 (Fri, 10 May 2013)
Log Message:
-----------
Added filtering of trivial axioms in pattern eval.
Modified Paths:
--------------
trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java 2013-05-09 15:57:17 UTC (rev 3971)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java 2013-05-10 06:39:31 UTC (rev 3972)
@@ -49,7 +49,6 @@
import org.dllearner.reasoning.SPARQLReasoner;
import org.dllearner.utilities.owl.DLLearnerDescriptionConvertVisitor;
import org.dllearner.utilities.owl.OWLClassExpressionToSPARQLConverter;
-import org.semanticweb.elk.reasoner.saturation.classes.SuperClassExpression;
import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.io.OWLObjectRenderer;
import org.semanticweb.owlapi.io.ToStringRenderer;
@@ -121,7 +120,7 @@
private double threshold = 0.6;
private OWLAnnotationProperty confidenceProperty = df.getOWLAnnotationProperty(IRI.create("http://dl-learner.org/pattern/confidence"));
- private long maxFragmentExtractionTime = TimeUnit.SECONDS.toMillis(10);
+ private long maxFragmentExtractionTime = TimeUnit.SECONDS.toMillis(60);
private OWLClassExpressionToSPARQLConverter converter = new OWLClassExpressionToSPARQLConverter();
private long maxExecutionTime = TimeUnit.SECONDS.toMillis(20);
private int queryLimit = 10000;
@@ -134,66 +133,6 @@
}
- public void run(SparqlEndpoint endpoint, OWLOntology ontology, File outputFile, int maxNrOfTestedClasses){
- ks = new SparqlEndpointKS(endpoint, cache);
- SPARQLReasoner reasoner = new SPARQLReasoner(ks, cache);
-
- //get the axiom patterns to evaluate
- List<OWLAxiom> patterns = getPatternsToEvaluate(ontology);
-
- //get all classes in KB
- Collection<NamedClass> classes = reasoner.getTypes(ns);
- List<NamedClass> classesList = new ArrayList<NamedClass>(classes);
- Collections.shuffle(classesList, new Random(123));
- classesList = classesList.subList(0, maxNrOfTestedClasses);
- classes = classesList;
-
- //for each pattern
- for (OWLAxiom pattern : patterns) {
- File file = new File(axiomRenderer.render(pattern).replace(" ", "_") + "-instantiations.ttl");
- if(!file.exists()){
- //if pattern is equivalent classes axiom, we need to get the subclass axiom where the named class is the subclass
- if(pattern.isOfType(AxiomType.EQUIVALENT_CLASSES)){
- Set<OWLSubClassOfAxiom> subClassOfAxioms = ((OWLEquivalentClassesAxiom)pattern).asOWLSubClassOfAxioms();
- for (OWLSubClassOfAxiom axiom : subClassOfAxioms) {
- if(!axiom.getSubClass().isAnonymous()){
- pattern = axiom;
- break;
- }
- }
- }
- if(pattern.isOfType(AxiomType.SUBCLASS_OF)){
- logger.info("Processing " + pattern + "...");
- Map<OWLAxiom, Score> axioms2Score = new LinkedHashMap<OWLAxiom, Score>();
- //for each class
- int i = 1;
- for (NamedClass cls : classes) {
- logger.info("Processing " + cls + "...");
-
- Map<OWLAxiom, Score> result = evaluateUsingFragmentExtraction(pattern, cls);
- axioms2Score.putAll(result);
-
- for (Entry<OWLAxiom, Score> entry : result.entrySet()) {
- OWLAxiom axiom = entry.getKey();
- Score score = entry.getValue();
- if(score.getAccuracy() >= threshold){
- logger.info(axiom + "(" + format.format(score.getAccuracy()) + ")");
- }
- }
-
- //wait some time to avoid flooding of endpoint
- try {
- Thread.sleep(waitingTime);
- } catch (InterruptedException e) {
- e.printStackTrace();
- }
-// if(i++ == 3) break;
- }
- save(pattern, axioms2Score, file);
- }
- }
- }
- }
public void runUsingFragmentExtraction(SparqlEndpoint endpoint, OWLOntology patternOntology, File outputFile, int maxNrOfTestedClasses){
ks = new SparqlEndpointKS(endpoint, cache);
@@ -210,6 +149,7 @@
Collections.shuffle(classesList, new Random(123));
classesList = classesList.subList(0, maxNrOfTestedClasses);
classes = classesList;
+// classes = Collections.singleton(new NamedClass("http://dbpedia.org/ontology/ChristianBishop"));
//get the maximum modal depth in the pattern axioms
int maxModalDepth = maxModalDepth(patterns);
@@ -238,26 +178,18 @@
OWLOntology ontology = null;
if(!file.exists()){
logger.info("Applying pattern " + pattern + "...");
- // if pattern is equivalent classes axiom, we need to get the
- // subclass axiom where the named class is the subclass
- Map<OWLAxiom, Score> axioms2Score = new LinkedHashMap<OWLAxiom, Score>();
+ Set<OWLAxiom> learnedAxioms = new HashSet<OWLAxiom>();
// for each class
for (NamedClass cls : classes) {
logger.info("...on class " + cls + "...");
Model fragment = class2Fragment.get(cls);
Map<OWLAxiom, Score> result = applyPattern(pattern,
df.getOWLClass(IRI.create(cls.getName())), fragment);
- axioms2Score.putAll(result);
-
- for (Entry<OWLAxiom, Score> entry : result.entrySet()) {
- OWLAxiom axiom = entry.getKey();
- Score score = entry.getValue();
- if (score.getAccuracy() >= threshold) {
- logger.info(axiom + "(" + format.format(score.getAccuracy()) + ")");
- }
- }
+ Set<OWLAxiom> annotatedAxioms = asAnnotatedAxioms(result);
+ filterOutTrivialAxioms(annotatedAxioms);
+ printAxioms(annotatedAxioms, threshold);
}
- ontology = save(pattern, axioms2Score, file);
+ ontology = save(pattern, learnedAxioms, file);
} else {
OWLOntologyManager man = OWLManager.createOWLOntologyManager();
try {
@@ -282,8 +214,32 @@
}
}
+ private Set<OWLAxiom> asAnnotatedAxioms(Map<OWLAxiom, Score> axioms2Score){
+ Set<OWLAxiom> annotatedAxioms = new HashSet<OWLAxiom>();
+ for (Entry<OWLAxiom, Score> entry : axioms2Score.entrySet()) {
+ OWLAxiom axiom = entry.getKey();
+ Score score = entry.getValue();
+ if(score.getAccuracy() >= threshold){
+ annotatedAxioms.add(axiom.getAnnotatedAxiom(Collections.singleton(df.getOWLAnnotation(confidenceProperty, df.getOWLLiteral(score.getAccuracy())))));
+
+ }
+ }
+ return annotatedAxioms;
+ }
+
+ private void printAxioms(Set<OWLAxiom> axioms, double threshold){
+ for (Iterator<OWLAxiom> iter = axioms.iterator(); iter.hasNext();) {
+ OWLAxiom axiom = iter.next();
+ double accuracy = getAccuracy(axiom);
+ if (accuracy >= threshold) {
+ logger.info(axiom + "(" + format.format(accuracy) + ")");
+ }
+ }
+ }
+
private List<OWLAxiom> createSample(OWLOntology ontology){
Set<OWLAxiom> axioms = ontology.getAxioms();
+ filterOutTrivialAxioms(axioms);
for (Iterator<OWLAxiom> iter = axioms.iterator(); iter.hasNext();) {
OWLAxiom axiom = iter.next();
double accuracy = getAccuracy(axiom);
@@ -300,49 +256,53 @@
}
if(remove){
iter.remove();
- } else {
- if(axiom.isOfType(AxiomType.EQUIVALENT_CLASSES)){
- Set<OWLSubClassOfAxiom> subClassOfAxioms = ((OWLEquivalentClassesAxiom)axiom).asOWLSubClassOfAxioms();
- for (OWLSubClassOfAxiom subClassOfAxiom : subClassOfAxioms) {
- if(!subClassOfAxiom.getSubClass().isAnonymous()){
- axiom = subClassOfAxiom;
+ }
+ }
+ }
+ List<OWLAxiom> axiomList = new ArrayList<OWLAxiom>(axioms);
+ Collections.shuffle(axiomList, new Random(123));
+ return axiomList.subList(0, Math.min(sampleSize, axiomList.size()));
+ }
+
+ private void filterOutTrivialAxioms(Set<OWLAxiom> axioms) {
+ for (Iterator<OWLAxiom> iter = axioms.iterator(); iter.hasNext();) {
+ OWLAxiom axiom = iter.next();
+ if (axiom.isOfType(AxiomType.EQUIVALENT_CLASSES)) {
+ Set<OWLSubClassOfAxiom> subClassOfAxioms = ((OWLEquivalentClassesAxiom) axiom).asOWLSubClassOfAxioms();
+ for (OWLSubClassOfAxiom subClassOfAxiom : subClassOfAxioms) {
+ if (!subClassOfAxiom.getSubClass().isAnonymous()) {
+ axiom = subClassOfAxiom;
+ break;
+ }
+ }
+ }
+ // check for some trivial axioms
+ if (axiom.isOfType(AxiomType.SUBCLASS_OF)) {
+ OWLClassExpression subClass = ((OWLSubClassOfAxiom) axiom).getSubClass();
+ OWLClassExpression superClass = ((OWLSubClassOfAxiom) axiom).getSuperClass();
+ if (superClass.isOWLThing()) {
+ iter.remove();
+ } else if (subClass.equals(superClass)) {
+ iter.remove();
+ } else if (superClass instanceof OWLObjectIntersectionOf) {
+ List<OWLClassExpression> operands = ((OWLObjectIntersectionOf) superClass).getOperandsAsList();
+
+ if (operands.size() == 1) {// how can this happen?
+ iter.remove();
+ } else if (operands.size() > ((OWLObjectIntersectionOf) superClass).getOperands().size()) {// duplicates
+ iter.remove();
+ } else {
+ for (OWLClassExpression op : operands) {
+ if (op.isOWLThing() || op.equals(subClass)) {
+ iter.remove();
break;
}
}
}
- //check for some trivial axioms
- if(axiom.isOfType(AxiomType.SUBCLASS_OF)){
- OWLClassExpression subClass = ((OWLSubClassOfAxiom)axiom).getSubClass();
- OWLClassExpression superClass = ((OWLSubClassOfAxiom)axiom).getSuperClass();
- if(superClass.isOWLThing()){
- iter.remove();
- } else if(subClass.equals(superClass)){
- iter.remove();
- } else if(superClass instanceof OWLObjectIntersectionOf){
- List<OWLClassExpression> operands = ((OWLObjectIntersectionOf) superClass).getOperandsAsList();
-
-
- if(operands.size() == 1){//how can this happen?
- iter.remove();
- } else if(operands.size() > ((OWLObjectIntersectionOf) superClass).getOperands().size()){//duplicates
- iter.remove();
- } else {
- for (OWLClassExpression op : operands) {
- if(op.isOWLThing() || op.equals(subClass)){
- iter.remove();
- break;
- }
- }
- }
- }
- }
}
-
}
+
}
- List<OWLAxiom> axiomList = new ArrayList<OWLAxiom>(axioms);
- Collections.shuffle(axiomList, new Random(123));
- return axiomList.subList(0, Math.min(sampleSize, axiomList.size()));
}
private double getAccuracy(OWLAxiom axiom){
@@ -432,12 +392,13 @@
}
}
logger.info("...got " + fragment.size() + " triples.");
- class2Fragment.put(cls, fragment);
try {
fragment.write(new FileOutputStream(file), "TURTLE");
} catch (FileNotFoundException e) {
e.printStackTrace();
}
+ filterModel(fragment);
+ class2Fragment.put(cls, fragment);
}
return class2Fragment;
}
@@ -453,6 +414,8 @@
}
if(st.getPredicate().hasURI("http://xmlns.com/foaf/0.1/depiction") || st.getPredicate().hasURI("http://dbpedia.org/ontology/thumbnail")){
statements2Remove.add(st);
+ } else if(!st.getPredicate().equals(RDF.type) && !st.getPredicate().getURI().startsWith("http://dbpedia.org/ontology/")){
+ statements2Remove.add(st);
}
}
model.remove(statements2Remove);
@@ -672,6 +635,9 @@
} else if(pattern.isOfType(AxiomType.SUBCLASS_OF)){
patternSubClass = ((OWLSubClassOfAxiom) pattern).getSubClass();
patternSuperClass = ((OWLSubClassOfAxiom) pattern).getSuperClass();
+ } else if(pattern.isOfType(AxiomType.SUBCLASS_OF)){
+ patternSubClass = ((OWLSubClassOfAxiom) pattern).getSubClass();
+ patternSuperClass = ((OWLSubClassOfAxiom) pattern).getSuperClass();
} else {
logger.warn("Pattern " + pattern + " not supported yet.");
return axioms2Score;
@@ -722,6 +688,7 @@
int total = resources.size();
for (OWLAxiom axiom : instantiations.elementSet()) {
int frequency = instantiations.count(axiom);
+// System.out.println(axiom + ":" + frequency);
Score score = computeScore(total, Math.min(total, frequency));
axioms2Score.put(axiom, score);
}
@@ -825,19 +792,10 @@
return template.asQuery();
}
- private OWLOntology save(OWLAxiom pattern, Map<OWLAxiom, Score> axioms2Score, File file){
+ private OWLOntology save(OWLAxiom pattern, Set<OWLAxiom> learnedAxioms, File file){
try {
- Set<OWLAxiom> annotatedAxioms = new HashSet<OWLAxiom>();
- for (Entry<OWLAxiom, Score> entry : axioms2Score.entrySet()) {
- OWLAxiom axiom = entry.getKey();
- Score score = entry.getValue();
- if(score.getAccuracy() >= threshold){
- annotatedAxioms.add(axiom.getAnnotatedAxiom(Collections.singleton(df.getOWLAnnotation(confidenceProperty, df.getOWLLiteral(score.getAccuracy())))));
-
- }
- }
OWLOntologyManager man = OWLManager.createOWLOntologyManager();
- OWLOntology ontology = man.createOntology(annotatedAxioms);
+ OWLOntology ontology = man.createOntology(learnedAxioms);
man.saveOntology(ontology, new TurtleOntologyFormat(), new FileOutputStream(file));
return ontology;
} catch (OWLOntologyCreationException e) {
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|
|
From: <lor...@us...> - 2013-05-09 15:57:21
|
Revision: 3971
http://sourceforge.net/p/dl-learner/code/3971
Author: lorenz_b
Date: 2013-05-09 15:57:17 +0000 (Thu, 09 May 2013)
Log Message:
-----------
Refactored pattern eval.
Modified Paths:
--------------
trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java 2013-05-09 15:22:50 UTC (rev 3970)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java 2013-05-09 15:57:17 UTC (rev 3971)
@@ -290,48 +290,54 @@
if(accuracy < sampleThreshold){
iter.remove();
} else {
- if(axiom.isOfType(AxiomType.EQUIVALENT_CLASSES)){
- Set<OWLSubClassOfAxiom> subClassOfAxioms = ((OWLEquivalentClassesAxiom)axiom).asOWLSubClassOfAxioms();
- for (OWLSubClassOfAxiom subClassOfAxiom : subClassOfAxioms) {
- if(!subClassOfAxiom.getSubClass().isAnonymous()){
- axiom = subClassOfAxiom;
- break;
+ String axiomString = axiomRenderer.render(axiom);
+ boolean remove = false;
+ for (String s : entites2Ignore) {
+ if(axiomString.contains(s)){
+ remove = true;
+ break;
+ }
+ }
+ if(remove){
+ iter.remove();
+ } else {
+ if(axiom.isOfType(AxiomType.EQUIVALENT_CLASSES)){
+ Set<OWLSubClassOfAxiom> subClassOfAxioms = ((OWLEquivalentClassesAxiom)axiom).asOWLSubClassOfAxioms();
+ for (OWLSubClassOfAxiom subClassOfAxiom : subClassOfAxioms) {
+ if(!subClassOfAxiom.getSubClass().isAnonymous()){
+ axiom = subClassOfAxiom;
+ break;
+ }
}
}
- }
- //check for some trivial axioms
- if(axiom.isOfType(AxiomType.SUBCLASS_OF)){
- OWLClassExpression subClass = ((OWLSubClassOfAxiom)axiom).getSubClass();
- OWLClassExpression superClass = ((OWLSubClassOfAxiom)axiom).getSuperClass();
- if(superClass.isOWLThing()){
- iter.remove();
- } else if(subClass.equals(superClass)){
- iter.remove();
- } else if(superClass instanceof OWLObjectIntersectionOf){
- List<OWLClassExpression> operands = ((OWLObjectIntersectionOf) superClass).getOperandsAsList();
-
-
- if(operands.size() == 1){//how can this happen?
+ //check for some trivial axioms
+ if(axiom.isOfType(AxiomType.SUBCLASS_OF)){
+ OWLClassExpression subClass = ((OWLSubClassOfAxiom)axiom).getSubClass();
+ OWLClassExpression superClass = ((OWLSubClassOfAxiom)axiom).getSuperClass();
+ if(superClass.isOWLThing()){
iter.remove();
- } else if(operands.size() > ((OWLObjectIntersectionOf) superClass).getOperands().size()){//duplicates
+ } else if(subClass.equals(superClass)){
iter.remove();
- } else {
- for (OWLClassExpression op : operands) {
- if(op.isOWLThing() || op.equals(subClass)){
- iter.remove();
- break;
+ } else if(superClass instanceof OWLObjectIntersectionOf){
+ List<OWLClassExpression> operands = ((OWLObjectIntersectionOf) superClass).getOperandsAsList();
+
+
+ if(operands.size() == 1){//how can this happen?
+ iter.remove();
+ } else if(operands.size() > ((OWLObjectIntersectionOf) superClass).getOperands().size()){//duplicates
+ iter.remove();
+ } else {
+ for (OWLClassExpression op : operands) {
+ if(op.isOWLThing() || op.equals(subClass)){
+ iter.remove();
+ break;
+ }
}
}
- }
- } else {
- String classString = superClass.toString();
- for (String s : entites2Ignore) {
- if(classString.contains(s)){
- iter.remove();
- }
- }
+ }
}
}
+
}
}
List<OWLAxiom> axiomList = new ArrayList<OWLAxiom>(axioms);
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|
|
From: <lor...@us...> - 2013-05-09 15:22:55
|
Revision: 3970
http://sourceforge.net/p/dl-learner/code/3970
Author: lorenz_b
Date: 2013-05-09 15:22:50 +0000 (Thu, 09 May 2013)
Log Message:
-----------
Refactored pattern eval.
Modified Paths:
--------------
trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java 2013-05-09 14:04:53 UTC (rev 3969)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java 2013-05-09 15:22:50 UTC (rev 3970)
@@ -317,7 +317,7 @@
iter.remove();
} else {
for (OWLClassExpression op : operands) {
- if(op.isOWLThing()){
+ if(op.isOWLThing() || op.equals(subClass)){
iter.remove();
break;
}
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|
|
From: <lor...@us...> - 2013-05-09 14:04:57
|
Revision: 3969
http://sourceforge.net/p/dl-learner/code/3969
Author: lorenz_b
Date: 2013-05-09 14:04:53 +0000 (Thu, 09 May 2013)
Log Message:
-----------
Refactored pattern eval.
Modified Paths:
--------------
trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java 2013-05-09 13:41:45 UTC (rev 3968)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java 2013-05-09 14:04:53 UTC (rev 3969)
@@ -81,6 +81,7 @@
import com.google.common.base.Joiner;
import com.google.common.collect.HashMultiset;
import com.google.common.collect.Multiset;
+import com.google.common.collect.Sets;
import com.google.common.hash.HashCode;
import com.google.common.hash.HashFunction;
import com.google.common.hash.Hashing;
@@ -127,6 +128,7 @@
private boolean sampling = true;
private double sampleThreshold = 0.8;
private int sampleSize = 100;
+ private Set<String> entites2Ignore = Sets.newHashSet("subject", "Concept", "wikiPage");
public OWLAxiomPatternUsageEvaluation() {
}
@@ -321,8 +323,13 @@
}
}
}
- } else if(superClass.toString().contains("Concept") || superClass.toString().contains("subject")){
- iter.remove();
+ } else {
+ String classString = superClass.toString();
+ for (String s : entites2Ignore) {
+ if(classString.contains(s)){
+ iter.remove();
+ }
+ }
}
}
}
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|
|
From: <lor...@us...> - 2013-05-09 13:41:49
|
Revision: 3968
http://sourceforge.net/p/dl-learner/code/3968
Author: lorenz_b
Date: 2013-05-09 13:41:45 +0000 (Thu, 09 May 2013)
Log Message:
-----------
Refactored pattern eval.
Modified Paths:
--------------
trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java 2013-05-09 13:27:03 UTC (rev 3967)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java 2013-05-09 13:41:45 UTC (rev 3968)
@@ -288,6 +288,15 @@
if(accuracy < sampleThreshold){
iter.remove();
} else {
+ if(axiom.isOfType(AxiomType.EQUIVALENT_CLASSES)){
+ Set<OWLSubClassOfAxiom> subClassOfAxioms = ((OWLEquivalentClassesAxiom)axiom).asOWLSubClassOfAxioms();
+ for (OWLSubClassOfAxiom subClassOfAxiom : subClassOfAxioms) {
+ if(!subClassOfAxiom.getSubClass().isAnonymous()){
+ axiom = subClassOfAxiom;
+ break;
+ }
+ }
+ }
//check for some trivial axioms
if(axiom.isOfType(AxiomType.SUBCLASS_OF)){
OWLClassExpression subClass = ((OWLSubClassOfAxiom)axiom).getSubClass();
@@ -297,11 +306,19 @@
} else if(subClass.equals(superClass)){
iter.remove();
} else if(superClass instanceof OWLObjectIntersectionOf){
- Set<OWLClassExpression> operands = ((OWLObjectIntersectionOf) superClass).getOperands();
- for (OWLClassExpression op : operands) {
- if(op.isOWLThing()){
- iter.remove();
- break;
+ List<OWLClassExpression> operands = ((OWLObjectIntersectionOf) superClass).getOperandsAsList();
+
+
+ if(operands.size() == 1){//how can this happen?
+ iter.remove();
+ } else if(operands.size() > ((OWLObjectIntersectionOf) superClass).getOperands().size()){//duplicates
+ iter.remove();
+ } else {
+ for (OWLClassExpression op : operands) {
+ if(op.isOWLThing()){
+ iter.remove();
+ break;
+ }
}
}
} else if(superClass.toString().contains("Concept") || superClass.toString().contains("subject")){
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|
|
From: <lor...@us...> - 2013-05-09 13:27:06
|
Revision: 3967
http://sourceforge.net/p/dl-learner/code/3967
Author: lorenz_b
Date: 2013-05-09 13:27:03 +0000 (Thu, 09 May 2013)
Log Message:
-----------
Refactored pattern eval.
Modified Paths:
--------------
trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java 2013-05-09 13:21:27 UTC (rev 3966)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java 2013-05-09 13:27:03 UTC (rev 3967)
@@ -212,8 +212,22 @@
//get the maximum modal depth in the pattern axioms
int maxModalDepth = maxModalDepth(patterns);
+ //check if we need the fragments
+ boolean fragmentsNeeded = false;
+ for (OWLAxiom pattern : patterns) {
+ //run if not already exists a result on disk
+ File file = new File(axiomRenderer.render(pattern).replace(" ", "_") + "-instantiations.ttl");
+ if(!file.exists()){
+ fragmentsNeeded = true;
+ break;
+ }
+ }
+
//extract fragment for each class only once
- Map<NamedClass, Model> class2Fragment = extractFragments(classes, maxModalDepth);
+ Map<NamedClass, Model> class2Fragment = null;
+ if(fragmentsNeeded){
+ class2Fragment = extractFragments(classes, maxModalDepth);
+ }
//for each pattern
for (OWLAxiom pattern : patterns) {
@@ -273,25 +287,26 @@
double accuracy = getAccuracy(axiom);
if(accuracy < sampleThreshold){
iter.remove();
- }
- //check for some trivial axioms
- if(axiom.isOfType(AxiomType.SUBCLASS_OF)){
- OWLClassExpression subClass = ((OWLSubClassOfAxiom)axiom).getSubClass();
- OWLClassExpression superClass = ((OWLSubClassOfAxiom)axiom).getSuperClass();
- if(superClass.isOWLThing()){
- iter.remove();
- } else if(subClass.equals(superClass)){
- iter.remove();
- } else if(superClass instanceof OWLObjectIntersectionOf){
- Set<OWLClassExpression> operands = ((OWLObjectIntersectionOf) superClass).getOperands();
- for (OWLClassExpression op : operands) {
- if(op.isOWLThing()){
- iter.remove();
- break;
+ } else {
+ //check for some trivial axioms
+ if(axiom.isOfType(AxiomType.SUBCLASS_OF)){
+ OWLClassExpression subClass = ((OWLSubClassOfAxiom)axiom).getSubClass();
+ OWLClassExpression superClass = ((OWLSubClassOfAxiom)axiom).getSuperClass();
+ if(superClass.isOWLThing()){
+ iter.remove();
+ } else if(subClass.equals(superClass)){
+ iter.remove();
+ } else if(superClass instanceof OWLObjectIntersectionOf){
+ Set<OWLClassExpression> operands = ((OWLObjectIntersectionOf) superClass).getOperands();
+ for (OWLClassExpression op : operands) {
+ if(op.isOWLThing()){
+ iter.remove();
+ break;
+ }
}
+ } else if(superClass.toString().contains("Concept") || superClass.toString().contains("subject")){
+ iter.remove();
}
- } else if(superClass.toString().contains("Concept") || superClass.toString().contains("subject")){
- iter.remove();
}
}
}
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|
|
From: <lor...@us...> - 2013-05-09 13:21:31
|
Revision: 3966
http://sourceforge.net/p/dl-learner/code/3966
Author: lorenz_b
Date: 2013-05-09 13:21:27 +0000 (Thu, 09 May 2013)
Log Message:
-----------
Refactored pattern eval.
Modified Paths:
--------------
trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java 2013-05-09 03:51:49 UTC (rev 3965)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java 2013-05-09 13:21:27 UTC (rev 3966)
@@ -6,6 +6,7 @@
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
+import java.io.IOException;
import java.io.UnsupportedEncodingException;
import java.net.SocketTimeoutException;
import java.net.URI;
@@ -17,6 +18,7 @@
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
+import java.util.Iterator;
import java.util.LinkedHashMap;
import java.util.LinkedList;
import java.util.List;
@@ -47,11 +49,13 @@
import org.dllearner.reasoning.SPARQLReasoner;
import org.dllearner.utilities.owl.DLLearnerDescriptionConvertVisitor;
import org.dllearner.utilities.owl.OWLClassExpressionToSPARQLConverter;
+import org.semanticweb.elk.reasoner.saturation.classes.SuperClassExpression;
import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.io.OWLObjectRenderer;
import org.semanticweb.owlapi.io.ToStringRenderer;
import org.semanticweb.owlapi.model.AxiomType;
import org.semanticweb.owlapi.model.IRI;
+import org.semanticweb.owlapi.model.OWLAnnotation;
import org.semanticweb.owlapi.model.OWLAnnotationProperty;
import org.semanticweb.owlapi.model.OWLAxiom;
import org.semanticweb.owlapi.model.OWLClass;
@@ -59,7 +63,9 @@
import org.semanticweb.owlapi.model.OWLDataFactory;
import org.semanticweb.owlapi.model.OWLEntity;
import org.semanticweb.owlapi.model.OWLEquivalentClassesAxiom;
+import org.semanticweb.owlapi.model.OWLLiteral;
import org.semanticweb.owlapi.model.OWLObjectComplementOf;
+import org.semanticweb.owlapi.model.OWLObjectIntersectionOf;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLOntologyCreationException;
import org.semanticweb.owlapi.model.OWLOntologyManager;
@@ -71,11 +77,14 @@
import uk.ac.manchester.cs.owl.owlapi.mansyntaxrenderer.ManchesterOWLSyntaxOWLObjectRendererImpl;
import uk.ac.manchester.cs.owlapi.dlsyntax.DLSyntaxObjectRenderer;
+import com.google.common.base.Charsets;
+import com.google.common.base.Joiner;
import com.google.common.collect.HashMultiset;
import com.google.common.collect.Multiset;
import com.google.common.hash.HashCode;
import com.google.common.hash.HashFunction;
import com.google.common.hash.Hashing;
+import com.google.common.io.Files;
import com.hp.hpl.jena.query.ParameterizedSparqlString;
import com.hp.hpl.jena.query.Query;
import com.hp.hpl.jena.query.QueryExecution;
@@ -115,6 +124,9 @@
private OWLClassExpressionToSPARQLConverter converter = new OWLClassExpressionToSPARQLConverter();
private long maxExecutionTime = TimeUnit.SECONDS.toMillis(20);
private int queryLimit = 10000;
+ private boolean sampling = true;
+ private double sampleThreshold = 0.8;
+ private int sampleSize = 100;
public OWLAxiomPatternUsageEvaluation() {
}
@@ -181,12 +193,12 @@
}
}
- public void runUsingFragmentExtraction(SparqlEndpoint endpoint, OWLOntology ontology, File outputFile, int maxNrOfTestedClasses){
+ public void runUsingFragmentExtraction(SparqlEndpoint endpoint, OWLOntology patternOntology, File outputFile, int maxNrOfTestedClasses){
ks = new SparqlEndpointKS(endpoint, cache);
SPARQLReasoner reasoner = new SPARQLReasoner(ks, cache);
//get the axiom patterns to evaluate
- List<OWLAxiom> patterns = getPatternsToEvaluate(ontology);
+ List<OWLAxiom> patterns = getPatternsToEvaluate(patternOntology);
//get all classes in KB
Collection<NamedClass> classes = reasoner.getTypes(ns);
@@ -207,6 +219,7 @@
for (OWLAxiom pattern : patterns) {
//run if not already exists a result on disk
File file = new File(axiomRenderer.render(pattern).replace(" ", "_") + "-instantiations.ttl");
+ OWLOntology ontology = null;
if(!file.exists()){
logger.info("Applying pattern " + pattern + "...");
// if pattern is equivalent classes axiom, we need to get the
@@ -228,11 +241,75 @@
}
}
}
- save(pattern, axioms2Score, file);
+ ontology = save(pattern, axioms2Score, file);
+ } else {
+ OWLOntologyManager man = OWLManager.createOWLOntologyManager();
+ try {
+ ontology = man.loadOntologyFromOntologyDocument(file);
+ } catch (OWLOntologyCreationException e) {
+ e.printStackTrace();
+ }
}
+ if(sampling){
+ List<OWLAxiom> sample = createSample(ontology);
+ List<String> lines = new ArrayList<String>();
+ for (OWLAxiom axiom : sample) {
+ double accuracy = getAccuracy(axiom);
+ lines.add(axiomRenderer.render(axiom) + "," + format.format(accuracy));
+ }
+ try {
+ Files.write(Joiner.on("\n").join(lines), new File(axiomRenderer.render(pattern).replace(" ", "_") + "-instantiations-sample.csv"), Charsets.UTF_8);
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+ }
}
}
+ private List<OWLAxiom> createSample(OWLOntology ontology){
+ Set<OWLAxiom> axioms = ontology.getAxioms();
+ for (Iterator<OWLAxiom> iter = axioms.iterator(); iter.hasNext();) {
+ OWLAxiom axiom = iter.next();
+ double accuracy = getAccuracy(axiom);
+ if(accuracy < sampleThreshold){
+ iter.remove();
+ }
+ //check for some trivial axioms
+ if(axiom.isOfType(AxiomType.SUBCLASS_OF)){
+ OWLClassExpression subClass = ((OWLSubClassOfAxiom)axiom).getSubClass();
+ OWLClassExpression superClass = ((OWLSubClassOfAxiom)axiom).getSuperClass();
+ if(superClass.isOWLThing()){
+ iter.remove();
+ } else if(subClass.equals(superClass)){
+ iter.remove();
+ } else if(superClass instanceof OWLObjectIntersectionOf){
+ Set<OWLClassExpression> operands = ((OWLObjectIntersectionOf) superClass).getOperands();
+ for (OWLClassExpression op : operands) {
+ if(op.isOWLThing()){
+ iter.remove();
+ break;
+ }
+ }
+ } else if(superClass.toString().contains("Concept") || superClass.toString().contains("subject")){
+ iter.remove();
+ }
+ }
+ }
+ List<OWLAxiom> axiomList = new ArrayList<OWLAxiom>(axioms);
+ Collections.shuffle(axiomList, new Random(123));
+ return axiomList.subList(0, Math.min(sampleSize, axiomList.size()));
+ }
+
+ private double getAccuracy(OWLAxiom axiom){
+ Set<OWLAnnotation> annotations = axiom.getAnnotations(confidenceProperty);
+ if(!annotations.isEmpty()){
+ OWLAnnotation annotation = annotations.iterator().next();
+ double accuracy = ((OWLLiteral)annotation.getValue()).parseDouble();
+ return accuracy;
+ }
+ return -1;
+ }
+
private int maxModalDepth(List<OWLAxiom> patterns) {
int maxModalDepth = 1;
for (OWLAxiom pattern : patterns) {
@@ -329,6 +406,9 @@
if(st.getPredicate().equals(RDF.type) && !st.getObject().asResource().getURI().startsWith("http://dbpedia.org/ontology/")){
statements2Remove.add(st);
}
+ if(st.getPredicate().hasURI("http://xmlns.com/foaf/0.1/depiction") || st.getPredicate().hasURI("http://dbpedia.org/ontology/thumbnail")){
+ statements2Remove.add(st);
+ }
}
model.remove(statements2Remove);
}
@@ -700,7 +780,7 @@
return template.asQuery();
}
- private void save(OWLAxiom pattern, Map<OWLAxiom, Score> axioms2Score, File file){
+ private OWLOntology save(OWLAxiom pattern, Map<OWLAxiom, Score> axioms2Score, File file){
try {
Set<OWLAxiom> annotatedAxioms = new HashSet<OWLAxiom>();
for (Entry<OWLAxiom, Score> entry : axioms2Score.entrySet()) {
@@ -714,6 +794,7 @@
OWLOntologyManager man = OWLManager.createOWLOntologyManager();
OWLOntology ontology = man.createOntology(annotatedAxioms);
man.saveOntology(ontology, new TurtleOntologyFormat(), new FileOutputStream(file));
+ return ontology;
} catch (OWLOntologyCreationException e) {
e.printStackTrace();
} catch (OWLOntologyStorageException e) {
@@ -721,6 +802,7 @@
} catch (FileNotFoundException e) {
e.printStackTrace();
}
+ return null;
}
private void save(Set<EvaluatedAxiom> evaluatedAxioms){
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|
|
From: <lor...@us...> - 2013-05-09 03:51:52
|
Revision: 3965
http://sourceforge.net/p/dl-learner/code/3965
Author: lorenz_b
Date: 2013-05-09 03:51:49 +0000 (Thu, 09 May 2013)
Log Message:
-----------
Refactored pattern eval.
Modified Paths:
--------------
trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java 2013-05-08 21:16:05 UTC (rev 3964)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java 2013-05-09 03:51:49 UTC (rev 3965)
@@ -85,7 +85,6 @@
import com.hp.hpl.jena.query.Syntax;
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.Resource;
import com.hp.hpl.jena.rdf.model.Statement;
import com.hp.hpl.jena.sparql.engine.http.QueryEngineHTTP;
@@ -137,44 +136,47 @@
//for each pattern
for (OWLAxiom pattern : patterns) {
- //if pattern is equivalent classes axiom, we need to get the subclass axiom where the named class is the subclass
- if(pattern.isOfType(AxiomType.EQUIVALENT_CLASSES)){
- Set<OWLSubClassOfAxiom> subClassOfAxioms = ((OWLEquivalentClassesAxiom)pattern).asOWLSubClassOfAxioms();
- for (OWLSubClassOfAxiom axiom : subClassOfAxioms) {
- if(!axiom.getSubClass().isAnonymous()){
- pattern = axiom;
- break;
+ File file = new File(axiomRenderer.render(pattern).replace(" ", "_") + "-instantiations.ttl");
+ if(!file.exists()){
+ //if pattern is equivalent classes axiom, we need to get the subclass axiom where the named class is the subclass
+ if(pattern.isOfType(AxiomType.EQUIVALENT_CLASSES)){
+ Set<OWLSubClassOfAxiom> subClassOfAxioms = ((OWLEquivalentClassesAxiom)pattern).asOWLSubClassOfAxioms();
+ for (OWLSubClassOfAxiom axiom : subClassOfAxioms) {
+ if(!axiom.getSubClass().isAnonymous()){
+ pattern = axiom;
+ break;
+ }
}
}
- }
- if(pattern.isOfType(AxiomType.SUBCLASS_OF)){
- logger.info("Processing " + pattern + "...");
- Map<OWLAxiom, Score> axioms2Score = new LinkedHashMap<OWLAxiom, Score>();
- //for each class
- int i = 1;
- for (NamedClass cls : classes) {
- logger.info("Processing " + cls + "...");
-
- Map<OWLAxiom, Score> result = evaluateUsingFragmentExtraction(pattern, cls);
- axioms2Score.putAll(result);
-
- for (Entry<OWLAxiom, Score> entry : result.entrySet()) {
- OWLAxiom axiom = entry.getKey();
- Score score = entry.getValue();
- if(score.getAccuracy() >= threshold){
- logger.info(axiom + "(" + format.format(score.getAccuracy()) + ")");
+ if(pattern.isOfType(AxiomType.SUBCLASS_OF)){
+ logger.info("Processing " + pattern + "...");
+ Map<OWLAxiom, Score> axioms2Score = new LinkedHashMap<OWLAxiom, Score>();
+ //for each class
+ int i = 1;
+ for (NamedClass cls : classes) {
+ logger.info("Processing " + cls + "...");
+
+ Map<OWLAxiom, Score> result = evaluateUsingFragmentExtraction(pattern, cls);
+ axioms2Score.putAll(result);
+
+ for (Entry<OWLAxiom, Score> entry : result.entrySet()) {
+ OWLAxiom axiom = entry.getKey();
+ Score score = entry.getValue();
+ if(score.getAccuracy() >= threshold){
+ logger.info(axiom + "(" + format.format(score.getAccuracy()) + ")");
+ }
}
+
+ //wait some time to avoid flooding of endpoint
+ try {
+ Thread.sleep(waitingTime);
+ } catch (InterruptedException e) {
+ e.printStackTrace();
+ }
+// if(i++ == 3) break;
}
-
- //wait some time to avoid flooding of endpoint
- try {
- Thread.sleep(waitingTime);
- } catch (InterruptedException e) {
- e.printStackTrace();
- }
-// if(i++ == 3) break;
+ save(pattern, axioms2Score, file);
}
- save(pattern, axioms2Score);
}
}
}
@@ -203,28 +205,31 @@
//for each pattern
for (OWLAxiom pattern : patterns) {
- logger.info("Applying pattern " + pattern + "...");
- // if pattern is equivalent classes axiom, we need to get the
- // subclass axiom where the named class is the subclass
- Map<OWLAxiom, Score> axioms2Score = new LinkedHashMap<OWLAxiom, Score>();
- // for each class
- for (NamedClass cls : classes) {
- logger.info("...on class " + cls + "...");
- Model fragment = class2Fragment.get(cls);
- Map<OWLAxiom, Score> result = applyPattern(pattern,
- df.getOWLClass(IRI.create(cls.getName())), fragment);
- axioms2Score.putAll(result);
+ //run if not already exists a result on disk
+ File file = new File(axiomRenderer.render(pattern).replace(" ", "_") + "-instantiations.ttl");
+ if(!file.exists()){
+ logger.info("Applying pattern " + pattern + "...");
+ // if pattern is equivalent classes axiom, we need to get the
+ // subclass axiom where the named class is the subclass
+ Map<OWLAxiom, Score> axioms2Score = new LinkedHashMap<OWLAxiom, Score>();
+ // for each class
+ for (NamedClass cls : classes) {
+ logger.info("...on class " + cls + "...");
+ Model fragment = class2Fragment.get(cls);
+ Map<OWLAxiom, Score> result = applyPattern(pattern,
+ df.getOWLClass(IRI.create(cls.getName())), fragment);
+ axioms2Score.putAll(result);
- for (Entry<OWLAxiom, Score> entry : result.entrySet()) {
- OWLAxiom axiom = entry.getKey();
- Score score = entry.getValue();
- if (score.getAccuracy() >= threshold) {
- logger.info(axiom + "(" + format.format(score.getAccuracy()) + ")");
+ for (Entry<OWLAxiom, Score> entry : result.entrySet()) {
+ OWLAxiom axiom = entry.getKey();
+ Score score = entry.getValue();
+ if (score.getAccuracy() >= threshold) {
+ logger.info(axiom + "(" + format.format(score.getAccuracy()) + ")");
+ }
}
}
+ save(pattern, axioms2Score, file);
}
- save(pattern, axioms2Score);
-
}
}
@@ -695,7 +700,7 @@
return template.asQuery();
}
- private void save(OWLAxiom pattern, Map<OWLAxiom, Score> axioms2Score){
+ private void save(OWLAxiom pattern, Map<OWLAxiom, Score> axioms2Score, File file){
try {
Set<OWLAxiom> annotatedAxioms = new HashSet<OWLAxiom>();
for (Entry<OWLAxiom, Score> entry : axioms2Score.entrySet()) {
@@ -708,8 +713,7 @@
}
OWLOntologyManager man = OWLManager.createOWLOntologyManager();
OWLOntology ontology = man.createOntology(annotatedAxioms);
- String filename = axiomRenderer.render(pattern).replace(" ", "_");
- man.saveOntology(ontology, new TurtleOntologyFormat(), new FileOutputStream(filename + "-instantiations.ttl"));
+ man.saveOntology(ontology, new TurtleOntologyFormat(), new FileOutputStream(file));
} catch (OWLOntologyCreationException e) {
e.printStackTrace();
} catch (OWLOntologyStorageException e) {
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|
|
From: <lor...@us...> - 2013-05-08 21:16:10
|
Revision: 3964
http://sourceforge.net/p/dl-learner/code/3964
Author: lorenz_b
Date: 2013-05-08 21:16:05 +0000 (Wed, 08 May 2013)
Log Message:
-----------
Refactored pattern eval.
Modified Paths:
--------------
trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java 2013-05-08 21:03:43 UTC (rev 3963)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java 2013-05-08 21:16:05 UTC (rev 3964)
@@ -204,44 +204,27 @@
//for each pattern
for (OWLAxiom pattern : patterns) {
logger.info("Applying pattern " + pattern + "...");
- //if pattern is equivalent classes axiom, we need to get the subclass axiom where the named class is the subclass
- if(pattern.isOfType(AxiomType.EQUIVALENT_CLASSES)){
- Set<OWLSubClassOfAxiom> subClassOfAxioms = ((OWLEquivalentClassesAxiom)pattern).asOWLSubClassOfAxioms();
- for (OWLSubClassOfAxiom axiom : subClassOfAxioms) {
- if(!axiom.getSubClass().isAnonymous()){
- pattern = axiom;
- break;
+ // if pattern is equivalent classes axiom, we need to get the
+ // subclass axiom where the named class is the subclass
+ Map<OWLAxiom, Score> axioms2Score = new LinkedHashMap<OWLAxiom, Score>();
+ // for each class
+ for (NamedClass cls : classes) {
+ logger.info("...on class " + cls + "...");
+ Model fragment = class2Fragment.get(cls);
+ Map<OWLAxiom, Score> result = applyPattern(pattern,
+ df.getOWLClass(IRI.create(cls.getName())), fragment);
+ axioms2Score.putAll(result);
+
+ for (Entry<OWLAxiom, Score> entry : result.entrySet()) {
+ OWLAxiom axiom = entry.getKey();
+ Score score = entry.getValue();
+ if (score.getAccuracy() >= threshold) {
+ logger.info(axiom + "(" + format.format(score.getAccuracy()) + ")");
}
}
}
- if(pattern.isOfType(AxiomType.SUBCLASS_OF)){
- Map<OWLAxiom, Score> axioms2Score = new LinkedHashMap<OWLAxiom, Score>();
- //for each class
- int i = 1;
- for (NamedClass cls : classes) {
- logger.info("...on class " + cls + "...");
- Model fragment = class2Fragment.get(cls);
- Map<OWLAxiom, Score> result = applyPattern((OWLSubClassOfAxiom) pattern, df.getOWLClass(IRI.create(cls.getName())), fragment);
- axioms2Score.putAll(result);
-
- for (Entry<OWLAxiom, Score> entry : result.entrySet()) {
- OWLAxiom axiom = entry.getKey();
- Score score = entry.getValue();
- if(score.getAccuracy() >= threshold){
- logger.info(axiom + "(" + format.format(score.getAccuracy()) + ")");
- }
- }
-
- //wait some time to avoid flooding of endpoint
- try {
- Thread.sleep(waitingTime);
- } catch (InterruptedException e) {
- e.printStackTrace();
- }
-// if(i++ == 3) break;
- }
- save(pattern, axioms2Score);
- }
+ save(pattern, axioms2Score);
+
}
}
@@ -541,19 +524,32 @@
return axioms2Score;
}
- private Map<OWLAxiom, Score> applyPattern(OWLSubClassOfAxiom pattern, OWLClass cls, Model fragment) {
+ private Map<OWLAxiom, Score> applyPattern(OWLAxiom pattern, OWLClass cls, Model fragment) {
Map<OWLAxiom, Score> axioms2Score = new HashMap<OWLAxiom, Score>();
- OWLClassExpression patternSubClass = pattern.getSubClass();
- OWLClassExpression patternSuperClass = pattern.getSuperClass();
+ OWLClassExpression patternSubClass = null;
+ OWLClassExpression patternSuperClass = null;
- patternSubClass = cls;
+ if(pattern.isOfType(AxiomType.EQUIVALENT_CLASSES)){
+ Set<OWLSubClassOfAxiom> subClassOfAxioms = ((OWLEquivalentClassesAxiom)pattern).asOWLSubClassOfAxioms();
+ for (OWLSubClassOfAxiom axiom : subClassOfAxioms) {
+ if(!axiom.getSubClass().isAnonymous()){
+ patternSubClass = axiom.getSubClass();
+ patternSuperClass = axiom.getSuperClass();
+ break;
+ }
+ }
+ } else if(pattern.isOfType(AxiomType.SUBCLASS_OF)){
+ patternSubClass = ((OWLSubClassOfAxiom) pattern).getSubClass();
+ patternSuperClass = ((OWLSubClassOfAxiom) pattern).getSuperClass();
+ } else {
+ logger.warn("Pattern " + pattern + " not supported yet.");
+ return axioms2Score;
+ }
-
-
Set<OWLEntity> signature = patternSuperClass.getSignature();
- signature.remove(patternSubClass);
- Query query = converter.asQuery("?x", df.getOWLObjectIntersectionOf(patternSubClass, patternSuperClass), signature);
+ signature.remove(patternSubClass.asOWLClass());
+ Query query = converter.asQuery("?x", df.getOWLObjectIntersectionOf(cls, patternSuperClass), signature);
logger.info("Running query\n" + query);
Map<OWLEntity, String> variablesMapping = converter.getVariablesMapping();
com.hp.hpl.jena.query.ResultSet rs = QueryExecutionFactory.create(query, fragment).execSelect();
@@ -565,7 +561,7 @@
resources.add(qs.getResource("x").getURI());
// get the IRIs for each variable
Map<OWLEntity, IRI> entity2IRIMap = new HashMap<OWLEntity, IRI>();
- entity2IRIMap.put(pattern.getSubClass().asOWLClass(), cls.getIRI());
+ entity2IRIMap.put(patternSubClass.asOWLClass(), cls.getIRI());
boolean skip = false;
for (OWLEntity entity : signature) {
String var = variablesMapping.get(entity);
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|
|
From: <lor...@us...> - 2013-05-08 21:03:48
|
Revision: 3963
http://sourceforge.net/p/dl-learner/code/3963
Author: lorenz_b
Date: 2013-05-08 21:03:43 +0000 (Wed, 08 May 2013)
Log Message:
-----------
Refactored pattern eval.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLClassExpressionToSPARQLConverter.java
trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java
Modified: trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLClassExpressionToSPARQLConverter.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLClassExpressionToSPARQLConverter.java 2013-05-08 19:07:53 UTC (rev 3962)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLClassExpressionToSPARQLConverter.java 2013-05-08 21:03:43 UTC (rev 3963)
@@ -1,5 +1,7 @@
package org.dllearner.utilities.owl;
+import java.util.ArrayList;
+import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
@@ -7,6 +9,7 @@
import java.util.Map;
import java.util.Set;
import java.util.Stack;
+import java.util.TreeSet;
import org.aksw.commons.collections.diff.ModelDiff;
import org.semanticweb.owlapi.apibinding.OWLManager;
@@ -58,6 +61,10 @@
import uk.ac.manchester.cs.owl.owlapi.OWLDataFactoryImpl;
import uk.ac.manchester.cs.owlapi.dlsyntax.DLSyntaxObjectRenderer;
+import com.google.common.collect.HashMultimap;
+import com.google.common.collect.Multimap;
+import com.google.common.collect.Multimaps;
+import com.google.common.collect.Sets;
import com.hp.hpl.jena.query.Query;
import com.hp.hpl.jena.query.QueryFactory;
import com.hp.hpl.jena.query.Syntax;
@@ -74,6 +81,8 @@
private OWLDataFactory df = new OWLDataFactoryImpl();
+ private Multimap<Integer, OWLEntity> properties = HashMultimap.create();
+
private Map<Integer, Boolean> intersection;
private Set<? extends OWLEntity> variableEntities = new HashSet<OWLEntity>();
@@ -147,6 +156,7 @@
private void reset(){
variablesMapping.clear();
variables.clear();
+ properties.clear();
classCnt = 0;
propCnt = 0;
indCnt = 0;
@@ -238,6 +248,9 @@
} else {
s = "<" + entity.toStringID() + ">";
}
+ if(entity.isOWLObjectProperty()){
+ properties.put(modalDepth(), entity);
+ }
return s;
}
@@ -269,6 +282,19 @@
for (OWLClassExpression operand : operands) {
operand.accept(this);
}
+ Collection<OWLEntity> props = properties.get(modalDepth());
+ if(props.size() > 1){
+ Collection<String> vars = new TreeSet<String>();
+ for (OWLEntity p : props) {
+ if(variablesMapping.containsKey(p)){
+ vars.add(variablesMapping.get(p));
+ }
+ }
+ if(vars.size() == 2){
+ List<String> varList = new ArrayList<String>(vars);
+ sparql += "FILTER(" + varList.get(0) + "!=" + varList.get(1) + ")";
+ }
+ }
leaveIntersection();
}
@@ -728,8 +754,14 @@
//variable entity
expr = df.getOWLObjectIntersectionOf(
df.getOWLObjectSomeValuesFrom(propR, clsB),
+ clsB, df.getOWLObjectSomeValuesFrom(propS, clsA));
+ query = converter.asQuery(rootVar, expr, Sets.newHashSet(propR, propS)).toString();
+ System.out.println(expr + "\n" + query);
+
+ expr = df.getOWLObjectIntersectionOf(
+ df.getOWLObjectSomeValuesFrom(propR, df.getOWLObjectIntersectionOf(df.getOWLObjectSomeValuesFrom(propS, clsA), clsC)),
clsB);
- query = converter.asQuery(rootVar, expr, Collections.singleton(propR)).toString();
+ query = converter.asQuery(rootVar, expr, Sets.newHashSet(propR, propS)).toString();
System.out.println(expr + "\n" + query);
}
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java 2013-05-08 19:07:53 UTC (rev 3962)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java 2013-05-08 21:03:43 UTC (rev 3963)
@@ -6,14 +6,10 @@
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.InputStream;
import java.io.UnsupportedEncodingException;
import java.net.SocketTimeoutException;
import java.net.URI;
import java.net.URL;
-import java.sql.Connection;
-import java.sql.DriverManager;
import java.sql.SQLException;
import java.text.DecimalFormat;
import java.util.ArrayList;
@@ -30,7 +26,6 @@
import java.util.Set;
import java.util.TreeSet;
import java.util.concurrent.TimeUnit;
-import java.util.prefs.Preferences;
import joptsimple.OptionException;
import joptsimple.OptionParser;
@@ -52,8 +47,6 @@
import org.dllearner.reasoning.SPARQLReasoner;
import org.dllearner.utilities.owl.DLLearnerDescriptionConvertVisitor;
import org.dllearner.utilities.owl.OWLClassExpressionToSPARQLConverter;
-import org.ini4j.IniPreferences;
-import org.ini4j.InvalidFileFormatException;
import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.io.OWLObjectRenderer;
import org.semanticweb.owlapi.io.ToStringRenderer;
@@ -92,7 +85,9 @@
import com.hp.hpl.jena.query.Syntax;
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.Resource;
+import com.hp.hpl.jena.rdf.model.Statement;
import com.hp.hpl.jena.sparql.engine.http.QueryEngineHTTP;
import com.hp.hpl.jena.sparql.engine.http.QueryExceptionHTTP;
import com.hp.hpl.jena.vocabulary.RDF;
@@ -298,6 +293,7 @@
} catch (FileNotFoundException e) {
e.printStackTrace();
}
+ filterModel(fragment);
class2Fragment.put(cls, fragment);
logger.info("...got " + fragment.size() + " triples.");
continue;
@@ -336,6 +332,19 @@
return class2Fragment;
}
+ private void filterModel(Model model){
+ List<Statement> statements2Remove = new ArrayList<Statement>();
+ for (Statement st : model.listStatements().toSet()) {
+ if(st.getObject().isLiteral()){
+ statements2Remove.add(st);
+ }
+ if(st.getPredicate().equals(RDF.type) && !st.getObject().asResource().getURI().startsWith("http://dbpedia.org/ontology/")){
+ statements2Remove.add(st);
+ }
+ }
+ model.remove(statements2Remove);
+ }
+
private Map<OWLAxiom, Score> evaluate1(OWLAxiom pattern, NamedClass cls){
Map<OWLAxiom, Score> axioms2Score = new HashMap<OWLAxiom, Score>();
@@ -540,15 +549,11 @@
patternSubClass = cls;
- // 2. execute SPARQL query on local model
- Query query = QueryFactory.create(
- "SELECT (COUNT(DISTINCT ?x) AS ?cnt) WHERE {" + converter.convert("?x", patternSubClass) + "}",
- Syntax.syntaxARQ);
- int subClassCnt = QueryExecutionFactory.create(query, fragment).execSelect().next().getLiteral("cnt").getInt();
+
Set<OWLEntity> signature = patternSuperClass.getSignature();
signature.remove(patternSubClass);
- query = converter.asQuery("?x", df.getOWLObjectIntersectionOf(patternSubClass, patternSuperClass), signature);
+ Query query = converter.asQuery("?x", df.getOWLObjectIntersectionOf(patternSubClass, patternSuperClass), signature);
logger.info("Running query\n" + query);
Map<OWLEntity, String> variablesMapping = converter.getVariablesMapping();
com.hp.hpl.jena.query.ResultSet rs = QueryExecutionFactory.create(query, fragment).execSelect();
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|
|
From: <lor...@us...> - 2013-05-08 19:07:57
|
Revision: 3962
http://sourceforge.net/p/dl-learner/code/3962
Author: lorenz_b
Date: 2013-05-08 19:07:53 +0000 (Wed, 08 May 2013)
Log Message:
-----------
Refactored pattern eval.
Modified Paths:
--------------
trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java 2013-05-08 17:47:19 UTC (rev 3961)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java 2013-05-08 19:07:53 UTC (rev 3962)
@@ -3,6 +3,7 @@
import static java.util.Arrays.asList;
import java.io.File;
+import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
@@ -27,6 +28,7 @@
import java.util.Map.Entry;
import java.util.Random;
import java.util.Set;
+import java.util.TreeSet;
import java.util.concurrent.TimeUnit;
import java.util.prefs.Preferences;
@@ -34,7 +36,6 @@
import joptsimple.OptionParser;
import joptsimple.OptionSet;
-import org.aksw.commons.collections.diff.ModelDiff;
import org.apache.log4j.Logger;
import org.coode.owlapi.turtle.TurtleOntologyFormat;
import org.dllearner.core.EvaluatedAxiom;
@@ -79,6 +80,9 @@
import com.google.common.collect.HashMultiset;
import com.google.common.collect.Multiset;
+import com.google.common.hash.HashCode;
+import com.google.common.hash.HashFunction;
+import com.google.common.hash.Hashing;
import com.hp.hpl.jena.query.ParameterizedSparqlString;
import com.hp.hpl.jena.query.Query;
import com.hp.hpl.jena.query.QueryExecution;
@@ -96,24 +100,18 @@
public class OWLAxiomPatternUsageEvaluation {
- private static final Logger logger = Logger.getLogger(OWLAxiomPatternUsageEvaluation.AxiomTypeCategory.class
- .getName());
+ private static final Logger logger = Logger.getLogger(OWLAxiomPatternUsageEvaluation.class.getName());
- enum AxiomTypeCategory{
- TBox, RBox, ABox
- }
private OWLObjectRenderer axiomRenderer = new ManchesterOWLSyntaxOWLObjectRendererImpl();
private OWLDataFactory df = new OWLDataFactoryImpl();
- private Connection conn;
- private ExtractionDBCache cache = new ExtractionDBCache("pattern-cache");
+ private ExtractionDBCache cache = new ExtractionDBCache("pattern-cache/db");
private SparqlEndpoint endpoint = SparqlEndpoint.getEndpointDBpedia();
private SparqlEndpointKS ks = new SparqlEndpointKS(endpoint, cache);//new LocalModelBasedSparqlEndpointKS(model);
private String ns = "http://dbpedia.org/ontology/";
- private boolean fancyLatex = false;
private DecimalFormat format = new DecimalFormat("00.0%");
private long waitingTime = TimeUnit.SECONDS.toMillis(3);
private double threshold = 0.6;
@@ -125,33 +123,8 @@
private int queryLimit = 10000;
public OWLAxiomPatternUsageEvaluation() {
- initDBConnection();
}
- 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();
- }
- }
public void run(SparqlEndpoint endpoint, OWLOntology ontology, File outputFile, int maxNrOfTestedClasses){
ks = new SparqlEndpointKS(endpoint, cache);
@@ -315,6 +288,21 @@
for (NamedClass cls : classes) {
logger.info("Extracting fragment for " + cls + "...");
Model fragment = ModelFactory.createDefaultModel();
+ //try to load from cache
+ HashFunction hf = Hashing.md5();
+ HashCode hc = hf.newHasher().putString(cls.getName()).hash();
+ File file = new File("pattern-cache/" + hc.toString() + ".ttl");
+ if(file.exists()){
+ try {
+ fragment.read(new FileInputStream(file), null, "TURTLE");
+ } catch (FileNotFoundException e) {
+ e.printStackTrace();
+ }
+ class2Fragment.put(cls, fragment);
+ logger.info("...got " + fragment.size() + " triples.");
+ continue;
+ }
+
//build the CONSTRUCT query
Query query = buildConstructQuery(cls, depth);
query.setLimit(queryLimit);
@@ -323,7 +311,8 @@
int offset = 0;
boolean hasMoreResults = true;
while(hasMoreResults && (System.currentTimeMillis() - startTime)<= maxFragmentExtractionTime){
- query.setOffset(offset);System.out.println(query);
+ query.setOffset(offset);
+ logger.info(query);
Model m = executeConstructQuery(query);
fragment.add(m);
if(m.size() == 0){
@@ -338,6 +327,11 @@
}
logger.info("...got " + fragment.size() + " triples.");
class2Fragment.put(cls, fragment);
+ try {
+ fragment.write(new FileOutputStream(file), "TURTLE");
+ } catch (FileNotFoundException e) {
+ e.printStackTrace();
+ }
}
return class2Fragment;
}
@@ -554,6 +548,72 @@
Set<OWLEntity> signature = patternSuperClass.getSignature();
signature.remove(patternSubClass);
+ query = converter.asQuery("?x", df.getOWLObjectIntersectionOf(patternSubClass, patternSuperClass), signature);
+ logger.info("Running query\n" + query);
+ Map<OWLEntity, String> variablesMapping = converter.getVariablesMapping();
+ com.hp.hpl.jena.query.ResultSet rs = QueryExecutionFactory.create(query, fragment).execSelect();
+ QuerySolution qs;
+ Set<String> resources = new HashSet<String>();
+ Multiset<OWLAxiom> instantiations = HashMultiset.create();
+ while (rs.hasNext()) {
+ qs = rs.next();
+ resources.add(qs.getResource("x").getURI());
+ // get the IRIs for each variable
+ Map<OWLEntity, IRI> entity2IRIMap = new HashMap<OWLEntity, IRI>();
+ entity2IRIMap.put(pattern.getSubClass().asOWLClass(), cls.getIRI());
+ boolean skip = false;
+ for (OWLEntity entity : signature) {
+ String var = variablesMapping.get(entity);
+ if(qs.get(var) == null){
+ logger.warn("Variable " + var + " is not bound.");
+ skip = true;
+ break;
+ }
+ if(qs.get(var).isLiteral()){
+ skip = true;
+ break;
+ }
+ Resource resource = qs.getResource(var);
+ if(entity.isOWLObjectProperty() && resource.hasURI(RDF.type.getURI())){
+ skip = true;
+ break;
+ }
+ entity2IRIMap.put(entity, IRI.create(resource.getURI()));
+ }
+ if(!skip){
+ // instantiate the pattern
+ OWLObjectDuplicator duplicator = new OWLObjectDuplicator(entity2IRIMap, df);
+ OWLAxiom patternInstantiation = duplicator.duplicateObject(pattern);
+ instantiations.add(patternInstantiation);
+ }
+ }
+ // compute the score
+ int total = resources.size();
+ for (OWLAxiom axiom : instantiations.elementSet()) {
+ int frequency = instantiations.count(axiom);
+ Score score = computeScore(total, Math.min(total, frequency));
+ axioms2Score.put(axiom, score);
+ }
+
+ return axioms2Score;
+ }
+
+ private Map<OWLAxiom, Score> applyPattern2(OWLSubClassOfAxiom pattern, OWLClass cls, Model fragment) {
+ Map<OWLAxiom, Score> axioms2Score = new HashMap<OWLAxiom, Score>();
+
+ OWLClassExpression patternSubClass = pattern.getSubClass();
+ OWLClassExpression patternSuperClass = pattern.getSuperClass();
+
+ patternSubClass = cls;
+
+ // 2. execute SPARQL query on local model
+ Query query = QueryFactory.create(
+ "SELECT (COUNT(DISTINCT ?x) AS ?cnt) WHERE {" + converter.convert("?x", patternSubClass) + "}",
+ Syntax.syntaxARQ);
+ int subClassCnt = QueryExecutionFactory.create(query, fragment).execSelect().next().getLiteral("cnt").getInt();
+
+ Set<OWLEntity> signature = patternSuperClass.getSignature();
+ signature.remove(patternSubClass);
query = converter.asQuery("?x", df.getOWLObjectIntersectionOf(patternSubClass, patternSuperClass), signature, true);
logger.info("Running query\n" + query);
Map<OWLEntity, String> variablesMapping = converter.getVariablesMapping();
@@ -679,7 +739,7 @@
public List<OWLAxiom> getPatternsToEvaluate(OWLOntology ontology){
List<OWLAxiom> axiomPatterns = new ArrayList<OWLAxiom>();
- axiomPatterns.addAll(ontology.getLogicalAxioms());
+ axiomPatterns.addAll(new TreeSet<OWLAxiom>(ontology.getLogicalAxioms()));
return axiomPatterns;
}
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|
|
From: <lor...@us...> - 2013-05-08 17:47:24
|
Revision: 3961
http://sourceforge.net/p/dl-learner/code/3961
Author: lorenz_b
Date: 2013-05-08 17:47:19 +0000 (Wed, 08 May 2013)
Log Message:
-----------
Refactored pattern eval.
Modified Paths:
--------------
trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java 2013-05-08 16:37:49 UTC (rev 3960)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java 2013-05-08 17:47:19 UTC (rev 3961)
@@ -551,12 +551,11 @@
"SELECT (COUNT(DISTINCT ?x) AS ?cnt) WHERE {" + converter.convert("?x", patternSubClass) + "}",
Syntax.syntaxARQ);
int subClassCnt = QueryExecutionFactory.create(query, fragment).execSelect().next().getLiteral("cnt").getInt();
- System.out.println(subClassCnt);
Set<OWLEntity> signature = patternSuperClass.getSignature();
signature.remove(patternSubClass);
query = converter.asQuery("?x", df.getOWLObjectIntersectionOf(patternSubClass, patternSuperClass), signature, true);
- System.out.println(query);
+ logger.info("Running query\n" + query);
Map<OWLEntity, String> variablesMapping = converter.getVariablesMapping();
com.hp.hpl.jena.query.ResultSet rs = QueryExecutionFactory.create(query, fragment).execSelect();
QuerySolution qs;
@@ -568,6 +567,11 @@
boolean skip = false;
for (OWLEntity entity : signature) {
String var = variablesMapping.get(entity);
+ if(qs.get(var) == null){
+ logger.warn("Variable " + var + " is not bound.");
+ skip = true;
+ break;
+ }
if(qs.get(var).isLiteral()){
skip = true;
break;
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