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[DL-Learner SVN] SF.net SVN: dl-learner:[3941] trunk
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From: <lor...@us...> - 2013-05-04 05:50:52
|
Revision: 3941
http://sourceforge.net/p/dl-learner/code/3941
Author: lorenz_b
Date: 2013-05-04 05:50:47 +0000 (Sat, 04 May 2013)
Log Message:
-----------
Some modifications in pattern detection script.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomPatternFinder.java
trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomRenamer.java
trunk/components-core/src/main/java/org/dllearner/kb/repository/tones/TONESRepository.java
trunk/interfaces/src/main/java/org/dllearner/cli/Enrichment.java
trunk/pom.xml
trunk/scripts/pom.xml
trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomPatternDetectionEvaluation.java
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomPatternFinder.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomPatternFinder.java 2013-05-03 08:49:17 UTC (rev 3940)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomPatternFinder.java 2013-05-04 05:50:47 UTC (rev 3941)
@@ -21,6 +21,7 @@
import java.util.Set;
import java.util.prefs.Preferences;
+import org.coode.owlapi.functionalparser.OWLFunctionalSyntaxOWLParser;
import org.dllearner.kb.dataset.OWLOntologyDataset;
import org.dllearner.kb.repository.OntologyRepository;
import org.dllearner.kb.repository.OntologyRepositoryEntry;
@@ -28,6 +29,7 @@
import org.ini4j.InvalidFileFormatException;
import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.io.OWLObjectRenderer;
+import org.semanticweb.owlapi.io.StringDocumentSource;
import org.semanticweb.owlapi.io.UnparsableOntologyException;
import org.semanticweb.owlapi.model.AxiomType;
import org.semanticweb.owlapi.model.IRI;
@@ -359,7 +361,9 @@
entries = entryList;
}
Multiset<OWLAxiom> allAxiomPatterns = HashMultiset.create();
+ int i = 1;
for (OntologyRepositoryEntry entry : entries) {
+ System.out.print(i + ": ");
URI uri = entry.getPhysicalURI();
// if(uri.toString().startsWith("http://rest.bioontology.org/bioportal/ontologies/download/42764")){
if (!ontologyProcessed(uri)) {
@@ -368,15 +372,19 @@
manager = OWLManager.createOWLOntologyManager();
OWLOntology ontology = manager.loadOntology(IRI.create(uri));
Multiset<OWLAxiom> axiomPatterns = HashMultiset.create();
- for (OWLLogicalAxiom axiom : ontology.getLogicalAxioms()) {
+ Set<OWLAxiom> logicalAxioms = new HashSet<OWLAxiom>();
+ for (AxiomType<?> type : AxiomType.AXIOM_TYPES) {
+ logicalAxioms.addAll(ontology.getAxioms(type, true));
+ }
+ for (OWLAxiom axiom : logicalAxioms) {
OWLAxiom renamedAxiom = renamer.rename(axiom);
axiomPatterns.add(renamedAxiom);
}
allAxiomPatterns.addAll(axiomPatterns);
addOntologyPatterns(uri, ontology, axiomPatterns);
- for (OWLAxiom owlAxiom : Multisets.copyHighestCountFirst(allAxiomPatterns).elementSet()) {
+// for (OWLAxiom owlAxiom : Multisets.copyHighestCountFirst(allAxiomPatterns).elementSet()) {
// System.out.println(owlAxiom + ": " + allAxiomPatterns.count(owlAxiom));
- }
+// }
manager.removeOntology(ontology);
} catch (OWLOntologyAlreadyExistsException e) {
e.printStackTrace();
@@ -384,6 +392,8 @@
e.printStackTrace();
addOntologyError(uri, e);
}
+ } else {
+ System.out.println("Already processed.");
}
}
@@ -401,5 +411,11 @@
org.coode.owlapi.functionalrenderer.OWLObjectRenderer r = new org.coode.owlapi.functionalrenderer.OWLObjectRenderer(man, ontology, sw);
axiom.accept(r);
System.out.println(sw.toString());
+ StringDocumentSource s = new StringDocumentSource("Ontology(<http://www.pattern.org>" + sw.toString() + ")");
+ OWLFunctionalSyntaxOWLParser p = new OWLFunctionalSyntaxOWLParser();
+ OWLOntology newOntology = man.createOntology();
+ p.parse(s, newOntology);
+ System.out.println(newOntology.getLogicalAxioms());
+
}
}
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomRenamer.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomRenamer.java 2013-05-03 08:49:17 UTC (rev 3940)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomRenamer.java 2013-05-04 05:50:47 UTC (rev 3941)
@@ -341,14 +341,13 @@
@Override
public void visit(OWLSubPropertyChainOfAxiom axiom) {
+ List<OWLObjectPropertyExpression> renamedSubPropertyChain = new ArrayList<OWLObjectPropertyExpression>();
+ for (OWLObjectPropertyExpression owlObjectPropertyExpression : axiom.getPropertyChain()) {
+ renamedSubPropertyChain.add(expressionRenamer.rename(owlObjectPropertyExpression));
+ }
OWLObjectPropertyExpression superProperty = axiom.getSuperProperty();
superProperty = expressionRenamer.rename(superProperty);
- List<OWLObjectPropertyExpression> subPropertyChain = axiom.getPropertyChain();
- List<OWLObjectPropertyExpression> renamedSubPropertyChain = axiom.getPropertyChain();
- for (OWLObjectPropertyExpression owlObjectPropertyExpression : subPropertyChain) {
- renamedSubPropertyChain.add(expressionRenamer.rename(owlObjectPropertyExpression));
- }
- renamedAxiom = df.getOWLSubPropertyChainOfAxiom(subPropertyChain, superProperty);
+ renamedAxiom = df.getOWLSubPropertyChainOfAxiom(renamedSubPropertyChain, superProperty);
}
@Override
Modified: trunk/components-core/src/main/java/org/dllearner/kb/repository/tones/TONESRepository.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/kb/repository/tones/TONESRepository.java 2013-05-03 08:49:17 UTC (rev 3940)
+++ trunk/components-core/src/main/java/org/dllearner/kb/repository/tones/TONESRepository.java 2013-05-04 05:50:47 UTC (rev 3941)
@@ -10,14 +10,18 @@
import java.util.Collections;
import java.util.List;
+import org.apache.log4j.Logger;
import org.dllearner.kb.repository.OntologyRepository;
import org.dllearner.kb.repository.OntologyRepositoryEntry;
+import org.dllearner.kb.repository.bioportal.BioPortalRepository;
import org.semanticweb.owlapi.model.IRI;
import org.semanticweb.owlapi.model.OWLOntologyIRIMapper;
import org.semanticweb.owlapi.util.OntologyIRIShortFormProvider;
public class TONESRepository implements OntologyRepository{
+ private static final Logger log = Logger.getLogger(TONESRepository.class);
+
private final String repositoryName = "TONES";
private final URI repositoryLocation = URI.create("http://owl.cs.manchester.ac.uk/repository");
@@ -91,6 +95,7 @@
catch (IOException e) {
e.printStackTrace();
}
+ log.info("Loaded " + entries.size() + " ontology entries from TONES.");
}
private class RepositoryEntry implements OntologyRepositoryEntry {
Modified: trunk/interfaces/src/main/java/org/dllearner/cli/Enrichment.java
===================================================================
--- trunk/interfaces/src/main/java/org/dllearner/cli/Enrichment.java 2013-05-03 08:49:17 UTC (rev 3940)
+++ trunk/interfaces/src/main/java/org/dllearner/cli/Enrichment.java 2013-05-04 05:50:47 UTC (rev 3941)
@@ -61,11 +61,14 @@
import joptsimple.OptionSpec;
import org.aksw.commons.jena_owlapi.Conversion;
+import org.apache.jena.riot.checker.CheckerLiterals;
+import org.apache.jena.riot.system.ErrorHandlerFactory;
import org.apache.log4j.ConsoleAppender;
import org.apache.log4j.Level;
import org.apache.log4j.Logger;
import org.apache.log4j.SimpleLayout;
import org.coode.owlapi.manchesterowlsyntax.ManchesterOWLSyntaxOntologyFormat;
+import org.coode.owlapi.turtle.TurtleOntologyFormat;
import org.dllearner.algorithms.celoe.CELOE;
import org.dllearner.algorithms.properties.AsymmetricObjectPropertyAxiomLearner;
import org.dllearner.algorithms.properties.DataPropertyDomainAxiomLearner;
@@ -127,6 +130,7 @@
import org.dllearner.utilities.datastructures.SortedSetTuple;
import org.dllearner.utilities.examples.AutomaticNegativeExampleFinderSPARQL2;
import org.dllearner.utilities.owl.OWLAPIAxiomConvertVisitor;
+import org.dllearner.utilities.owl.OWLEntityTypeAdder;
import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.io.RDFXMLOntologyFormat;
import org.semanticweb.owlapi.io.SystemOutDocumentTarget;
@@ -212,7 +216,7 @@
// restrict tested number of entities per type (only for testing purposes);
// should be set to -1 in production mode
- int maxEntitiesPerType = -1;
+ int maxEntitiesPerType = 5;
// number of axioms which will be learned/considered (only applies to
// some learners)
@@ -462,7 +466,7 @@
ksFragment = ksCached;
rc = rcCached;
} else {
- System.out.print("extracting fragment ... ");
+ System.out.print("extracting fragment ... ");//com.hp.hpl.jena.shared.impl.JenaParameters.enableEagerLiteralValidation = true;
startTime = System.currentTimeMillis();
ConciseBoundedDescriptionGenerator cbdGen = new ConciseBoundedDescriptionGeneratorImpl(ks.getEndpoint(), cache, 2);
Model model = ModelFactory.createDefaultModel();
@@ -471,6 +475,7 @@
model.add(cbd);
}
filter(model);
+ OWLEntityTypeAdder.addEntityTypes(model);
runTime = System.currentTimeMillis() - startTime;
System.out.println("done (" + model.size()+ " triples found in " + runTime + " ms)");
OWLOntology ontology = asOWLOntology(model);
@@ -768,6 +773,13 @@
model.write(fos, "TURTLE", null);
OWLOntologyManager man = OWLManager.createOWLOntologyManager();
OWLOntology ontology = man.loadOntologyFromOntologyDocument(new ByteArrayInputStream(baos.toByteArray()));
+ try {
+ man.saveOntology(ontology, new TurtleOntologyFormat(), new FileOutputStream("error.owl"));
+ } catch (OWLOntologyStorageException e) {
+ e.printStackTrace();
+ } catch (FileNotFoundException e) {
+ e.printStackTrace();
+ }
return ontology;
} catch (OWLOntologyCreationException e) {
e.printStackTrace();
@@ -797,6 +809,7 @@
// fix URIs with spaces
Resource newSubject = (Resource) subject;
RDFNode newObject = object;
+ boolean validTriple = true;
if (subject.isURIResource()) {
String uri = subject.asResource().getURI();
if (uri.contains(" ")) {
@@ -814,8 +827,11 @@
if (lit.getDatatype() == null || lit.getDatatype().equals(XSD.STRING)) {
newObject = model.createLiteral("shortened", "en");
}
+ validTriple = CheckerLiterals.checkLiteral(object.asNode(), ErrorHandlerFactory.errorHandlerNoLogging, 1l, 1l);
}
- statementsToAdd.add(model.createStatement(newSubject, st.getPredicate(), newObject));
+ if(validTriple){
+ statementsToAdd.add(model.createStatement(newSubject, st.getPredicate(), newObject));
+ }
statementsToRemove.add(st);
}
Modified: trunk/pom.xml
===================================================================
--- trunk/pom.xml 2013-05-03 08:49:17 UTC (rev 3940)
+++ trunk/pom.xml 2013-05-04 05:50:47 UTC (rev 3941)
@@ -123,7 +123,8 @@
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-distribution</artifactId>
- <version>3.4.4</version>
+ <version>3.4.3</version>
+ <type>pom</type>
</dependency>
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
@@ -379,7 +380,7 @@
<dependency>
<groupId>mysql</groupId>
<artifactId>mysql-connector-java</artifactId>
- <version>5.1.13</version>
+ <version>5.1.24</version>
</dependency>
<!--GWT Dependencies -->
Modified: trunk/scripts/pom.xml
===================================================================
--- trunk/scripts/pom.xml 2013-05-03 08:49:17 UTC (rev 3940)
+++ trunk/scripts/pom.xml 2013-05-04 05:50:47 UTC (rev 3941)
@@ -116,6 +116,7 @@
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-distribution</artifactId>
+ <type>pom</type>
</dependency>
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomPatternDetectionEvaluation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomPatternDetectionEvaluation.java 2013-05-03 08:49:17 UTC (rev 3940)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomPatternDetectionEvaluation.java 2013-05-04 05:50:47 UTC (rev 3941)
@@ -11,17 +11,34 @@
import java.sql.SQLException;
import java.util.Arrays;
import java.util.Collection;
+import java.util.LinkedHashMap;
+import java.util.Map;
+import java.util.Map.Entry;
import java.util.prefs.Preferences;
+import org.coode.owlapi.functionalparser.OWLFunctionalSyntaxOWLParser;
import org.dllearner.algorithms.pattern.OWLAxiomPatternFinder;
import org.dllearner.kb.repository.OntologyRepository;
import org.dllearner.kb.repository.bioportal.BioPortalRepository;
import org.dllearner.kb.repository.tones.TONESRepository;
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.OWLParserException;
+import org.semanticweb.owlapi.io.StringDocumentSource;
+import org.semanticweb.owlapi.io.ToStringRenderer;
+import org.semanticweb.owlapi.model.OWLAxiom;
+import org.semanticweb.owlapi.model.OWLOntology;
+import org.semanticweb.owlapi.model.OWLOntologyCreationException;
+import org.semanticweb.owlapi.model.UnloadableImportException;
+import uk.ac.manchester.cs.owl.owlapi.mansyntaxrenderer.ManchesterOWLSyntaxOWLObjectRendererImpl;
+import uk.ac.manchester.cs.owlapi.dlsyntax.DLSyntaxObjectRenderer;
+
public class OWLAxiomPatternDetectionEvaluation {
+ private OWLObjectRenderer axiomRenderer = new ManchesterOWLSyntaxOWLObjectRendererImpl();
private Connection conn;
public OWLAxiomPatternDetectionEvaluation() {
@@ -59,6 +76,9 @@
//create statistics for the repositories
makeRepositoryStatistics(repositories);
+
+ //get top n TBox, RBox and ABox patterns
+ makePatternStatistics(repositories);
}
private void analyze(Collection<OntologyRepository> repositories){
@@ -69,6 +89,35 @@
}
}
+ private void makePatternStatistics(Collection<OntologyRepository> repositories){
+ int n = 10;
+ String latex = "";
+ Map<OWLAxiom, Integer> topNTBoxAxiomPatterns = getTopNTBoxAxiomPatterns(n);
+ latex += asLatex("Total TBox", topNTBoxAxiomPatterns) + "\n\n";
+ Map<OWLAxiom, Integer> topNRBoxAxiomPatterns = getTopNRBoxAxiomPatterns(n);
+ latex += asLatex("Total RBox", topNRBoxAxiomPatterns) + "\n\n";
+ Map<OWLAxiom, Integer> topNABoxAxiomPatterns = getTopNABoxAxiomPatterns(n);
+ latex += asLatex("Total ABox", topNABoxAxiomPatterns) + "\n\n";
+
+ //get top n TBox, RBox and ABox patterns by repository
+
+ Map<OntologyRepository, Map<OWLAxiom, Integer>> topNTBoxAxiomPatternsByRepository = getTopNTBoxAxiomPatterns(repositories, n);
+ Map<OntologyRepository, Map<OWLAxiom, Integer>> topNRBoxAxiomPatternsByRepository = getTopNRBoxAxiomPatterns(repositories, n);
+ Map<OntologyRepository, Map<OWLAxiom, Integer>> topNABoxAxiomPatternsByRepository = getTopNABoxAxiomPatterns(repositories, n);
+ for (OntologyRepository repository : repositories) {
+ latex += asLatex(repository.getName() + " TBox", topNTBoxAxiomPatternsByRepository.get(repository)) + "\n\n";
+ latex += asLatex(repository.getName() + " RBox", topNRBoxAxiomPatternsByRepository.get(repository)) + "\n\n";
+ latex += asLatex(repository.getName() + " ABox", topNABoxAxiomPatternsByRepository.get(repository)) + "\n\n";
+ }
+ try {
+ new FileOutputStream("pattern-statistics.tex").write(latex.getBytes());
+ } catch (FileNotFoundException e) {
+ e.printStackTrace();
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+ }
+
private void makeRepositoryStatistics(Collection<OntologyRepository> repositories){
String latexTable = "\\begin{tabular}{lrr|rrr|rrr|rrr|rrr}";
latexTable += "\\toprule\n";
@@ -147,7 +196,7 @@
ps.setString(1, repository.getName());
minNumberOfAboxAxioms = count(ps);
//get max number of abox axioms
- ps = conn.prepareStatement("SELECT MAX(tbox_axioms) FROM Ontology WHERE repository=? AND iri NOT LIKE 'ERROR%'");
+ ps = conn.prepareStatement("SELECT MAX(abox_axioms) FROM Ontology WHERE repository=? AND iri NOT LIKE 'ERROR%'");
ps.setString(1, repository.getName());
maxNumberOfAboxAxioms = count(ps);
//get avg number of abox axioms
@@ -186,6 +235,193 @@
}
}
+ private String asLatex(String title, Map<OWLAxiom, Integer> topN){
+ String latexTable = "\\begin{table}\n";
+ latexTable += "\\begin{tabular}{lr}\n";
+ latexTable += "\\toprule\n";
+ latexTable += "Pattern & Frequency\\\\\\midrule\n";
+
+ for (Entry<OWLAxiom, Integer> entry : topN.entrySet()) {
+ OWLAxiom axiom = entry.getKey();
+ Integer frequency = entry.getValue();
+
+ latexTable += axiomRenderer.render(axiom) + " & " + frequency + "\\\\\n";
+
+ }
+ latexTable += "\\bottomrule\\end{tabular}\n";
+ latexTable += "\\caption{" + title + "}\n";
+ latexTable += "\\end{table}\n";
+ return latexTable;
+ }
+
+ private Map<OWLAxiom, Integer> getTopNTBoxAxiomPatterns(int n){
+ Map<OWLAxiom, Integer> topN = new LinkedHashMap<OWLAxiom, Integer>();
+ PreparedStatement ps;
+ ResultSet rs;
+ try {
+ ps = conn.prepareStatement("SELECT pattern,SUM(occurrences) FROM " +
+ "Ontology_Pattern OP, Pattern P, Ontology O WHERE " +
+ "(P.id=OP.pattern_id AND O.id=OP.ontology_id AND P.axiom_type=?) " +
+ "GROUP BY P.id ORDER BY SUM(`OP`.`occurrences`) DESC LIMIT ?");
+ ps.setString(1, "TBox");
+ ps.setInt(2, n);
+ rs = ps.executeQuery();
+ while(rs.next()){
+ topN.put(asOWLAxiom(rs.getString(1)), rs.getInt(2));
+ }
+ } catch(SQLException e){
+ e.printStackTrace();
+ }
+ return topN;
+ }
+
+ private Map<OntologyRepository, Map<OWLAxiom, Integer>> getTopNTBoxAxiomPatterns(Collection<OntologyRepository> repositories, int n){
+ Map<OntologyRepository, Map<OWLAxiom, Integer>> topNByRepository = new LinkedHashMap<OntologyRepository, Map<OWLAxiom,Integer>>();
+ PreparedStatement ps;
+ ResultSet rs;
+ //for each repository
+ for (OntologyRepository repository : repositories) {
+ Map<OWLAxiom, Integer> topN = new LinkedHashMap<OWLAxiom, Integer>();
+ try {
+ //get number of ontologies
+ ps = conn.prepareStatement("SELECT pattern,SUM(occurrences) FROM " +
+ "Ontology_Pattern OP, Pattern P, Ontology O WHERE " +
+ "(P.id=OP.pattern_id AND O.id=OP.ontology_id AND O.repository=? AND P.axiom_type=?) " +
+ "GROUP BY P.id ORDER BY SUM(`OP`.`occurrences`) DESC LIMIT ?");
+ ps.setString(1, repository.getName());
+ ps.setString(2, "TBox");
+ ps.setInt(3, n);
+ rs = ps.executeQuery();
+ while(rs.next()){
+ topN.put(asOWLAxiom(rs.getString(1)), rs.getInt(2));
+ }
+ } catch(SQLException e){
+ e.printStackTrace();
+ }
+ topNByRepository.put(repository, topN);
+ }
+ return topNByRepository;
+ }
+
+ private Map<OWLAxiom, Integer> getTopNRBoxAxiomPatterns(int n){
+ Map<OWLAxiom, Integer> topN = new LinkedHashMap<OWLAxiom, Integer>();
+ PreparedStatement ps;
+ ResultSet rs;
+ try {
+ ps = conn.prepareStatement("SELECT pattern,SUM(occurrences) FROM " +
+ "Ontology_Pattern OP, Pattern P, Ontology O WHERE " +
+ "(P.id=OP.pattern_id AND O.id=OP.ontology_id AND P.axiom_type=?) " +
+ "GROUP BY P.id ORDER BY SUM(`OP`.`occurrences`) DESC LIMIT ?");
+ ps.setString(1, "RBox");
+ ps.setInt(2, n);
+ rs = ps.executeQuery();
+ while(rs.next()){
+ topN.put(asOWLAxiom(rs.getString(1)), rs.getInt(2));
+ }
+ } catch(SQLException e){
+ e.printStackTrace();
+ }
+ return topN;
+ }
+
+ private Map<OntologyRepository, Map<OWLAxiom, Integer>> getTopNRBoxAxiomPatterns(Collection<OntologyRepository> repositories, int n){
+ Map<OntologyRepository, Map<OWLAxiom, Integer>> topNByRepository = new LinkedHashMap<OntologyRepository, Map<OWLAxiom,Integer>>();
+ PreparedStatement ps;
+ ResultSet rs;
+ //for each repository
+ for (OntologyRepository repository : repositories) {
+ Map<OWLAxiom, Integer> topN = new LinkedHashMap<OWLAxiom, Integer>();
+ try {
+ //get number of ontologies
+ ps = conn.prepareStatement("SELECT pattern,SUM(occurrences) FROM " +
+ "Ontology_Pattern OP, Pattern P, Ontology O WHERE " +
+ "(P.id=OP.pattern_id AND O.id=OP.ontology_id AND O.repository=? AND P.axiom_type=?) " +
+ "GROUP BY P.id ORDER BY SUM(`OP`.`occurrences`) DESC LIMIT ?");
+ ps.setString(1, repository.getName());
+ ps.setString(2, "RBox");
+ ps.setInt(3, n);
+ rs = ps.executeQuery();
+ while(rs.next()){
+ topN.put(asOWLAxiom(rs.getString(1)), rs.getInt(2));
+ }
+ } catch(SQLException e){
+ e.printStackTrace();
+ }
+ topNByRepository.put(repository, topN);
+ }
+ return topNByRepository;
+ }
+
+ private Map<OWLAxiom, Integer> getTopNABoxAxiomPatterns(int n){
+ Map<OWLAxiom, Integer> topN = new LinkedHashMap<OWLAxiom, Integer>();
+ PreparedStatement ps;
+ ResultSet rs;
+ try {
+ ps = conn.prepareStatement("SELECT pattern,SUM(occurrences) FROM " +
+ "Ontology_Pattern OP, Pattern P, Ontology O WHERE " +
+ "(P.id=OP.pattern_id AND O.id=OP.ontology_id AND P.axiom_type=?) " +
+ "GROUP BY P.id ORDER BY SUM(`OP`.`occurrences`) DESC LIMIT ?");
+ ps.setString(1, "ABox");
+ ps.setInt(2, n);
+ rs = ps.executeQuery();
+ while(rs.next()){
+ topN.put(asOWLAxiom(rs.getString(1)), rs.getInt(2));
+ }
+ } catch(SQLException e){
+ e.printStackTrace();
+ }
+ return topN;
+ }
+
+ private Map<OntologyRepository, Map<OWLAxiom, Integer>> getTopNABoxAxiomPatterns(Collection<OntologyRepository> repositories, int n){
+ Map<OntologyRepository, Map<OWLAxiom, Integer>> topNByRepository = new LinkedHashMap<OntologyRepository, Map<OWLAxiom,Integer>>();
+ PreparedStatement ps;
+ ResultSet rs;
+ //for each repository
+ for (OntologyRepository repository : repositories) {
+ Map<OWLAxiom, Integer> topN = new LinkedHashMap<OWLAxiom, Integer>();
+ try {
+ //get number of ontologies
+ ps = conn.prepareStatement("SELECT pattern,SUM(occurrences) FROM " +
+ "Ontology_Pattern OP, Pattern P, Ontology O WHERE " +
+ "(P.id=OP.pattern_id AND O.id=OP.ontology_id AND O.repository=? AND P.axiom_type=?) " +
+ "GROUP BY P.id ORDER BY SUM(`OP`.`occurrences`) DESC LIMIT ?");
+ ps.setString(1, repository.getName());
+ ps.setString(2, "ABox");
+ ps.setInt(3, n);
+ rs = ps.executeQuery();
+ while(rs.next()){
+ topN.put(asOWLAxiom(rs.getString(1)), rs.getInt(2));
+ }
+ } catch(SQLException e){
+ e.printStackTrace();
+ }
+ topNByRepository.put(repository, topN);
+ }
+ return topNByRepository;
+ }
+
+ private OWLAxiom asOWLAxiom(String functionalSyntaxAxiomString){
+ try {
+ StringDocumentSource s = new StringDocumentSource("Ontology(<http://www.pattern.org>" + functionalSyntaxAxiomString + ")");
+ OWLFunctionalSyntaxOWLParser p = new OWLFunctionalSyntaxOWLParser();
+ OWLOntology newOntology = OWLManager.createOWLOntologyManager().createOntology();
+ p.parse(s, newOntology);
+ if(!newOntology.getLogicalAxioms().isEmpty()){
+ return newOntology.getLogicalAxioms().iterator().next();
+ }
+ } catch (UnloadableImportException e) {
+ e.printStackTrace();
+ } catch (OWLOntologyCreationException e) {
+ e.printStackTrace();
+ } catch (OWLParserException e) {
+ e.printStackTrace();
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+ return null;
+ }
+
private int count(PreparedStatement ps) throws SQLException{
ResultSet rs = ps.executeQuery();
rs.next();
@@ -193,6 +429,7 @@
}
public static void main(String[] args) throws Exception {
+// ToStringRenderer.getInstance().setRenderer(new DLSyntaxObjectRenderer());
new OWLAxiomPatternDetectionEvaluation().run(Arrays.asList(
new TONESRepository(), new BioPortalRepository()));
}
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