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[DL-Learner SVN] SF.net SVN: dl-learner:[1867] trunk/src/dl-learner/org/dllearner/examples
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From: <jen...@us...> - 2009-09-28 14:35:55
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Revision: 1867
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=1867&view=rev
Author: jenslehmann
Date: 2009-09-28 14:35:48 +0000 (Mon, 28 Sep 2009)
Log Message:
-----------
converted conservation + other properties
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/examples/Carcinogenesis.java
trunk/src/dl-learner/org/dllearner/examples/MonogenicDiseases.java
Modified: trunk/src/dl-learner/org/dllearner/examples/Carcinogenesis.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/examples/Carcinogenesis.java 2009-09-28 07:30:22 UTC (rev 1866)
+++ trunk/src/dl-learner/org/dllearner/examples/Carcinogenesis.java 2009-09-28 14:35:48 UTC (rev 1867)
@@ -484,7 +484,7 @@
return ret;
}
- private static void appendPosExamples(File file, List<Individual> examples) {
+ public static void appendPosExamples(File file, List<Individual> examples) {
StringBuffer content = new StringBuffer();
for(Individual example : examples) {
if(learnCarcinogenic)
@@ -495,7 +495,7 @@
Files.appendFile(file, content.toString());
}
- private static void appendNegExamples(File file, List<Individual> examples) {
+ public static void appendNegExamples(File file, List<Individual> examples) {
StringBuffer content = new StringBuffer();
for(Individual example : examples) {
if(learnCarcinogenic)
Modified: trunk/src/dl-learner/org/dllearner/examples/MonogenicDiseases.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/examples/MonogenicDiseases.java 2009-09-28 07:30:22 UTC (rev 1866)
+++ trunk/src/dl-learner/org/dllearner/examples/MonogenicDiseases.java 2009-09-28 14:35:48 UTC (rev 1867)
@@ -26,15 +26,23 @@
import java.sql.ResultSet;
import java.sql.SQLException;
import java.sql.Statement;
+import java.util.LinkedList;
+import java.util.List;
import java.util.prefs.BackingStoreException;
import java.util.prefs.Preferences;
import org.dllearner.core.owl.ClassAssertionAxiom;
+import org.dllearner.core.owl.Datatype;
+import org.dllearner.core.owl.DatatypeProperty;
+import org.dllearner.core.owl.DatatypePropertyDomainAxiom;
+import org.dllearner.core.owl.DatatypePropertyRangeAxiom;
+import org.dllearner.core.owl.DoubleDatatypePropertyAssertion;
import org.dllearner.core.owl.Individual;
import org.dllearner.core.owl.KB;
import org.dllearner.core.owl.NamedClass;
import org.dllearner.core.owl.SubClassAxiom;
import org.dllearner.reasoning.OWLAPIReasoner;
+import org.dllearner.utilities.Files;
import org.dllearner.utilities.Helper;
import org.ini4j.IniFile;
@@ -49,6 +57,7 @@
private static URI ontologyURI = URI.create("http://dl-learner.org/mutation");
private static File owlFile = new File("examples/mutation/mutation.owl");
+ private static File confFile = new File("examples/mutation/mutation.conf");
public static void main(String[] args) throws ClassNotFoundException, BackingStoreException, SQLException {
@@ -97,8 +106,49 @@
NamedClass protHydroDecClass = new NamedClass(getURI("ProteinHydroDecreasingMutation"));
kb.addAxiom(new SubClassAxiom(protHydroIncClass, mutationClass));
kb.addAxiom(new SubClassAxiom(protHydroUnchangedClass, mutationClass));
- kb.addAxiom(new SubClassAxiom(protHydroDecClass, mutationClass));
+ kb.addAxiom(new SubClassAxiom(protHydroDecClass, mutationClass));
+ // polarity
+ NamedClass protPolIncClass = new NamedClass(getURI("ProteinPolarityIncreasingMutation"));
+ NamedClass protPolUnchangedClass = new NamedClass(getURI("ProteinPolarityUnchangedMutation"));
+ NamedClass protPolDecClass = new NamedClass(getURI("ProteinPolarityDecreasingMutation"));
+ kb.addAxiom(new SubClassAxiom(protPolIncClass, mutationClass));
+ kb.addAxiom(new SubClassAxiom(protPolUnchangedClass, mutationClass));
+ kb.addAxiom(new SubClassAxiom(protPolDecClass, mutationClass));
+
+ // score
+ DatatypeProperty scoreProp = new DatatypeProperty(getURI("modifScore"));
+ kb.addAxiom(new DatatypePropertyDomainAxiom(scoreProp, mutationClass));
+ kb.addAxiom(new DatatypePropertyRangeAxiom(scoreProp, Datatype.DOUBLE));
+
+ // g_p
+ NamedClass gpIncClass = new NamedClass(getURI("GPIncreasingMutation"));
+ NamedClass gpUnchangedClass = new NamedClass(getURI("GPUnchangedMutation"));
+ NamedClass gpDecClass = new NamedClass(getURI("GPDecreasingMutation"));
+ kb.addAxiom(new SubClassAxiom(gpIncClass, mutationClass));
+ kb.addAxiom(new SubClassAxiom(gpUnchangedClass, mutationClass));
+ kb.addAxiom(new SubClassAxiom(gpDecClass, mutationClass));
+
+ // conservation_wt
+ DatatypeProperty conservationWTProp = new DatatypeProperty(getURI("convservationWT"));
+ kb.addAxiom(new DatatypePropertyDomainAxiom(conservationWTProp, mutationClass));
+ kb.addAxiom(new DatatypePropertyRangeAxiom(conservationWTProp, Datatype.DOUBLE));
+
+ // conservation_mut
+ DatatypeProperty conservationMutProp = new DatatypeProperty(getURI("convservationMut"));
+ kb.addAxiom(new DatatypePropertyDomainAxiom(conservationMutProp, mutationClass));
+ kb.addAxiom(new DatatypePropertyRangeAxiom(conservationMutProp, Datatype.DOUBLE));
+
+ // freq_at_pos
+ DatatypeProperty freqAtPosProp = new DatatypeProperty(getURI("freqAtPos"));
+ kb.addAxiom(new DatatypePropertyDomainAxiom(freqAtPosProp, mutationClass));
+ kb.addAxiom(new DatatypePropertyRangeAxiom(freqAtPosProp, Datatype.DOUBLE));
+
+ // cluster_5res_size
+ DatatypeProperty cluster5ResSizeProp = new DatatypeProperty(getURI("cluster_5res_size"));
+ kb.addAxiom(new DatatypePropertyDomainAxiom(cluster5ResSizeProp, mutationClass));
+ kb.addAxiom(new DatatypePropertyRangeAxiom(cluster5ResSizeProp, Datatype.DOUBLE));
+
// select all data
Statement stmt = conn.createStatement();
ResultSet rs = stmt.executeQuery("SELECT * FROM " + table);
@@ -125,10 +175,39 @@
kb.addAxiom(new ClassAssertionAxiom(protChargeChangedClass, mutationInd));
}
- // size change is represented via 3 classes
+ // hydro...
String modifHydro = rs.getString("modif_hydrophobicity");
convertThreeValuedColumn(kb, mutationInd, modifHydro, protHydroIncClass, protHydroUnchangedClass, protHydroDecClass);
-
+
+ // polarity
+ String modifPolarity = rs.getString("modif_polarity");
+ convertThreeValuedColumn(kb, mutationInd, modifPolarity, protPolIncClass, protPolUnchangedClass, protPolDecClass);
+
+ // modif_score
+ double modifScore = rs.getDouble("modif_score");
+ kb.addAxiom(new DoubleDatatypePropertyAssertion(scoreProp, mutationInd, modifScore));
+
+ // g_p
+ String gp = rs.getString("g_p");
+ convertThreeValuedColumn(kb, mutationInd, gp, gpIncClass, gpUnchangedClass, gpDecClass);
+
+ // modif_score
+ double conservationWT = rs.getDouble("conservation_wt");
+ kb.addAxiom(new DoubleDatatypePropertyAssertion(conservationWTProp, mutationInd, conservationWT));
+
+ // modif_score
+ double conservationMut = rs.getDouble("conservation_mut");
+ kb.addAxiom(new DoubleDatatypePropertyAssertion(conservationMutProp, mutationInd, conservationMut));
+
+ // freq_at_pos
+ double freqAtPos = rs.getDouble("freq_at_pos");
+ kb.addAxiom(new DoubleDatatypePropertyAssertion(freqAtPosProp, mutationInd, freqAtPos));
+
+ // freq_at_pos
+ double cluster5ResSize = rs.getDouble("cluster_5res_size");
+ kb.addAxiom(new DoubleDatatypePropertyAssertion(cluster5ResSizeProp, mutationInd, cluster5ResSize));
+
+
count++;
}
@@ -139,8 +218,39 @@
long writeDuration = System.nanoTime() - startWriteTime;
System.out.println("OK (time: " + Helper.prettyPrintNanoSeconds(writeDuration) + "; file size: " + owlFile.length()/1024 + " KB).");
+ // selecting examples
+ // -> only a fraction of examples are selected as positive/negative
+ rs = stmt.executeQuery("SELECT * FROM " + table + " WHERE " //lower(phenotype) not like 'polymorphism' AND "
+ + " (gain_contact is not null) && (gain_contact != 0)");
+ List<Individual> posExamples = new LinkedList<Individual>();
+ List<Individual> negExamples = new LinkedList<Individual>();
+ while(rs.next()) {
+ int mutationID = rs.getInt("id");
+ String phenotype = rs.getString("phenotype");
+ if(phenotype.toLowerCase().contains("polymorphism")) {
+ negExamples.add(new Individual(getURI("mutation" + mutationID)));
+ } else {
+ posExamples.add(new Individual(getURI("mutation" + mutationID)));
+ }
+ }
+
+ // writing conf file
+ Files.clearFile(confFile);
+ String confHeader = "import(\"" + owlFile.getName() + "\");\n\n";
+ confHeader += "reasoner = fastInstanceChecker;\n";
+ confHeader += "algorithm = refexamples;\n";
+ confHeader += "refexamples.noisePercentage = 31;\n";
+ confHeader += "refexamples.startClass = \"" + getURI("Mutation") + "\";\n";
+ confHeader += "refexamples.writeSearchTree = false;\n";
+ confHeader += "refexamples.searchTreeFile = \"log/mutation/searchTree.log\";\n";
+ confHeader += "\n";
+ Files.appendFile(confFile, confHeader);
+ Carcinogenesis.appendPosExamples(confFile, posExamples);
+ Carcinogenesis.appendNegExamples(confFile, negExamples);
+
long runTime = System.nanoTime() - startTime;
System.out.println("Database successfully converted in " + Helper.prettyPrintNanoSeconds(runTime) + ".");
+
}
// a table column with values "+", "=", "-" is converted to subclasses
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