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[DL-Learner SVN] SF.net SVN: dl-learner:[2357] trunk
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From: <jen...@us...> - 2010-10-08 13:04:23
|
Revision: 2357
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=2357&view=rev
Author: jenslehmann
Date: 2010-10-08 13:04:14 +0000 (Fri, 08 Oct 2010)
Log Message:
-----------
- org.dllearner.examples package now only exists in scripts module
- merged modifications on this package (always used highest revision)
Added Paths:
-----------
trunk/scripts/src/main/java/org/dllearner/examples/FlagScript.java
trunk/scripts/src/main/java/org/dllearner/examples/MonogenicDiseases.java
trunk/scripts/src/main/java/org/dllearner/examples/Script.java
Removed Paths:
-------------
trunk/components-core/src/main/java/org/dllearner/examples/
trunk/scripts/src/main/java/org/dllearner/examples/MonogenicDiseases.java
Copied: trunk/scripts/src/main/java/org/dllearner/examples/FlagScript.java (from rev 2356, trunk/components-core/src/main/java/org/dllearner/examples/flags/FlagScript.java)
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/examples/FlagScript.java (rev 0)
+++ trunk/scripts/src/main/java/org/dllearner/examples/FlagScript.java 2010-10-08 13:04:14 UTC (rev 2357)
@@ -0,0 +1,22 @@
+/**
+ *
+ */
+package org.dllearner.examples.flags;
+
+import org.dllearner.examples.flags.Script;
+
+/**
+ * @author flo
+ *
+ */
+public class FlagScript {
+
+ /**
+ * @param args
+ */
+ public static void main(String[] args) {
+ // TODO Auto-generated method stub
+ Script.createKB();
+ }
+
+}
Deleted: trunk/scripts/src/main/java/org/dllearner/examples/MonogenicDiseases.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/examples/MonogenicDiseases.java 2010-10-08 11:26:35 UTC (rev 2356)
+++ trunk/scripts/src/main/java/org/dllearner/examples/MonogenicDiseases.java 2010-10-08 13:04:14 UTC (rev 2357)
@@ -1,464 +0,0 @@
-/**
- * Copyright (C) 2007-2009, Jens Lehmann
- *
- * This file is part of DL-Learner.
- *
- * DL-Learner is free software; you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation; either version 3 of the License, or
- * (at your option) any later version.
- *
- * DL-Learner is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
- *
- */
-package org.dllearner.examples;
-
-import java.io.File;
-import java.sql.Connection;
-import java.sql.DriverManager;
-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;
-import org.semanticweb.owlapi.model.IRI;
-
-/**
- * Converts SM2PH database to an OWL ontology. To run the script, please
- * copy mutant.ini.dist to mutant.ini first and adapt the database connection.
- *
- * @author Jens Lehmann
- *
- */
-public class MonogenicDiseases {
-
- private static IRI ontologyURI = IRI.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");
-
- // whether to generate a class containing the positive examples
- private static boolean generatePosExampleClass = true;
- // set to true if accessing PostreSQL and false for MySQL
- private static boolean pgSQL = true;
- // generate fragment => limits the number of individuals in the ontology
- // to speed up learning
-// private static boolean onlyFragment = true;
-
- public static void main(String[] args) throws ClassNotFoundException, BackingStoreException, SQLException {
-
- // reading values for db connection from ini file
- String iniFile = "src/dl-learner/org/dllearner/examples/mutation.ini";
- Preferences prefs = new IniFile(new File(iniFile));
- String dbServer = prefs.node("database").get("server", null);
- String dbName = prefs.node("database").get("db", null);
- String dbPort = prefs.node("database").get("port", null);
- String dbUser = prefs.node("database").get("user", null);
- String dbPass = prefs.node("database").get("pass", null);
- String table = prefs.node("database").get("table", null);
-
- // connect to database
- String url = "jdbc:";
- if(pgSQL) {
- Class.forName("org.postgresql.Driver");
- // adapt the port if necessary
- url += "postgresql://"+dbServer+":"+dbPort+"/"+dbName;
- } else {
- Class.forName("com.mysql.jdbc.Driver");
- url += "mysql://"+dbServer+":"+dbPort+"/"+dbName;
- }
- Connection conn = DriverManager.getConnection(url, dbUser, dbPass);
- System.out.println("Successfully connected to database.");
-
- // prepare ontology
- long startTime = System.nanoTime();
- KB kb = new KB();
- NamedClass mutationClass = new NamedClass(getURI("Mutation"));
-
- NamedClass deleteriousMutationClass = new NamedClass(getURI("DeletoriousMutation"));
-
- // size change
- NamedClass protSizeIncClass = new NamedClass(getURI("ProteinSizeIncreasingMutation"));
- NamedClass protSizeUnchangedClass = new NamedClass(getURI("ProteinSizeUnchangedMutation"));
- NamedClass protSizeDecClass = new NamedClass(getURI("ProteinSizeDecreasingMutation"));
- kb.addAxiom(new SubClassAxiom(protSizeIncClass, mutationClass));
- kb.addAxiom(new SubClassAxiom(protSizeUnchangedClass, mutationClass));
- kb.addAxiom(new SubClassAxiom(protSizeDecClass, mutationClass));
-
- // charge
- NamedClass protChargeIncClass = new NamedClass(getURI("ProteinChargeIncreasingMutation"));
- NamedClass protChargeUnchangedClass = new NamedClass(getURI("ProteinChargeUnchangedMutation"));
- NamedClass protChargeDecClass = new NamedClass(getURI("ProteinChargeDecreasingMutation"));
- NamedClass protChargeChangedClass = new NamedClass(getURI("ProteinChargeChangedMutation"));
- kb.addAxiom(new SubClassAxiom(protChargeIncClass, mutationClass));
- kb.addAxiom(new SubClassAxiom(protChargeUnchangedClass, mutationClass));
- kb.addAxiom(new SubClassAxiom(protChargeDecClass, mutationClass));
- kb.addAxiom(new SubClassAxiom(protChargeChangedClass, mutationClass));
- // TODO: maybe inc and plus are subclasses of changed
-
- // hydrophobicity
- NamedClass protHydroIncClass = new NamedClass(getURI("ProteinHydroIncreasingMutation"));
- NamedClass protHydroUnchangedClass = new NamedClass(getURI("ProteinHydroUnchangedMutation"));
- NamedClass protHydroDecClass = new NamedClass(getURI("ProteinHydroDecreasingMutation"));
- kb.addAxiom(new SubClassAxiom(protHydroIncClass, mutationClass));
- kb.addAxiom(new SubClassAxiom(protHydroUnchangedClass, 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("cluster5resSize"));
- kb.addAxiom(new DatatypePropertyDomainAxiom(cluster5ResSizeProp, mutationClass));
- kb.addAxiom(new DatatypePropertyRangeAxiom(cluster5ResSizeProp, Datatype.DOUBLE));
-
- // secondary_struc
- NamedClass scHelixClass = new NamedClass(getURI("SCHelixMutation"));
- NamedClass scSheetClass = new NamedClass(getURI("SCSheetMutation"));
- NamedClass scUndeterminedClass = new NamedClass(getURI("SCUndeterminedMutation"));
- kb.addAxiom(new SubClassAxiom(scHelixClass, mutationClass));
- kb.addAxiom(new SubClassAxiom(scSheetClass, mutationClass));
- kb.addAxiom(new SubClassAxiom(scUndeterminedClass, mutationClass));
-
- // gain_contact
- DatatypeProperty gainContactProp = new DatatypeProperty(getURI("gainContact"));
- kb.addAxiom(new DatatypePropertyDomainAxiom(gainContactProp, mutationClass));
- kb.addAxiom(new DatatypePropertyRangeAxiom(gainContactProp, Datatype.DOUBLE));
-
- // lost_contact
- DatatypeProperty lostContactProp = new DatatypeProperty(getURI("lostContact"));
- kb.addAxiom(new DatatypePropertyDomainAxiom(lostContactProp, mutationClass));
- kb.addAxiom(new DatatypePropertyRangeAxiom(lostContactProp, Datatype.DOUBLE));
-
- // identical_contact
- DatatypeProperty identicalContactProp = new DatatypeProperty(getURI("identicalContact"));
- kb.addAxiom(new DatatypePropertyDomainAxiom(identicalContactProp, mutationClass));
- kb.addAxiom(new DatatypePropertyRangeAxiom(identicalContactProp, Datatype.DOUBLE));
-
- // gain_n1_contact
- DatatypeProperty gainN1ContactProp = new DatatypeProperty(getURI("gainN1Contact"));
- kb.addAxiom(new DatatypePropertyDomainAxiom(gainN1ContactProp, mutationClass));
- kb.addAxiom(new DatatypePropertyRangeAxiom(gainN1ContactProp, Datatype.DOUBLE));
-
- // lost_n1_contact
- DatatypeProperty lostN1ContactProp = new DatatypeProperty(getURI("lostN1Contact"));
- kb.addAxiom(new DatatypePropertyDomainAxiom(lostN1ContactProp, mutationClass));
- kb.addAxiom(new DatatypePropertyRangeAxiom(lostN1ContactProp, Datatype.DOUBLE));
-
- // identical_n1_contact
- DatatypeProperty identicalN1ContactProp = new DatatypeProperty(getURI("identicalN1Contact"));
- kb.addAxiom(new DatatypePropertyDomainAxiom(identicalN1ContactProp, mutationClass));
- kb.addAxiom(new DatatypePropertyRangeAxiom(identicalN1ContactProp, Datatype.DOUBLE));
-
- // wt_accessibility
- DatatypeProperty wtAccessibilityProp = new DatatypeProperty(getURI("wtAccessibility"));
- kb.addAxiom(new DatatypePropertyDomainAxiom(wtAccessibilityProp, mutationClass));
- kb.addAxiom(new DatatypePropertyRangeAxiom(wtAccessibilityProp, Datatype.DOUBLE));
-
- // mut_accessibility
- DatatypeProperty mutAccessibilityProp = new DatatypeProperty(getURI("mutAccessibility"));
- kb.addAxiom(new DatatypePropertyDomainAxiom(mutAccessibilityProp, mutationClass));
- kb.addAxiom(new DatatypePropertyRangeAxiom(mutAccessibilityProp, Datatype.DOUBLE));
-
- // cluster3d_10
- DatatypeProperty cluster3D10Prop = new DatatypeProperty(getURI("cluster3d10"));
- kb.addAxiom(new DatatypePropertyDomainAxiom(cluster3D10Prop, mutationClass));
- kb.addAxiom(new DatatypePropertyRangeAxiom(cluster3D10Prop, Datatype.DOUBLE));
-
- // cluster3d_20
- DatatypeProperty cluster3D20Prop = new DatatypeProperty(getURI("cluster3d20"));
- kb.addAxiom(new DatatypePropertyDomainAxiom(cluster3D20Prop, mutationClass));
- kb.addAxiom(new DatatypePropertyRangeAxiom(cluster3D20Prop, Datatype.DOUBLE));
-
- // cluster3d_30
- DatatypeProperty cluster3D30Prop = new DatatypeProperty(getURI("cluster3d30"));
- kb.addAxiom(new DatatypePropertyDomainAxiom(cluster3D30Prop, mutationClass));
- kb.addAxiom(new DatatypePropertyRangeAxiom(cluster3D30Prop, Datatype.DOUBLE));
-
- // TODO: stability missing
-
- // reliability_deltag
- DatatypeProperty reliabilityDeltagProp = new DatatypeProperty(getURI("reliabilityDeltag"));
- kb.addAxiom(new DatatypePropertyDomainAxiom(reliabilityDeltagProp, mutationClass));
- kb.addAxiom(new DatatypePropertyRangeAxiom(reliabilityDeltagProp, Datatype.DOUBLE));
-
- if(generatePosExampleClass) {
- kb.addAxiom(new SubClassAxiom(deleteriousMutationClass, mutationClass));
- }
-
- // select data (restricted to pos/neg examples for efficiency)
- Statement stmt = conn.createStatement();
- ResultSet rs = null;
- if(pgSQL) {
- // join tables
- rs = stmt.executeQuery("SELECT * FROM fiche_mutant, mutants WHERE fiche_mutant.id = mutants.id AND(gain_contact is not null)");
- } else {
- rs = stmt.executeQuery("SELECT * FROM " + table + " WHERE (gain_contact is not null) AND (gain_contact != 0)");
- }
-
- int count = 0;
- while(rs.next()) {
- // generate an individual for each entry in the table
- int mutationID = rs.getInt("id");
- Individual mutationInd = new Individual(getURI("mutation" + mutationID));
-
- // size change is represented via 3 classes
- String modifSize = rs.getString("modif_size");
- convertThreeValuedColumn(kb, mutationInd, modifSize, protSizeIncClass, protSizeUnchangedClass, protSizeDecClass);
-
- // charge is done via 4 classes
- String modifCharge = rs.getString("modif_charge");
- if(modifCharge.equals("+")) {
- kb.addAxiom(new ClassAssertionAxiom(protChargeIncClass, mutationInd));
- } else if(modifCharge.equals("=")) {
- kb.addAxiom(new ClassAssertionAxiom(protChargeUnchangedClass, mutationInd));
- } else if(modifCharge.equals("-")) {
- kb.addAxiom(new ClassAssertionAxiom(protChargeDecClass, mutationInd));
- } else if(modifCharge.equals("!=")) {
- kb.addAxiom(new ClassAssertionAxiom(protChargeChangedClass, mutationInd));
- }
-
- // 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));
-
- // secondary struc
- String secStruc = rs.getString("secondary_struc");
- if(secStruc.equals("HELIX")) {
- kb.addAxiom(new ClassAssertionAxiom(scHelixClass, mutationInd));
- } else if(secStruc.equals("SHEET")) {
- kb.addAxiom(new ClassAssertionAxiom(scSheetClass, mutationInd));
- } else if(secStruc.equals("0")) {
- kb.addAxiom(new ClassAssertionAxiom(scUndeterminedClass, mutationInd));
- }
-
- // TODO: Wert null soll hier auch vorkommen, aber existiert in der DB nicht.
- // gain_contact
- double gainContact = rs.getDouble("gain_contact");
- kb.addAxiom(new DoubleDatatypePropertyAssertion(gainContactProp, mutationInd, gainContact));
-
- // lost_contact
- double lostContact = rs.getDouble("lost_contact");
- kb.addAxiom(new DoubleDatatypePropertyAssertion(lostContactProp, mutationInd, lostContact));
-
- // identical_contact
- double identicalContact = rs.getDouble("identical_contact");
- kb.addAxiom(new DoubleDatatypePropertyAssertion(identicalContactProp, mutationInd, identicalContact));
-
- // gain_n1_contact
- double gainN1Contact = rs.getDouble("gain_n1_contact");
- kb.addAxiom(new DoubleDatatypePropertyAssertion(gainN1ContactProp, mutationInd, gainN1Contact));
-
- // lost_n1_contact
- double lostN1Contact = rs.getDouble("lost_n1_contact");
- kb.addAxiom(new DoubleDatatypePropertyAssertion(lostN1ContactProp, mutationInd, lostN1Contact));
-
- // identical_n1_contact
- double identicalN1Contact = rs.getDouble("identical_n1_contact");
- kb.addAxiom(new DoubleDatatypePropertyAssertion(identicalN1ContactProp, mutationInd, identicalN1Contact));
-
- // TODO Vorsicht bei 0-Werten in den weitern Feldern (klären, ob in dem
- // Fall gar nichts geschrieben werden soll)
-
- // wt_accessibility
- double wtAccessibility = rs.getDouble("wt_accessibility");
- kb.addAxiom(new DoubleDatatypePropertyAssertion(wtAccessibilityProp, mutationInd, wtAccessibility));
-
- // mut_accessibility
- double mutAccessibility = rs.getDouble("mut_accessibility");
- kb.addAxiom(new DoubleDatatypePropertyAssertion(mutAccessibilityProp, mutationInd, mutAccessibility));
-
- // cluster3d_10
- double cluster3D10 = rs.getDouble("cluster3d_10");
- kb.addAxiom(new DoubleDatatypePropertyAssertion(cluster3D10Prop, mutationInd, cluster3D10));
-
- // cluster3d_20
- double cluster3D20 = rs.getDouble("cluster3d_20");
- kb.addAxiom(new DoubleDatatypePropertyAssertion(cluster3D20Prop, mutationInd, cluster3D20));
-
- // cluster3d_30
- double cluster3D30 = rs.getDouble("cluster3d_30");
- kb.addAxiom(new DoubleDatatypePropertyAssertion(cluster3D30Prop, mutationInd, cluster3D30));
-
- // TODO: stability missing
-
- // reliability_deltag
- double reliabilityDeltag = rs.getDouble("reliability_deltag");
- kb.addAxiom(new DoubleDatatypePropertyAssertion(reliabilityDeltagProp, mutationInd, reliabilityDeltag));
-
- // generate a class with all positive examples (optional)
- if(generatePosExampleClass) {
- String phenotype = rs.getString("phenotype");
- if(!phenotype.toLowerCase().contains("polymorphism")) {
- kb.addAxiom(new ClassAssertionAxiom(deleteriousMutationClass, mutationInd));
- }
- }
-
-
- count++;
- }
-
- // writing generated knowledge base
- System.out.print("Writing OWL file ... ");
- long startWriteTime = System.nanoTime();
- OWLAPIReasoner.exportKBToOWL(owlFile, kb, ontologyURI);
- long writeDuration = System.nanoTime() - startWriteTime;
- System.out.println("OK (entities: " + count + "; time: " + Helper.prettyPrintNanoSeconds(writeDuration) + "; file size: " + owlFile.length()/1024 + " KB).");
-
- // selecting examples
- // -> only a fraction of examples are selected as positive/negative
- if(pgSQL) {
- rs = stmt.executeQuery("SELECT * FROM fiche_mutant, mutants WHERE fiche_mutant.id=mutants.id AND " //lower(phenotype) not like 'polymorphism' AND "
- + " (gain_contact is not null)"); // AND (gain_contact != 0)");
- } else {
- rs = stmt.executeQuery("SELECT * FROM " + table + " WHERE " //lower(phenotype) not like 'polymorphism' AND "
- + " (gain_contact is not null) AND (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 += "problem = classLearning;\n";
- confHeader += "classLearning.classToDescribe = \"" + deleteriousMutationClass + "\";\n";
- confHeader += "classLearning.accuracyMethod = \"fmeasure\";\n";
- confHeader += "classLearning.approxAccuracy = 0.03;\n";
-
-// confHeader += "problem = posNegLPStandard;\n";
-// confHeader += "posNegLPStandard.useApproximations = true;\n";
-// confHeader += "posNegLPStandard.accuracyMethod = \"fmeasure\";\n";
-// confHeader += "posNegLPStandard.approxAccuracy = 0.03;\n";
-
- confHeader += "algorithm = celoe;\n";
- confHeader += "celoe.maxExecutionTimeInSeconds = 10;\n";
- confHeader += "celoe.noisePercentage = 10;\n";
- confHeader += "celoe.singleSuggestionMode = true;\n";
- confHeader += "celoe.useNegation = true;\n";
-
-// confHeader += "refexamples.noisePercentage = 15;\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);
- if(!generatePosExampleClass) {
- Carcinogenesis.appendPosExamples(confFile, posExamples);
- Carcinogenesis.appendNegExamples(confFile, negExamples);
- }
-
- long runTime = System.nanoTime() - startTime;
- System.out.println("Conf file written with " + posExamples.size() + " positive and " + negExamples.size() + " negative examples.");
- System.out.println("Database successfully converted in " + Helper.prettyPrintNanoSeconds(runTime) + ".");
-
- }
-
- // a table column with values "+", "=", "-" is converted to subclasses
- private static void convertThreeValuedColumn(KB kb, Individual mutationInd, String value, NamedClass plusClass, NamedClass equalClass, NamedClass minusClass) {
- if(value.equals("+")) {
- kb.addAxiom(new ClassAssertionAxiom(plusClass, mutationInd));
- } else if(value.equals("=")) {
- kb.addAxiom(new ClassAssertionAxiom(equalClass, mutationInd));
- } else if(value.equals("-")) {
- kb.addAxiom(new ClassAssertionAxiom(minusClass, mutationInd));
- }
- }
-
- private static String getURI(String name) {
- return ontologyURI + "#" + name;
- }
-}
Copied: trunk/scripts/src/main/java/org/dllearner/examples/MonogenicDiseases.java (from rev 2356, trunk/components-core/src/main/java/org/dllearner/examples/MonogenicDiseases.java)
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/examples/MonogenicDiseases.java (rev 0)
+++ trunk/scripts/src/main/java/org/dllearner/examples/MonogenicDiseases.java 2010-10-08 13:04:14 UTC (rev 2357)
@@ -0,0 +1,762 @@
+/**
+ * Copyright (C) 2007-2009, Jens Lehmann
+ *
+ * This file is part of DL-Learner.
+ *
+ * DL-Learner is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * DL-Learner is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+package org.dllearner.examples;
+
+import java.io.File;
+import java.sql.Connection;
+import java.sql.DriverManager;
+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;
+import org.semanticweb.owlapi.model.IRI;
+
+/**
+ * Converts SM2PH database to an OWL ontology. To run the script, please
+ * copy mutant.ini.dist to mutant.ini first and adapt the database connection.
+ *
+ * @author Jens Lehmann
+ *
+ */
+public class MonogenicDiseases {
+
+//---> OPTIONS:
+ private static int algorithmus = 1; // 1 = pos/neg Algorithmus 2 = Celoe
+ private static boolean writeAlephFiles = true; // Add AlephFiles
+ private static boolean writeYYFiles = true; // Add YinYangFiles
+ private static int posEx = 25; // Number of pos-Ex.
+ private static int negEx = 25; // Number of neg-Ex.
+ private static boolean cvAleph = true; // add Files for Aleph 10-Fold Cross Validation
+
+//<--- OPTIONS end
+
+ private static IRI ontologyURI = IRI.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");
+ private static File badFile = new File("examples/mutation/mutation1.n"); // AlephFile
+ private static File posFile = new File("examples/mutation/mutation1.f"); // AlephFile
+ private static File yybadFile = new File("examples/mutation/mutationNegatives.txt"); //YYFile
+ private static File yyposFile = new File("examples/mutation/mutationPositives.txt"); //YYFile
+
+ private static File split1n = new File("examples/mutation/split1.n");
+ private static File split1f = new File("examples/mutation/split1.f");
+ private static File split2n = new File("examples/mutation/split2.n");
+ private static File split2f = new File("examples/mutation/split2.f");
+ private static File split3n = new File("examples/mutation/split3.n");
+ private static File split3f = new File("examples/mutation/split3.f");
+ private static File split4n = new File("examples/mutation/split4.n");
+ private static File split4f = new File("examples/mutation/split4.f");
+ private static File split5n = new File("examples/mutation/split5.n");
+ private static File split5f = new File("examples/mutation/split5.f");
+ private static File split6n = new File("examples/mutation/split6.n");
+ private static File split6f = new File("examples/mutation/split6.f");
+ private static File split7n = new File("examples/mutation/split7.n");
+ private static File split7f = new File("examples/mutation/split7.f");
+ private static File split8n = new File("examples/mutation/split8.n");
+ private static File split8f = new File("examples/mutation/split8.f");
+ private static File split9n = new File("examples/mutation/split9.n");
+ private static File split9f = new File("examples/mutation/split9.f");
+ private static File split10n = new File("examples/mutation/split10.n");
+ private static File split10f = new File("examples/mutation/split10.f");
+
+
+
+ // whether to generate a class containing the positive examples
+ private static boolean generatePosExampleClass = false;
+ // set to true if accessing PostreSQL and false for MySQL
+ private static boolean pgSQL = true;
+ // generate fragment => limits the number of individuals in the ontology
+ // to speed up learning
+ private static boolean learnMutation = true;
+ // private static boolean onlyFragment = true;
+
+ public static void main(String[] args) throws ClassNotFoundException, BackingStoreException, SQLException {
+
+ if (algorithmus == 1) { // LearnAlgo-Check
+ generatePosExampleClass = false;
+ }
+
+ if (algorithmus == 2) { // LearnAlgo-Check
+ generatePosExampleClass = true;
+ }
+
+
+ // reading values for db connection from ini file
+ String iniFile = "src/dl-learner/org/dllearner/examples/mutation.ini";
+ Preferences prefs = new IniFile(new File(iniFile));
+ String dbServer = prefs.node("database").get("server", null);
+ String dbName = prefs.node("database").get("db", null);
+ String dbPort = prefs.node("database").get("port", null);
+ String dbUser = prefs.node("database").get("user", null);
+ String dbPass = prefs.node("database").get("pass", null);
+ String table = prefs.node("database").get("table", null);
+
+ // connect to database
+ String url = "jdbc:";
+ if(pgSQL) {
+ Class.forName("org.postgresql.Driver");
+ // adapt the port if necessary
+ url += "postgresql://"+dbServer+":"+dbPort+"/"+dbName;
+ } else {
+ Class.forName("com.mysql.jdbc.Driver");
+ url += "mysql://"+dbServer+":"+dbPort+"/"+dbName;
+ }
+ Connection conn = DriverManager.getConnection(url, dbUser, dbPass);
+ System.out.println("Successfully connected to database.");
+
+ // prepare ontology
+ long startTime = System.nanoTime();
+ KB kb = new KB();
+ NamedClass mutationClass = new NamedClass(getURI("Mutation"));
+
+ NamedClass deleteriousMutationClass = new NamedClass(getURI("DeletoriousMutation"));
+
+ // size change
+ NamedClass protSizeIncClass = new NamedClass(getURI("ProteinSizeIncreasingMutation"));
+ NamedClass protSizeUnchangedClass = new NamedClass(getURI("ProteinSizeUnchangedMutation"));
+ NamedClass protSizeDecClass = new NamedClass(getURI("ProteinSizeDecreasingMutation"));
+ kb.addAxiom(new SubClassAxiom(protSizeIncClass, mutationClass));
+ kb.addAxiom(new SubClassAxiom(protSizeUnchangedClass, mutationClass));
+ kb.addAxiom(new SubClassAxiom(protSizeDecClass, mutationClass));
+
+ // charge
+ NamedClass protChargeIncClass = new NamedClass(getURI("ProteinChargeIncreasingMutation"));
+ NamedClass protChargeUnchangedClass = new NamedClass(getURI("ProteinChargeUnchangedMutation"));
+ NamedClass protChargeDecClass = new NamedClass(getURI("ProteinChargeDecreasingMutation"));
+ NamedClass protChargeChangedClass = new NamedClass(getURI("ProteinChargeChangedMutation"));
+ kb.addAxiom(new SubClassAxiom(protChargeIncClass, mutationClass));
+ kb.addAxiom(new SubClassAxiom(protChargeUnchangedClass, mutationClass));
+ kb.addAxiom(new SubClassAxiom(protChargeDecClass, mutationClass));
+ kb.addAxiom(new SubClassAxiom(protChargeChangedClass, mutationClass));
+ // TODO: maybe inc and plus are subclasses of changed
+
+ // hydrophobicity
+ NamedClass protHydroIncClass = new NamedClass(getURI("ProteinHydroIncreasingMutation"));
+ NamedClass protHydroUnchangedClass = new NamedClass(getURI("ProteinHydroUnchangedMutation"));
+ NamedClass protHydroDecClass = new NamedClass(getURI("ProteinHydroDecreasingMutation"));
+ kb.addAxiom(new SubClassAxiom(protHydroIncClass, mutationClass));
+ kb.addAxiom(new SubClassAxiom(protHydroUnchangedClass, 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("cluster5resSize"));
+ kb.addAxiom(new DatatypePropertyDomainAxiom(cluster5ResSizeProp, mutationClass));
+ kb.addAxiom(new DatatypePropertyRangeAxiom(cluster5ResSizeProp, Datatype.DOUBLE));
+
+ // secondary_struc
+ NamedClass scHelixClass = new NamedClass(getURI("SCHelixMutation"));
+ NamedClass scSheetClass = new NamedClass(getURI("SCSheetMutation"));
+ NamedClass scUndeterminedClass = new NamedClass(getURI("SCUndeterminedMutation"));
+ kb.addAxiom(new SubClassAxiom(scHelixClass, mutationClass));
+ kb.addAxiom(new SubClassAxiom(scSheetClass, mutationClass));
+ kb.addAxiom(new SubClassAxiom(scUndeterminedClass, mutationClass));
+
+ // gain_contact
+ DatatypeProperty gainContactProp = new DatatypeProperty(getURI("gainContact"));
+ kb.addAxiom(new DatatypePropertyDomainAxiom(gainContactProp, mutationClass));
+ kb.addAxiom(new DatatypePropertyRangeAxiom(gainContactProp, Datatype.DOUBLE));
+
+ // lost_contact
+ DatatypeProperty lostContactProp = new DatatypeProperty(getURI("lostContact"));
+ kb.addAxiom(new DatatypePropertyDomainAxiom(lostContactProp, mutationClass));
+ kb.addAxiom(new DatatypePropertyRangeAxiom(lostContactProp, Datatype.DOUBLE));
+
+ // identical_contact
+ DatatypeProperty identicalContactProp = new DatatypeProperty(getURI("identicalContact"));
+ kb.addAxiom(new DatatypePropertyDomainAxiom(identicalContactProp, mutationClass));
+ kb.addAxiom(new DatatypePropertyRangeAxiom(identicalContactProp, Datatype.DOUBLE));
+
+ // gain_n1_contact
+ DatatypeProperty gainN1ContactProp = new DatatypeProperty(getURI("gainN1Contact"));
+ kb.addAxiom(new DatatypePropertyDomainAxiom(gainN1ContactProp, mutationClass));
+ kb.addAxiom(new DatatypePropertyRangeAxiom(gainN1ContactProp, Datatype.DOUBLE));
+
+ // lost_n1_contact
+ DatatypeProperty lostN1ContactProp = new DatatypeProperty(getURI("lostN1Contact"));
+ kb.addAxiom(new DatatypePropertyDomainAxiom(lostN1ContactProp, mutationClass));
+ kb.addAxiom(new DatatypePropertyRangeAxiom(lostN1ContactProp, Datatype.DOUBLE));
+
+ // identical_n1_contact
+ DatatypeProperty identicalN1ContactProp = new DatatypeProperty(getURI("identicalN1Contact"));
+ kb.addAxiom(new DatatypePropertyDomainAxiom(identicalN1ContactProp, mutationClass));
+ kb.addAxiom(new DatatypePropertyRangeAxiom(identicalN1ContactProp, Datatype.DOUBLE));
+
+ // wt_accessibility
+ DatatypeProperty wtAccessibilityProp = new DatatypeProperty(getURI("wtAccessibility"));
+ kb.addAxiom(new DatatypePropertyDomainAxiom(wtAccessibilityProp, mutationClass));
+ kb.addAxiom(new DatatypePropertyRangeAxiom(wtAccessibilityProp, Datatype.DOUBLE));
+
+ // mut_accessibility
+ DatatypeProperty mutAccessibilityProp = new DatatypeProperty(getURI("mutAccessibility"));
+ kb.addAxiom(new DatatypePropertyDomainAxiom(mutAccessibilityProp, mutationClass));
+ kb.addAxiom(new DatatypePropertyRangeAxiom(mutAccessibilityProp, Datatype.DOUBLE));
+
+ // cluster3d_10
+ DatatypeProperty cluster3D10Prop = new DatatypeProperty(getURI("cluster3d10"));
+ kb.addAxiom(new DatatypePropertyDomainAxiom(cluster3D10Prop, mutationClass));
+ kb.addAxiom(new DatatypePropertyRangeAxiom(cluster3D10Prop, Datatype.DOUBLE));
+
+ // cluster3d_20
+ DatatypeProperty cluster3D20Prop = new DatatypeProperty(getURI("cluster3d20"));
+ kb.addAxiom(new DatatypePropertyDomainAxiom(cluster3D20Prop, mutationClass));
+ kb.addAxiom(new DatatypePropertyRangeAxiom(cluster3D20Prop, Datatype.DOUBLE));
+
+ // cluster3d_30
+ DatatypeProperty cluster3D30Prop = new DatatypeProperty(getURI("cluster3d30"));
+ kb.addAxiom(new DatatypePropertyDomainAxiom(cluster3D30Prop, mutationClass));
+ kb.addAxiom(new DatatypePropertyRangeAxiom(cluster3D30Prop, Datatype.DOUBLE));
+
+ // TODO: stability missing
+
+ // reliability_deltag
+ DatatypeProperty reliabilityDeltagProp = new DatatypeProperty(getURI("reliabilityDeltag"));
+ kb.addAxiom(new DatatypePropertyDomainAxiom(reliabilityDeltagProp, mutationClass));
+ kb.addAxiom(new DatatypePropertyRangeAxiom(reliabilityDeltagProp, Datatype.DOUBLE));
+
+ if(generatePosExampleClass) {
+ kb.addAxiom(new SubClassAxiom(deleteriousMutationClass, mutationClass));
+ }
+
+ // select data (restricted to pos/neg examples for efficiency)
+ Statement stmt = conn.createStatement();
+ ResultSet rs = null;
+ if(pgSQL) {
+ // join tables
+ rs = stmt.executeQuery("SELECT * FROM fiche_mutant, mutants WHERE fiche_mutant.id = mutants.id AND(gain_contact is not null)");
+ } else {
+ rs = stmt.executeQuery("SELECT * FROM " + table + " WHERE (gain_contact is not null) AND (gain_contact != 0)");
+ }
+
+int count = 1;
+int pos_count = 0;
+int neg_count = 1;
+
+
+ if (writeAlephFiles){ // Clear AlephFiles
+ Files.clearFile(badFile);
+ Files.clearFile(posFile);
+ }
+
+ if (writeYYFiles) { // Clear YinYangFiles
+ Files.clearFile(yybadFile);
+ Files.clearFile(yyposFile);
+ }
+
+ if (cvAleph) { // Clear Aleph CV-Files
+ Files.clearFile(split1n);
+ Files.clearFile(split1f);
+ Files.clearFile(split2n);
+ Files.clearFile(split2f);
+ Files.clearFile(split3n);
+ Files.clearFile(split3f);
+ Files.clearFile(split4n);
+ Files.clearFile(split4f);
+ Files.clearFile(split5n);
+ Files.clearFile(split5f);
+ Files.clearFile(split6n);
+ Files.clearFile(split6f);
+ Files.clearFile(split7n);
+ Files.clearFile(split7f);
+ Files.clearFile(split8n);
+ Files.clearFile(split8f);
+ Files.clearFile(split9n);
+ Files.clearFile(split9f);
+ Files.clearFile(split10n);
+ Files.clearFile(split10f);
+ }
+
+ int kp = 1; // k for CV positiv
+ int kn = 1; // k for CV negativ
+ int peps = posEx/10; // positiv Examples per Splitfile
+ int neps = negEx/10; // negative Examples per Splitfile
+ int aneg = 0; // aktuell negativ
+ int apos = 0; // aktuell positiv
+
+
+ while((rs.next()) && ((pos_count < posEx) || (neg_count < negEx))) {
+
+
+
+ // generate an individual for each entry in the table
+ int mutationID = rs.getInt("id");
+ Individual mutationInd = new Individual(getURI("mutation" + mutationID));
+
+
+ String pt = rs.getString("phenotype");
+ if ((pt.toLowerCase().contains("polymorphism"))&&( neg_count<=negEx )) {
+ if (writeAlephFiles) {
+ Files.appendFile(badFile, "deleterious(id"+mutationID+").\n");
+ }
+ if (writeYYFiles) {
+ Files.appendFile(yybadFile, "http://example.com/mutation/mutation#mutation"+mutationID+"\n");
+ }
+ if (cvAleph){
+ switch (kn) {
+ case 1:
+ aneg++;
+ Files.appendFile(split1n, "deleterious(id"+mutationID+").\n");
+ if (aneg == neps) {aneg = 0; kn++;}
+ break;
+ case 2:
+ aneg++;
+ Files.appendFile(split2n, "deleterious(id"+mutationID+").\n");
+ if (aneg == neps) {aneg = 0; kn++;}
+ break;
+ case 3:
+ aneg++;
+ Files.appendFile(split3n, "deleterious(id"+mutationID+").\n");
+ if (aneg == neps) {aneg = 0; kn++;}
+ break;
+ case 4:
+ aneg++;
+ Files.appendFile(split4n, "deleterious(id"+mutationID+").\n");
+ if (aneg == neps) {aneg = 0; kn++;}
+ break;
+ case 5:
+ aneg++;
+ Files.appendFile(split5n, "deleterious(id"+mutationID+").\n");
+ if (aneg == neps) {aneg = 0; kn++;}
+ break;
+ case 6:
+ aneg++;
+ Files.appendFile(split6n, "deleterious(id"+mutationID+").\n");
+ if (aneg == neps) {aneg = 0; kn++;}
+ break;
+ case 7:
+ aneg++;
+ Files.appendFile(split7n, "deleterious(id"+mutationID+").\n");
+ if (aneg == neps) {aneg = 0; kn++;}
+ break;
+ case 8:
+ aneg++;
+ Files.appendFile(split8n, "deleterious(id"+mutationID+").\n");
+ if (aneg == neps) {aneg = 0; kn++;}
+ break;
+ case 9:
+ aneg++;
+ Files.appendFile(split9n, "deleterious(id"+mutationID+").\n");
+ if (aneg == neps) {aneg = 0; kn++;}
+ break;
+ case 10:
+ aneg++;
+ Files.appendFile(split10n, "deleterious(id"+mutationID+").\n");
+// if (aneg == neps) {aneg = 0; kn++;}
+ break;
+// case 11: // without comment its round negExamples / 10
+// break;
+ }
+ }
+
+ neg_count++;
+ }
+ if ((!pt.toLowerCase().contains("polymorphism"))&& ( pos_count<=posEx)) {
+ if (writeAlephFiles) {
+ Files.appendFile(posFile, "deleterious(id"+mutationID+").\n");
+ }
+ if (writeYYFiles) {
+ Files.appendFile(yyposFile, "http://example.com/mutation/mutation#mutation"+mutationID+"\n");
+ }
+ if (cvAleph){
+ switch (kp) {
+ case 1:
+ apos++;
+ Files.appendFile(split1f, "deleterious(id"+mutationID+").\n");
+ if (apos == peps) {apos = 0; kp++;}
+ break;
+ case 2:
+ apos++;
+ Files.appendFile(split2f, "deleterious(id"+mutationID+").\n");
+ if (apos == peps) {apos = 0; kp++;}
+ break;
+ case 3:
+ apos++;
+ Files.appendFile(split3f, "deleterious(id"+mutationID+").\n");
+ if (apos == peps) {apos = 0; kp++;}
+ break;
+ case 4:
+ apos++;
+ Files.appendFile(split4f, "deleterious(id"+mutationID+").\n");
+ if (apos == peps) {apos = 0; kp++;}
+ break;
+ case 5:
+ apos++;
+ Files.appendFile(split5f, "deleterious(id"+mutationID+").\n");
+ if (apos == peps) {apos = 0; kp++;}
+ break;
+ case 6:
+ apos++;
+ Files.appendFile(split6f, "deleterious(id"+mutationID+").\n");
+ if (apos == peps) {apos = 0; kp++;}
+ break;
+ case 7:
+ apos++;
+ Files.appendFile(split7f, "deleterious(id"+mutationID+").\n");
+ if (apos == peps) {apos = 0; kp++;}
+ break;
+ case 8:
+ apos++;
+ Files.appendFile(split8f, "deleterious(id"+mutationID+").\n");
+ if (apos == peps) {apos = 0; kp++;}
+ break;
+ case 9:
+ apos++;
+ Files.appendFile(split9f, "deleterious(id"+mutationID+").\n");
+ if (apos == peps) {apos = 0; kp++;}
+ break;
+ case 10:
+ apos++;
+ Files.appendFile(split10f, "deleterious(id"+mutationID+").\n");
+// if (apos == peps) {apos = 0; kp++;}
+ break;
+// case 11: // without comments its round to posExamples / 10
+// break;
+ }
+ }
+
+
+ pos_count++;
+ }
+
+ if ((pt.toLowerCase().contains("polymorphism"))&&( neg_count > negEx )) {
+ continue;
+ }
+ if ((!pt.toLowerCase().contains("polymorphism"))&& ( pos_count > posEx)) {
+ continue;
+ }
+
+
+ // size change is represented via 3 classes
+ String modifSize = rs.getString("modif_size");
+ convertThreeValuedColumn(kb, mutationInd, modifSize, protSizeIncClass, protSizeUnchangedClass, protSizeDecClass);
+
+ // charge is done via 4 classes
+ String modifCharge = rs.getString("modif_charge");
+ if(modifCharge.equals("+")) {
+ kb.addAxiom(new ClassAssertionAxiom(protChargeIncClass, mutationInd));
+ } else if(modifCharge.equals("=")) {
+ kb.addAxiom(new ClassAssertionAxiom(protChargeUnchangedClass, mutationInd));
+ } else if(modifCharge.equals("-")) {
+ kb.addAxiom(new ClassAssertionAxiom(protChargeDecClass, mutationInd));
+ } else if(modifCharge.equals("!=")) {
+ kb.addAxiom(new ClassAssertionAxiom(protChargeChangedClass, mutationInd));
+ }
+
+ // 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));
+
+ // secondary struc
+ String secStruc = rs.getString("secondary_struc");
+ if(secStruc.equals("HELIX")) {
+ kb.addAxiom(new ClassAssertionAxiom(scHelixClass, mutationInd));
+ } else if(secStruc.equals("SHEET")) {
+ kb.addAxiom(new ClassAssertionAxiom(scSheetClass, mutationInd));
+ } else if(secStruc.equals("0")) {
+ kb.addAxiom(new ClassAssertionAxiom(scUndeterminedClass, mutationInd));
+ }
+
+ // TODO: Wert null soll hier auch vorkommen, aber existiert in der DB nicht.
+ // gain_contact
+ double gainContact = rs.getDouble("gain_contact");
+ kb.addAxiom(new DoubleDatatypePropertyAssertion(gainContactProp, mutationInd, gainContact));
+
+ // lost_contact
+ double lostContact = rs.getDouble("lost_contact");
+ kb.addAxiom(new DoubleDatatypePropertyAssertion(lostContactProp, mutationInd, lostContact));
+
+ // identical_contact
+ double identicalContact = rs.getDouble("identical_contact");
+ kb.addAxiom(new DoubleDatatypePropertyAssertion(identicalContactProp, mutationInd, identicalContact));
+
+ // gain_n1_contact
+ double gainN1Contact = rs.getDouble("gain_n1_contact");
+ kb.addAxiom(new DoubleDatatypePropertyAssertion(gainN1ContactProp, mutationInd, gainN1Contact));
+
+ // lost_n1_contact
+ double lostN1Contact = rs.getDouble("lost_n1_contact");
+ kb.addAxiom(new DoubleDatatypePropertyAssertion(lostN1ContactProp, mutationInd, lostN1Contact));
+
+ // identical_n1_contact
+ double identicalN1Contact = rs.getDouble("identical_n1_contact");
+ kb.addAxiom(new DoubleDatatypePropertyAssertion(identicalN1ContactProp, mutationInd, identicalN1Contact));
+
+ // TODO Vorsicht bei 0-Werten in den weitern Feldern (klaeren, ob in dem
+ // Fall gar nichts geschrieben werden soll)
+
+ // wt_accessibility
+ double wtAccessibility = rs.getDouble("wt_accessibility");
+ kb.addAxiom(new DoubleDatatypePropertyAssertion(wtAccessibilityProp, mutationInd, wtAccessibility));
+
+ // mut_accessibility
+ double mutAccessibility = rs.getDouble("mut_accessibility");
+ kb.addAxiom(new DoubleDatatypePropertyAssertion(mutAccessibilityProp, mutationInd, mutAccessibility));
+
+ // cluster3d_10
+ double cluster3D10 = rs.getDouble("cluster3d_10");
+ kb.addAxiom(new DoubleDatatypePropertyAssertion(cluster3D10Prop, mutationInd, cluster3D10));
+
+ // cluster3d_20
+ double cluster3D20 = rs.getDouble("cluster3d_20");
+ kb.addAxiom(new DoubleDatatypePropertyAssertion(cluster3D20Prop, mutationInd, cluster3D20));
+
+ // cluster3d_30
+ double cluster3D30 = rs.getDouble("cluster3d_30");
+ kb.addAxiom(new DoubleDatatypePropertyAssertion(cluster3D30Prop, mutationInd, cluster3D30));
+
+ // TODO: stability missing
+
+ // reliability_deltag
+ double reliabilityDeltag = rs.getDouble("reliability_deltag");
+ kb.addAxiom(new DoubleDatatypePropertyAssertion(reliabilityDeltagProp, mutationInd, reliabilityDeltag));
+
+ // generate a class with all positive examples (optional)
+ if(generatePosExampleClass) {
+ String phenotype = rs.getString("phenotype");
+
+
+ if(!phenotype.toLowerCase().contains("polymorphism")) {
+ kb.addAxiom(new ClassAssertionAxiom(deleteriousMutationClass, mutationInd));
+ }
+
+ }
+
+// String pt = rs.getString("phenotype");
+// if (pt.toLowerCase().contains("polymorphism")) { neg_count++; }
+// if (!pt.toLowerCase().contains("polymorphism")) { pos_count++; }
+
+
+ count++;
+ }
+
+ // writing generated knowledge base
+ System.out.print("Writing OWL file ... ");
+ long startWriteTime = System.nanoTime();
+ OWLAPIReasoner.exportKBToOWL(owlFile, kb, ontologyURI);
+ long writeDuration = System.nanoTime() - startWriteTime;
+ System.out.println("OK (entities: " + count + "; time: " + Helper.prettyPrintNanoSeconds(writeDuration) + "; file size: " + owlFile.length()/1024 + " KB).");
+
+
+
+ // selecting examples
+ // -> only a fraction of examples are selected as positive/negative
+ if(pgSQL) {
+ rs = stmt.executeQuery("SELECT * FROM fiche_mutant, mutants WHERE fiche_mutant.id=mutants.id AND " //lower(phenotype) not like 'polymorphism' AND "
+ + " (gain_contact is not null)"); // AND (gain_contact != 0)");
+ } else {
+ rs = stmt.executeQuery("SELECT * FROM " + table + " WHERE " //lower(phenotype) not like 'polymorphism' AND "
+ + " (gain_contact is not null) AND (gain_contact != 0)");
+ }
+ List<Individual> posExamples = new LinkedList<Individual>();
+ List<Individual> negExamples = new LinkedList<Individual>();
+
+count = 1;
+pos_count = 0;
+neg_count = 0;
+
+
+
+ while((rs.next()) && (pos_count < posEx) || (neg_count < negEx)) {
+ int mutationID = rs.getInt("id");
+ String phenotype = rs.getString("phenotype");
+// if(phenotype.toLowerCase().contains("polymorphism")) {
+// negExamples.add(new Individual(getURI("mutation" + mutationID))); neg_count++;
+// } else {
+// posExamples.add(new Individual(getURI("mutation" + mutationID))); pos_count++;
+// }
+
+ if((phenotype.toLowerCase().contains("polymorphism")) && (neg_count < negEx)) {
+ negExamples.add(new Individual(getURI("mutation" + mutationID))); neg_count++;
+ }
+ if((!phenotype.toLowerCase().contains("polymorphism")) && (pos_count < posEx)) {
+ posExamples.add(new Individual(getURI("mutation" + mutationID))); pos_count++;
+ }
+
+
+count++;
+ }
+
+ // writing conf file
+ Files.clearFile(confFile);
+ String confHeader = "import(\"" + owlFile.getName() + "\");\n\n";
+ confHeader += "reasoner = fastInstanceChecker;\n";
+
+ if (algorithmus == 1) {
+ confHeader += "problem = posNegLPStandard;\n";
+ confHeader += "posNegLPStandard.useApproximations = true;\n";
+ confHeader += "posNegLPStandard.accuracyMethod = \"fmeasure\";\n";
+ confHeader += "posNegLPStandard.approxAccuracy = 0.03;\n";
+ confHeader += "refexamples.noisePercentage = 15;\n";
+ confHeader += "refexamples.startClass = \"" + getURI("Mutation") + "\";\n";
+ confHeader += "refexamples.writeSearchTree = false;\n";
+ confHeader += "refexamples.searchTreeFile = \"log/mutation/searchTree.log\";\n";
+
+ confHeader += "\n";
+ }
+
+ if (algorithmus == 2)
+ {
+ confHeader += "problem = classLearning;\n";
+ confHeader += "classLearning.classToDescribe = \"" + deleteriousMutationClass + "\";\n";
+ confHeader += "classLearning.accuracyMethod = \"fmeasure\";\n";
+ confHeader += "classLearning.approxAccuracy = 0.03;\n";
+ confHeader += "algorithm = celoe;\n";
+ confHeader += "celoe.maxExecutionTimeInSeconds = 10;\n";
+ confHeader += "celoe.noisePercentage = 10;\n";
+ confHeader += "celoe.singleSuggestionMode = true;\n";
+ confHeader += "celoe.useNegation = true;\n";
+
+ confHeader += "\n";
+ }
+
+ Files.appendFile(confFile, confHeader);
+ if(!generatePosExampleClass) {
+ MonogenicDiseases.appendPosExamples(confFile, posExamples);
+ MonogenicDiseases.appendNegExamples(confFile, negExamples);
+ }
+
+ long runTime = System.nanoTime() - startTime;
+ System.out.println("Conf file written with " + posExamples.size() + " positive and " + negExamples.size() + " negative examples.");
+ System.out.println("Database successfully converted in " + Helper.prettyPrintNanoSeconds(runTime) + ".");
+
+ if (writeAlephFiles) System.out.println("Added Aleph Files.");
+ if (writeYYFiles) System.out.println("Added YinYang Files.");
+ if (cvAleph) System.out.println("Added Aleph Split Filles for 10-Fold CrossValidation.");
+
+ }
+
+ // a table column with values "+", "=", "-" is converted to subclasses
+ private static void convertThreeValuedColumn(KB kb, Individual mutationInd, String value, NamedClass plusClass, NamedClass equalClass, NamedClass minusClass) {
+ if(value.equals("+")) {
+ kb.addAxiom(new ClassAssertionAxiom(plusClass, mutationInd));
+ } else if(value.equals("=")) {
+ kb.addAxiom(new ClassAssertionAxiom(equalClass, mutationInd));
+ } else if(value.equals("-")) {
+ kb.addAxiom(new ClassAssertionAxiom(minusClass, mutationInd));
+ }
+ }
+
+ private static String getURI(String name) {
+ return ontologyURI + "#" + name;
+ }
+
+ public static void appendPosExamples(File file, List<Individual> examples) {
+ StringBuffer content = new StringBuffer();
+ for(Individual example : examples) {
+ if(learnMutation)
+ content.append("+\""+example.toString()+"\"\n");
+ else
+ content.append("-\""+example.toString()+"\"\n");
+ }
+ Files.appendFile(file, content.toString());
+ }
+
+ public static void appendNegExamples(File file, List<Individual> examples) {
+ StringBuffer content = new StringBuffer();
+ for(Individual example : examples) {
+ if(learnMutation)
+ content.append("-\""+example.toString()+"\"\n");
+ else
+ content.append("+\""+example.toString()+"\"\n");
+ }
+ Files.appendFile(file, content.toString());
+ }
+}
Copied: trunk/scripts/src/main/java/org/dllearner/examples/Script.java (from rev 2356, trunk/components-core/src/main/java/org/dllearner/examples/flags/Script.java)
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/examples/Script.java (rev 0)
+++ trunk/scripts/src/main/java/org/dllearner/examples/Script.java 2010-10-08 13:04:14 UTC (rev 2357)
@@ -0,0 +1,739 @@
+/**
+ *
+ */
+package org.dllearner.examples.flags;
+
+import org.dllearner.core.OntologyFormat;
+import org.dllearner.core.owl.BooleanDatatypePropertyAssertion;
+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.ObjectProperty;
+import org.dllearner.core.owl.ObjectPropertyAssertion;
+import org.dllearner.core.owl.ObjectPropertyDomainAxiom;
+import org.dllearner.core.owl.ObjectPropertyRangeAxiom;
+import org.dllearner.core.owl.StringDatatypePropertyAssertion;
+import org.semanticweb.owlapi.model.*;
+
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.HashMap;
+
+/**
+ * @author flo
+ *
+ */
+public class Script {
+
+ private static final String flagDataPath = "C:/temp/Uni/Semantic Web Praktikum 10/flag.data";
+ //private static final String flagNamesPath = "D:/Dokumente/Uni/Semantic Web Praktikum 10/flag.names";
+ private static final String kbOutputPath = "D:/Dokumente/develop/java/eclipseWorkspace/DL-Learner/examples/flags/flag.owl";
+ private static final String dataSeparator = ",";
+ //private static String ontoIri = "http://www.semanticweb.org/owlapi/ontologies/uniLpz/semWeb";
+
+ /*private static final String ontoFlagClassName = "Flag";
+ private static final String ontoCountryClassName = "Country";
+ private static String ontoLandmassClassName = "Landmass";
+ private static String ontoHemisphereClassName = "Hemisphere";
+ private static String ontoLanguageClassName = "Language";
+ private static String ontoLanguageGroupClassName = "LanguageGroup";
+ private static String ontoReligionClassName = "Religion";
+ private static String ontoReligionGroupClassName = "ReligionGroup";
+ private static String ontoColorClassName = "Color";*/
+ private static final String ontoFlagClassName = "Flag";
+ private static final String ontoCountryClassName = "";
+ private static String ontoLandmassClassName = "";
+ private static String ontoHemisphereClassName = "";
+ private static String ontoLanguageClassName = "";
+ private static String ontoLanguageGroupClassName = "";
+ private static String ontoReligionClassName = "";
+ private static String ontoReligionGroupClassName = "";
+ private static String ontoColorClassName = "";
+
+ private static final String iriSeperator = "#";
+
+ //private static OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
+ //private static OWLDataFactory factory = manager.getOWLDataFactory();
+
+ //OWLClass flagClass = factory.getOWLClass(IRI.create(ontoIri + iriSeperator + ontoFlagClassName));
+
+ private static final KB kb = new KB();
+ private static ArrayList<Individual> flags = new ArrayList<Individual>();
+ private static ArrayList<Individual> countries = new ArrayList<Individual>();
+
+
+ /*private static NamedClass Flag = new NamedClass(getIRI(onto...
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