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[DL-Learner SVN] SF.net SVN: dl-learner:[1874] trunk/src/dl-learner/org/dllearner/examples/ MonogenicDiseases.java
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From: <jen...@us...> - 2009-10-02 15:57:27
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Revision: 1874
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=1874&view=rev
Author: jenslehmann
Date: 2009-10-02 15:50:46 +0000 (Fri, 02 Oct 2009)
Log Message:
-----------
continued mutation database conversion
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/examples/MonogenicDiseases.java
Modified: trunk/src/dl-learner/org/dllearner/examples/MonogenicDiseases.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/examples/MonogenicDiseases.java 2009-10-02 14:47:52 UTC (rev 1873)
+++ trunk/src/dl-learner/org/dllearner/examples/MonogenicDiseases.java 2009-10-02 15:50:46 UTC (rev 1874)
@@ -145,13 +145,83 @@
kb.addAxiom(new DatatypePropertyRangeAxiom(freqAtPosProp, Datatype.DOUBLE));
// cluster_5res_size
- DatatypeProperty cluster5ResSizeProp = new DatatypeProperty(getURI("cluster_5res_size"));
+ DatatypeProperty cluster5ResSizeProp = new DatatypeProperty(getURI("cluster5resSize"));
kb.addAxiom(new DatatypePropertyDomainAxiom(cluster5ResSizeProp, mutationClass));
kb.addAxiom(new DatatypePropertyRangeAxiom(cluster5ResSizeProp, Datatype.DOUBLE));
- // select all data
+ // 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));
+
+ // select data (restricted to pos/neg examples for efficiency)
Statement stmt = conn.createStatement();
- ResultSet rs = stmt.executeQuery("SELECT * FROM " + table);
+ ResultSet rs = stmt.executeQuery("SELECT * FROM " + table + " WHERE (gain_contact is not null) && (gain_contact != 0)");
int count = 0;
while(rs.next()) {
@@ -207,7 +277,70 @@
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));
+
count++;
}
@@ -239,7 +372,7 @@
String confHeader = "import(\"" + owlFile.getName() + "\");\n\n";
confHeader += "reasoner = fastInstanceChecker;\n";
confHeader += "algorithm = refexamples;\n";
- confHeader += "refexamples.noisePercentage = 31;\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";
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