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[DL-Learner SVN] SF.net SVN: dl-learner: [631] trunk/src/dl-learner/org/dllearner
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From: <jen...@us...> - 2008-02-23 09:10:53
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Revision: 631
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=631&view=rev
Author: jenslehmann
Date: 2008-02-23 01:10:40 -0800 (Sat, 23 Feb 2008)
Log Message:
-----------
carcinogenesis mapping extended
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/core/owl/KB.java
trunk/src/dl-learner/org/dllearner/examples/Carcinogenesis.java
Modified: trunk/src/dl-learner/org/dllearner/core/owl/KB.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/KB.java 2008-02-22 21:58:43 UTC (rev 630)
+++ trunk/src/dl-learner/org/dllearner/core/owl/KB.java 2008-02-23 09:10:40 UTC (rev 631)
@@ -8,6 +8,7 @@
public class KB implements KBElement {
+ // private Set<Axiom> axioms = new HashSet<Axiom>();
private Set<AssertionalAxiom> abox = new HashSet<AssertionalAxiom>();
private Set<TerminologicalAxiom> tbox = new HashSet<TerminologicalAxiom>();
private Set<PropertyAxiom> rbox = new HashSet<PropertyAxiom>();
@@ -239,6 +240,23 @@
public void accept(KBElementVisitor visitor) {
visitor.visit(this);
- }
+ }
+
+ /**
+ * Returns all axioms in the ontology. Note that calling this
+ * method is not efficient for large knowledge bases, since
+ * internally all axioms are separated into ABox, RBox, and
+ * TBox, which means that a union of these sets is computed
+ * and returned here.
+ *
+ * @return All axioms in the ontology.
+ */
+ public Set<Axiom> getAxioms() {
+ Set<Axiom> axioms = new HashSet<Axiom>();
+ axioms.addAll(abox);
+ axioms.addAll(rbox);
+ axioms.addAll(tbox);
+ return axioms;
+ }
}
Modified: trunk/src/dl-learner/org/dllearner/examples/Carcinogenesis.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/examples/Carcinogenesis.java 2008-02-22 21:58:43 UTC (rev 630)
+++ trunk/src/dl-learner/org/dllearner/examples/Carcinogenesis.java 2008-02-23 09:10:40 UTC (rev 631)
@@ -24,6 +24,7 @@
import java.io.IOException;
import java.net.URI;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.HashMap;
import java.util.LinkedList;
import java.util.List;
@@ -82,14 +83,27 @@
// mapping of symbols to names of chemical elements
private static Map<String, String> chemElements;
- // types of atoms and bonds
+ // structures in newgroups.pl
+ private static Set<String> newGroups = new TreeSet<String>();
+
+ // types of atoms, bonds, and structures
private static Set<String> atomTypes = new TreeSet<String>();
private static Set<String> bondTypes = new TreeSet<String>();
+ private static Set<String> structureTypes = new TreeSet<String>();
// we need a counter for bonds, because they are instances in OWL
// but not in Prolog
private static int bondNr = 0;
+ private static int structureNr = 0;
+ // list of all compounds
+ private static Set<String> compounds = new TreeSet<String>();
+ // compounds with positive ames test
+ private static Set<String> compoundsAmes = new TreeSet<String>();
+
+ // list of all "hasProperty" test
+ private static Set<String> tests = new TreeSet<String>();
+
/**
* @param args
* No arguments supported.
@@ -100,8 +114,8 @@
public static void main(String[] args) throws FileNotFoundException, IOException,
ParseException {
- String[] files = new String[] { "ames.pl", "atoms.pl", "bonds.pl", "gentoxprops.pl",
- "ind_nos.pl", "ind_pos.pl", "newgroups.pl",
+ String[] files = new String[] { "newgroups.pl", "ames.pl", "atoms.pl", "bonds.pl", "gentoxprops.pl",
+ "ind_nos.pl", "ind_pos.pl",
// "train.b" => not a pure Prolog file but Progol/Aleph specific
};
File owlFile = new File("examples/carcinogenesis/pte.owl");
@@ -133,6 +147,7 @@
// prepare mapping
KB kb = new KB();
createChemElementsMapping();
+ createNewGroups();
// create subclasses of atom
NamedClass atomClass = getAtomicConcept("Atom");
for (String element : chemElements.values()) {
@@ -161,6 +176,20 @@
for (Axiom axiom : axioms)
kb.addAxiom(axiom);
}
+ // special handling for ames test (we assume the ames test
+ // was performed on all compounds but only the positive ones
+ // are in ames.pl [the rest is negative in Prolog by CWA], so
+ // we add negative test results here)
+ for(String compound : compounds) {
+ if(!compoundsAmes.contains(compound)) {
+ BooleanDatatypePropertyAssertion ames = getBooleanDatatypePropertyAssertion(compound, "amesTestPositive", false);
+ kb.addAxiom(ames);
+ }
+ }
+
+ // TODO: disjoint classes axioms
+ // TODO: all different axiom (UNA)
+
duration = System.nanoTime() - startTime;
time = Helper.prettyPrintNanoSeconds(duration, false, false);
System.out.println("OK (" + time + ").");
@@ -210,7 +239,7 @@
// on "Testing Status of Agents at NTP"
}
- private static List<Axiom> mapClause(Clause clause) {
+ private static List<Axiom> mapClause(Clause clause) throws IOException, ParseException {
List<Axiom> axioms = new LinkedList<Axiom>();
Atom head = clause.getHead();
String headName = head.getName();
@@ -228,7 +257,7 @@
String compoundName = head.getArgument(0).toPLString();
BooleanDatatypePropertyAssertion ames = getBooleanDatatypePropertyAssertion(compoundName, "amesTestPositive", true);
axioms.add(ames);
-
+ compoundsAmes.add(compoundName);
} else if (headName.equals("atm")) {
String compoundName = head.getArgument(0).toPLString();
String atomName = head.getArgument(1).toPLString();
@@ -237,7 +266,8 @@
double charge = Double.parseDouble(head.getArgument(4).toPLString());
// make the compound an instance of the Compound class
ClassAssertionAxiom cmpAxiom = getConceptAssertion("Compound", compoundName);
- axioms.add(cmpAxiom);
+ axioms.add(cmpAxiom);
+ compounds.add(compoundName);
// relate compound and atom
ObjectPropertyAssertion ra = getRoleAssertion("hasAtom", compoundName, atomName);
axioms.add(ra);
@@ -282,12 +312,55 @@
ObjectPropertyAssertion op2 = getRoleAssertion("inBond", bondInstance, atom2Name);
axioms.add(op1);
axioms.add(op2);
+ } else if (headName.equals("has_property")) {
+ String compoundName = head.getArgument(0).toPLString();
+ String testName = head.getArgument(1).toPLString();
+ boolean testResult = Boolean.parseBoolean(head.getArgument(2).toPLString());
+ // create a new datatype property if it does not exist already
+ if(!tests.contains(testName)) {
+ String axiom1 = "DPDOMAIN(" + getURI2(testName) + ") = " + getURI2("Compound") + ".\n";
+ String axiom2 = "DPRANGE(" + getURI2(testName) + ") = BOOLEAN.\n";
+ KB kb = KBParser.parseKBFile(axiom1 + axiom2);
+ axioms.addAll(kb.getAxioms());
+ }
+ // create an axiom with the test result
+ DatatypePropertyAssertion dpa = getBooleanDatatypePropertyAssertion(compoundName, testName,
+ testResult);
+ axioms.add(dpa);
+ // either parse this or ashby_alert - not both - ashby_alert contains
+ // all information in ind already
+ } else if (headName.equals("ind")) {
+ String compoundName = head.getArgument(0).toPLString();
+ String structureName = head.getArgument(1).toPLString();
+ int count = Integer.parseInt(head.getArgument(2).toPLString());
+ // upper case first letter
+ String structureClass = structureName.substring(0,1).toUpperCase() + structureName.substring(1);;
+ String structureInstance = structureName + "-" + structureNr;
+
+ if (!bondTypes.contains(structureClass)) {
+ NamedClass subClass = getAtomicConcept(structureClass);
+ SubClassAxiom sc = new SubClassAxiom(subClass, getAtomicConcept("Structure"));
+ axioms.add(sc);
+ structureTypes.add(structureClass);
+ }
+
+ for(int i=0; i<count; i++) {
+ ObjectPropertyAssertion op = getRoleAssertion("hasStructure", compoundName, structureInstance);
+ axioms.add(op);
+ // make e.g. halide10-382 instance of Bond-3
+ ClassAssertionAxiom ca = getConceptAssertion(structureClass, structureInstance);
+ axioms.add(ca);
+ structureNr++;
+ }
+ } else if (headName.equals("ashby_alert")) {
+ // ... currently ignored ...
+ } else if (newGroups.contains(headName)) {
} else {
// print clauses which are not supported yet
System.out.println("unsupported clause");
System.out.println(clause.toPLString());
System.out.println(clause);
-// System.exit(0);
+ System.exit(0);
}
return axioms;
}
@@ -419,4 +492,19 @@
chemElements.put("v", "Vanadium");
chemElements.put("zn", "Zinc");
}
+
+ private static void createNewGroups() {
+ String[] groups = new String[] {"six_ring", "non_ar_6c_ring",
+ "ketone", "amine", "alcohol", "ether", "ar_halide",
+ "five_ring", "non_ar_5c_ring", "alkyl_halide",
+ "methyl", "non_ar_hetero_5_ring", "nitro", "sulfo",
+ "methoxy", "amine", "aldehyde", "sulfide",
+ "non_ar_hetero_6_ring", "phenol", "carboxylic_acid",
+ "ester", "imine",
+ };
+
+ List<String> list = Arrays.asList(groups);
+ newGroups.addAll(list);
+ }
+
}
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