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[DL-Learner SVN] SF.net SVN: dl-learner: [611] trunk/src/dl-learner/org/dllearner
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From: <jen...@us...> - 2008-02-19 14:28:37
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Revision: 611
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=611&view=rev
Author: jenslehmann
Date: 2008-02-19 06:28:23 -0800 (Tue, 19 Feb 2008)
Log Message:
-----------
- continued carcinogenesis mapper
- fixed bug in KB file (relevant for component creation in ComponentManager)
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/examples/Carcinogenesis.java
trunk/src/dl-learner/org/dllearner/kb/KBFile.java
Modified: trunk/src/dl-learner/org/dllearner/examples/Carcinogenesis.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/examples/Carcinogenesis.java 2008-02-19 13:20:01 UTC (rev 610)
+++ trunk/src/dl-learner/org/dllearner/examples/Carcinogenesis.java 2008-02-19 14:28:23 UTC (rev 611)
@@ -73,79 +73,77 @@
public class Carcinogenesis {
private static URI ontologyURI = URI.create("http://dl-learner.org/carcinogenesis");
+
+ // directory of Prolog files
+ private static String prologDirectory = "examples/carcinogenesis/prolog/";
// mapping of symbols to names of chemical elements
- private static Map<String,String> chemElements;
-
+ private static Map<String, String> chemElements;
+
// types of atoms and bonds
private static Set<String> atomTypes = new TreeSet<String>();
private static Set<String> bondTypes = new TreeSet<String>();
-
+
// we need a counter for bonds, because they are instances in OWL
// but not in Prolog
private static int bondNr = 0;
-
+
/**
* @param args
* No arguments supported.
+ * @throws IOException
+ * @throws FileNotFoundException
+ * @throws ParseException
*/
- public static void main(String[] args) {
+ public static void main(String[] args) throws FileNotFoundException, IOException,
+ ParseException {
- String prologDirectory = "examples/carcinogenesis/prolog/";
String[] files = new String[] { "ames.pl", "atoms.pl", "bonds.pl", "gentoxprops.pl",
"ind_nos.pl", "ind_pos.pl", "newgroups.pl",
// "train.b" => not a pure Prolog file but Progol/Aleph specific
};
File owlFile = new File("examples/carcinogenesis/pte.owl");
-
+
Program program = null;
long startTime, duration;
String time;
- try {
- // reading files
- System.out.print("Reading in carcinogenesis Prolog files ... ");
- startTime = System.nanoTime();
- String content = "";
- for (String file : files) {
- content += Files.readFile(new File(prologDirectory + file));
- }
- duration = System.nanoTime() - startTime;
- time = Helper.prettyPrintNanoSeconds(duration, false, false);
- System.out.println("OK (" + time + ").");
-
- // parsing files
- System.out.print("Parsing Prolog files ... ");
- startTime = System.nanoTime();
- PrologParser pp = new PrologParser();
- program = pp.parseProgram(content);
- duration = System.nanoTime() - startTime;
- time = Helper.prettyPrintNanoSeconds(duration, false, false);
- System.out.println("OK (" + time + ").");
- } catch (ParseException e) {
- e.printStackTrace();
- } catch (FileNotFoundException e) {
- e.printStackTrace();
- } catch (IOException e) {
- e.printStackTrace();
+ // reading files
+ System.out.print("Reading in carcinogenesis Prolog files ... ");
+ startTime = System.nanoTime();
+ String content = "";
+ for (String file : files) {
+ content += Files.readFile(new File(prologDirectory + file));
}
+ duration = System.nanoTime() - startTime;
+ time = Helper.prettyPrintNanoSeconds(duration, false, false);
+ System.out.println("OK (" + time + ").");
+ // parsing files
+ System.out.print("Parsing Prolog files ... ");
+ startTime = System.nanoTime();
+ PrologParser pp = new PrologParser();
+ program = pp.parseProgram(content);
+ duration = System.nanoTime() - startTime;
+ time = Helper.prettyPrintNanoSeconds(duration, false, false);
+ System.out.println("OK (" + time + ").");
+
// prepare mapping
- KB kb = new KB();
+ KB kb = new KB();
createChemElementsMapping();
// create subclasses of atom
NamedClass atomClass = getAtomicConcept("Atom");
- for(String element : chemElements.values()) {
+ for (String element : chemElements.values()) {
NamedClass elClass = getAtomicConcept(element);
SubClassAxiom sc = new SubClassAxiom(elClass, atomClass);
kb.addAxiom(sc);
}
// define properties including domain and range
// ... TODO ...
-
+
// mapping clauses to axioms
System.out.print("Mapping clauses to axioms ... ");
- startTime = System.nanoTime();
+ startTime = System.nanoTime();
ArrayList<Clause> clauses = program.getClauses();
for (Clause clause : clauses) {
List<Axiom> axioms = mapClause(clause);
@@ -154,7 +152,7 @@
}
duration = System.nanoTime() - startTime;
time = Helper.prettyPrintNanoSeconds(duration, false, false);
- System.out.println("OK (" + time + ").");
+ System.out.println("OK (" + time + ").");
// writing generated knowledge base
System.out.print("Writing OWL file ... ");
@@ -162,7 +160,27 @@
OWLAPIReasoner.exportKBToOWL(owlFile, kb, ontologyURI);
duration = System.nanoTime() - startTime;
time = Helper.prettyPrintNanoSeconds(duration, false, false);
- System.out.println("OK (" + time + ").");
+ System.out.println("OK (" + time + ").");
+
+ // generating conf files
+ File confTrainFile = new File("examples/carcinogenesis/train.conf");
+ String confHeader = "";
+ Files.appendFile(confTrainFile, confHeader);
+
+ // generating training examples
+ File trainingFilePositives = new File(prologDirectory + "train.f");
+ File trainingFileNegatives = new File(prologDirectory + "train.n");
+
+ List<Individual> posTrainExamples = getExamples(trainingFilePositives);
+ List<Individual> negTrainExamples = getExamples(trainingFileNegatives);
+ appendPosExamples(confTrainFile, posTrainExamples);
+ appendNegExamples(confTrainFile, negTrainExamples);
+
+ // generating testExamples
+// File confTestFile = new File("examples/carcinogenesis/test.conf");
+// File testFilePositives = new File(prologDirectory + "train.f");
+// File testFileNegatives = new File(prologDirectory + "train.n");
+//
}
private static List<Axiom> mapClause(Clause clause) {
@@ -180,14 +198,14 @@
String type = head.getArgument(3).toPLString();
double charge = Double.parseDouble(head.getArgument(4).toPLString());
// relate compound and atom
- ObjectPropertyAssertion ra = getRoleAssertion("hasAtom", compoundName, atomName);
+ ObjectPropertyAssertion ra = getRoleAssertion("hasAtom", compoundName, atomName);
axioms.add(ra);
// atom is made instance of the correct class
String atomClass = getAtomClass(elementName, type);
- ClassAssertionAxiom ca = getConceptAssertion(atomClass,atomName);
+ ClassAssertionAxiom ca = getConceptAssertion(atomClass, atomName);
axioms.add(ca);
// write subclass axiom if doesn't exist already
- if(!atomTypes.contains(atomClass)) {
+ if (!atomTypes.contains(atomClass)) {
NamedClass subClass = getAtomicConcept(atomClass);
NamedClass superClass = getAtomicConcept(getFullElementName(elementName));
SubClassAxiom sc = new SubClassAxiom(subClass, superClass);
@@ -195,9 +213,10 @@
atomTypes.add(atomClass);
}
// charge of atom
- DatatypePropertyAssertion dpa = getDoubleDatatypePropertyAssertion(atomName, "charge", charge);
+ DatatypePropertyAssertion dpa = getDoubleDatatypePropertyAssertion(atomName, "charge",
+ charge);
axioms.add(dpa);
- } else if(headName.equals("bond")) {
+ } else if (headName.equals("bond")) {
String compoundName = head.getArgument(0).toPLString();
String atom1Name = head.getArgument(1).toPLString();
String atom2Name = head.getArgument(2).toPLString();
@@ -207,10 +226,10 @@
ObjectPropertyAssertion op = getRoleAssertion("hasBond", compoundName, "bond" + bondNr);
axioms.add(op);
// make Bond-X subclass of Bond if that hasn't been done already
- if(!bondTypes.contains(bondClass)) {
+ if (!bondTypes.contains(bondClass)) {
NamedClass subClass = getAtomicConcept(bondClass);
SubClassAxiom sc = new SubClassAxiom(subClass, getAtomicConcept("Bond"));
- axioms.add(sc);
+ axioms.add(sc);
bondTypes.add(bondClass);
}
// make e.g. bond382 instance of Bond-3
@@ -226,46 +245,77 @@
// print clauses which are not supported yet
System.out.println("unsupported clause");
System.out.println(clause.toPLString());
- System.out.println(clause);
+ System.out.println(clause);
}
return axioms;
}
+
+ // takes a *.f or *.n file as input and returns the
+ // contained examples
+ private static List<Individual> getExamples(File file) throws FileNotFoundException, IOException, ParseException {
+ String content = Files.readFile(new File(prologDirectory + file));
+ PrologParser pp = new PrologParser();
+ Program programPos = pp.parseProgram(content);
+ List<Individual> ret = new LinkedList<Individual>();
+ for(Clause c : programPos.getClauses()) {
+ String example = c.getHead().getArgument(0).toPLString();
+ ret.add(getIndividual(example));
+ }
+ return ret;
+ }
+ private static void appendPosExamples(File file, List<Individual> examples) {
+ StringBuffer content = new StringBuffer();
+ for(Individual example : examples) {
+ content.append("+\""+example.toString()+"\"");
+ }
+ Files.appendFile(file, content.toString());
+ }
+
+ private static void appendNegExamples(File file, List<Individual> examples) {
+ StringBuffer content = new StringBuffer();
+ for(Individual example : examples) {
+ content.append("-\""+example.toString()+"\"");
+ }
+ Files.appendFile(file, content.toString());
+ }
+
private static String getAtomClass(String element, String atomType) {
return getFullElementName(element) + "-" + atomType;
}
-
+
private static ClassAssertionAxiom getConceptAssertion(String concept, String i) {
Individual ind = getIndividual(i);
NamedClass c = getAtomicConcept(concept);
- return new ClassAssertionAxiom(c,ind);
+ return new ClassAssertionAxiom(c, ind);
}
-
+
private static ObjectPropertyAssertion getRoleAssertion(String role, String i1, String i2) {
Individual ind1 = getIndividual(i1);
Individual ind2 = getIndividual(i2);
ObjectProperty ar = getRole(role);
- return new ObjectPropertyAssertion(ar,ind1,ind2);
+ return new ObjectPropertyAssertion(ar, ind1, ind2);
}
-
- private static DoubleDatatypePropertyAssertion getDoubleDatatypePropertyAssertion(String individual, String datatypeProperty, double value) {
+
+ private static DoubleDatatypePropertyAssertion getDoubleDatatypePropertyAssertion(
+ String individual, String datatypeProperty, double value) {
Individual ind = getIndividual(individual);
DatatypeProperty dp = getDatatypeProperty(datatypeProperty);
- return new DoubleDatatypePropertyAssertion(dp,ind,value);
- }
-
+ return new DoubleDatatypePropertyAssertion(dp, ind, value);
+ }
+
private static Individual getIndividual(String name) {
return new Individual(ontologyURI + "#" + name);
- }
-
+ }
+
private static ObjectProperty getRole(String name) {
return new ObjectProperty(ontologyURI + "#" + name);
- }
-
+ }
+
private static DatatypeProperty getDatatypeProperty(String name) {
return new DatatypeProperty(ontologyURI + "#" + name);
- }
-
+ }
+
private static NamedClass getAtomicConcept(String name) {
return new NamedClass(ontologyURI + "#" + name);
}
@@ -274,15 +324,15 @@
// return corresponding element or throw an error if it
// is not in the list
String result = chemElements.get(abbreviation);
- if(result == null)
+ if (result == null)
throw new Error("Unknown element " + abbreviation);
else
- return result;
- }
-
+ return result;
+ }
+
// create chemical element list
private static void createChemElementsMapping() {
- chemElements = new HashMap<String,String>();
+ chemElements = new HashMap<String, String>();
chemElements.put("as", "Arsenic");
chemElements.put("ba", "Barium");
chemElements.put("br", "Bromine");
Modified: trunk/src/dl-learner/org/dllearner/kb/KBFile.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/KBFile.java 2008-02-19 13:20:01 UTC (rev 610)
+++ trunk/src/dl-learner/org/dllearner/kb/KBFile.java 2008-02-19 14:28:23 UTC (rev 611)
@@ -61,6 +61,13 @@
private KB kb;
/**
+ * Default constructor (needed for reflection in ComponentManager).
+ */
+ public KBFile() {
+
+ }
+
+ /**
* Constructor allowing you to treat an already existing KB object
* as a KBFile knowledge source. Use it sparingly, because the
* standard way to create components is via
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