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[DL-Learner SVN] SF.net SVN: dl-learner: [535] trunk/src/dl-learner/org/dllearner
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From: <jen...@us...> - 2008-02-10 17:52:44
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Revision: 535
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=535&view=rev
Author: jenslehmann
Date: 2008-02-10 09:52:40 -0800 (Sun, 10 Feb 2008)
Log Message:
-----------
started Prolog to OWL mapping for carcinogenesis data
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/core/dl/KB.java
trunk/src/dl-learner/org/dllearner/examples/Carcinogenesis.java
trunk/src/dl-learner/org/dllearner/examples/PokerTransformer.java
trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java
trunk/src/dl-learner/org/dllearner/utilities/Files.java
Added Paths:
-----------
trunk/src/dl-learner/org/dllearner/examples/PokerCard.java
trunk/src/dl-learner/org/dllearner/examples/PokerHand.java
Removed Paths:
-------------
trunk/src/dl-learner/org/dllearner/examples/Card.java
trunk/src/dl-learner/org/dllearner/examples/Hand.java
Modified: trunk/src/dl-learner/org/dllearner/core/dl/KB.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/dl/KB.java 2008-02-10 16:08:51 UTC (rev 534)
+++ trunk/src/dl-learner/org/dllearner/core/dl/KB.java 2008-02-10 17:52:40 UTC (rev 535)
@@ -134,6 +134,24 @@
return tbox;
}
+ /**
+ * Convenience method, which adds an axiom to ABox, RBox, or
+ * TBox depending on whether it is an assertional, role, or
+ * terminological axiom.
+ *
+ * @param axiom Axiom to add.
+ */
+ public void addAxiom(Axiom axiom) {
+ if(axiom instanceof AssertionalAxiom)
+ addABoxAxiom((AssertionalAxiom) axiom);
+ else if(axiom instanceof RBoxAxiom)
+ addRBoxAxiom((RBoxAxiom) axiom);
+ else if(axiom instanceof TerminologicalAxiom)
+ addTBoxAxiom((TerminologicalAxiom) axiom);
+ else
+ throw new Error(axiom + " has unsupported axiom type.");
+ }
+
public void addABoxAxiom(AssertionalAxiom axiom) {
abox.add(axiom);
}
Modified: trunk/src/dl-learner/org/dllearner/examples/Carcinogenesis.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/examples/Carcinogenesis.java 2008-02-10 16:08:51 UTC (rev 534)
+++ trunk/src/dl-learner/org/dllearner/examples/Carcinogenesis.java 2008-02-10 17:52:40 UTC (rev 535)
@@ -22,11 +22,25 @@
import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
+import java.net.URI;
+import java.util.ArrayList;
+import java.util.LinkedList;
+import java.util.List;
+import org.dllearner.core.dl.AtomicConcept;
+import org.dllearner.core.dl.AtomicRole;
+import org.dllearner.core.dl.Axiom;
+import org.dllearner.core.dl.Individual;
+import org.dllearner.core.dl.KB;
+import org.dllearner.core.dl.RoleAssertion;
import org.dllearner.parser.ParseException;
import org.dllearner.parser.PrologParser;
+import org.dllearner.prolog.Atom;
+import org.dllearner.prolog.Clause;
import org.dllearner.prolog.Program;
+import org.dllearner.reasoning.OWLAPIReasoner;
import org.dllearner.utilities.Files;
+import org.dllearner.utilities.Helper;
/**
* This class maps the carcinogenesis Prolog files to an OWL file. In a first
@@ -34,23 +48,60 @@
* applying mapping Prolog clauses to OWL axioms through domain specific mapping
* rules.
*
+ * The carcinogenesis Prolog files are available here:
+ * http://web.comlab.ox.ac.uk/oucl/research/areas/machlearn/cancer.html
+ *
+ * .f files contain positive and .n files contain negative examples. pte1.n and
+ * pte.f contain the PTE-1 challenge examples. train.n and train.f contain other
+ * examples which can be used to train for PTE-1.
+ *
+ * The PTE-2 directory contains PTE-2 files, i.e. all substances referred to in
+ * those files are only those of the PTE-2 challenge.
+ *
* @author Jens Lehmann
*
*/
public class Carcinogenesis {
+ private static URI ontologyURI = URI.create("http://dl-learner.org/carcinogenesis");
+
/**
* @param args
+ * No arguments supported.
*/
public static void main(String[] args) {
+ 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 {
- String prologFile = "examples/carcinogenesis/prolog/atoms.pl";
- File file = new File(prologFile);
- String content = Files.readFile(file);
+ // 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 program = pp.parseProgram(content);
- System.out.println(program.toPLString());
+ 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) {
@@ -59,6 +110,66 @@
e.printStackTrace();
}
+ // mapping clauses to axioms
+ System.out.print("Mapping clauses to axioms ... ");
+ startTime = System.nanoTime();
+ ArrayList<Clause> clauses = program.getClauses();
+ KB kb = new KB();
+ for (Clause clause : clauses) {
+ List<Axiom> axioms = mapClause(clause);
+ for (Axiom axiom : axioms)
+ kb.addAxiom(axiom);
+ }
+ duration = System.nanoTime() - startTime;
+ time = Helper.prettyPrintNanoSeconds(duration, false, false);
+ System.out.println("OK (" + time + ").");
+
+ // writing generated knowledge base
+ System.out.print("Writing OWL file ... ");
+ startTime = System.nanoTime();
+ OWLAPIReasoner.exportKBToOWL(owlFile, kb, ontologyURI);
+ duration = System.nanoTime() - startTime;
+ time = Helper.prettyPrintNanoSeconds(duration, false, false);
+ System.out.println("OK (" + time + ").");
}
+ private static List<Axiom> mapClause(Clause clause) {
+ List<Axiom> axioms = new LinkedList<Axiom>();
+ Atom head = clause.getHead();
+ String headName = head.getName();
+ // Body body = clause.getBody();
+ // ArrayList<Literal> literals = body.getLiterals();
+ if (headName.equals("atm")) {
+ // System.out.println(clause.toPLString());
+ // System.out.println(clause);
+ String compoundName = head.getArgument(0).toPLString();
+ String atomName = head.getArgument(1).toPLString();
+ RoleAssertion ra = getRoleAssertion("hasAtom", compoundName, atomName);
+ axioms.add(ra);
+ } else {
+
+ }
+ return axioms;
+ }
+
+ private static RoleAssertion getRoleAssertion(String role, String i1, String i2) {
+ Individual ind1 = getIndividual(i1);
+ Individual ind2 = getIndividual(i2);
+ AtomicRole ar = getRole(role);
+ return new RoleAssertion(ar,ind1,ind2);
+ }
+
+ private static Individual getIndividual(String name) {
+ return new Individual(ontologyURI + "#" + name);
+ }
+
+ private static AtomicRole getRole(String name) {
+ return new AtomicRole(ontologyURI + "#" + name);
+ }
+
+ @SuppressWarnings({"unused"})
+ private static AtomicConcept getAtomicConcept(String name) {
+ return new AtomicConcept(ontologyURI + "#" + name);
+ }
+
}
Deleted: trunk/src/dl-learner/org/dllearner/examples/Card.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/examples/Card.java 2008-02-10 16:08:51 UTC (rev 534)
+++ trunk/src/dl-learner/org/dllearner/examples/Card.java 2008-02-10 17:52:40 UTC (rev 535)
@@ -1,71 +0,0 @@
-package org.dllearner.examples;
-
-public class Card {
-
- private int suit;
- private int rank;
-
- /**
- *
- * @param suit Ordinal (1-4) representing {Hearts, Spades, Diamonds, Clubs}.
- * @param rank Numerical (1-13) representing (Ace, 2, 3, ... , Queen, King)
- */
- public Card(int suit, int rank) {
- this.suit = suit;
- this.rank = rank;
- }
-
- public String getSuitString() {
- switch(suit) {
- case 1: return "hearts";
- case 2: return "spades";
- case 3: return "diamonds";
- case 4: return "clubs";
- }
- throw new Error("Unknown suit code " + suit);
- }
-
- public String getRankString() {
- switch(rank) {
- case 1: return "ace";
- case 2: return "two";
- case 3: return "three";
- case 4: return "four";
- case 5: return "five";
- case 6: return "six";
- case 7: return "seven";
- case 8: return "eight";
- case 9: return "nine";
- case 10: return "ten";
- case 11: return "jack";
- case 12: return "queen";
- case 13: return "king";
- }
- throw new Error("Unknown rank code " + rank);
- }
-
- public boolean hasSameSuit(Card card) {
- return (suit == card.getSuit());
- }
-
- public boolean hasSameRank(Card card) {
- return (rank == card.getRank());
- }
-
- // prüft, ob übergebene Karte den nächsten Rank hat
- public boolean hasNextRank(Card card) {
- // Spezialfall Ass: Vorgänger von 2 und Nachfolger von König
- if(rank+1 == card.getRank() || (rank==13 && card.getRank()==1))
- return true;
- else
- return false;
- }
-
- public int getRank() {
- return rank;
- }
-
- public int getSuit() {
- return suit;
- }
-}
Deleted: trunk/src/dl-learner/org/dllearner/examples/Hand.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/examples/Hand.java 2008-02-10 16:08:51 UTC (rev 534)
+++ trunk/src/dl-learner/org/dllearner/examples/Hand.java 2008-02-10 17:52:40 UTC (rev 535)
@@ -1,38 +0,0 @@
-package org.dllearner.examples;
-
-public class Hand {
-
- private Card[] cards;
- int handType;
-
- /**
- *
- * @param cards
- * @param hand
- * Ordinal (0-9)
- *
- * 0: Nothing in hand; not a recognized poker hand
- * 1: One pair; one pair of equal ranks within five cards
- * 2: Two pairs; two pairs of equal ranks within five cards
- * 3: Three of a kind; three equal ranks within five cards
- * 4: Straight; five cards, sequentially ranked with no gaps
- * 5: Flush; five cards with the same suit
- * 6: Full house; pair + different rank three of a kind
- * 7: Four of a kind; four equal ranks within five cards
- * 8: Straight flush; straight + flush
- * 9: Royal flush; {Ace, King, Queen, Jack, Ten} + flush
- */
- public Hand(Card[] cards, int hand) {
- this.cards = cards;
- this.handType = hand;
- }
-
- public Card[] getCards() {
- return cards;
- }
-
- public int getHandType() {
- return handType;
- }
-
-}
Copied: trunk/src/dl-learner/org/dllearner/examples/PokerCard.java (from rev 533, trunk/src/dl-learner/org/dllearner/examples/Card.java)
===================================================================
--- trunk/src/dl-learner/org/dllearner/examples/PokerCard.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/examples/PokerCard.java 2008-02-10 17:52:40 UTC (rev 535)
@@ -0,0 +1,76 @@
+package org.dllearner.examples;
+
+/**
+ * A poker card has one of 4 suits and 13 ranks.
+ * @author Jens Lehmann
+ *
+ */
+public class PokerCard {
+
+ private int suit;
+ private int rank;
+
+ /**
+ *
+ * @param suit Ordinal (1-4) representing {Hearts, Spades, Diamonds, Clubs}.
+ * @param rank Numerical (1-13) representing (Ace, 2, 3, ... , Queen, King)
+ */
+ public PokerCard(int suit, int rank) {
+ this.suit = suit;
+ this.rank = rank;
+ }
+
+ public String getSuitString() {
+ switch(suit) {
+ case 1: return "hearts";
+ case 2: return "spades";
+ case 3: return "diamonds";
+ case 4: return "clubs";
+ }
+ throw new Error("Unknown suit code " + suit);
+ }
+
+ public String getRankString() {
+ switch(rank) {
+ case 1: return "ace";
+ case 2: return "two";
+ case 3: return "three";
+ case 4: return "four";
+ case 5: return "five";
+ case 6: return "six";
+ case 7: return "seven";
+ case 8: return "eight";
+ case 9: return "nine";
+ case 10: return "ten";
+ case 11: return "jack";
+ case 12: return "queen";
+ case 13: return "king";
+ }
+ throw new Error("Unknown rank code " + rank);
+ }
+
+ public boolean hasSameSuit(PokerCard card) {
+ return (suit == card.getSuit());
+ }
+
+ public boolean hasSameRank(PokerCard card) {
+ return (rank == card.getRank());
+ }
+
+ // prüft, ob übergebene Karte den nächsten Rank hat
+ public boolean hasNextRank(PokerCard card) {
+ // Spezialfall Ass: Vorgänger von 2 und Nachfolger von König
+ if(rank+1 == card.getRank() || (rank==13 && card.getRank()==1))
+ return true;
+ else
+ return false;
+ }
+
+ public int getRank() {
+ return rank;
+ }
+
+ public int getSuit() {
+ return suit;
+ }
+}
Copied: trunk/src/dl-learner/org/dllearner/examples/PokerHand.java (from rev 533, trunk/src/dl-learner/org/dllearner/examples/Hand.java)
===================================================================
--- trunk/src/dl-learner/org/dllearner/examples/PokerHand.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/examples/PokerHand.java 2008-02-10 17:52:40 UTC (rev 535)
@@ -0,0 +1,44 @@
+package org.dllearner.examples;
+
+/**
+ * A poker hand consists of 5 cards.
+ *
+ * @author Jens Lehmann
+ *
+ */
+public class PokerHand {
+
+ private PokerCard[] cards;
+ int handType;
+
+ /**
+ *
+ * @param cards
+ * @param hand
+ * Ordinal (0-9)
+ *
+ * 0: Nothing in hand; not a recognized poker hand
+ * 1: One pair; one pair of equal ranks within five cards
+ * 2: Two pairs; two pairs of equal ranks within five cards
+ * 3: Three of a kind; three equal ranks within five cards
+ * 4: Straight; five cards, sequentially ranked with no gaps
+ * 5: Flush; five cards with the same suit
+ * 6: Full house; pair + different rank three of a kind
+ * 7: Four of a kind; four equal ranks within five cards
+ * 8: Straight flush; straight + flush
+ * 9: Royal flush; {Ace, King, Queen, Jack, Ten} + flush
+ */
+ public PokerHand(PokerCard[] cards, int hand) {
+ this.cards = cards;
+ this.handType = hand;
+ }
+
+ public PokerCard[] getCards() {
+ return cards;
+ }
+
+ public int getHandType() {
+ return handType;
+ }
+
+}
Modified: trunk/src/dl-learner/org/dllearner/examples/PokerTransformer.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/examples/PokerTransformer.java 2008-02-10 16:08:51 UTC (rev 534)
+++ trunk/src/dl-learner/org/dllearner/examples/PokerTransformer.java 2008-02-10 17:52:40 UTC (rev 535)
@@ -60,27 +60,27 @@
lineNumber++;
}
- List<Hand> hands = new LinkedList<Hand>();
+ List<PokerHand> hands = new LinkedList<PokerHand>();
for(String s : pokerExamples) {
// System.out.println(s);
StringTokenizer st = new StringTokenizer(s,",");
// 5 Karten einlesen
- Card[] cards = new Card[5];
+ PokerCard[] cards = new PokerCard[5];
for(int i=0; i<=4; i++) {
String suit = st.nextToken();
String rank = st.nextToken();
- cards[i] = new Card(new Integer(suit),new Integer(rank));
+ cards[i] = new PokerCard(new Integer(suit),new Integer(rank));
}
// Klasse auslesen
String handType = st.nextToken();
- Hand hand = new Hand(cards, new Integer(handType));
+ PokerHand hand = new PokerHand(cards, new Integer(handType));
// prüfen, ob Deck schon existiert (nicht gerade effizient,
// aber OK)
boolean handExists = false;
- for(Hand d : hands) {
+ for(PokerHand d : hands) {
if(equalDecks(d,hand)) {
handExists = true;
break;
@@ -112,7 +112,7 @@
// für jede Karte die entsprechende Ausgabe machen
int handNumber = 0;
- for(Hand deck : hands) {
+ for(PokerHand deck : hands) {
String handID = "hand" + handNumber;
// Ausgabe der Hand (damit für Reasoner klar ist, dass es
@@ -120,10 +120,10 @@
write(fos, "deck("+handID+").");
int cardNumber = handNumber*5;
- Card[] cards = deck.getCards();
+ PokerCard[] cards = deck.getCards();
// for(Card card : deck.getCards()) {
for(int i=0; i<5; i++) {
- Card card = cards[i];
+ PokerCard card = cards[i];
String cardID = "card" + cardNumber;
// Ausgabe der Karte (damit klar ist, dass es sich um ein
@@ -139,7 +139,7 @@
// sameSuit, nextRank und sameRank ausgeben
for(int j=i+1; j<5; j++) {
- Card otherCard = cards[j];
+ PokerCard otherCard = cards[j];
String otherCardID = "card" + (handNumber*5+j);
if(card.hasSameSuit(otherCard))
write(fos, "sameSuit("+cardID+","+otherCardID+").");
@@ -150,7 +150,7 @@
// nextRank ist nicht symmetrisch, deshalb müssen alle
// 4 anderen Karten geprüft werden
for(int j=0; j<5; j++) {
- Card otherCard = cards[j];
+ PokerCard otherCard = cards[j];
String otherCardID = "card" + (handNumber*5+j);
if(card.hasNextRank(otherCard)) {
// Spezialfall: Ass
@@ -217,8 +217,8 @@
}
}
- public boolean equalDecks(Hand deck1, Hand deck2) {
- Card[] deck1Cards = deck1.getCards();
+ public boolean equalDecks(PokerHand deck1, PokerHand deck2) {
+ PokerCard[] deck1Cards = deck1.getCards();
for(int i=0; i<5; i++) {
if(!isInCards(deck1Cards[i],deck2))
return false;
@@ -226,8 +226,8 @@
return true;
}
- public boolean isInCards(Card card, Hand deck) {
- Card[] cards = deck.getCards();
+ public boolean isInCards(PokerCard card, PokerHand deck) {
+ PokerCard[] cards = deck.getCards();
for(int j=0; j<5; j++) {
// Test auf Gleichheit
if(card.getSuit()==cards[j].getSuit() && card.getRank()==cards[j].getRank())
@@ -236,8 +236,8 @@
return false;
}
- public boolean hasKing(Hand deck) {
- Card[] cards = deck.getCards();
+ public boolean hasKing(PokerHand deck) {
+ PokerCard[] cards = deck.getCards();
for(int j=0; j<5; j++) {
if(cards[j].getRank()==13)
return true;
Modified: trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java 2008-02-10 16:08:51 UTC (rev 534)
+++ trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java 2008-02-10 17:52:40 UTC (rev 535)
@@ -19,6 +19,7 @@
*/
package org.dllearner.reasoning;
+import java.io.File;
import java.net.URI;
import java.net.URISyntaxException;
import java.net.URL;
@@ -83,6 +84,9 @@
import org.semanticweb.owl.model.OWLOntologyChangeException;
import org.semanticweb.owl.model.OWLOntologyCreationException;
import org.semanticweb.owl.model.OWLOntologyManager;
+import org.semanticweb.owl.model.OWLOntologyStorageException;
+import org.semanticweb.owl.model.UnknownOWLOntologyException;
+import org.semanticweb.owl.util.SimpleURIMapper;
/**
* Mapping to OWL API reasoner interface. The OWL API currently
@@ -521,6 +525,29 @@
return new AtomicConcept(owlClass.getURI().toString());
}
+ public static void exportKBToOWL(File owlOutputFile, KB kb, URI ontologyURI) {
+ OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
+ //URI ontologyURI = URI.create("http://example.com");
+ URI physicalURI = owlOutputFile.toURI();
+ SimpleURIMapper mapper = new SimpleURIMapper(ontologyURI, physicalURI);
+ manager.addURIMapper(mapper);
+ OWLOntology ontology;
+ try {
+ ontology = manager.createOntology(ontologyURI);
+ OWLAPIReasoner.fillOWLAPIOntology(manager, ontology, kb);
+ manager.saveOntology(ontology);
+ } catch (OWLOntologyCreationException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ } catch (UnknownOWLOntologyException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ } catch (OWLOntologyStorageException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ }
+
public static OWLObjectProperty getOWLAPIDescription(AtomicRole role) {
return staticFactory.getOWLObjectProperty(URI.create(role.getName()));
}
Modified: trunk/src/dl-learner/org/dllearner/utilities/Files.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/Files.java 2008-02-10 16:08:51 UTC (rev 534)
+++ trunk/src/dl-learner/org/dllearner/utilities/Files.java 2008-02-10 17:52:40 UTC (rev 535)
@@ -20,13 +20,11 @@
package org.dllearner.utilities;
import java.io.BufferedReader;
-import java.io.DataInputStream;
import java.io.File;
-import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
+import java.io.FileReader;
import java.io.IOException;
-import java.io.InputStreamReader;
/**
* @author Jens Lehmann
@@ -42,15 +40,14 @@
* @return Content of the file.
*/
public static String readFile(File file) throws FileNotFoundException, IOException {
- FileInputStream fstream = new FileInputStream(file);
- DataInputStream in = new DataInputStream(fstream);
- BufferedReader br = new BufferedReader(new InputStreamReader(in));
+ BufferedReader br = new BufferedReader(new FileReader(file));
String line;
StringBuffer content = new StringBuffer();
while ((line = br.readLine()) != null) {
content.append(line);
+ content.append(System.getProperty("line.separator"));
}
- in.close();
+ br.close();
return content.toString();
}
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