matching between ontology classes (not instances)

owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/classmatch/ClassMatcher.java

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+package org.monarchinitiative.owlsim.compute.classmatch;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Set;
+import java.util.stream.Collectors;
+
+import javax.inject.Inject;
+
+import org.monarchinitiative.owlsim.kb.BMKnowledgeBase;
+import org.monarchinitiative.owlsim.kb.LabelMapper;
+
+import com.googlecode.javaewah.EWAHCompressedBitmap;
+
+/**
+ * Finds matches between classes in the KB
+ * 
+ * @author cjm
+ *
+ */
+public class ClassMatcher {
+
+    BMKnowledgeBase kb;
+    
+   
+    @Inject
+    public ClassMatcher(BMKnowledgeBase kb) {
+        super();
+        this.kb = kb;
+    }
+
+    /**
+     * Find best match for every class in ont1, where the best
+     * match is in ont2
+     * 
+     * @param qOnt
+     * @param tOnt
+     * @return
+     */
+    public List<SimpleClassMatch> matchOntologies(String qOnt, String tOnt) {
+        Set<String> qids = getClassIdsByOntology(qOnt);
+        Set<String> tids = getClassIdsByOntology(tOnt);
+        return matchClassSets(qids, tids);
+    }
+
+    public List<SimpleClassMatch> matchClassSets(Set<String> qids,
+            Set<String> tids) {
+        ArrayList<SimpleClassMatch> matches = new ArrayList<>();
+        for (String q : qids) {
+            matches.add(getBestMatch(q, tids));
+        }
+        return matches;
+    }
+
+    private SimpleClassMatch getBestMatch(String q, Set<String> tids) {
+        EWAHCompressedBitmap qbm = kb.getSuperClassesBM(q);
+        double bestEqScore = 0.0;
+        String best = null;
+        for (String t : tids) {
+            EWAHCompressedBitmap tbm = kb.getSuperClassesBM(t);
+            int numInQueryAndInTarget = qbm.andCardinality(tbm);
+            int numInQueryOrInTarget = qbm.orCardinality(tbm);
+            double eqScore = numInQueryAndInTarget / (double) numInQueryOrInTarget;
+            if (eqScore > bestEqScore) {
+                bestEqScore = eqScore;
+                best = t;
+            }
+        }
+            
+        EWAHCompressedBitmap tbm = kb.getSuperClassesBM(best);
+        int numInQueryAndInTarget = qbm.andCardinality(tbm);
+        double subClassScore = numInQueryAndInTarget / (double) qbm.cardinality();
+        double superClassScore = numInQueryAndInTarget / (double) tbm.cardinality();
+            
+        LabelMapper lm = kb.getLabelMapper();
+        return new SimpleClassMatch(q, best,
+                lm.getArbitraryLabel(q),
+                lm.getArbitraryLabel(best),
+                bestEqScore,
+                subClassScore,
+                superClassScore);
+    }
+
+    public Set<String> getClassIdsByOntology(String ont) {
+        return kb.getClassIdsInSignature().stream().filter(x -> isIn(x, ont)).collect(Collectors.toSet());
+    }
+
+    public boolean isIn(String id, String ont) {
+        // TODO - use curie util
+        return id.startsWith(ont+":") || id.contains("/"+ont+"_");      
+    }
+
+}

owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/classmatch/SimpleClassMatch.java

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+package org.monarchinitiative.owlsim.compute.classmatch;
+
+public class SimpleClassMatch {
+    
+    private String queryClassId;
+    private String matchClassId;
+    private String queryClassLabel;
+    private String matchClassLabel;
+    
+    private double eqScore;
+    private double subClassScore;
+    private double superClassScore;
+    public SimpleClassMatch(String queryClassId, String matchClassId,
+            String queryClassLabel, String matchClassLabel, double eqScore,
+            double subClassScore, double superClassScore) {
+        super();
+        this.queryClassId = queryClassId;
+        this.matchClassId = matchClassId;
+        this.queryClassLabel = queryClassLabel;
+        this.matchClassLabel = matchClassLabel;
+        this.eqScore = eqScore;
+        this.subClassScore = subClassScore;
+        this.superClassScore = superClassScore;
+    }
+    /**
+     * @return the queryClassId
+     */
+    public String getQueryClassId() {
+        return queryClassId;
+    }
+    /**
+     * @param queryClassId the queryClassId to set
+     */
+    public void setQueryClassId(String queryClassId) {
+        this.queryClassId = queryClassId;
+    }
+    /**
+     * @return the matchClassId
+     */
+    public String getMatchClassId() {
+        return matchClassId;
+    }
+    /**
+     * @param matchClassId the matchClassId to set
+     */
+    public void setMatchClassId(String matchClassId) {
+        this.matchClassId = matchClassId;
+    }
+    /**
+     * @return the queryClassLabel
+     */
+    public String getQueryClassLabel() {
+        return queryClassLabel;
+    }
+    /**
+     * @param queryClassLabel the queryClassLabel to set
+     */
+    public void setQueryClassLabel(String queryClassLabel) {
+        this.queryClassLabel = queryClassLabel;
+    }
+    /**
+     * @return the matchClassLabel
+     */
+    public String getMatchClassLabel() {
+        return matchClassLabel;
+    }
+    /**
+     * @param matchClassLabel the matchClassLabel to set
+     */
+    public void setMatchClassLabel(String matchClassLabel) {
+        this.matchClassLabel = matchClassLabel;
+    }
+    /**
+     * @return the eqScore
+     */
+    public double getEqScore() {
+        return eqScore;
+    }
+    /**
+     * @param eqScore the eqScore to set
+     */
+    public void setEqScore(double eqScore) {
+        this.eqScore = eqScore;
+    }
+    /**
+     * @return the subClassScore
+     */
+    public double getSubClassScore() {
+        return subClassScore;
+    }
+    /**
+     * @param subClassScore the subClassScore to set
+     */
+    public void setSubClassScore(double subClassScore) {
+        this.subClassScore = subClassScore;
+    }
+    /**
+     * @return the superClassScore
+     */
+    public double getSuperClassScore() {
+        return superClassScore;
+    }
+    /**
+     * @param superClassScore the superClassScore to set
+     */
+    public void setSuperClassScore(double superClassScore) {
+        this.superClassScore = superClassScore;
+    }
+    /* (non-Javadoc)
+     * @see java.lang.Object#toString()
+     */
+    @Override
+    public String toString() {
+        return "SimpleClassMatch [queryClassId=" + queryClassId
+                + ", matchClassId=" + matchClassId + ", queryClassLabel="
+                + queryClassLabel + ", matchClassLabel=" + matchClassLabel
+                + ", eqScore=" + eqScore + ", subClassScore=" + subClassScore
+                + ", superClassScore=" + superClassScore + "]";
+    }
+    
+    
+    
+
+}

owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/classmatch/package-info.java

@@ -0,0 +1,8 @@
+/**
+ * 
+ */
+/**
+ * @author cjm
+ *
+ */
+package org.monarchinitiative.owlsim.compute.classmatch;

owlsim-core/src/test/java/org/monarchinitiative/owlsim/compute/classmatch/ClassMatcherTest.java

@@ -0,0 +1,59 @@
+package org.monarchinitiative.owlsim.compute.classmatch;
+
+import static org.junit.Assert.*;
+
+import java.net.URISyntaxException;
+import java.net.URL;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.junit.Test;
+import org.monarchinitiative.owlsim.compute.mica.AbstractMICAStoreTest;
+import org.monarchinitiative.owlsim.compute.mica.MICAStore;
+import org.monarchinitiative.owlsim.compute.mica.impl.MICAStoreImpl;
+import org.monarchinitiative.owlsim.compute.mica.impl.NoRootException;
+import org.monarchinitiative.owlsim.compute.stats.KBStatsCalculator;
+import org.monarchinitiative.owlsim.io.OWLLoader;
+import org.monarchinitiative.owlsim.kb.BMKnowledgeBase;
+import org.monarchinitiative.owlsim.kb.LabelMapper;
+import org.semanticweb.owlapi.model.IRI;
+import org.semanticweb.owlapi.model.OWLOntologyCreationException;
+
+import com.google.monitoring.runtime.instrumentation.common.com.google.common.io.Resources;
+
+public class ClassMatcherTest {
+
+    protected BMKnowledgeBase kb;
+    protected ClassMatcher classMatcher;
+    private Logger LOG = Logger.getLogger(ClassMatcherTest.class);
+
+    protected void load(String fn, String... ontfns) throws OWLOntologyCreationException, URISyntaxException, NoRootException {
+        OWLLoader loader = new OWLLoader();
+        LOG.info("Loading: "+fn);
+        loader.load(IRI.create(Resources.getResource(fn)));
+        for (String ontfn : ontfns) {
+            URL res = getClass().getResource(ontfn);
+            LOG.info("RES="+res);
+            loader.loadOntologies(res.getFile());
+        }
+        kb = loader.createKnowledgeBaseInterface();
+        classMatcher = new ClassMatcher(kb);
+    }
+    
+    @Test
+    public void selfTest() throws OWLOntologyCreationException, URISyntaxException, NoRootException {
+        load("mp-subset.ttl");
+        LabelMapper lm = kb.getLabelMapper();
+        
+        List<SimpleClassMatch> matches = classMatcher.matchOntologies("MP", "MP");
+        
+        int numNonSelfMatches = 0;
+        for (SimpleClassMatch m : matches) {
+            if (!m.getQueryClassId().equals(m.getMatchClassId())) {
+                numNonSelfMatches++;
+            }
+        }
+        assertEquals(0, numNonSelfMatches);
+    }
+
+}

owlsim-services/src/main/java/org/monarchinitiative/owlsim/services/resources/OntologyMatchResource.java

@@ -0,0 +1,66 @@
+package org.monarchinitiative.owlsim.services.resources;
+
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.concurrent.TimeUnit;
+
+import javax.inject.Inject;
+import javax.ws.rs.GET;
+import javax.ws.rs.Path;
+import javax.ws.rs.PathParam;
+import javax.ws.rs.Produces;
+import javax.ws.rs.QueryParam;
+import javax.ws.rs.core.MediaType;
+
+import org.monarchinitiative.owlsim.compute.classmatch.ClassMatcher;
+import org.monarchinitiative.owlsim.compute.classmatch.SimpleClassMatch;
+import org.monarchinitiative.owlsim.compute.cpt.IncoherentStateException;
+import org.monarchinitiative.owlsim.compute.matcher.NegationAwareProfileMatcher;
+import org.monarchinitiative.owlsim.compute.matcher.ProfileMatcher;
+import org.monarchinitiative.owlsim.kb.filter.AnonIndividualFilter;
+import org.monarchinitiative.owlsim.kb.filter.TypeFilter;
+import org.monarchinitiative.owlsim.kb.filter.UnknownFilterException;
+import org.monarchinitiative.owlsim.model.match.MatchSet;
+import org.monarchinitiative.owlsim.model.match.ProfileQuery;
+import org.monarchinitiative.owlsim.model.match.ProfileQueryFactory;
+import org.monarchinitiative.owlsim.services.exceptions.NonNegatedMatcherException;
+import org.monarchinitiative.owlsim.services.exceptions.UnknownMatcherException;
+
+import com.codahale.metrics.annotation.Timed;
+import com.wordnik.swagger.annotations.Api;
+import com.wordnik.swagger.annotations.ApiOperation;
+import com.wordnik.swagger.annotations.ApiParam;
+
+import io.dropwizard.jersey.caching.CacheControl;
+
+@Path("/ontomatch")
+@Api(value = "/ontomatch", description = "ontology match services")
+@Produces({MediaType.APPLICATION_JSON})
+public class OntologyMatchResource {
+
+    @Inject
+    ClassMatcher classMatcher;
+
+    @GET
+    @Path("/{queryOntology}/{targetOntology}")
+    @Timed
+    @CacheControl(maxAge = 2, maxAgeUnit = TimeUnit.HOURS)
+    @ApiOperation(value = "Match", response = MatchSet.class,
+    notes = "Additional notes on the match resource.")
+    public List<SimpleClassMatch> getMatches(
+            @ApiParam(value = "base ontology, e.g. MP",
+            required = true) @PathParam("queryOntology") String queryOntology,
+            @ApiParam(value = "ontology to be matched, e.g. HP",
+            required = true) @PathParam("targetOntology") String targetOntology)
+                    throws UnknownFilterException, IncoherentStateException {
+        List<SimpleClassMatch> matches = 
+                classMatcher.matchOntologies(queryOntology, targetOntology);
+        return matches;
+    }
+
+    // TODO - API for comparing two entities
+
+}