org.apache.ctakes.relationextractor.ae.baselines.Baseline3EntityMentionPairRelationExtractorAnnotator.java Source code

Introduction

Here is the source code for org.apache.ctakes.relationextractor.ae.baselines.Baseline3EntityMentionPairRelationExtractorAnnotator.java

Source

/*
 * Licensed to the Apache Software Foundation (ASF) under one
 * or more contributor license agreements.  See the NOTICE file
 * distributed with this work for additional information
 * regarding copyright ownership.  The ASF licenses this file
 * to you under the Apache License, Version 2.0 (the
 * "License"); you may not use this file except in compliance
 * with the License.  You may obtain a copy of the License at
 *
 *   http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing,
 * software distributed under the License is distributed on an
 * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
 * KIND, either express or implied.  See the License for the
 * specific language governing permissions and limitations
 * under the License.
 */
package org.apache.ctakes.relationextractor.ae.baselines;

import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;

import org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator;
import org.apache.ctakes.typesystem.type.syntax.BaseToken;
import org.apache.ctakes.typesystem.type.textsem.EntityMention;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
import org.apache.uima.fit.util.JCasUtil;
import org.apache.uima.jcas.JCas;
import org.apache.uima.jcas.tcas.Annotation;
import org.cleartk.ml.Feature;

import com.google.common.base.Function;
import com.google.common.base.Functions;
import com.google.common.collect.Ordering;

/**
 * This baseline links each anatomical site with the closest entity of a type  
 * that's suitable for location_of, as long as there is no intervening anatomical site. 
 */
public class Baseline3EntityMentionPairRelationExtractorAnnotator extends RelationExtractorAnnotator {

    @Override
    public Class<? extends Annotation> getCoveringClass() {
        return Sentence.class;
    }

    @Override
    public List<IdentifiedAnnotationPair> getCandidateRelationArgumentPairs(JCas identifiedAnnotationView,
            Annotation sentence) {

        List<EntityMention> entityMentions = JCasUtil.selectCovered(identifiedAnnotationView, EntityMention.class,
                sentence);

        List<EntityMention> anatomicalSites = getAnatomicalSites(entityMentions);
        List<EntityMention> entitiesSuitableForLocationOf = getEntitiesSuitableForLocationOf(entityMentions);

        if ((anatomicalSites.size() < 1) || (entitiesSuitableForLocationOf.size() < 1)) {
            return new ArrayList<IdentifiedAnnotationPair>();
        }

        List<IdentifiedAnnotationPair> result = new ArrayList<IdentifiedAnnotationPair>();
        Set<EntityMention> alreadyLinked = new HashSet<EntityMention>();

        for (EntityMention anatomicalSite : anatomicalSites) {
            EntityMention nearestEntity = getNearestEntity(identifiedAnnotationView, anatomicalSite,
                    entitiesSuitableForLocationOf);

            // don't link if there's an another anatomical site between this one and its nearest entity
            if (checkForAnatomicalSiteBetween(identifiedAnnotationView, anatomicalSite, nearestEntity)) {
                continue;
            }

            // make sure this entity isn't already linked to an anatomical site
            if (!alreadyLinked.contains(nearestEntity)) {
                result.add(new IdentifiedAnnotationPair(anatomicalSite, nearestEntity));
                alreadyLinked.add(nearestEntity);
            }
        }

        return result;
    }

    /*
     * Return entity mentions that are anatomical types (i.e. typeId is 6)
     */
    private static List<EntityMention> getAnatomicalSites(List<EntityMention> entityMentions) {

        List<EntityMention> anatomicalSites = new ArrayList<EntityMention>();

        for (EntityMention entityMention : entityMentions) {
            if (entityMention.getTypeID() == 6) {
                anatomicalSites.add(entityMention);
            }
        }

        return anatomicalSites;
    }

    /*
     * Return entity mentions that qualityf to be the arg2 of location_of relation (i.e. 2, 3, or 5)
     */
    private static List<EntityMention> getEntitiesSuitableForLocationOf(List<EntityMention> entityMentions) {

        HashSet<Integer> okArg2Types = new HashSet<Integer>(Arrays.asList(2, 3, 5));
        List<EntityMention> suitableEntities = new ArrayList<EntityMention>();

        for (EntityMention entityMention : entityMentions) {
            if (okArg2Types.contains(entityMention.getTypeID())) {
                suitableEntities.add(entityMention);
            }
        }

        return suitableEntities;
    }

    /*
     * Find the entity nearest to the anatomical site
     */
    private static EntityMention getNearestEntity(JCas jCas, EntityMention anatomicalSite,
            List<EntityMention> entityMentions) {

        // token distance from anatomical site to other entity mentions
        Map<EntityMention, Integer> distanceToEntities = new HashMap<EntityMention, Integer>();

        for (EntityMention entityMention : entityMentions) {
            List<BaseToken> baseTokens = JCasUtil.selectBetween(jCas, BaseToken.class, anatomicalSite,
                    entityMention);
            distanceToEntities.put(entityMention, baseTokens.size());
        }

        List<EntityMention> sortedEntityMentions = new ArrayList<EntityMention>(distanceToEntities.keySet());
        Function<EntityMention, Integer> getValue = Functions.forMap(distanceToEntities);
        Collections.sort(sortedEntityMentions, Ordering.natural().onResultOf(getValue));

        return sortedEntityMentions.get(0);
    }

    /*
     * Return true if there's an anatomical site entity mention between two entities.
     */
    private static boolean checkForAnatomicalSiteBetween(JCas jCas, EntityMention entity1, EntityMention entity2) {

        for (EntityMention entityMention : JCasUtil.selectBetween(jCas, EntityMention.class, entity1, entity2)) {
            if (entityMention.getTypeID() == 6) {
                return true;
            }
        }

        return false;
    }

    @Override
    public String classify(List<Feature> features) {
        return "location_of";
    }
}