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From dlig...@apache.org
Subject svn commit: r1672104 - /ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/ManagesTreatsRelationExtractorAnnotator.java
Date Wed, 08 Apr 2015 15:20:01 GMT
Author: dligach
Date: Wed Apr  8 15:20:01 2015
New Revision: 1672104

URL: http://svn.apache.org/r1672104
Log:
annotates manages/treats relation

Added:
    ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/ManagesTreatsRelationExtractorAnnotator.java
  (with props)

Added: ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/ManagesTreatsRelationExtractorAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/ManagesTreatsRelationExtractorAnnotator.java?rev=1672104&view=auto
==============================================================================
--- ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/ManagesTreatsRelationExtractorAnnotator.java
(added)
+++ ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/ManagesTreatsRelationExtractorAnnotator.java
Wed Apr  8 15:20:01 2015
@@ -0,0 +1,110 @@
+/**
+ * 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;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation;
+import org.apache.ctakes.typesystem.type.relation.ManagesTreatsTextRelation;
+import org.apache.ctakes.typesystem.type.relation.RelationArgument;
+import org.apache.ctakes.typesystem.type.textsem.AnatomicalSiteMention;
+import org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import org.apache.ctakes.typesystem.type.textsem.MedicationMention;
+import org.apache.ctakes.typesystem.type.textsem.ProcedureMention;
+import org.apache.ctakes.typesystem.type.textsem.SignSymptomMention;
+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;
+
+/**
+ * Identifies manages/treats relation.
+ * 
+ * arg1: drug, procedure
+ * arg2: disease/disorder, sign/symptom, anatomical site
+ */
+public class ManagesTreatsRelationExtractorAnnotator extends RelationExtractorAnnotator {
+
+  @Override
+  protected Class<? extends BinaryTextRelation> getRelationClass() {
+    return ManagesTreatsTextRelation.class;
+  }
+
+  @Override
+  public List<IdentifiedAnnotationPair> getCandidateRelationArgumentPairs(
+      JCas identifiedAnnotationView,
+      Annotation sentence) {
+
+    List<IdentifiedAnnotation> arg1s = new ArrayList<>();
+    List<MedicationMention> medications = 
+        JCasUtil.selectCovered(identifiedAnnotationView, MedicationMention.class, sentence);

+    List<ProcedureMention> procedures = 
+        JCasUtil.selectCovered(identifiedAnnotationView, ProcedureMention.class, sentence);
+    arg1s.addAll(medications);
+    arg1s.addAll(procedures);
+    
+    List<IdentifiedAnnotation> arg2s = new ArrayList<>();
+    List<DiseaseDisorderMention> diseaseDisorders = 
+        JCasUtil.selectCovered(identifiedAnnotationView, DiseaseDisorderMention.class, sentence);
+    List<SignSymptomMention> signSymptoms = 
+        JCasUtil.selectCovered(identifiedAnnotationView, SignSymptomMention.class, sentence);
+    List<AnatomicalSiteMention> anatomicalSites =  
+        JCasUtil.selectCovered(identifiedAnnotationView, AnatomicalSiteMention.class, sentence);
+    arg2s.addAll(diseaseDisorders);
+    arg2s.addAll(signSymptoms);
+    arg2s.addAll(anatomicalSites);
+    
+    List<IdentifiedAnnotationPair> pairs = new ArrayList<>();
+    for(IdentifiedAnnotation arg1 : arg1s) {
+      for(IdentifiedAnnotation arg2 : arg2s) {
+        pairs.add(new IdentifiedAnnotationPair(arg1, arg2));
+      }
+    }
+    
+    return pairs;
+  }
+
+  @Override
+  protected void createRelation(
+      JCas jCas,
+      IdentifiedAnnotation arg1,
+      IdentifiedAnnotation arg2,
+      String predictedCategory) {
+    RelationArgument relArg1 = new RelationArgument(jCas);
+    relArg1.setArgument(arg1);
+    relArg1.setRole("Argument");
+    relArg1.addToIndexes();
+    RelationArgument relArg2 = new RelationArgument(jCas);
+    relArg2.setArgument(arg2);
+    relArg2.setRole("Related_to");
+    relArg2.addToIndexes();
+    ManagesTreatsTextRelation relation = new ManagesTreatsTextRelation(jCas);
+    relation.setArg1(relArg1);
+    relation.setArg2(relArg2);
+    relation.setCategory(predictedCategory);
+    relation.addToIndexes();
+  }
+
+  @Override
+  protected Class<? extends Annotation> getCoveringClass() {
+    return Sentence.class;
+  }
+}

Propchange: ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/ManagesTreatsRelationExtractorAnnotator.java
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