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Posted to commits@ctakes.apache.org by dl...@apache.org on 2013/06/04 20:31:34 UTC
svn commit: r1489548 -
/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/SelectiveRelationAnnotationViewer.java
Author: dligach
Date: Tue Jun 4 18:31:21 2013
New Revision: 1489548
URL: http://svn.apache.org/r1489548
Log:
display the relations whose arg1 is defined in a separate file
Added:
ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/SelectiveRelationAnnotationViewer.java
Added: ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/SelectiveRelationAnnotationViewer.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/SelectiveRelationAnnotationViewer.java?rev=1489548&view=auto
==============================================================================
--- ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/SelectiveRelationAnnotationViewer.java (added)
+++ ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/SelectiveRelationAnnotationViewer.java Tue Jun 4 18:31:21 2013
@@ -0,0 +1,220 @@
+/**
+ * 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.pipelines;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.util.Arrays;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Scanner;
+import java.util.Set;
+
+import org.apache.ctakes.relationextractor.eval.XMIReader;
+import org.apache.ctakes.typesystem.type.refsem.OntologyConcept;
+import org.apache.ctakes.typesystem.type.refsem.UmlsConcept;
+import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import org.apache.ctakes.typesystem.type.textspan.Sentence;
+import org.apache.uima.UimaContext;
+import org.apache.uima.analysis_engine.AnalysisEngine;
+import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.cas.CAS;
+import org.apache.uima.cas.CASException;
+import org.apache.uima.cas.FeatureStructure;
+import org.apache.uima.collection.CollectionReader;
+import org.apache.uima.jcas.JCas;
+import org.apache.uima.jcas.cas.FSArray;
+import org.apache.uima.resource.ResourceInitializationException;
+import org.cleartk.util.Options_ImplBase;
+import org.kohsuke.args4j.Option;
+import org.uimafit.component.JCasAnnotator_ImplBase;
+import org.uimafit.factory.AnalysisEngineFactory;
+import org.uimafit.factory.CollectionReaderFactory;
+import org.uimafit.pipeline.SimplePipeline;
+import org.uimafit.util.JCasUtil;
+
+/**
+ * View relation instances in xmi files. Only display the relations
+ * whose arg1s are specified in a dictionary of CUIs.
+ *
+ * @author dmitriy dligach
+ */
+public class SelectiveRelationAnnotationViewer {
+
+ public static class Options extends Options_ImplBase {
+
+ @Option(
+ name = "--input-dir",
+ usage = "specify the path to the directory containing the clinical notes to be processed",
+ required = true)
+ public File inputDirectory;
+ }
+
+ public static void main(String[] args) throws Exception {
+
+ Options options = new Options();
+ options.parseOptions(args);
+
+ List<File> trainFiles = Arrays.asList(options.inputDirectory.listFiles());
+ CollectionReader collectionReader = getCollectionReader(trainFiles);
+
+ AnalysisEngine relationExtractorPrinter = AnalysisEngineFactory.createPrimitive(
+ RelationExtractorPrinter.class);
+
+ SimplePipeline.runPipeline(collectionReader, relationExtractorPrinter);
+ }
+
+ /*
+ * Displays the relations whose arg1 is specified in a dictionary file.
+ */
+ public static class RelationExtractorPrinter extends JCasAnnotator_ImplBase {
+
+ // file containing one cui per line
+ private String dictionaryPath = "cuis.txt";
+ private Set<String> cuiDictionary;
+
+ @Override
+ public void initialize(UimaContext aContext) throws ResourceInitializationException {
+ super.initialize(aContext);
+ cuiDictionary = getCustomizedDictionary(dictionaryPath);
+ }
+
+ @Override
+ public void process(JCas jCas) throws AnalysisEngineProcessException {
+
+ JCas systemView;
+ try {
+ systemView = jCas.getView(CAS.NAME_DEFAULT_SOFA);
+ } catch (CASException e) {
+ throw new AnalysisEngineProcessException(e);
+ }
+
+ for(BinaryTextRelation binaryTextRelation : JCasUtil.select(systemView, BinaryTextRelation.class)) {
+ IdentifiedAnnotation entity1; // entity whose role is "Argument"
+ IdentifiedAnnotation entity2; // entity whose role is "Related_to"
+
+ if(binaryTextRelation.getArg1().getRole().equals("Argument")) {
+ entity1 = (IdentifiedAnnotation) binaryTextRelation.getArg1().getArgument();
+ entity2 = (IdentifiedAnnotation) binaryTextRelation.getArg2().getArgument();
+ } else {
+ entity1 = (IdentifiedAnnotation) binaryTextRelation.getArg2().getArgument();
+ entity2 = (IdentifiedAnnotation) binaryTextRelation.getArg1().getArgument();
+ }
+
+ String category = binaryTextRelation.getCategory();
+ String arg1 = entity1.getCoveredText().toLowerCase();
+ String arg2 = entity2.getCoveredText().toLowerCase();
+ int type1 = entity1.getTypeID();
+ int type2 = entity2.getTypeID();
+
+ // first argument has to be an anatomical site
+ if(type1 != 6) {
+ continue;
+ }
+ // skip location_of(anatomical site, anatomical site)
+ if(type1 == 6 && type2 == 6) {
+ continue;
+ }
+ // "to" is not a valid disease/disorder
+ if(type2 == 3 && arg2.equals("to")) {
+ continue;
+ }
+
+ // print relations as long as arg1 exists in the dictionary
+ Set<String> codes = getOntologyConceptCodes(entity1);
+ codes.retainAll(cuiDictionary);
+ if(codes.size() > 0) {
+ // print relation and its arguments: location_of(colon/6, colon cancer/2)
+ System.out.format("%s(%s/%d, %s/%d)\n", category, arg1, type1, arg2, type2);
+ List<Sentence> sentences = JCasUtil.selectCovering(systemView, Sentence.class, entity1.getBegin(), entity1.getEnd());
+ System.out.println(sentences.get(0).getCoveredText());
+ System.out.println();
+ }
+ }
+ }
+ }
+
+ private static CollectionReader getCollectionReader(List<File> items) throws Exception {
+
+ // convert the List<File> to a String[]
+ String[] paths = new String[items.size()];
+ for (int i = 0; i < paths.length; ++i) {
+ paths[i] = items.get(i).getPath();
+ }
+
+ // return a reader that will load each of the XMI files
+ return CollectionReaderFactory.createCollectionReader(
+ XMIReader.class,
+ XMIReader.PARAM_FILES,
+ paths);
+ }
+
+ /**
+ * Get the CUIs, RxNorm codes specified for this entity.
+ */
+ public static HashSet<String> getOntologyConceptCodes(IdentifiedAnnotation identifiedAnnotation) {
+
+ HashSet<String> codes = new HashSet<String>();
+
+ FSArray fsArray = identifiedAnnotation.getOntologyConceptArr();
+ if(fsArray == null) {
+ return codes;
+ }
+
+ for(FeatureStructure featureStructure : fsArray.toArray()) {
+ OntologyConcept ontologyConcept = (OntologyConcept) featureStructure;
+
+ if(ontologyConcept instanceof UmlsConcept) {
+ UmlsConcept umlsConcept = (UmlsConcept) ontologyConcept;
+ String code = umlsConcept.getCui();
+ codes.add(code);
+ } else { // SNOMED or RxNorm
+ String code = ontologyConcept.getCodingScheme() + ontologyConcept.getCode();
+ codes.add(code);
+ }
+ }
+
+ return codes;
+ }
+
+ /**
+ * Read comma separate file containing target CUIs.
+ */
+ public static Set<String> getCustomizedDictionary(String path) {
+
+ Set<String> cuis = new HashSet<String>();
+
+ File file = new File(path);
+ Scanner scan = null;
+ try {
+ scan = new Scanner(file);
+ } catch (FileNotFoundException e) {
+ System.err.println("couldn't open file: " + path);
+ return cuis;
+ }
+
+ while(scan.hasNextLine()) {
+ String line = scan.nextLine();
+ cuis.add(line);
+ }
+
+ return cuis;
+ }
+}