finding medical terms given string through ctakes(UMLS)

[Ks Sunder]

Hi All,

I have written below code..

package com.shyam.Test;

import java.util.ArrayList;

import java.util.Arrays;

import java.util.Collection;

import org.apache.ctakes.clinicalpipeline.ClinicalPipelineFactory;

import org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator;

import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;

import org.apache.uima.UIMAException;

import org.apache.uima.analysis_engine.AnalysisEngineDescription;

import org.apache.uima.analysis_engine.AnalysisEngineProcessException;

import org.apache.uima.cas.CASRuntimeException;

import org.apache.uima.fit.factory.JCasFactory;

import org.apache.uima.fit.pipeline.SimplePipeline;

import org.apache.uima.fit.util.JCasUtil;

import org.apache.uima.jcas.JCas;

import org.apache.uima.resource.ResourceInitializationException;

public class DefaultPipeLine {

public static void main(String[] args) {

      try {

  final String note = " History of diabetes and hypertension."

                          + " Mother had breast cancer."

                          + " Sister with multiple sclerosis."

                          + " The patient is suffering from extreme pain due to shark bite."

                          + " Recommend continuing use of aspirin, oxycodone, and coumadin."

                          + " Continue exercise for obesity and hypertension.";

                      

                    

  final JCas jcas = JCasFactory.createJCas();

  jcas.setDocumentText( note );

   // final AnalysisEngineDescription aed = ClinicalPipelineFactory.getDefaultPipeline();

            final AnalysisEngineDescription aed = ClinicalPipelineFactory.getFastPipeline();  // Outputs from default and fast pipelines are identical

            // final AnalysisEngineDescription uml = UmlsDictionaryLookupAnnotator.createAnnotatorDescription();

             

           

             SimplePipeline.runPipeline( jcas, aed );

  

  final Collection<String> codes = new ArrayList<>();

  for ( IdentifiedAnnotation entity : JCasUtil.select( jcas, IdentifiedAnnotation.class ) ) {

     System.out.println( "Entity: " + entity.getCoveredText()

                         + " === Polarity: " + entity.getPolarity()

     );

               //  System.out.println("!!!!!!!!!! Task is Completed !!!!!!!!!!!!!!!");

     

  }

  

  

} catch (CASRuntimeException e) {

// TODO Auto-generated catch block

e.printStackTrace();

} catch (AnalysisEngineProcessException e) {

// TODO Auto-generated catch block

e.printStackTrace();

} catch (ResourceInitializationException e) {

// TODO Auto-generated catch block

e.printStackTrace();

} catch (UIMAException e) {

// TODO Auto-generated catch block

e.printStackTrace();

}

   }

}

o/p is :

Entity: History of === Polarity: 1

Entity: History === Polarity: 1

Entity: diabetes === Polarity: 1

Entity: hypertension === Polarity: 1

Entity: breast cancer === Polarity: 1

Entity: breast === Polarity: 1

Entity: cancer === Polarity: 1

Entity: multiple sclerosis === Polarity: 1

Entity: sclerosis === Polarity: 1

Entity: pain === Polarity: 1

Entity: shark bite === Polarity: 1

Entity: bite === Polarity: 1

Entity: bite === Polarity: 1

Entity: aspirin === Polarity: 1

Entity: oxycodone === Polarity: 1

Entity: oxycodone === Polarity: 1

Entity: coumadin === Polarity: 1

Entity: exercise === Polarity: 1

Entity: obesity === Polarity: 1

Entity: hypertension === Polarity: 1

im getting non medical and medical terms , so how can avoid non medical terms , i want o/p is only medical terms .

please help me.

regards,

shyam k.