Package org.apache.ctakes.typesystem.type.refsem

Examples of org.apache.ctakes.typesystem.type.refsem.UmlsConcept

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    HashSet<String> uniqueCuis = new HashSet<String>();
    if(mentions == null) return null;
    for(int i = 0; i < mentions.size(); i++){
      if(mentions.get(i) instanceof UmlsConcept){
        UmlsConcept concept = (UmlsConcept) mentions.get(i);
        uniqueCuis.add(concept.getCui());
      }
    }
   
    for(String cui : uniqueCuis){
      if(t.getPolarity() == CONST.NE_POLARITY_NEGATION_PRESENT) buff.append("-");
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    //logger.info("hasConcept: " + hasConcept);
    OntologyConcept ontologyConcept = (OntologyConcept)firstConceptFS;
    boolean isRxnorm = false;
    boolean isUmls = false;

    UmlsConcept umlsConcept = null;
    if (ontologyConcept == null)
    {
      // do nothing -- leave isRxnorm and isUmls as false
      return null;
    }
    if (ontologyConcept instanceof UmlsConcept)
    {
      isUmls = true;
      umlsConcept = (UmlsConcept)firstConceptFS;
    } else
    {
      isRxnorm = "RXNORM".equalsIgnoreCase(ontologyConcept.getCodingScheme());
    }
   
    //logger.info(String.format("isUmls: %b; isRxnorm: %b", isUmls, isRxnorm));
   
    if (isRxnorm)
    {
      return ConceptType.TREATMENT;
    } else if (!isUmls) // is not umls and is not rxnorm
    {
      return null;
    }
   
    // if we're continuing, this means we are umls (and we are not rxnorm)
   
    String tui = umlsConcept.getTui();
    //logger.info(String.format("tui: %s", tui));
   
    ConceptType conceptType = null;
    if (problemSet.contains(tui))
    {
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   private Collection<UmlsConcept> createConceptCol( final JCas jcas, final String cui, final String tui,
                                        final Collection<String> snomedCodesCol ) {
      final String codingSchemeKey = props.getProperty( CODING_SCHEME_PRP_KEY );
      final List<UmlsConcept> conceptList = new ArrayList<UmlsConcept>();
      for ( String snomedCode : snomedCodesCol ) {
         final UmlsConcept uc = new UmlsConcept( jcas );
         uc.setCode( snomedCode );
         uc.setCodingScheme( codingSchemeKey );
         uc.setCui( cui );
         uc.setTui( tui );
         conceptList.add( uc );
      }
      return conceptList;
   }
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    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 { // RxNorm
        String code = ontologyConcept.getCodingScheme() + ontologyConcept.getCode();
        codes.add(code);
      }
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    OntologyConcept ontologyConcept;
    if (mention.getTypeID() == CONST.NE_TYPE_ID_DRUG) {
      ontologyConcept = new OntologyConcept(jCas);
      ontologyConcept.setCode(code);
    } else {
      UmlsConcept umlsConcept = new UmlsConcept(jCas);
      umlsConcept.setCui(code);
      ontologyConcept = umlsConcept;
    }
    ontologyConcept.addToIndexes();
    mention.setOntologyConceptArr(new FSArray(jCas, 1));
    mention.setOntologyConceptArr(0, ontologyConcept);
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Related Classes of org.apache.ctakes.typesystem.type.refsem.UmlsConcept

  • org.apache.ctakes.assertion.cr.MiPACQKnowtatorXMLReader
  • org.apache.ctakes.assertion.medfacts.ConceptLookup
  • org.apache.ctakes.clinicalpipeline.runtime.BagOfCUIsGenerator
  • org.apache.ctakes.core.ae.SHARPKnowtatorXMLReader
  • org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedConsumerImpl
  • org.apache.ctakes.dictionary.lookup2.consumer.DefaultTermConsumer
  • org.apache.ctakes.dictionary.lookup2.consumer.WsdTermConsumer
  • org.apache.ctakes.relationextractor.pipelines.SelectiveRelationAnnotationViewer
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