Examples of ConceptType

Examples of org.mitre.medfacts.i2b2.annotation.ConceptType

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    // 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))
    {
      conceptType = ConceptType.PROBLEM;
    } else if (testSet.contains(tui))
    {
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Examples of org.mitre.medfacts.i2b2.annotation.ConceptType

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      concept.setOriginalEntityExternalId(annotation.getAddress());

      FSArray ontologyConceptArray = annotation
          .getOntologyConceptArr();

      ConceptType conceptType = ConceptLookup
          .lookupConceptType(ontologyConceptArray);

      //logger.info(String.format("got concept type: %s", conceptType));

      // now always generating a concept annotation whether or not the
      // conceptType is null (previously, we only generated a concept
      // annotation if the conceptType was not null)
      if (conceptType != null)
      {
        concept.setConceptType(conceptType.toString());
      }
      concept.addToIndexes();

      //logger.info("finished adding new Concept annotation. " + concept);
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Examples of org.mitre.medfacts.i2b2.annotation.ConceptType

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    // 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))
    {
      conceptType = ConceptType.PROBLEM;
    } else if (testSet.contains(tui))
    {
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Examples of org.mitre.medfacts.i2b2.annotation.ConceptType

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      concept.setOriginalEntityExternalId(annotation.getAddress());

      FSArray ontologyConceptArray = annotation
          .getOntologyConceptArr();

      ConceptType conceptType = ConceptLookup
          .lookupConceptType(ontologyConceptArray);

      //logger.info(String.format("got concept type: %s", conceptType));

      // now always generating a concept annotation whether or not the
      // conceptType is null (previously, we only generated a concept
      // annotation if the conceptType was not null)
      if (conceptType != null)
      {
        concept.setConceptType(conceptType.toString());
      }
      concept.addToIndexes();

      //logger.info("finished adding new Concept annotation. " + concept);
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Examples of org.mitre.medfacts.i2b2.annotation.ConceptType

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        logger.info("  begin assertion");
        logger.info("  assertion: " + a.toString());
        //Concept assertion = new Concept(jcas);

        org.mitre.medfacts.i2b2.annotation.AssertionAnnotation i2b2Assertion = (org.mitre.medfacts.i2b2.annotation.AssertionAnnotation)a;
        ConceptType conceptType = i2b2Assertion.getConceptType();

        IdentifiedAnnotation entityOrEventMention = null;
        if (conceptType.equals(ConceptType.TREATMENT))
        {
          entityOrEventMention = new EventMention(jcas);
        } else
        {
          entityOrEventMention = new EntityMention(jcas);
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Examples of org.mitre.medfacts.i2b2.annotation.ConceptType

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      concept.setOriginalEntityExternalId(annotation.getAddress());

      FSArray ontologyConceptArray = annotation
          .getOntologyConceptArr();

      ConceptType conceptType = ConceptLookup
          .lookupConceptType(ontologyConceptArray);

      //logger.info(String.format("got concept type: %s", conceptType));

      // now always generating a concept annotation whether or not the
      // conceptType is null (previously, we only generated a concept
      // annotation if the conceptType was not null)
      if (conceptType != null)
      {
        concept.setConceptType(conceptType.toString());
      }
      concept.addToIndexes();

      //logger.info("finished adding new Concept annotation. " + concept);
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Examples of org.mitre.medfacts.i2b2.annotation.ConceptType

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    // 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))
    {
      conceptType = ConceptType.PROBLEM;
    } else if (testSet.contains(tui))
    {
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