Package org.mitre.medfacts.i2b2.processors

Examples of org.mitre.medfacts.i2b2.processors.ScopeFileProcessor

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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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      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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        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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      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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    // 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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        String cueSubTypeString = matcher.group(11);
        CueSubType cueSubType = CueSubType.valueOf(cueSubTypeString.toUpperCase());
        String scopeRefString = matcher.group(12);
        int scopeRef = Integer.parseInt(scopeRefString);

        CueAnnotation a2 = new CueAnnotation();
        a2.setCueSubType(cueSubType);
        a2.setScopeIdReference(scopeRef);
        annotation = a2;
        break;
    }
    annotation.setConceptText(conceptText);
    annotation.setBegin(new Location(beginLine, beginCharacter));
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            }
          }

          if (a instanceof CueAnnotation)
          {
            CueAnnotation cue = (CueAnnotation)a;
            if (checkForEnabledFeature("cue"))
            {
              String cueType = cue.getCueSubType().toString();
              int cueBegin = cue.getBegin().getTokenOffset();
              if (cueBegin < conceptBeginTokenOffset) {
                  trainingInstance.addFeature("cue_" + cueType + "_left");
                  if ((conceptBeginTokenOffset - cueBegin) < 4) {
                      trainingInstance.addFeature("cue_" + cueType + "_left_3");
                  }
              } else {
                  int cueEnd = cue.getEnd().getTokenOffset();
                  trainingInstance.addFeature("cue_" + cueType + "_right");
                  if ((cueEnd - conceptEndTokenOffset) < 4) {
                      trainingInstance.addFeature("cue_" + cueType + "_right_3");
                  }
              }
            }
            if (checkForEnabledFeature("inCue"))
            {
              trainingInstance.addFeature("in_cue_" + currentToken);
            }
            if (checkForEnabledFeature("inCueForScopeId"))
            {
              trainingInstance.addFeature("in_cue_for_scope_id_" + cue.getScopeIdReference() + "_" + currentToken);
            }
          }

          if (checkForEnabledFeature("zone"))
          {
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            }
          }

          if (a instanceof CueAnnotation)
          {
            CueAnnotation cue = (CueAnnotation)a;
            if (checkForEnabledFeature("cue"))
            {
              String cueType = cue.getCueSubType().toString();
              int cueBegin = cue.getBegin().getTokenOffset();
              if (cueBegin < conceptBeginTokenOffset) {
                  trainingInstance.addFeature("cue_" + cueType + "_left");
                  if ((conceptBeginTokenOffset - cueBegin) < 4) {
                      trainingInstance.addFeature("cue_" + cueType + "_left_3");
                  }
              } else {
                  int cueEnd = cue.getEnd().getTokenOffset();
                  trainingInstance.addFeature("cue_" + cueType + "_right");
                  if ((cueEnd - conceptEndTokenOffset) < 4) {
                      trainingInstance.addFeature("cue_" + cueType + "_right_3");
                  }
              }
            }
            if (checkForEnabledFeature("inCue"))
            {
              trainingInstance.addFeature("in_cue_" + currentToken);
            }
            if (checkForEnabledFeature("inCueForScopeId"))
            {
              trainingInstance.addFeature("in_cue_for_scope_id_" + cue.getScopeIdReference() + "_" + currentToken);
            }
          }

          if (a instanceof CueWordAnnotation)
          {
            CueWordAnnotation cueWord = (CueWordAnnotation)a;
            String cueWordType = cueWord.getCueWordType().toString();
            String cueWordText = cueWord.getCueWordText();
            String escapedCueWordText = escapeFeatureName(cueWordText);
            String escapedCueWordClass = null;
            String cueWordClass = cueWord.getCueWordClass();
            boolean cueWordClassIsNotEmpty = (cueWordClass != null) && (!cueWordClass.isEmpty());
            if (checkForEnabledFeature("cueWordClassValue") && cueWordClassIsNotEmpty)
            {
              escapedCueWordClass = escapeFeatureName(cueWordClass);
            }

            if (checkForEnabledFeature("cueWordTextPositional"))
            {
              int cueWordBegin = cueWord.getBegin().getTokenOffset();
              int cueWordEnd = cueWord.getEnd().getTokenOffset();
              if (cueWordBegin < conceptBeginTokenOffset) {
                  trainingInstance.addFeature("cueWordTextPositional_" + escapedCueWordText + "_left");
                  if ((conceptBeginTokenOffset - cueWordBegin) < 4) {
                      trainingInstance.addFeature("cueWordTextPositional_" + escapedCueWordText + "_left_3");
                  }
              } else if (cueWordBegin > conceptEndTokenOffset) {
                    trainingInstance.addFeature("cueWordTextPositional_" + escapedCueWordText + "_right");
                    if ((cueWordEnd - conceptEndTokenOffset) < 4) {
                        trainingInstance.addFeature("cueWordTextPositional_" + escapedCueWordText + "_right_3");
                    }
              } else {
                  trainingInstance.addFeature("cueWordTextPositional_" + escapedCueWordText + "_within");
              }
            }
            if (checkForEnabledFeature("cueWordTypePositional"))
            {
              int cueWordBegin = cueWord.getBegin().getTokenOffset();
              int cueWordEnd = cueWord.getEnd().getTokenOffset();
              if (cueWordBegin < conceptBeginTokenOffset) {
                  trainingInstance.addFeature("cueWordTypePositional_" + cueWordType + "_left");
                  if ((conceptBeginTokenOffset - cueWordBegin) < 4) {
                      trainingInstance.addFeature("cueWordTypePositional_" + cueWordType + "_left_3");
                  }
              } else if (cueWordBegin > conceptEndTokenOffset) {
                    trainingInstance.addFeature("cueWordTypePositional_" + cueWordType + "_right");
                    if ((cueWordEnd - conceptEndTokenOffset) < 4) {
                        trainingInstance.addFeature("cueWordTypePositional_" + cueWordType + "_right_3");
                    }
              } else {
                  trainingInstance.addFeature("cueWordTypePositional_" + cueWordType + "_within");
              }
            }
            if (checkForEnabledFeature("cueWordClassPositional") && cueWordClassIsNotEmpty)
            {
              int cueWordBegin = cueWord.getBegin().getTokenOffset();
              int cueWordEnd = cueWord.getEnd().getTokenOffset();
              if (cueWordBegin < conceptBeginTokenOffset) {
                  trainingInstance.addFeature("cueWordClassPositional_" + escapedCueWordClass + "_left");
                  if ((conceptBeginTokenOffset - cueWordBegin) < 4) {
                      trainingInstance.addFeature("cueWordClassPositional_" + escapedCueWordClass + "_left_3");
                  }
              } else if (cueWordBegin > conceptEndTokenOffset) {
                    trainingInstance.addFeature("cueWordClassPositional_" + escapedCueWordClass + "_right");
                    if ((cueWordEnd - conceptEndTokenOffset) < 4) {
                        trainingInstance.addFeature("cueWordClassPositional_" + escapedCueWordClass + "_right_3");
                    }
              } else {
                  trainingInstance.addFeature("cueWordClassPositional_" + escapedCueWordClass + "_within");
              }
            }
            if (checkForEnabledFeature("cueWordTextValue"))
            {
              trainingInstance.addFeature("cueWordTextValue_" + escapedCueWordText);
            }
            if (checkForEnabledFeature("cueWordTypeValue") && cueWord.getCueWordType() != null)
            {
              trainingInstance.addFeature("cueWordTypeValue_" + cueWord.getCueWordType().toString());
            }
            if (checkForEnabledFeature("cueWordClassValue") && cueWord.getCueWordClass() != null && !cueWord.getCueWordClass().isEmpty())
            {
              trainingInstance.addFeature("cueWordClassValue_" + escapedCueWordClass);
            }
          }

          if (checkForEnabledFeature("zone"))
          {
            if (a instanceof ZoneAnnotation)
            {
              ZoneAnnotation zone = (ZoneAnnotation)a;
              final String zoneFeatureName = "zone_" + escapeFeatureName(zone.getZoneName());
              //logger.info("### zone feature: " + zoneFeatureName);
              trainingInstance.addFeature(zoneFeatureName);
            }
          }
        }
        if (scopeCount > 0)
        {
          if (checkForEnabledFeature("scopeCountNumber"))
          {
            trainingInstance.addFeature("scope_count_" + scopeCount);
          }
          if (checkForEnabledFeature("scopeCountEvenOrOdd"))
          {
            boolean scopeCountIsEven = (scopeCount % 2) == 0;
            trainingInstance.addFeature("scope_count_" + (scopeCountIsEven ? "even" : "odd"));
          }
        }
      }

      //Features based on negation and speculation scopes enclosing the text of the entire training instance -Alex Yeh
      int enclosingNegationScopeCnt = 0;
      int enclosingSpeculationScopeCnt = 0;
      AssertionAnnotation assertForTI = trainingInstance.getAssertAnnotateForTI();
      //Count number of enclosing negation and speculation scopes
      for (ScopeAnnotation enclosingScope : assertForTI.getEnclosingScopes())
      {
        CueAnnotation cueForScope = enclosingScope.getCueForScope();
        CueSubType scopeType = cueForScope.getCueSubType();
        if (scopeType == CueSubType.NEGATION) enclosingNegationScopeCnt++;
        else if (scopeType == CueSubType.SPECULATION) enclosingSpeculationScopeCnt++;
        else logger.info(String.format("WARNING: CUE %s%n  FOR SCOPE %s%n ENCLOSING %s%n is neither a negation nor speculation cue%n", cueForScope, enclosingScope,assertForTI));
      }
      if (checkForEnabledFeature("statusRuleMixNMatchFeature"))
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            ScopeAnnotation scope = (ScopeAnnotation)current;
            int scopeId = scope.getScopeId();
            scopeIdMap.put(scopeId, scope);
        } else if (current instanceof CueAnnotation)
        {
            CueAnnotation cue = (CueAnnotation)current;
            int scopeIdForThisCue = cue.getScopeIdReference();
            cueForScopeIdMap.put(scopeIdForThisCue, cue);
        }
    }

    for (Entry<Integer, ScopeAnnotation> current : scopeIdMap.entrySet())
    {
        int currentId = current.getKey();
        ScopeAnnotation scope = current.getValue();

        CueAnnotation cue = cueForScopeIdMap.get(currentId);
        scope.setCueForScope(cue);
    }
    //For testing -Alex Yeh
//    logger.info(String.format("CUES for SCOPES in FILE %s%n", textFilename);
//    logger.info(String.format("  MAP size: %s.%n", scopeIdMap.entrySet().size());
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        annotation = a1;
        break;
      case CUE:
        String cueSubTypeString = matcher.group(11);
        CueSubType cueSubType = CueSubType.valueOf(cueSubTypeString.toUpperCase());
        String scopeRefString = matcher.group(12);
        int scopeRef = Integer.parseInt(scopeRefString);

        CueAnnotation a2 = new CueAnnotation();
        a2.setCueSubType(cueSubType);
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Related Classes of org.mitre.medfacts.i2b2.processors.ScopeFileProcessor

  • edu.mayo.bmi.uima.core.type.syntax.BaseToken
  • edu.mayo.bmi.uima.core.type.textspan.Sentence
  • org.apache.commons.cli.CommandLine
  • org.apache.commons.cli.CommandLineParser
  • org.apache.commons.cli.GnuParser
  • org.apache.commons.cli.Options
  • org.apache.ctakes.assertion.medfacts.AssertionAnalysisEngine
  • org.apache.ctakes.assertion.medfacts.ConceptConverterAnalysisEngine
  • org.apache.ctakes.assertion.medfacts.ConceptLookup
  • org.apache.ctakes.assertion.medfacts.Converti2b2AnnotationsToCTAKES
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