Examples of org.apache.ctakes.typesystem.type.textsem.EventMention

Package org.apache.ctakes.typesystem.type.textsem

Examples of org.apache.ctakes.typesystem.type.textsem.EventMention

org.apache.ctakes.typesystem.type.textsem.EventMention


  jCas.setDocumentText(a.sentenceText);
  DocumentID documentID = new DocumentID(jCas);
  documentID.setDocumentID("doc" + a.lineNumber);
  documentID.addToIndexes();
  EventMention ia = new EventMention(jCas);
  ia.setBegin(Integer.parseInt(a.begin));
  ia.setEnd(Integer.parseInt(a.end));
  if (!skipReadingValuesJustReadText) ia.setPolarity(Integer.parseInt(a.polarity));
  ia.addToIndexes();


}

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        delayedFeatures.add(new DelayedFeature(mention, "bodyLaterality", bodyLaterality));
        KnowtatorAnnotation bodySide = annotationSlots.remove("body_side");
        delayedFeatures.add(new DelayedFeature(mention, "bodySide", bodySide));


      } else if ("Clinical_attribute".equals(annotation.type)) {
        EventMention mention = new EventMention(jCas, coveringSpan.begin, coveringSpan.end);
        addIdentifiedAnnotationFeatures(
            annotation,
            mention,
            jCas,
            CONST.NE_TYPE_ID_CLINICAL_ATTRIBUTE,
            stringSlots,
            booleanSlots,
            annotationSlots,
            idAnnotationMap,
            delayedFeatures);


      } else if ("Devices".equals(annotation.type)) {
        EntityMention mention = new EntityMention(jCas, coveringSpan.begin, coveringSpan.end);
        addIdentifiedAnnotationFeatures(
            annotation,
            mention,
            jCas,
            CONST.NE_TYPE_ID_DEVICE,
            stringSlots,
            booleanSlots,
            annotationSlots,
            idAnnotationMap,
            delayedFeatures);


      } else if (getDiseaseDisorderKnowtatorClasses().contains(annotation.type)) {
        DiseaseDisorderMention mention = new DiseaseDisorderMention(jCas, coveringSpan.begin, coveringSpan.end);
        addIdentifiedAnnotationFeatures(
            annotation,
            mention,
            jCas,
            CONST.NE_TYPE_ID_DISORDER,
            stringSlots,
            booleanSlots,
            annotationSlots,
            idAnnotationMap,
            delayedFeatures);
        KnowtatorAnnotation alleviatingFactor = annotationSlots.remove("alleviating_factor");
        delayedFeatures.add(DelayedRelationFeature.forArg2(
            mention,
            "alleviatingFactor",
            alleviatingFactor,
            ManagesTreatsTextRelation.class,
            EventMention.class));
        KnowtatorAnnotation signOrSymptom = annotationSlots.remove("associated_sign_or_symptom");
        delayedFeatures.add(DelayedRelationFeature.forArg1(
            mention,
            "associatedSignSymptom",
            signOrSymptom,
            ManifestationOfTextRelation.class,
            EventMention.class));
        KnowtatorAnnotation bodyLaterality = annotationSlots.remove("body_laterality");
        delayedFeatures.add(new DelayedFeature(mention, "bodyLaterality", bodyLaterality));
        KnowtatorAnnotation bodyLocation = annotationSlots.remove("body_location");
        delayedFeatures.add(DelayedRelationFeature.forArg1(
            mention,
            "bodyLocation",
            bodyLocation,
            LocationOfTextRelation.class,
            AnatomicalSiteMention.class));
        KnowtatorAnnotation bodySide = annotationSlots.remove("body_side");
        delayedFeatures.add(new DelayedFeature(mention, "bodySide", bodySide));
        KnowtatorAnnotation course = annotationSlots.remove("course");
        delayedFeatures.add(DelayedRelationFeature.forArg1(
            mention,
            "course",
            course,
            DegreeOfTextRelation.class,
            CourseModifier.class));
        KnowtatorAnnotation exacerbatingFactor = annotationSlots.remove("exacerbating_factor");
        delayedFeatures.add(DelayedRelationFeature.forArg2(
            mention,
            "exacerbatingFactor",
            exacerbatingFactor,
            ComplicatesDisruptsTextRelation.class,
            EventMention.class));
        KnowtatorAnnotation severity = annotationSlots.remove("severity");
        delayedFeatures.add(DelayedRelationFeature.forArg1(
            mention,
            "severity",
            severity,
            DegreeOfTextRelation.class,
            SeverityModifier.class));


      } else if ("Lab".equals(annotation.type)) {
        LabMention mention = new LabMention(jCas, coveringSpan.begin, coveringSpan.end);
        addIdentifiedAnnotationFeatures(
            annotation,
            mention,
            jCas,
            CONST.NE_TYPE_ID_LAB,
            stringSlots,
            booleanSlots,
            annotationSlots,
            idAnnotationMap,
            delayedFeatures);
        KnowtatorAnnotation ordinal = annotationSlots.remove("ordinal_interpretation");
        delayedFeatures.add(DelayedRelationFeature.forArg1(
            mention,
            "ordinalInterpretation",
            ordinal,
            DegreeOfTextRelation.class,
            LabInterpretationModifier.class));
        KnowtatorAnnotation referenceRange = annotationSlots.remove("reference_range_narrative");
        delayedFeatures.add(new DelayedFeature(mention, "referenceRangeNarrative", referenceRange));
        KnowtatorAnnotation labValue = annotationSlots.remove("lab_value");
        delayedFeatures.add(DelayedRelationFeature.forArg1(
            mention,
            "labValue",
            labValue,
            ResultOfTextRelation.class,
            LabValueModifier.class));


      } else if (getMedicationKnowtatorClasses().contains(annotation.type)) {
        MedicationMention mention = new MedicationMention(jCas, coveringSpan.begin, coveringSpan.end);
        addIdentifiedAnnotationFeatures(
            annotation,
            mention,
            jCas,
            CONST.NE_TYPE_ID_DRUG,
            stringSlots,
            booleanSlots,
            annotationSlots,
            idAnnotationMap,
            delayedFeatures);
        KnowtatorAnnotation allergy = annotationSlots.remove("allergy_indicator");
        delayedFeatures.add(new DelayedFeature(mention, "medicationAllergy", allergy));
        KnowtatorAnnotation changeStatus = annotationSlots.remove("change_status_model");
        delayedFeatures.add(new DelayedFeature(mention, "medicationStatusChange", changeStatus));
        KnowtatorAnnotation dosage = annotationSlots.remove("dosage_model");
        delayedFeatures.add(new DelayedFeature(mention, "medicationDosage", dosage));
        KnowtatorAnnotation duration = annotationSlots.remove("duration_model");
        delayedFeatures.add(new DelayedFeature(mention, "medicationDuration", duration));
        KnowtatorAnnotation form = annotationSlots.remove("form_model");
        delayedFeatures.add(new DelayedFeature(mention, "medicationForm", form));
        KnowtatorAnnotation frequency = annotationSlots.remove("frequency_model");
        delayedFeatures.add(new DelayedFeature(mention, "medicationFrequency", frequency));
        KnowtatorAnnotation route = annotationSlots.remove("route_model");
        delayedFeatures.add(new DelayedFeature(mention, "medicationRoute", route));
        KnowtatorAnnotation startDate = annotationSlots.remove("start_date");
        delayedFeatures.add(new DelayedFeature(mention, "startDate", startDate));
        KnowtatorAnnotation strength = annotationSlots.remove("strength_model");
        delayedFeatures.add(new DelayedFeature(mention, "medicationStrength", strength));


      } else if ("Phenomena".equals(annotation.type)) {
        EventMention mention = new EventMention(jCas, coveringSpan.begin, coveringSpan.end);
        addIdentifiedAnnotationFeatures(
            annotation,
            mention,
            jCas,
            CONST.NE_TYPE_ID_PHENOMENA,
            stringSlots,
            booleanSlots,
            annotationSlots,
            idAnnotationMap,
            delayedFeatures);


      } else if (getProcedureKnowtatorClasses().contains(annotation.type)) {
        ProcedureMention mention = new ProcedureMention(jCas, coveringSpan.begin, coveringSpan.end);
        addIdentifiedAnnotationFeatures(
            annotation,
            mention,
            jCas,
            CONST.NE_TYPE_ID_PROCEDURE,
            stringSlots,
            booleanSlots,
            annotationSlots,
            idAnnotationMap,
            delayedFeatures);
        KnowtatorAnnotation bodyLaterality = annotationSlots.remove("body_laterality");
        delayedFeatures.add(new DelayedFeature(mention, "bodyLaterality", bodyLaterality));
        KnowtatorAnnotation bodyLocation = annotationSlots.remove("body_location");
        delayedFeatures.add(DelayedRelationFeature.forArg1(
            mention,
            "bodyLocation",
            bodyLocation,
            LocationOfTextRelation.class,
            AnatomicalSiteMention.class));
        KnowtatorAnnotation bodySide = annotationSlots.remove("body_side");
        delayedFeatures.add(new DelayedFeature(mention, "bodySide", bodySide));
        KnowtatorAnnotation device = annotationSlots.remove("device");
        delayedFeatures.add(new DelayedFeature(mention, "procedureDevice", device));
        KnowtatorAnnotation method = annotationSlots.remove("method");
        delayedFeatures.add(new DelayedFeature(mention, "method", method));


      } else if (getSignSymptomKnowtatorClasses().contains(annotation.type)) {
        SignSymptomMention mention = new SignSymptomMention(jCas, coveringSpan.begin, coveringSpan.end);
        addIdentifiedAnnotationFeatures(
            annotation,
            mention,
            jCas,
            CONST.NE_TYPE_ID_FINDING,
            stringSlots,
            booleanSlots,
            annotationSlots,
            idAnnotationMap,
            delayedFeatures);
        KnowtatorAnnotation alleviatingFactor = annotationSlots.remove("alleviating_factor");
        delayedFeatures.add(DelayedRelationFeature.forArg2(
            mention,
            "alleviatingFactor",
            alleviatingFactor,
            ManagesTreatsTextRelation.class,
            ProcedureMention.class));
        KnowtatorAnnotation bodyLaterality = annotationSlots.remove("body_laterality");
        delayedFeatures.add(new DelayedFeature(mention, "bodyLaterality", bodyLaterality));
        KnowtatorAnnotation bodyLocation = annotationSlots.remove("body_location");
        delayedFeatures.add(DelayedRelationFeature.forArg1(
            mention,
            "bodyLocation",
            bodyLocation,
            LocationOfTextRelation.class,
            AnatomicalSiteMention.class));
        KnowtatorAnnotation bodySide = annotationSlots.remove("body_side");
        delayedFeatures.add(new DelayedFeature(mention, "bodySide", bodySide));
        KnowtatorAnnotation course = annotationSlots.remove("course");
        delayedFeatures.add(DelayedRelationFeature.forArg1(
            mention,
            "course",
            course,
            DegreeOfTextRelation.class,
            CourseModifier.class));
        KnowtatorAnnotation exacerbatingFactor = annotationSlots.remove("exacerbating_factor");
        delayedFeatures.add(DelayedRelationFeature.forArg2(
            mention,
            "exacerbatingFactor",
            exacerbatingFactor,
            ComplicatesDisruptsTextRelation.class,
            EventMention.class));
        KnowtatorAnnotation severity = annotationSlots.remove("severity");
        delayedFeatures.add(DelayedRelationFeature.forArg1(
            mention,
            "severity",
            severity,
            DegreeOfTextRelation.class,
            SeverityModifier.class));


      } else if ("EVENT".equals(annotation.type)) {


        // collect the event properties (setting defaults as necessary)
        EventProperties eventProperties = new EventProperties(jCas);
        eventProperties.setCategory(stringSlots.remove("type"));
        if (eventProperties.getCategory() == null) {
          eventProperties.setCategory("N/A");
        }
        eventProperties.setContextualModality(stringSlots.remove("contextualmoduality"));
        if (eventProperties.getContextualModality() == null) {
          eventProperties.setContextualModality("ACTUAL");
        }
        eventProperties.setContextualAspect(stringSlots.remove("contextualaspect"));
        if (eventProperties.getContextualAspect() == null) {
          eventProperties.setContextualAspect("N/A");
        }
        eventProperties.setDegree(stringSlots.remove("degree"));
        if (eventProperties.getDegree() == null) {
          eventProperties.setDegree("N/A");
        }
        eventProperties.setDocTimeRel(stringSlots.remove("DocTimeRel"));
        if (eventProperties.getDocTimeRel() == null) {
          LOGGER.warn(String.format(
              "assuming docTimeRel=OVERLAP for annotation with id \"%s\"",
              annotation.id));
          eventProperties.setDocTimeRel("OVERLAP");
        }
        eventProperties.setPermanence(stringSlots.remove("permanence"));
        if (eventProperties.getPermanence() == null) {
          eventProperties.setPermanence("UNDETERMINED");
        }
        String polarityStr = stringSlots.remove("polarity");
        int polarity;
        if (polarityStr == null || polarityStr.equals("POS")) {
          polarity = CONST.NE_POLARITY_NEGATION_ABSENT;
        } else if (polarityStr.equals("NEG")) {
          polarity = CONST.NE_POLARITY_NEGATION_PRESENT;
        } else {
          throw new IllegalArgumentException("Invalid polarity: " + polarityStr);
        }
        eventProperties.setPolarity(polarity);


        // create the event object
        Event event = new Event(jCas);
        event.setConfidence(1.0f);
        event.setDiscoveryTechnique(CONST.NE_DISCOVERY_TECH_GOLD_ANNOTATION);


        // create the event mention
        EventMention eventMention = new EventMention(jCas, coveringSpan.begin, coveringSpan.end);
        eventMention.setConfidence(1.0f);
        eventMention.setDiscoveryTechnique(CONST.NE_DISCOVERY_TECH_GOLD_ANNOTATION);


        // add the links between event, mention and properties
        event.setProperties(eventProperties);
        event.setMentions(new FSArray(jCas, 1));
        event.setMentions(0, eventMention);
        eventMention.setEvent(event);


        // add the annotations to the indexes
        eventProperties.addToIndexes();
        event.addToIndexes();
        eventMention.addToIndexes();
        idAnnotationMap.put(annotation.id, eventMention);


      } else if ("DOCTIME".equals(annotation.type)) {
        TimeMention timeMention = new TimeMention(jCas, coveringSpan.begin, coveringSpan.end);
        timeMention.setTimeClass(annotation.type);

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        newGoldEntityMention.addToIndexes();
      }


      for (EventMention oldSystemEventMention : JCasUtil.select(jCas, EventMention.class))
      {
        EventMention newGoldEventMention = new EventMention(goldView, oldSystemEventMention.getBegin(), oldSystemEventMention.getEnd());
        
        // copying assertion fields
        newGoldEventMention.setDiscoveryTechnique(oldSystemEventMention.getDiscoveryTechnique());
        newGoldEventMention.setUncertainty(oldSystemEventMention.getUncertainty());
        newGoldEventMention.setConditional(oldSystemEventMention.getConditional());
        newGoldEventMention.setGeneric(oldSystemEventMention.getGeneric());
        newGoldEventMention.setPolarity(oldSystemEventMention.getPolarity());
        newGoldEventMention.setSubject(oldSystemEventMention.getSubject());
        newGoldEventMention.setHistoryOf(oldSystemEventMention.getHistoryOf());


        // copying non-assertion fields
        newGoldEventMention.setConfidence(oldSystemEventMention.getConfidence());
        newGoldEventMention.setTypeID(oldSystemEventMention.getTypeID());


        newGoldEventMention.addToIndexes();
      }
      
      // TODO do we need to copy supporting feature structures (particularly ontology concept array)??


    } // end of method ReferenceIdentifiedAnnotationsSystemToGoldCopier.process()

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            || type==CONST.NE_TYPE_ID_DRUG
            || type==CONST.NE_TYPE_ID_FINDING
            || type==CONST.NE_TYPE_ID_PROCEDURE
            || type==CONST.NE_TYPE_ID_ANATOMICAL_SITE
            ) {
          eMention = new EventMention(initView, first.start, last.end);
        } else {
          eMention = new IdentifiedAnnotation(initView, first.start, last.end);
        }
        
        // set easy attributes

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        newGoldEntityMention.addToIndexes();
      }


      for (EventMention oldSystemEventMention : JCasUtil.select(jCas, EventMention.class))
      {
        EventMention newGoldEventMention = new EventMention(goldView, oldSystemEventMention.getBegin(), oldSystemEventMention.getEnd());
        
        // copying assertion fields
        newGoldEventMention.setDiscoveryTechnique(oldSystemEventMention.getDiscoveryTechnique());
        newGoldEventMention.setUncertainty(oldSystemEventMention.getUncertainty());
        newGoldEventMention.setConditional(oldSystemEventMention.getConditional());
        newGoldEventMention.setGeneric(oldSystemEventMention.getGeneric());
        newGoldEventMention.setPolarity(oldSystemEventMention.getPolarity());
        newGoldEventMention.setSubject(oldSystemEventMention.getSubject());
        newGoldEventMention.setHistoryOf(oldSystemEventMention.getHistoryOf());


        // copying non-assertion fields
        newGoldEventMention.setConfidence(oldSystemEventMention.getConfidence());
        newGoldEventMention.setTypeID(oldSystemEventMention.getTypeID());


        newGoldEventMention.addToIndexes();
      }
      
      // TODO do we need to copy supporting feature structures (particularly ontology concept array)??


    } // end of method ReferenceIdentifiedAnnotationsSystemToGoldCopier.process()

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          Point pair = new Point(Integer.parseInt(m.group(2)), Integer.parseInt(m.group(3)));
          if(word2char.containsKey(pair)){
            int charOffset = word2char.get(pair);
            int end = charOffset + m.group(1).length();
//            Entity entity = new Entity(jcas);
            EventMention mention = new EventMention(jcas, charOffset, end);


            // set default values...
            mention.setPolarity(CONST.NE_POLARITY_NEGATION_ABSENT);
            mention.setConditional(CONST.NE_CONDITIONAL_FALSE);
            mention.setUncertainty(CONST.NE_UNCERTAINTY_ABSENT);
            mention.setGeneric(CONST.NE_GENERIC_FALSE);
            mention.setSubject(CONST.ATTR_SUBJECT_PATIENT);


            // set non-default values. mappings follow MITRE's conventions (see AssertionAnalysisEngine)
            if(m.group(7).equals("absent")){
//              negSet.add(charOffset+"-"+end);
              mention.setPolarity(CONST.NE_POLARITY_NEGATION_PRESENT);
            }else if(m.group(7).equals("hypothetical")){
//              hypothSet.add(charOffset+"-"+end);
              mention.setConditional(CONST.NE_CONDITIONAL_TRUE);
            }else if(m.group(7).equals("possible")){
//              possSet.add(charOffset+"-"+end);
              mention.setUncertainty(CONST.NE_UNCERTAINTY_PRESENT);
            }else if(m.group(7).equals("associated_with_someone_else")){
//              nasSet.add(charOffset+"-"+end);
              mention.setSubject(CONST.ATTR_SUBJECT_FAMILY_MEMBER); // the most common non-patient case
            }else if(m.group(7).equals("conditional")){ // no good mapping.
////              condSet.add(charOffset+"-"+end);
//              mention.setConditional(true);
////            }else if(m.group(7).equals("present")){
////              presSet.add(charOffset+"-"+end);    // NOTE: There is no "present" setting, it is an inference from other things not being set.
            }
            mention.addToIndexes();
          }
        }
      }
    }

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        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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        delayedFeatures.add(new DelayedFeature(mention, "bodyLaterality", bodyLaterality));
        KnowtatorAnnotation bodySide = annotationSlots.remove("body_side");
        delayedFeatures.add(new DelayedFeature(mention, "bodySide", bodySide));


      } else if ("Clinical_attribute".equals(annotation.type)) {
        EventMention mention = new EventMention(jCas, coveringSpan.begin, coveringSpan.end);
        addIdentifiedAnnotationFeatures(
            annotation,
            mention,
            jCas,
            CONST.NE_TYPE_ID_CLINICAL_ATTRIBUTE,
            stringSlots,
            booleanSlots,
            annotationSlots,
            idAnnotationMap,
            delayedFeatures);


      } else if ("Devices".equals(annotation.type)) {
        EntityMention mention = new EntityMention(jCas, coveringSpan.begin, coveringSpan.end);
        addIdentifiedAnnotationFeatures(
            annotation,
            mention,
            jCas,
            CONST.NE_TYPE_ID_DEVICE,
            stringSlots,
            booleanSlots,
            annotationSlots,
            idAnnotationMap,
            delayedFeatures);


      } else if ("Disease_Disorder".equals(annotation.type)) {
        DiseaseDisorderMention mention = new DiseaseDisorderMention(jCas, coveringSpan.begin, coveringSpan.end);
        addIdentifiedAnnotationFeatures(
            annotation,
            mention,
            jCas,
            CONST.NE_TYPE_ID_DISORDER,
            stringSlots,
            booleanSlots,
            annotationSlots,
            idAnnotationMap,
            delayedFeatures);
        KnowtatorAnnotation alleviatingFactor = annotationSlots.remove("alleviating_factor");
        delayedFeatures.add(DelayedRelationFeature.forArg2(
            mention,
            "alleviatingFactor",
            alleviatingFactor,
            ManagesTreatsTextRelation.class,
            EventMention.class));
        KnowtatorAnnotation signOrSymptom = annotationSlots.remove("associated_sign_or_symptom");
        delayedFeatures.add(DelayedRelationFeature.forArg1(
            mention,
            "associatedSignSymptom",
            signOrSymptom,
            ManifestationOfTextRelation.class,
            EventMention.class));
        KnowtatorAnnotation bodyLaterality = annotationSlots.remove("body_laterality");
        delayedFeatures.add(new DelayedFeature(mention, "bodyLaterality", bodyLaterality));
        KnowtatorAnnotation bodyLocation = annotationSlots.remove("body_location");
        delayedFeatures.add(DelayedRelationFeature.forArg1(
            mention,
            "bodyLocation",
            bodyLocation,
            LocationOfTextRelation.class,
            AnatomicalSiteMention.class));
        KnowtatorAnnotation bodySide = annotationSlots.remove("body_side");
        delayedFeatures.add(new DelayedFeature(mention, "bodySide", bodySide));
        KnowtatorAnnotation course = annotationSlots.remove("course");
        delayedFeatures.add(DelayedRelationFeature.forArg1(
            mention,
            "course",
            course,
            DegreeOfTextRelation.class,
            CourseModifier.class));
        KnowtatorAnnotation exacerbatingFactor = annotationSlots.remove("exacerbating_factor");
        delayedFeatures.add(DelayedRelationFeature.forArg2(
            mention,
            "exacerbatingFactor",
            exacerbatingFactor,
            ComplicatesDisruptsTextRelation.class,
            EventMention.class));
        KnowtatorAnnotation severity = annotationSlots.remove("severity");
        delayedFeatures.add(DelayedRelationFeature.forArg1(
            mention,
            "severity",
            severity,
            DegreeOfTextRelation.class,
            SeverityModifier.class));


      } else if ("Lab".equals(annotation.type)) {
        LabMention mention = new LabMention(jCas, coveringSpan.begin, coveringSpan.end);
        addIdentifiedAnnotationFeatures(
            annotation,
            mention,
            jCas,
            CONST.NE_TYPE_ID_LAB,
            stringSlots,
            booleanSlots,
            annotationSlots,
            idAnnotationMap,
            delayedFeatures);
        KnowtatorAnnotation ordinal = annotationSlots.remove("ordinal_interpretation");
        delayedFeatures.add(DelayedRelationFeature.forArg1(
            mention,
            "ordinalInterpretation",
            ordinal,
            DegreeOfTextRelation.class,
            LabInterpretationModifier.class));
        KnowtatorAnnotation referenceRange = annotationSlots.remove("reference_range_narrative");
        delayedFeatures.add(new DelayedFeature(mention, "referenceRangeNarrative", referenceRange));
        KnowtatorAnnotation labValue = annotationSlots.remove("lab_value");
        delayedFeatures.add(DelayedRelationFeature.forArg1(
            mention,
            "labValue",
            labValue,
            ResultOfTextRelation.class,
            LabValueModifier.class));


      } else if ("Medications/Drugs".equals(annotation.type)) {
        MedicationMention mention = new MedicationMention(jCas, coveringSpan.begin, coveringSpan.end);
        addIdentifiedAnnotationFeatures(
            annotation,
            mention,
            jCas,
            CONST.NE_TYPE_ID_DRUG,
            stringSlots,
            booleanSlots,
            annotationSlots,
            idAnnotationMap,
            delayedFeatures);
        KnowtatorAnnotation allergy = annotationSlots.remove("allergy_indicator");
        delayedFeatures.add(new DelayedFeature(mention, "medicationAllergy", allergy));
        KnowtatorAnnotation changeStatus = annotationSlots.remove("change_status_model");
        delayedFeatures.add(new DelayedFeature(mention, "medicationStatusChange", changeStatus));
        KnowtatorAnnotation dosage = annotationSlots.remove("dosage_model");
        delayedFeatures.add(new DelayedFeature(mention, "medicationDosage", dosage));
        KnowtatorAnnotation duration = annotationSlots.remove("duration_model");
        delayedFeatures.add(new DelayedFeature(mention, "medicationDuration", duration));
        KnowtatorAnnotation form = annotationSlots.remove("form_model");
        delayedFeatures.add(new DelayedFeature(mention, "medicationForm", form));
        KnowtatorAnnotation frequency = annotationSlots.remove("frequency_model");
        delayedFeatures.add(new DelayedFeature(mention, "medicationFrequency", frequency));
        KnowtatorAnnotation route = annotationSlots.remove("route_model");
        delayedFeatures.add(new DelayedFeature(mention, "medicationRoute", route));
        KnowtatorAnnotation startDate = annotationSlots.remove("start_date");
        delayedFeatures.add(new DelayedFeature(mention, "startDate", startDate));
        KnowtatorAnnotation strength = annotationSlots.remove("strength_model");
        delayedFeatures.add(new DelayedFeature(mention, "medicationStrength", strength));


      } else if ("Phenomena".equals(annotation.type)) {
        EventMention mention = new EventMention(jCas, coveringSpan.begin, coveringSpan.end);
        addIdentifiedAnnotationFeatures(
            annotation,
            mention,
            jCas,
            CONST.NE_TYPE_ID_PHENOMENA,
            stringSlots,
            booleanSlots,
            annotationSlots,
            idAnnotationMap,
            delayedFeatures);


      } else if ("Procedure".equals(annotation.type)) {
        ProcedureMention mention = new ProcedureMention(jCas, coveringSpan.begin, coveringSpan.end);
        addIdentifiedAnnotationFeatures(
            annotation,
            mention,
            jCas,
            CONST.NE_TYPE_ID_PROCEDURE,
            stringSlots,
            booleanSlots,
            annotationSlots,
            idAnnotationMap,
            delayedFeatures);
        KnowtatorAnnotation bodyLaterality = annotationSlots.remove("body_laterality");
        delayedFeatures.add(new DelayedFeature(mention, "bodyLaterality", bodyLaterality));
        KnowtatorAnnotation bodyLocation = annotationSlots.remove("body_location");
        delayedFeatures.add(DelayedRelationFeature.forArg1(
            mention,
            "bodyLocation",
            bodyLocation,
            LocationOfTextRelation.class,
            AnatomicalSiteMention.class));
        KnowtatorAnnotation bodySide = annotationSlots.remove("body_side");
        delayedFeatures.add(new DelayedFeature(mention, "bodySide", bodySide));
        KnowtatorAnnotation device = annotationSlots.remove("device");
        delayedFeatures.add(new DelayedFeature(mention, "procedureDevice", device));
        KnowtatorAnnotation method = annotationSlots.remove("method");
        delayedFeatures.add(new DelayedFeature(mention, "method", method));


      } else if ("Sign_symptom".equals(annotation.type)) {
        SignSymptomMention mention = new SignSymptomMention(jCas, coveringSpan.begin, coveringSpan.end);
        addIdentifiedAnnotationFeatures(
            annotation,
            mention,
            jCas,
            CONST.NE_TYPE_ID_FINDING,
            stringSlots,
            booleanSlots,
            annotationSlots,
            idAnnotationMap,
            delayedFeatures);
        KnowtatorAnnotation alleviatingFactor = annotationSlots.remove("alleviating_factor");
        delayedFeatures.add(DelayedRelationFeature.forArg2(
            mention,
            "alleviatingFactor",
            alleviatingFactor,
            ManagesTreatsTextRelation.class,
            ProcedureMention.class));
        KnowtatorAnnotation bodyLaterality = annotationSlots.remove("body_laterality");
        delayedFeatures.add(new DelayedFeature(mention, "bodyLaterality", bodyLaterality));
        KnowtatorAnnotation bodyLocation = annotationSlots.remove("body_location");
        delayedFeatures.add(DelayedRelationFeature.forArg1(
            mention,
            "bodyLocation",
            bodyLocation,
            LocationOfTextRelation.class,
            AnatomicalSiteMention.class));
        KnowtatorAnnotation bodySide = annotationSlots.remove("body_side");
        delayedFeatures.add(new DelayedFeature(mention, "bodySide", bodySide));
        KnowtatorAnnotation course = annotationSlots.remove("course");
        delayedFeatures.add(DelayedRelationFeature.forArg1(
            mention,
            "course",
            course,
            DegreeOfTextRelation.class,
            CourseModifier.class));
        KnowtatorAnnotation exacerbatingFactor = annotationSlots.remove("exacerbating_factor");
        delayedFeatures.add(DelayedRelationFeature.forArg2(
            mention,
            "exacerbatingFactor",
            exacerbatingFactor,
            ComplicatesDisruptsTextRelation.class,
            EventMention.class));
        KnowtatorAnnotation severity = annotationSlots.remove("severity");
        delayedFeatures.add(DelayedRelationFeature.forArg1(
            mention,
            "severity",
            severity,
            DegreeOfTextRelation.class,
            SeverityModifier.class));


      } else if ("EVENT".equals(annotation.type)) {


        // collect the event properties (setting defaults as necessary)
        EventProperties eventProperties = new EventProperties(jCas);
        eventProperties.setCategory(stringSlots.remove("type"));
        if (eventProperties.getCategory() == null) {
          eventProperties.setCategory("N/A");
        }
        eventProperties.setContextualModality(stringSlots.remove("contextualmoduality"));
        if (eventProperties.getContextualModality() == null) {
          eventProperties.setContextualModality("ACTUAL");
        }
        eventProperties.setContextualAspect(stringSlots.remove("contextualaspect"));
        if (eventProperties.getContextualAspect() == null) {
          eventProperties.setContextualAspect("N/A");
        }
        eventProperties.setDegree(stringSlots.remove("degree"));
        if (eventProperties.getDegree() == null) {
          eventProperties.setDegree("N/A");
        }
        eventProperties.setDocTimeRel(stringSlots.remove("DocTimeRel"));
        if (eventProperties.getDocTimeRel() == null) {
          LOGGER.warn(String.format(
              "assuming docTimeRel=OVERLAP for annotation with id \"%s\"",
              annotation.id));
          eventProperties.setDocTimeRel("OVERLAP");
        }
        eventProperties.setPermanence(stringSlots.remove("permanence"));
        if (eventProperties.getPermanence() == null) {
          eventProperties.setPermanence("UNDETERMINED");
        }
        String polarityStr = stringSlots.remove("polarity");
        int polarity;
        if (polarityStr == null || polarityStr.equals("POS")) {
          polarity = CONST.NE_POLARITY_NEGATION_ABSENT;
        } else if (polarityStr.equals("NEG")) {
          polarity = CONST.NE_POLARITY_NEGATION_PRESENT;
        } else {
          throw new IllegalArgumentException("Invalid polarity: " + polarityStr);
        }
        eventProperties.setPolarity(polarity);


        // create the event object
        Event event = new Event(jCas);
        event.setConfidence(1.0f);
        event.setDiscoveryTechnique(CONST.NE_DISCOVERY_TECH_GOLD_ANNOTATION);


        // create the event mention
        EventMention eventMention = new EventMention(jCas, coveringSpan.begin, coveringSpan.end);
        eventMention.setConfidence(1.0f);
        eventMention.setDiscoveryTechnique(CONST.NE_DISCOVERY_TECH_GOLD_ANNOTATION);


        // add the links between event, mention and properties
        event.setProperties(eventProperties);
        event.setMentions(new FSArray(jCas, 1));
        event.setMentions(0, eventMention);
        eventMention.setEvent(event);


        // add the annotations to the indexes
        eventProperties.addToIndexes();
        event.addToIndexes();
        eventMention.addToIndexes();
        idAnnotationMap.put(annotation.id, eventMention);


      } else if ("DOCTIME".equals(annotation.type)) {
        TimeMention timeMention = new TimeMention(jCas, coveringSpan.begin, coveringSpan.end);
        timeMention.setTimeClass(annotation.type);

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            EntityMention entityMention = (EntityMention) ia;
            logger.error("Need to implement cases for handling EntityMention " + entityMention + " within relation: " + relation);
            logger.error("   severity " + severity + " in relation " + relation + " with/to " + entityMention);
            logger.error("   Using covered text: severity " + severity.getCoveredText() + " in relation " + relation + " with/to " + entityMention.getCoveredText());
          } else { 
            EventMention eventMention = (EventMention) ia;
            if (eventMention instanceof DiseaseDisorderMention) {
              DiseaseDisorderMention ddm = (DiseaseDisorderMention) eventMention;
              logger.error("Need to implement attr for " + relation + " for DiseaseDisorderMention"); 
            } else if (eventMention instanceof SignSymptomMention) {
              SignSymptomMention ssm = (SignSymptomMention) eventMention;
              ssm.setSeverity(degreeOfTextRelation);
            } else {
              logger.error("Need to implement more cases for handling EventMention " + eventMention + " within relation: " + relation);
            }
          }
          
        } else if (relation.equals("location_of")) {


          EntityMention arg2Arg = (EntityMention) arg2.getArgument(); // wrongly created as EntityMention prior to 3.0
          IdentifiedAnnotation ia = mapToMentions.get(arg2Arg);


          if (ia instanceof EntityMention) {
            
            // Note you apparently can have an AnatomicalSiteMention be the location_of an AnatomicalSiteMention
            // from running rec041, end up with things like "Left lower extremity"  location_of "common femoral vein"
            // and "left renal vein" in relation location_of to anatomical site mention "renal vein"
            // and "vein" in relation location_of to anatomical site mention "renal vein"
            EntityMention entityMention = (EntityMention) ia;
            IdentifiedAnnotation location = (IdentifiedAnnotation) arg1.getArgument();
            IdentifiedAnnotation loc = (IdentifiedAnnotation)mapToMentions.get(location);
            if (loc instanceof AnatomicalSiteMention) { 
              AnatomicalSiteMention asm = (AnatomicalSiteMention) loc;
              //asm.setBodyLocation(binaryTextRelation); // uncomment iff AnatomicalSiteMention ends up with a bodyLocation attribute
            } else {
              logger.error("Need to implement cases for handling EntityMention " + entityMention + " within relation: " + relation);
              logger.error("   loc " + loc + " in relation " + relation + " with/to " + entityMention);
              logger.error("   Using covered text: loc " + loc.getCoveredText() + " in relation " + relation + " with/to " + entityMention.getCoveredText());
            }


          } else { 
            
            EventMention eventMention = (EventMention) ia;


            if (eventMention instanceof DiseaseDisorderMention) { //(eventMention.getTypeID()==CONST.NE_TYPE_ID_DISORDER) { 
              DiseaseDisorderMention ddm = (DiseaseDisorderMention) eventMention;
              ddm.setBodyLocation(locationOfTextRelation);
            } else if (eventMention instanceof ProcedureMention) { //(eventMention.getTypeID()==CONST.NE_TYPE_ID_PROCEDURE) {

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        newGoldEntityMention.addToIndexes();
      }


      for (EventMention oldSystemEventMention : JCasUtil.select(jCas, EventMention.class))
      {
        EventMention newGoldEventMention = new EventMention(goldView, oldSystemEventMention.getBegin(), oldSystemEventMention.getEnd());
        
        // copying assertion fields
        newGoldEventMention.setDiscoveryTechnique(oldSystemEventMention.getDiscoveryTechnique());
        newGoldEventMention.setUncertainty(oldSystemEventMention.getUncertainty());
        newGoldEventMention.setConditional(oldSystemEventMention.getConditional());
        newGoldEventMention.setGeneric(oldSystemEventMention.getGeneric());
        newGoldEventMention.setPolarity(oldSystemEventMention.getPolarity());
        newGoldEventMention.setSubject(oldSystemEventMention.getSubject());


        // copying non-assertion fields
        newGoldEventMention.setConfidence(oldSystemEventMention.getConfidence());


        newGoldEventMention.addToIndexes();
      }
      
      // TODO do we need to copy supporting feature structures (particularly ontology concept array)??


    } // end of method ReferenceIdentifiedAnnotationsSystemToGoldCopier.process()

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