Package org.apache.ctakes.core.knowtator

Examples of org.apache.ctakes.core.knowtator.KnowtatorAnnotation


            stringSlots,
            booleanSlots,
            annotationSlots,
            idAnnotationMap,
            delayedFeatures);
        KnowtatorAnnotation bodySide = annotationSlots.remove("body_side");
        if (bodySide != null) {
          delayedFeatures.add(new DelayedFeature<EntityMention>(entityMention, bodySide) {
            @Override
            protected void setValue(TOP valueAnnotation) {
              // TODO: this.annotation.setBodySide(...)
            }
          });
        }
        KnowtatorAnnotation bodyLaterality = annotationSlots.remove("body_laterality");
        if (bodyLaterality != null) {
          delayedFeatures.add(new DelayedFeature<EntityMention>(entityMention, bodyLaterality) {
            @Override
            protected void setValue(TOP valueAnnotation) {
              // TODO: this.annotation.setBodyLaterality(...)
            }
          });
        }

      } else if ("Disease_Disorder".equals(annotation.type)) {
        EntityMention entityMention = new EntityMention(jCas, coveringSpan.begin, coveringSpan.end);
        addEntityMentionFeatures(
            annotation,
            entityMention,
            jCas,
            CONST.NE_TYPE_ID_DISORDER,
            stringSlots,
            booleanSlots,
            annotationSlots,
            idAnnotationMap,
            delayedFeatures);
        KnowtatorAnnotation bodyLocation = annotationSlots.remove("body_location");
        if (bodyLocation != null) {
          delayedFeatures.add(new DelayedFeature<EntityMention>(entityMention, bodyLocation) {
            @Override
            protected void setValue(TOP valueAnnotation) {
              // TODO: this.annotation.setBodyLocation(...)
            }
          });
        }
        KnowtatorAnnotation severity = annotationSlots.remove("severity");
        if (severity != null) {
          delayedFeatures.add(new DelayedFeature<EntityMention>(entityMention, severity) {
            @Override
            protected void setValue(TOP valueAnnotation) {
              // TODO: this.annotation.setSeverity(...)
            }
          });
        }

      } else if ("Medications/Drugs".equals(annotation.type)) {
        EntityMention entityMention = new EntityMention(jCas, coveringSpan.begin, coveringSpan.end);
        addEntityMentionFeatures(
            annotation,
            entityMention,
            jCas,
            CONST.NE_TYPE_ID_DRUG,
            stringSlots,
            booleanSlots,
            annotationSlots,
            idAnnotationMap,
            delayedFeatures);

      } else if ("Phenomena".equals(annotation.type)) {
        EntityMention entityMention = new EntityMention(jCas, coveringSpan.begin, coveringSpan.end);
        addEntityMentionFeatures(
            annotation,
            entityMention,
            jCas,
            CONST.NE_TYPE_ID_UNKNOWN /* TODO: is this the correct type? */,
            stringSlots,
            booleanSlots,
            annotationSlots,
            idAnnotationMap,
            delayedFeatures);

      } else if ("Procedure".equals(annotation.type)) {
        EntityMention entityMention = new EntityMention(jCas, coveringSpan.begin, coveringSpan.end);
        addEntityMentionFeatures(
            annotation,
            entityMention,
            jCas,
            CONST.NE_TYPE_ID_PROCEDURE,
            stringSlots,
            booleanSlots,
            annotationSlots,
            idAnnotationMap,
            delayedFeatures);
        KnowtatorAnnotation bodyLocation = annotationSlots.remove("body_location");
        if (bodyLocation != null) {
          delayedFeatures.add(new DelayedFeature<EntityMention>(entityMention, bodyLocation) {
            @Override
            protected void setValue(TOP valueAnnotation) {
              // TODO: this.annotation.setBodyLocation(...)
            }
          });
        }
        KnowtatorAnnotation historyOf = annotationSlots.remove("historyOf_CU");
        if (historyOf != null) {
          delayedFeatures.add(new DelayedFeature<EntityMention>(entityMention, historyOf) {
            @Override
            protected void setValue(TOP valueAnnotation) {
              // TODO: this.annotation.setHistoryOf(...)
            }
          });
        }

      } else if ("Sign_symptom".equals(annotation.type)) {
        EntityMention entityMention = new EntityMention(jCas, coveringSpan.begin, coveringSpan.end);
        addEntityMentionFeatures(
            annotation,
            entityMention,
            jCas,
            CONST.NE_TYPE_ID_FINDING,
            stringSlots,
            booleanSlots,
            annotationSlots,
            idAnnotationMap,
            delayedFeatures);
        KnowtatorAnnotation bodyLocation = annotationSlots.remove("body_location");
        if (bodyLocation != null) {
          delayedFeatures.add(new DelayedFeature<EntityMention>(entityMention, bodyLocation) {
            @Override
            protected void setValue(TOP valueAnnotation) {
              // TODO: this.annotation.setBodyLocation(...)
            }
          });
        }
        KnowtatorAnnotation severity = annotationSlots.remove("severity");
        if (severity != null) {
          delayedFeatures.add(new DelayedFeature<EntityMention>(entityMention, severity) {
            @Override
            protected void setValue(TOP valueAnnotation) {
              // TODO: this.annotation.setSeverity(...)
            }
          });
        }

      } 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) {
          // TODO: this should not be necessary - DocTimeRel should always be specified
          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)) {
        // TODO

      } else if ("SECTIONTIME".equals(annotation.type)) {
        // TODO

      } else if ("TIMEX3".equals(annotation.type)) {
        String timexClass = stringSlots.remove("class");
        TimeMention timeMention = new TimeMention(jCas, coveringSpan.begin, coveringSpan.end);
        timeMention.addToIndexes();
        idAnnotationMap.put(annotation.id, timeMention);
        // TODO

      } else if ("generic_class".equals(annotation.type)) {
        // TODO: there's currently no Generic in the type system
        boolean value = booleanSlots.remove("generic_normalization");
        Modifier modifier = new Modifier(jCas, coveringSpan.begin, coveringSpan.end);
        // modifier.setNormalizedForm(...);
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("severity_class".equals(annotation.type)) {
        Severity severity = new Severity(jCas);
        severity.setValue(stringSlots.remove("severity_normalization"));
        severity.addToIndexes();
        Modifier modifier = new Modifier(jCas, coveringSpan.begin, coveringSpan.end);
        modifier.setNormalizedForm(severity);
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("conditional_class".equals(annotation.type)) {
View Full Code Here


    entityMention.setPolarity(negation == null
        ? CONST.NE_POLARITY_NEGATION_ABSENT
        : negation == true ? CONST.NE_POLARITY_NEGATION_PRESENT : CONST.NE_POLARITY_NEGATION_ABSENT);

    // negation must be delayed until the Negation annotations are present
    KnowtatorAnnotation negationIndicator = annotationSlots.remove("negation_indicator_CU");
    if (negationIndicator != null) {
      delayedFeatures.add(new DelayedFeature<EntityMention>(entityMention, negationIndicator) {
        @Override
        protected void setValue(TOP valueAnnotation) {
          // TODO: this.annotation.setPolarity(...)
        }
      });
    }

    // conditional must be delayed until the Conditional annotations are present
    KnowtatorAnnotation conditional = annotationSlots.remove("conditional_CU");
    if (conditional != null) {
      delayedFeatures.add(new DelayedFeature<EntityMention>(entityMention, conditional) {
        @Override
        protected void setValue(TOP valueAnnotation) {
          // TODO: this.annotation.setConditional(...)
        }
      });
    }

    // uncertainty must be delayed until the Uncertainty annotations are present
    KnowtatorAnnotation uncertainty = annotationSlots.remove("uncertainty_indicator_CU");
    if (uncertainty != null) {
      delayedFeatures.add(new DelayedFeature<EntityMention>(entityMention, uncertainty) {
        @Override
        protected void setValue(TOP valueAnnotation) {
          // TODO: this.annotation.setUncertainty(...)
        }
      });
    }

    // subject must be delayed until the Subject annotations are present
    KnowtatorAnnotation subject = annotationSlots.remove("subject_CU");
    if (subject != null) {
      delayedFeatures.add(new DelayedFeature<EntityMention>(entityMention, subject) {
        @Override
        protected void setValue(TOP valueAnnotation) {
          // TODO: this.annotation.setSubject(...)
View Full Code Here

            stringSlots,
            booleanSlots,
            annotationSlots,
            idAnnotationMap,
            delayedFeatures);
        KnowtatorAnnotation bodyLaterality = annotationSlots.remove("body_laterality");
        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);
        timeMention.addToIndexes();
        idAnnotationMap.put(annotation.id, timeMention);

      } else if ("SECTIONTIME".equals(annotation.type)) {
        TimeMention timeMention = new TimeMention(jCas, coveringSpan.begin, coveringSpan.end);
        timeMention.setTimeClass(annotation.type);
        timeMention.addToIndexes();
        idAnnotationMap.put(annotation.id, timeMention);

      } else if ("TIMEX3".equals(annotation.type)) {
        String timexClass = stringSlots.remove("class");
        TimeMention timeMention = new TimeMention(jCas, coveringSpan.begin, coveringSpan.end);
        timeMention.setTimeClass(timexClass);
        timeMention.addToIndexes();
        idAnnotationMap.put(annotation.id, timeMention);
       
      } else if ("conditional_class".equals(annotation.type)) {
        Boolean value = booleanSlots.remove("conditional_normalization");
        ConditionalModifier modifier = new ConditionalModifier(jCas, coveringSpan.begin, coveringSpan.end);
        modifier.setConditional(value == null ? false : value);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("generic_class".equals(annotation.type)) {
        Boolean value = booleanSlots.remove("generic_normalization");
        GenericModifier modifier = new GenericModifier(jCas, coveringSpan.begin, coveringSpan.end);
        modifier.setGeneric(value == null ? false : value);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("negation_indicator_class".equals(annotation.type)) {
        String value = stringSlots.remove("negation_indicator_normalization");
        PolarityModifier modifier = new PolarityModifier(jCas, coveringSpan.begin, coveringSpan.end);
        if (value == null) {
          LOGGER.warn(String.format(
              "assuming NE_POLARITY_NEGATION_PRESENT for %s with id \"%s\"",
              format(modifier),
              annotation.id));
          modifier.setPolarity(CONST.NE_POLARITY_NEGATION_PRESENT);
        } else if (value.equals("negation_absent")) {
          modifier.setPolarity(CONST.NE_POLARITY_NEGATION_ABSENT);
        } else if (value.equals("negation_present")) {
          modifier.setPolarity(CONST.NE_POLARITY_NEGATION_PRESENT);
        } else {
          throw new UnsupportedOperationException("Invalid negation: " + value);
        }
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("uncertainty_indicator_class".equals(annotation.type)) {
        String value = stringSlots.remove("uncertainty_indicator_normalization");
        UncertaintyModifier modifier = new UncertaintyModifier(jCas, coveringSpan.begin, coveringSpan.end);
        if (value == null) {
          LOGGER.warn(String.format(
              "assuming NE_UNCERTAINTY_PRESENT for %s with id \"%s\"",
              format(modifier),
              annotation.id));
          modifier.setUncertainty(CONST.NE_UNCERTAINTY_PRESENT);
        } else if (value.equals("indicator_absent")) {
          modifier.setUncertainty(CONST.NE_UNCERTAINTY_ABSENT);
        } else if (value.equals("indicator_present")) {
          modifier.setUncertainty(CONST.NE_UNCERTAINTY_PRESENT);
        } else {
          throw new UnsupportedOperationException("Invalid uncertainty: " + value);
        }
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("Person".equals(annotation.type)) {
        String value = stringSlots.remove("subject_normalization_CU");
        String uimaValue = SUBJECT_KNOWTATOR_TO_UIMA_MAP.get(value);
        String code = stringSlots.remove("associatedCode");
        String uimaCode = SUBJECT_KNOWTATOR_TO_UIMA_MAP.get(code);
        if (value != null && uimaValue == null) {
          LOGGER.error(String.format(
              "unrecognized subject value \"%s\" for annotation with id \"%s\"",
              value,
              annotation.id));
        }
        if (code != null && uimaCode == null) {
          LOGGER.error(String.format(
              "unrecognized subject code \"%s\" for annotation with id \"%s\"",
              code,
              annotation.id));
        }
        if (uimaValue != null && uimaCode != null && !uimaValue.equals(uimaCode)) {
          LOGGER.error(String.format(
              "subject value \"%s\" and code \"%s\" are inconsistent for annotation with id \"%s\"",
              value,
              code,
              annotation.id));
        }
        String subject = uimaValue != null ? uimaValue : uimaCode;
        if (subject == null && this.setDefaults) {
          subject = SHARPKnowtatorXMLDefaults.getSubject();
        }
        SubjectModifier modifier = new SubjectModifier(jCas, coveringSpan.begin, coveringSpan.end);
        modifier.setSubject(subject);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("historyOf_indicator_class".equals(annotation.type)) {
        String value = stringSlots.remove("historyOf_normalization");
        HistoryOfModifier modifier = new HistoryOfModifier(jCas, coveringSpan.begin, coveringSpan.end);
        if (null == value) {
          if (this.setDefaults) {
            modifier.setHistoryOf(SHARPKnowtatorXMLDefaults.getHistoryOf());
          }
        } else if ("historyOf_present".equals(value)) {
          modifier.setHistoryOf(CONST.NE_HISTORY_OF_PRESENT);
        } else if ("historyOf_absent".equals(value)) {
          modifier.setHistoryOf(CONST.NE_HISTORY_OF_ABSENT);
        } else {
          LOGGER.error(String.format(
              "unrecognized history-of value \"%s\" on annotation with id \"%s\"",
              value,
              annotation.id));
        }
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("distal_or_proximal".equals(annotation.type)) {
        String value = stringSlots.remove("distal_or_proximal_normalization");
        BodyLateralityModifier modifier = new BodyLateralityModifier(jCas, coveringSpan.begin, coveringSpan.end);
        BodyLaterality attribute = new BodyLaterality(jCas);
        if (value == null) {
          LOGGER.warn(String.format(
              "assuming \"%s\" for %s with id \"%s\"",
              CONST.ATTR_BODYLATERALITY_UNMARKED,
              format(modifier),
              annotation.id));
          value = CONST.ATTR_BODYLATERALITY_UNMARKED;
        } else if (!value.equals(CONST.ATTR_BODYLATERALITY_DISTAL) &&
            !value.equals(CONST.ATTR_BODYLATERALITY_PROXIMAL) &&
            !value.equals(CONST.ATTR_BODYLATERALITY_UNMARKED)) {
          throw new UnsupportedOperationException("Invalid BodyLaterality: " + value);
        }
        attribute.setValue(value);
        attribute.addToIndexes();
        modifier.setNormalizedForm(attribute);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("superior_or_inferior".equals(annotation.type)) {
        String value = stringSlots.remove("superior_or_inferior_normalization");
        BodyLateralityModifier modifier = new BodyLateralityModifier(jCas, coveringSpan.begin, coveringSpan.end);
        BodyLaterality attribute = new BodyLaterality(jCas);
        if (value == null) {
          LOGGER.warn(String.format(
              "assuming \"%s\" for %s with id \"%s\"",
              CONST.ATTR_BODYLATERALITY_UNMARKED,
              format(modifier),
              annotation.id));
          value = CONST.ATTR_BODYLATERALITY_UNMARKED;
        } else if (!value.equals(CONST.ATTR_BODYLATERALITY_DISTAL) &&
            !value.equals(CONST.ATTR_BODYLATERALITY_SUPERIOR) &&
            !value.equals(CONST.ATTR_BODYLATERALITY_INFERIOR)) {
          throw new UnsupportedOperationException("Invalid BodyLaterality: " + value);
        }
        attribute.setValue(value);
        attribute.addToIndexes();
        modifier.setNormalizedForm(attribute);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("medial_or_lateral".equals(annotation.type)) {
        String value = stringSlots.remove("medial_or_lateral_normalization");
       
        BodyLateralityModifier modifier = new BodyLateralityModifier(jCas, coveringSpan.begin, coveringSpan.end);
        BodyLaterality attribute = new BodyLaterality(jCas);
        if (value == null) {
          LOGGER.warn(String.format(
              "assuming \"%s\" for %s with id \"%s\"",
              CONST.ATTR_BODYLATERALITY_UNMARKED,
              format(modifier),
              annotation.id));
          value = CONST.ATTR_BODYLATERALITY_UNMARKED;
        } else if (!value.equals(CONST.ATTR_BODYLATERALITY_DISTAL) &&
            !value.equals(CONST.ATTR_BODYLATERALITY_MEDIAL) &&
            !value.equals(CONST.ATTR_BODYLATERALITY_LATERAL)) {
          throw new UnsupportedOperationException("Invalid BodyLaterality: " + value);
        }
        attribute.setValue(value);
        attribute.addToIndexes();
        modifier.setNormalizedForm(attribute);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("dorsal_or_ventral".equals(annotation.type)) {
        String value = stringSlots.remove("dorsal_or_ventral_normalization");
       
        BodyLateralityModifier modifier = new BodyLateralityModifier(jCas, coveringSpan.begin, coveringSpan.end);
        BodyLaterality attribute = new BodyLaterality(jCas);
        if (value == null) {
          LOGGER.warn(String.format(
              "assuming \"%s\" for %s with id \"%s\"",
              CONST.ATTR_BODYLATERALITY_UNMARKED,
              format(modifier),
              annotation.id));
          value = CONST.ATTR_BODYLATERALITY_UNMARKED;
        } else if (!value.equals(CONST.ATTR_BODYLATERALITY_DISTAL) &&
            !value.equals(CONST.ATTR_BODYLATERALITY_DORSAL) &&
            !value.equals(CONST.ATTR_BODYLATERALITY_VENTRAL)) {
          throw new UnsupportedOperationException("Invalid BodyLaterality: " + value);
        }
        attribute.setValue(value);
        attribute.addToIndexes();
        modifier.setNormalizedForm(attribute);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("body_side_class".equals(annotation.type)) {
        BodySide attribute = new BodySide(jCas);
        attribute.setValue(stringSlots.remove("body_side_normalization"));
        attribute.addToIndexes();
        BodySideModifier modifier = new BodySideModifier(jCas, coveringSpan.begin, coveringSpan.end);
        modifier.setNormalizedForm(attribute);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("course_class".equals(annotation.type)) {
        Course attribute = new Course(jCas);
        attribute.setValue(stringSlots.remove("course_normalization"));
        attribute.addToIndexes();
        CourseModifier modifier = new CourseModifier(jCas, coveringSpan.begin, coveringSpan.end);
        modifier.setTypeID(CONST.MODIFIER_TYPE_ID_COURSE_CLASS);
        modifier.setNormalizedForm(attribute);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("estimated_flag_indicator".equals(annotation.type)) {
        boolean value = booleanSlots.remove("estimated_normalization");
        LabEstimatedModifier modifier = new LabEstimatedModifier(jCas, coveringSpan.begin, coveringSpan.end);
        modifier.setIndicated(value);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("lab_interpretation_indicator".equals(annotation.type)) {
        String value = stringSlots.remove("lab_interpretation_normalization");
        LabInterpretationModifier modifier = new LabInterpretationModifier(jCas, coveringSpan.begin, coveringSpan.end);
        modifier.setTypeID(CONST.MODIFIER_TYPE_ID_LAB_INTERPRETATION_INDICATOR);
        modifier.setValue(value);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("reference_range".equals(annotation.type)) {
        LabReferenceRangeModifier modifier = new LabReferenceRangeModifier(jCas, coveringSpan.begin, coveringSpan.end);
        LabReferenceRange attribute = new LabReferenceRange(jCas);
        attribute.setValue(modifier.getCoveredText());
        attribute.addToIndexes();
        modifier.setNormalizedForm(attribute);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("Value".equals(annotation.type)) {
        KnowtatorAnnotation unit = annotationSlots.remove("value_unit");
        KnowtatorAnnotation number = annotationSlots.remove("value_number");
        LabValue attribute = new LabValue(jCas);
        if (unit != null) {
          KnowtatorAnnotation.Span unitSpan = unit.getCoveringSpan();
          String unitString = text.substring(unitSpan.begin, unitSpan.end);
          attribute.setUnit(unitString);
        }
        if (number != null) {
          KnowtatorAnnotation.Span numberSpan = number.getCoveringSpan();
          String numberString = text.substring(numberSpan.begin, numberSpan.end);
          attribute.setNumber(numberString);
        }
        attribute.addToIndexes();
        LabValueModifier modifier = new LabValueModifier(jCas, coveringSpan.begin, coveringSpan.end);
        modifier.setNormalizedForm(attribute);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("Value number".equals(annotation.type)) {
        // already handled in "Value" above

      } else if ("Value unit".equals(annotation.type)) {
        // already handled in "Value" above

      } else if ("allergy_indicator_class".equals(annotation.type)) {
        String value = stringSlots.remove("allergy_indicator_normalization");
        MedicationAllergyModifier modifier = new MedicationAllergyModifier(jCas, coveringSpan.begin, coveringSpan.end);
        if (null == value) {
          modifier.setIndicated(false);
        } else if ("indicator_present".equals(value)) {
          modifier.setIndicated(true);
        } else if ("indicator_absent".equals(value)) {
          modifier.setIndicated(false);
        } else {
          LOGGER.error(String.format(
              "unrecognized allergy-indicator value \"%s\" on annotation with id \"%s\"",
              value,
              annotation.id));
        }
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("Dosage".equals(annotation.type)) {
        String value = stringSlots.remove("dosage_values");
        MedicationDosage attribute = new MedicationDosage(jCas);
        attribute.setValue(value);
        attribute.addToIndexes();
        MedicationDosageModifier modifier = new MedicationDosageModifier(jCas, coveringSpan.begin, coveringSpan.end);
        modifier.setNormalizedForm(attribute);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("Duration".equals(annotation.type)) {
        String value = stringSlots.remove("duration_values");
        MedicationDuration attribute = new MedicationDuration(jCas);
        attribute.setValue(value);
        attribute.addToIndexes();
        MedicationDurationModifier modifier = new MedicationDurationModifier(jCas, coveringSpan.begin, coveringSpan.end);
        modifier.setNormalizedForm(attribute);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("Form".equals(annotation.type)) {
        String value = stringSlots.remove("form_values");
        MedicationForm attribute = new MedicationForm(jCas);
        attribute.setValue(value);
        attribute.addToIndexes();
        MedicationFormModifier modifier = new MedicationFormModifier(jCas, coveringSpan.begin, coveringSpan.end);
        modifier.setNormalizedForm(attribute);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);
       
      } else if ("Frequency".equals(annotation.type)) {
        KnowtatorAnnotation unit = annotationSlots.remove("frequency_unit");
        KnowtatorAnnotation number = annotationSlots.remove("frequency_number");
        MedicationFrequency attribute = new MedicationFrequency(jCas);
        if (unit != null) {
          String unitString = unit.stringSlots.get("frequency_unit_values");
          attribute.setUnit(unitString);
        }
        if (number != null) {
          String numberString = number.stringSlots.get("frequency_number_normalization");
          attribute.setNumber(numberString);
        }
        attribute.addToIndexes();
        MedicationFrequencyModifier modifier = new MedicationFrequencyModifier(jCas, coveringSpan.begin, coveringSpan.end);
        modifier.setNormalizedForm(attribute);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("Frequency number".equals(annotation.type)) {
        // already handled in "Frequency" above
        stringSlots.remove("frequency_number_normalization");

      } else if ("Frequency unit".equals(annotation.type)) {
        // already handled in "Frequency" above
        stringSlots.remove("frequency_unit_values");

      } else if ("Route".equals(annotation.type)) {
        String value = stringSlots.remove("route_values");
        MedicationRoute attribute = new MedicationRoute(jCas);
        attribute.setValue(value);
        attribute.addToIndexes();
        MedicationRouteModifier modifier = new MedicationRouteModifier(jCas, coveringSpan.begin, coveringSpan.end);
        modifier.setNormalizedForm(attribute);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);
       
      } else if ("Status change".equals(annotation.type)) {
        String value = stringSlots.remove("change_status_value");
        MedicationStatusChange attribute = new MedicationStatusChange(jCas);
        attribute.setValue(value);
        attribute.addToIndexes();
        MedicationStatusChangeModifier modifier = new MedicationStatusChangeModifier(jCas, coveringSpan.begin, coveringSpan.end);
        modifier.setNormalizedForm(attribute);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("Strength".equals(annotation.type)) {
        KnowtatorAnnotation unit = annotationSlots.remove("strength_unit");
        KnowtatorAnnotation number = annotationSlots.remove("strength_number");
        MedicationStrength attribute = new MedicationStrength(jCas);
        if (unit != null) {
          KnowtatorAnnotation.Span unitSpan = unit.getCoveringSpan();
          String unitString = text.substring(unitSpan.begin, unitSpan.end);
          attribute.setUnit(unitString);
        }
        if (number != null) {
          KnowtatorAnnotation.Span numberSpan = number.getCoveringSpan();
          String numberString = text.substring(numberSpan.begin, numberSpan.end);
          attribute.setNumber(numberString);
        }
        attribute.addToIndexes();
        MedicationStrengthModifier modifier = new MedicationStrengthModifier(jCas, coveringSpan.begin, coveringSpan.end);
View Full Code Here

    mention.setPolarity(negation == null
        ? CONST.NE_POLARITY_NEGATION_ABSENT
        : negation == true ? CONST.NE_POLARITY_NEGATION_PRESENT : CONST.NE_POLARITY_NEGATION_ABSENT);

    // add features for conditional, generic, etc.
    KnowtatorAnnotation conditional = annotationSlots.remove("conditional_CU");
    delayedFeatures.add(new DelayedFeatureFromFeature(mention, "conditional", conditional));
    KnowtatorAnnotation generic = annotationSlots.remove("generic_CU");
    delayedFeatures.add(new DelayedFeatureFromFeature(mention, "generic", generic));
    KnowtatorAnnotation historyOf = annotationSlots.remove("historyOf_CU");
    delayedFeatures.add(new DelayedFeatureFromFeature(mention, "historyOf", historyOf));
    KnowtatorAnnotation negationIndicator = annotationSlots.remove("negation_indicator_CU");
    delayedFeatures.add(new DelayedFeatureFromFeature(mention, "polarity", negationIndicator));
    KnowtatorAnnotation subject = annotationSlots.remove("subject_CU");
    delayedFeatures.add(new DelayedFeatureFromFeature(mention, "subject", subject) {
      @Override
      public void setValueFrom(Map<String, ? extends TOP> annotationMap) {
        super.setValueFrom(annotationMap);
        if (mention.getSubject() == null) {
          mention.setSubject(CONST.ATTR_SUBJECT_PATIENT);
        }
      }
    });
    KnowtatorAnnotation uncertainty = annotationSlots.remove("uncertainty_indicator_CU");
    delayedFeatures.add(new DelayedFeatureFromFeature(mention, "uncertainty", uncertainty));

    // convert status as necessary
    String status = stringSlots.remove("Status");
    if (status != null) {
View Full Code Here

            stringSlots,
            booleanSlots,
            annotationSlots,
            idAnnotationMap,
            delayedFeatures);
        KnowtatorAnnotation bodyLaterality = annotationSlots.remove("body_laterality");
        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);
        timeMention.addToIndexes();
        idAnnotationMap.put(annotation.id, timeMention);

      } else if ("SECTIONTIME".equals(annotation.type)) {
        TimeMention timeMention = new TimeMention(jCas, coveringSpan.begin, coveringSpan.end);
        timeMention.setTimeClass(annotation.type);
        timeMention.addToIndexes();
        idAnnotationMap.put(annotation.id, timeMention);

      } else if ("TIMEX3".equals(annotation.type)) {
        String timexClass = stringSlots.remove("class");
        TimeMention timeMention = new TimeMention(jCas, coveringSpan.begin, coveringSpan.end);
        timeMention.setTimeClass(timexClass);
        timeMention.addToIndexes();
        idAnnotationMap.put(annotation.id, timeMention);
       
      } else if ("conditional_class".equals(annotation.type)) {
        Boolean value = booleanSlots.remove("conditional_normalization");
        ConditionalModifier modifier = new ConditionalModifier(jCas, coveringSpan.begin, coveringSpan.end);
        modifier.setConditional(value == null ? false : value);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("generic_class".equals(annotation.type)) {
        Boolean value = booleanSlots.remove("generic_normalization");
        GenericModifier modifier = new GenericModifier(jCas, coveringSpan.begin, coveringSpan.end);
        modifier.setGeneric(value == null ? false : value);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("negation_indicator_class".equals(annotation.type)) {
        String value = stringSlots.remove("negation_indicator_normalization");
        PolarityModifier modifier = new PolarityModifier(jCas, coveringSpan.begin, coveringSpan.end);
        if (value == null) {
          LOGGER.warn(String.format(
              "assuming NE_POLARITY_NEGATION_PRESENT for %s with id \"%s\"",
              format(modifier),
              annotation.id));
          modifier.setPolarity(CONST.NE_POLARITY_NEGATION_PRESENT);
        } else if (value.equals("negation_absent")) {
          modifier.setPolarity(CONST.NE_POLARITY_NEGATION_ABSENT);
        } else if (value.equals("negation_present")) {
          modifier.setPolarity(CONST.NE_POLARITY_NEGATION_PRESENT);
        } else {
          throw new UnsupportedOperationException("Invalid negation: " + value);
        }
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("uncertainty_indicator_class".equals(annotation.type)) {
        String value = stringSlots.remove("uncertainty_indicator_normalization");
        UncertaintyModifier modifier = new UncertaintyModifier(jCas, coveringSpan.begin, coveringSpan.end);
        if (value == null) {
          LOGGER.warn(String.format(
              "assuming NE_UNCERTAINTY_PRESENT for %s with id \"%s\"",
              format(modifier),
              annotation.id));
          modifier.setUncertainty(CONST.NE_UNCERTAINTY_PRESENT);
        } else if (value.equals("indicator_absent")) {
          modifier.setUncertainty(CONST.NE_UNCERTAINTY_ABSENT);
        } else if (value.equals("indicator_present")) {
          modifier.setUncertainty(CONST.NE_UNCERTAINTY_PRESENT);
        } else {
          throw new UnsupportedOperationException("Invalid uncertainty: " + value);
        }
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("Person".equals(annotation.type)) {
        String value = stringSlots.remove("subject_normalization_CU");
        String uimaValue = SUBJECT_KNOWTATOR_TO_UIMA_MAP.get(value);
        String code = stringSlots.remove("associatedCode");
        String uimaCode = SUBJECT_KNOWTATOR_TO_UIMA_MAP.get(code);
        if (value != null && uimaValue == null) {
          LOGGER.error(String.format(
              "unrecognized subject value \"%s\" for annotation with id \"%s\"",
              value,
              annotation.id));
        }
        if (code != null && uimaCode == null) {
          LOGGER.error(String.format(
              "unrecognized subject code \"%s\" for annotation with id \"%s\"",
              code,
              annotation.id));
        }
        if (uimaValue != null && uimaCode != null && !uimaValue.equals(uimaCode)) {
          LOGGER.error(String.format(
              "subject value \"%s\" and code \"%s\" are inconsistent for annotation with id \"%s\"",
              value,
              code,
              annotation.id));
        }
        String subject = uimaValue != null ? uimaValue : uimaCode;
        if (subject == null && this.setDefaults) {
          subject = SHARPKnowtatorXMLDefaults.getSubject();
        }
        SubjectModifier modifier = new SubjectModifier(jCas, coveringSpan.begin, coveringSpan.end);
        modifier.setSubject(subject);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("historyOf_indicator_class".equals(annotation.type)) {
        String value = stringSlots.remove("historyOf_normalization");
        HistoryOfModifier modifier = new HistoryOfModifier(jCas, coveringSpan.begin, coveringSpan.end);
        if (null == value) {
          if (this.setDefaults) {
            modifier.setHistoryOf(SHARPKnowtatorXMLDefaults.getHistoryOf());
          }
        } else if ("historyOf_present".equals(value)) {
          modifier.setHistoryOf(CONST.NE_HISTORY_OF_PRESENT);
        } else if ("historyOf_absent".equals(value)) {
          modifier.setHistoryOf(CONST.NE_HISTORY_OF_ABSENT);
        } else {
          LOGGER.error(String.format(
              "unrecognized history-of value \"%s\" on annotation with id \"%s\"",
              value,
              annotation.id));
        }
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("distal_or_proximal".equals(annotation.type)) {
        String value = stringSlots.remove("distal_or_proximal_normalization");
        BodyLateralityModifier modifier = new BodyLateralityModifier(jCas, coveringSpan.begin, coveringSpan.end);
        BodyLaterality attribute = new BodyLaterality(jCas);
        if (value == null) {
          LOGGER.warn(String.format(
              "assuming \"%s\" for %s with id \"%s\"",
              CONST.ATTR_BODYLATERALITY_UNMARKED,
              format(modifier),
              annotation.id));
          value = CONST.ATTR_BODYLATERALITY_UNMARKED;
        } else if (!value.equals(CONST.ATTR_BODYLATERALITY_DISTAL) &&
            !value.equals(CONST.ATTR_BODYLATERALITY_PROXIMAL) &&
            !value.equals(CONST.ATTR_BODYLATERALITY_UNMARKED)) {
          throw new UnsupportedOperationException("Invalid BodyLaterality: " + value);
        }
        attribute.setValue(value);
        attribute.addToIndexes();
        modifier.setNormalizedForm(attribute);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("superior_or_inferior".equals(annotation.type)) {
        String value = stringSlots.remove("superior_or_inferior_normalization");
        BodyLateralityModifier modifier = new BodyLateralityModifier(jCas, coveringSpan.begin, coveringSpan.end);
        BodyLaterality attribute = new BodyLaterality(jCas);
        if (value == null) {
          LOGGER.warn(String.format(
              "assuming \"%s\" for %s with id \"%s\"",
              CONST.ATTR_BODYLATERALITY_UNMARKED,
              format(modifier),
              annotation.id));
          value = CONST.ATTR_BODYLATERALITY_UNMARKED;
        } else if (!value.equals(CONST.ATTR_BODYLATERALITY_DISTAL) &&
            !value.equals(CONST.ATTR_BODYLATERALITY_SUPERIOR) &&
            !value.equals(CONST.ATTR_BODYLATERALITY_INFERIOR)) {
          throw new UnsupportedOperationException("Invalid BodyLaterality: " + value);
        }
        attribute.setValue(value);
        attribute.addToIndexes();
        modifier.setNormalizedForm(attribute);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("medial_or_lateral".equals(annotation.type)) {
        String value = stringSlots.remove("medial_or_lateral_normalization");
       
        BodyLateralityModifier modifier = new BodyLateralityModifier(jCas, coveringSpan.begin, coveringSpan.end);
        BodyLaterality attribute = new BodyLaterality(jCas);
        if (value == null) {
          LOGGER.warn(String.format(
              "assuming \"%s\" for %s with id \"%s\"",
              CONST.ATTR_BODYLATERALITY_UNMARKED,
              format(modifier),
              annotation.id));
          value = CONST.ATTR_BODYLATERALITY_UNMARKED;
        } else if (!value.equals(CONST.ATTR_BODYLATERALITY_DISTAL) &&
            !value.equals(CONST.ATTR_BODYLATERALITY_MEDIAL) &&
            !value.equals(CONST.ATTR_BODYLATERALITY_LATERAL)) {
          throw new UnsupportedOperationException("Invalid BodyLaterality: " + value);
        }
        attribute.setValue(value);
        attribute.addToIndexes();
        modifier.setNormalizedForm(attribute);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("dorsal_or_ventral".equals(annotation.type)) {
        String value = stringSlots.remove("dorsal_or_ventral_normalization");
       
        BodyLateralityModifier modifier = new BodyLateralityModifier(jCas, coveringSpan.begin, coveringSpan.end);
        BodyLaterality attribute = new BodyLaterality(jCas);
        if (value == null) {
          LOGGER.warn(String.format(
              "assuming \"%s\" for %s with id \"%s\"",
              CONST.ATTR_BODYLATERALITY_UNMARKED,
              format(modifier),
              annotation.id));
          value = CONST.ATTR_BODYLATERALITY_UNMARKED;
        } else if (!value.equals(CONST.ATTR_BODYLATERALITY_DISTAL) &&
            !value.equals(CONST.ATTR_BODYLATERALITY_DORSAL) &&
            !value.equals(CONST.ATTR_BODYLATERALITY_VENTRAL)) {
          throw new UnsupportedOperationException("Invalid BodyLaterality: " + value);
        }
        attribute.setValue(value);
        attribute.addToIndexes();
        modifier.setNormalizedForm(attribute);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("body_side_class".equals(annotation.type)) {
        BodySide attribute = new BodySide(jCas);
        attribute.setValue(stringSlots.remove("body_side_normalization"));
        attribute.addToIndexes();
        BodySideModifier modifier = new BodySideModifier(jCas, coveringSpan.begin, coveringSpan.end);
        modifier.setNormalizedForm(attribute);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("course_class".equals(annotation.type)) {
        Course attribute = new Course(jCas);
        attribute.setValue(stringSlots.remove("course_normalization"));
        attribute.addToIndexes();
        CourseModifier modifier = new CourseModifier(jCas, coveringSpan.begin, coveringSpan.end);
        modifier.setTypeID(CONST.MODIFIER_TYPE_ID_COURSE_CLASS);
        modifier.setNormalizedForm(attribute);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("estimated_flag_indicator".equals(annotation.type)) {
        boolean value = booleanSlots.remove("estimated_normalization");
        LabEstimatedModifier modifier = new LabEstimatedModifier(jCas, coveringSpan.begin, coveringSpan.end);
        modifier.setIndicated(value);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("lab_interpretation_indicator".equals(annotation.type)) {
        String value = stringSlots.remove("lab_interpretation_normalization");
        LabInterpretationModifier modifier = new LabInterpretationModifier(jCas, coveringSpan.begin, coveringSpan.end);
        modifier.setTypeID(CONST.MODIFIER_TYPE_ID_LAB_INTERPRETATION_INDICATOR);
        modifier.setValue(value);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("reference_range".equals(annotation.type)) {
        LabReferenceRangeModifier modifier = new LabReferenceRangeModifier(jCas, coveringSpan.begin, coveringSpan.end);
        LabReferenceRange attribute = new LabReferenceRange(jCas);
        attribute.setValue(modifier.getCoveredText());
        attribute.addToIndexes();
        modifier.setNormalizedForm(attribute);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("Value".equals(annotation.type)) {
        KnowtatorAnnotation unit = annotationSlots.remove("value_unit");
        KnowtatorAnnotation number = annotationSlots.remove("value_number");
        LabValue attribute = new LabValue(jCas);
        if (unit != null) {
          KnowtatorAnnotation.Span unitSpan = unit.getCoveringSpan();
          String unitString = text.substring(unitSpan.begin, unitSpan.end);
          attribute.setUnit(unitString);
        }
        if (number != null) {
          KnowtatorAnnotation.Span numberSpan = number.getCoveringSpan();
          String numberString = text.substring(numberSpan.begin, numberSpan.end);
          attribute.setNumber(numberString);
        }
        attribute.addToIndexes();
        LabValueModifier modifier = new LabValueModifier(jCas, coveringSpan.begin, coveringSpan.end);
        modifier.setNormalizedForm(attribute);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("Value number".equals(annotation.type)) {
        // already handled in "Value" above

      } else if ("Value unit".equals(annotation.type)) {
        // already handled in "Value" above

      } else if ("allergy_indicator_class".equals(annotation.type)) {
        String value = stringSlots.remove("allergy_indicator_normalization");
        MedicationAllergyModifier modifier = new MedicationAllergyModifier(jCas, coveringSpan.begin, coveringSpan.end);
        if (null == value) {
          modifier.setIndicated(false);
        } else if ("indicator_present".equals(value)) {
          modifier.setIndicated(true);
        } else if ("indicator_absent".equals(value)) {
          modifier.setIndicated(false);
        } else {
          LOGGER.error(String.format(
              "unrecognized allergy-indicator value \"%s\" on annotation with id \"%s\"",
              value,
              annotation.id));
        }
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("Dosage".equals(annotation.type)) {
        String value = stringSlots.remove("dosage_values");
        MedicationDosage attribute = new MedicationDosage(jCas);
        attribute.setValue(value);
        attribute.addToIndexes();
        MedicationDosageModifier modifier = new MedicationDosageModifier(jCas, coveringSpan.begin, coveringSpan.end);
        modifier.setNormalizedForm(attribute);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("Duration".equals(annotation.type)) {
        String value = stringSlots.remove("duration_values");
        MedicationDuration attribute = new MedicationDuration(jCas);
        attribute.setValue(value);
        attribute.addToIndexes();
        MedicationDurationModifier modifier = new MedicationDurationModifier(jCas, coveringSpan.begin, coveringSpan.end);
        modifier.setNormalizedForm(attribute);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("Form".equals(annotation.type)) {
        String value = stringSlots.remove("form_values");
        MedicationForm attribute = new MedicationForm(jCas);
        attribute.setValue(value);
        attribute.addToIndexes();
        MedicationFormModifier modifier = new MedicationFormModifier(jCas, coveringSpan.begin, coveringSpan.end);
        modifier.setNormalizedForm(attribute);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);
       
      } else if ("Frequency".equals(annotation.type)) {
        KnowtatorAnnotation unit = annotationSlots.remove("frequency_unit");
        KnowtatorAnnotation number = annotationSlots.remove("frequency_number");
        MedicationFrequency attribute = new MedicationFrequency(jCas);
        if (unit != null) {
          String unitString = unit.stringSlots.get("frequency_unit_values");
          attribute.setUnit(unitString);
        }
        if (number != null) {
          String numberString = number.stringSlots.get("frequency_number_normalization");
          attribute.setNumber(numberString);
        }
        attribute.addToIndexes();
        MedicationFrequencyModifier modifier = new MedicationFrequencyModifier(jCas, coveringSpan.begin, coveringSpan.end);
        modifier.setNormalizedForm(attribute);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("Frequency number".equals(annotation.type)) {
        // already handled in "Frequency" above
        stringSlots.remove("frequency_number_normalization");

      } else if ("Frequency unit".equals(annotation.type)) {
        // already handled in "Frequency" above
        stringSlots.remove("frequency_unit_values");

      } else if ("Route".equals(annotation.type)) {
        String value = stringSlots.remove("route_values");
        MedicationRoute attribute = new MedicationRoute(jCas);
        attribute.setValue(value);
        attribute.addToIndexes();
        MedicationRouteModifier modifier = new MedicationRouteModifier(jCas, coveringSpan.begin, coveringSpan.end);
        modifier.setNormalizedForm(attribute);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);
       
      } else if ("Status change".equals(annotation.type)) {
        String value = stringSlots.remove("change_status_value");
        MedicationStatusChange attribute = new MedicationStatusChange(jCas);
        attribute.setValue(value);
        attribute.addToIndexes();
        MedicationStatusChangeModifier modifier = new MedicationStatusChangeModifier(jCas, coveringSpan.begin, coveringSpan.end);
        modifier.setNormalizedForm(attribute);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("Strength".equals(annotation.type)) {
        KnowtatorAnnotation unit = annotationSlots.remove("strength_unit");
        KnowtatorAnnotation number = annotationSlots.remove("strength_number");
        MedicationStrength attribute = new MedicationStrength(jCas);
        if (unit != null) {
          KnowtatorAnnotation.Span unitSpan = unit.getCoveringSpan();
          String unitString = text.substring(unitSpan.begin, unitSpan.end);
          attribute.setUnit(unitString);
        }
        if (number != null) {
          KnowtatorAnnotation.Span numberSpan = number.getCoveringSpan();
          String numberString = text.substring(numberSpan.begin, numberSpan.end);
          attribute.setNumber(numberString);
        }
        attribute.addToIndexes();
        MedicationStrengthModifier modifier = new MedicationStrengthModifier(jCas, coveringSpan.begin, coveringSpan.end);
View Full Code Here

    mention.setPolarity(negation == null
        ? CONST.NE_POLARITY_NEGATION_ABSENT
        : negation == true ? CONST.NE_POLARITY_NEGATION_PRESENT : CONST.NE_POLARITY_NEGATION_ABSENT);

    // add features for conditional, generic, etc.
    KnowtatorAnnotation conditional = annotationSlots.remove("conditional_CU");
    delayedFeatures.add(new DelayedFeatureFromFeature(mention, "conditional", conditional));
    KnowtatorAnnotation generic = annotationSlots.remove("generic_CU");
    delayedFeatures.add(new DelayedFeatureFromFeature(mention, "generic", generic));
    KnowtatorAnnotation historyOf = annotationSlots.remove("historyOf_CU");
    delayedFeatures.add(new DelayedFeatureFromFeature(mention, "historyOf", historyOf));
    KnowtatorAnnotation negationIndicator = annotationSlots.remove("negation_indicator_CU");
    delayedFeatures.add(new DelayedFeatureFromFeature(mention, "polarity", negationIndicator));
    KnowtatorAnnotation subject = annotationSlots.remove("subject_CU");
    delayedFeatures.add(new DelayedFeatureFromFeature(mention, "subject", subject) {
      @Override
      public void setValueFrom(Map<String, ? extends TOP> annotationMap) {
        super.setValueFrom(annotationMap);
        if (mention.getSubject() == null) {
          mention.setSubject(CONST.ATTR_SUBJECT_PATIENT);
        }
      }
    });
    KnowtatorAnnotation uncertainty = annotationSlots.remove("uncertainty_indicator_CU");
    delayedFeatures.add(new DelayedFeatureFromFeature(mention, "uncertainty", uncertainty));

    // convert status as necessary
    String status = stringSlots.remove("Status");
    if (status != null) {
View Full Code Here

            stringSlots,
            booleanSlots,
            annotationSlots,
            idAnnotationMap,
            delayedFeatures);
        KnowtatorAnnotation bodyLaterality = annotationSlots.remove("body_laterality");
        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);
        timeMention.addToIndexes();
        idAnnotationMap.put(annotation.id, timeMention);

      } else if ("SECTIONTIME".equals(annotation.type)) {
        TimeMention timeMention = new TimeMention(jCas, coveringSpan.begin, coveringSpan.end);
        timeMention.setTimeClass(annotation.type);
        timeMention.addToIndexes();
        idAnnotationMap.put(annotation.id, timeMention);

      } else if ("TIMEX3".equals(annotation.type)) {
        String timexClass = stringSlots.remove("class");
        TimeMention timeMention = new TimeMention(jCas, coveringSpan.begin, coveringSpan.end);
        timeMention.setTimeClass(timexClass);
        timeMention.addToIndexes();
        idAnnotationMap.put(annotation.id, timeMention);
       
      } else if ("conditional_class".equals(annotation.type)) {
        Boolean value = booleanSlots.remove("conditional_normalization");
        ConditionalModifier modifier = new ConditionalModifier(jCas, coveringSpan.begin, coveringSpan.end);
        modifier.setConditional(value == null ? false : value);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("generic_class".equals(annotation.type)) {
        Boolean value = booleanSlots.remove("generic_normalization");
        GenericModifier modifier = new GenericModifier(jCas, coveringSpan.begin, coveringSpan.end);
        modifier.setGeneric(value == null ? false : value);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("negation_indicator_class".equals(annotation.type)) {
        String value = stringSlots.remove("negation_indicator_normalization");
        PolarityModifier modifier = new PolarityModifier(jCas, coveringSpan.begin, coveringSpan.end);
        if (value == null) {
          LOGGER.warn(String.format(
              "assuming NE_POLARITY_NEGATION_PRESENT for %s with id \"%s\"",
              format(modifier),
              annotation.id));
          modifier.setPolarity(CONST.NE_POLARITY_NEGATION_PRESENT);
        } else if (value.equals("negation_absent")) {
          modifier.setPolarity(CONST.NE_POLARITY_NEGATION_ABSENT);
        } else if (value.equals("negation_present")) {
          modifier.setPolarity(CONST.NE_POLARITY_NEGATION_PRESENT);
        } else {
          throw new UnsupportedOperationException("Invalid negation: " + value);
        }
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("uncertainty_indicator_class".equals(annotation.type)) {
        String value = stringSlots.remove("uncertainty_indicator_normalization");
        UncertaintyModifier modifier = new UncertaintyModifier(jCas, coveringSpan.begin, coveringSpan.end);
        if (value == null) {
          LOGGER.warn(String.format(
              "assuming NE_UNCERTAINTY_PRESENT for %s with id \"%s\"",
              format(modifier),
              annotation.id));
          modifier.setUncertainty(CONST.NE_UNCERTAINTY_PRESENT);
        } else if (value.equals("indicator_absent")) {
          modifier.setUncertainty(CONST.NE_UNCERTAINTY_ABSENT);
        } else if (value.equals("indicator_present")) {
          modifier.setUncertainty(CONST.NE_UNCERTAINTY_PRESENT);
        } else {
          throw new UnsupportedOperationException("Invalid uncertainty: " + value);
        }
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("Person".equals(annotation.type)) {
        String value = stringSlots.remove("subject_normalization_CU");
        String uimaValue = SUBJECT_KNOWTATOR_TO_UIMA_MAP.get(value);
        String code = stringSlots.remove("associatedCode");
        String uimaCode = SUBJECT_KNOWTATOR_TO_UIMA_MAP.get(code);
        if (value != null && uimaValue == null) {
          LOGGER.error(String.format(
              "unrecognized subject value \"%s\" for annotation with id \"%s\"",
              value,
              annotation.id));
        }
        if (code != null && uimaCode == null) {
          LOGGER.error(String.format(
              "unrecognized subject code \"%s\" for annotation with id \"%s\"",
              code,
              annotation.id));
        }
        if (uimaValue != null && uimaCode != null && !uimaValue.equals(uimaCode)) {
          LOGGER.error(String.format(
              "subject value \"%s\" and code \"%s\" are inconsistent for annotation with id \"%s\"",
              value,
              code,
              annotation.id));
        }
        String subject = uimaValue != null ? uimaValue : uimaCode;
        if (subject == null && this.setDefaults) {
          subject = SHARPKnowtatorXMLDefaults.getSubject();
        }
        SubjectModifier modifier = new SubjectModifier(jCas, coveringSpan.begin, coveringSpan.end);
        modifier.setSubject(subject);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("historyOf_indicator_class".equals(annotation.type)) {
        String value = stringSlots.remove("historyOf_normalization");
        HistoryOfModifier modifier = new HistoryOfModifier(jCas, coveringSpan.begin, coveringSpan.end);
        if (null == value) {
          if (this.setDefaults) {
            modifier.setHistoryOf(SHARPKnowtatorXMLDefaults.getHistoryOf());
          }
        } else if ("historyOf_present".equals(value)) {
          modifier.setHistoryOf(CONST.NE_HISTORY_OF_PRESENT);
        } else if ("historyOf_absent".equals(value)) {
          modifier.setHistoryOf(CONST.NE_HISTORY_OF_ABSENT);
        } else {
          LOGGER.error(String.format(
              "unrecognized history-of value \"%s\" on annotation with id \"%s\"",
              value,
              annotation.id));
        }
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("distal_or_proximal".equals(annotation.type)) {
        String value = stringSlots.remove("distal_or_proximal_normalization");
        BodyLateralityModifier modifier = new BodyLateralityModifier(jCas, coveringSpan.begin, coveringSpan.end);
        BodyLaterality attribute = new BodyLaterality(jCas);
        if (value == null) {
          LOGGER.warn(String.format(
              "assuming \"%s\" for %s with id \"%s\"",
              CONST.ATTR_BODYLATERALITY_UNMARKED,
              format(modifier),
              annotation.id));
          value = CONST.ATTR_BODYLATERALITY_UNMARKED;
        } else if (!value.equals(CONST.ATTR_BODYLATERALITY_DISTAL) &&
            !value.equals(CONST.ATTR_BODYLATERALITY_PROXIMAL) &&
            !value.equals(CONST.ATTR_BODYLATERALITY_UNMARKED)) {
          throw new UnsupportedOperationException("Invalid BodyLaterality: " + value);
        }
        attribute.setValue(value);
        attribute.addToIndexes();
        modifier.setNormalizedForm(attribute);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("superior_or_inferior".equals(annotation.type)) {
        String value = stringSlots.remove("superior_or_inferior_normalization");
        BodyLateralityModifier modifier = new BodyLateralityModifier(jCas, coveringSpan.begin, coveringSpan.end);
        BodyLaterality attribute = new BodyLaterality(jCas);
        if (value == null) {
          LOGGER.warn(String.format(
              "assuming \"%s\" for %s with id \"%s\"",
              CONST.ATTR_BODYLATERALITY_UNMARKED,
              format(modifier),
              annotation.id));
          value = CONST.ATTR_BODYLATERALITY_UNMARKED;
        } else if (!value.equals(CONST.ATTR_BODYLATERALITY_DISTAL) &&
            !value.equals(CONST.ATTR_BODYLATERALITY_SUPERIOR) &&
            !value.equals(CONST.ATTR_BODYLATERALITY_INFERIOR)) {
          throw new UnsupportedOperationException("Invalid BodyLaterality: " + value);
        }
        attribute.setValue(value);
        attribute.addToIndexes();
        modifier.setNormalizedForm(attribute);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("medial_or_lateral".equals(annotation.type)) {
        String value = stringSlots.remove("medial_or_lateral_normalization");
       
        BodyLateralityModifier modifier = new BodyLateralityModifier(jCas, coveringSpan.begin, coveringSpan.end);
        BodyLaterality attribute = new BodyLaterality(jCas);
        if (value == null) {
          LOGGER.warn(String.format(
              "assuming \"%s\" for %s with id \"%s\"",
              CONST.ATTR_BODYLATERALITY_UNMARKED,
              format(modifier),
              annotation.id));
          value = CONST.ATTR_BODYLATERALITY_UNMARKED;
        } else if (!value.equals(CONST.ATTR_BODYLATERALITY_DISTAL) &&
            !value.equals(CONST.ATTR_BODYLATERALITY_MEDIAL) &&
            !value.equals(CONST.ATTR_BODYLATERALITY_LATERAL)) {
          throw new UnsupportedOperationException("Invalid BodyLaterality: " + value);
        }
        attribute.setValue(value);
        attribute.addToIndexes();
        modifier.setNormalizedForm(attribute);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("dorsal_or_ventral".equals(annotation.type)) {
        String value = stringSlots.remove("dorsal_or_ventral_normalization");
       
        BodyLateralityModifier modifier = new BodyLateralityModifier(jCas, coveringSpan.begin, coveringSpan.end);
        BodyLaterality attribute = new BodyLaterality(jCas);
        if (value == null) {
          LOGGER.warn(String.format(
              "assuming \"%s\" for %s with id \"%s\"",
              CONST.ATTR_BODYLATERALITY_UNMARKED,
              format(modifier),
              annotation.id));
          value = CONST.ATTR_BODYLATERALITY_UNMARKED;
        } else if (!value.equals(CONST.ATTR_BODYLATERALITY_DISTAL) &&
            !value.equals(CONST.ATTR_BODYLATERALITY_DORSAL) &&
            !value.equals(CONST.ATTR_BODYLATERALITY_VENTRAL)) {
          throw new UnsupportedOperationException("Invalid BodyLaterality: " + value);
        }
        attribute.setValue(value);
        attribute.addToIndexes();
        modifier.setNormalizedForm(attribute);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("body_side_class".equals(annotation.type)) {
        BodySide attribute = new BodySide(jCas);
        attribute.setValue(stringSlots.remove("body_side_normalization"));
        attribute.addToIndexes();
        BodySideModifier modifier = new BodySideModifier(jCas, coveringSpan.begin, coveringSpan.end);
        modifier.setNormalizedForm(attribute);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("course_class".equals(annotation.type)) {
        Course attribute = new Course(jCas);
        attribute.setValue(stringSlots.remove("course_normalization"));
        attribute.addToIndexes();
        CourseModifier modifier = new CourseModifier(jCas, coveringSpan.begin, coveringSpan.end);
        modifier.setTypeID(CONST.MODIFIER_TYPE_ID_COURSE_CLASS);
        modifier.setNormalizedForm(attribute);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("estimated_flag_indicator".equals(annotation.type)) {
        boolean value = booleanSlots.remove("estimated_normalization");
        LabEstimatedModifier modifier = new LabEstimatedModifier(jCas, coveringSpan.begin, coveringSpan.end);
        modifier.setIndicated(value);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("lab_interpretation_indicator".equals(annotation.type)) {
        String value = stringSlots.remove("lab_interpretation_normalization");
        LabInterpretationModifier modifier = new LabInterpretationModifier(jCas, coveringSpan.begin, coveringSpan.end);
        modifier.setTypeID(CONST.MODIFIER_TYPE_ID_LAB_INTERPRETATION_INDICATOR);
        modifier.setValue(value);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("reference_range".equals(annotation.type)) {
        LabReferenceRangeModifier modifier = new LabReferenceRangeModifier(jCas, coveringSpan.begin, coveringSpan.end);
        LabReferenceRange attribute = new LabReferenceRange(jCas);
        attribute.setValue(modifier.getCoveredText());
        attribute.addToIndexes();
        modifier.setNormalizedForm(attribute);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("Value".equals(annotation.type)) {
        KnowtatorAnnotation unit = annotationSlots.remove("value_unit");
        KnowtatorAnnotation number = annotationSlots.remove("value_number");
        LabValue attribute = new LabValue(jCas);
        if (unit != null) {
          KnowtatorAnnotation.Span unitSpan = unit.getCoveringSpan();
          String unitString = text.substring(unitSpan.begin, unitSpan.end);
          attribute.setUnit(unitString);
        }
        if (number != null) {
          KnowtatorAnnotation.Span numberSpan = number.getCoveringSpan();
          String numberString = text.substring(numberSpan.begin, numberSpan.end);
          attribute.setNumber(numberString);
        }
        attribute.addToIndexes();
        LabValueModifier modifier = new LabValueModifier(jCas, coveringSpan.begin, coveringSpan.end);
        modifier.setNormalizedForm(attribute);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("Value number".equals(annotation.type)) {
        // already handled in "Value" above

      } else if ("Value unit".equals(annotation.type)) {
        // already handled in "Value" above

      } else if ("allergy_indicator_class".equals(annotation.type)) {
        String value = stringSlots.remove("allergy_indicator_normalization");
        MedicationAllergyModifier modifier = new MedicationAllergyModifier(jCas, coveringSpan.begin, coveringSpan.end);
        if (null == value) {
          modifier.setIndicated(false);
        } else if ("indicator_present".equals(value)) {
          modifier.setIndicated(true);
        } else if ("indicator_absent".equals(value)) {
          modifier.setIndicated(false);
        } else {
          LOGGER.error(String.format(
              "unrecognized allergy-indicator value \"%s\" on annotation with id \"%s\"",
              value,
              annotation.id));
        }
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("Dosage".equals(annotation.type)) {
        String value = stringSlots.remove("dosage_values");
        MedicationDosage attribute = new MedicationDosage(jCas);
        attribute.setValue(value);
        attribute.addToIndexes();
        MedicationDosageModifier modifier = new MedicationDosageModifier(jCas, coveringSpan.begin, coveringSpan.end);
        modifier.setNormalizedForm(attribute);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("Duration".equals(annotation.type)) {
        String value = stringSlots.remove("duration_values");
        MedicationDuration attribute = new MedicationDuration(jCas);
        attribute.setValue(value);
        attribute.addToIndexes();
        MedicationDurationModifier modifier = new MedicationDurationModifier(jCas, coveringSpan.begin, coveringSpan.end);
        modifier.setNormalizedForm(attribute);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("Form".equals(annotation.type)) {
        String value = stringSlots.remove("form_values");
        MedicationForm attribute = new MedicationForm(jCas);
        attribute.setValue(value);
        attribute.addToIndexes();
        MedicationFormModifier modifier = new MedicationFormModifier(jCas, coveringSpan.begin, coveringSpan.end);
        modifier.setNormalizedForm(attribute);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);
       
      } else if ("Frequency".equals(annotation.type)) {
        KnowtatorAnnotation unit = annotationSlots.remove("frequency_unit");
        KnowtatorAnnotation number = annotationSlots.remove("frequency_number");
        MedicationFrequency attribute = new MedicationFrequency(jCas);
        if (unit != null) {
          String unitString = unit.stringSlots.get("frequency_unit_values");
          attribute.setUnit(unitString);
        }
        if (number != null) {
          String numberString = number.stringSlots.get("frequency_number_normalization");
          attribute.setNumber(numberString);
        }
        attribute.addToIndexes();
        MedicationFrequencyModifier modifier = new MedicationFrequencyModifier(jCas, coveringSpan.begin, coveringSpan.end);
        modifier.setNormalizedForm(attribute);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("Frequency number".equals(annotation.type)) {
        // already handled in "Frequency" above
        stringSlots.remove("frequency_number_normalization");

      } else if ("Frequency unit".equals(annotation.type)) {
        // already handled in "Frequency" above
        stringSlots.remove("frequency_unit_values");

      } else if ("Route".equals(annotation.type)) {
        String value = stringSlots.remove("route_values");
        MedicationRoute attribute = new MedicationRoute(jCas);
        attribute.setValue(value);
        attribute.addToIndexes();
        MedicationRouteModifier modifier = new MedicationRouteModifier(jCas, coveringSpan.begin, coveringSpan.end);
        modifier.setNormalizedForm(attribute);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);
       
      } else if ("Status change".equals(annotation.type)) {
        String value = stringSlots.remove("change_status_value");
        MedicationStatusChange attribute = new MedicationStatusChange(jCas);
        attribute.setValue(value);
        attribute.addToIndexes();
        MedicationStatusChangeModifier modifier = new MedicationStatusChangeModifier(jCas, coveringSpan.begin, coveringSpan.end);
        modifier.setNormalizedForm(attribute);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("Strength".equals(annotation.type)) {
        KnowtatorAnnotation unit = annotationSlots.remove("strength_unit");
        KnowtatorAnnotation number = annotationSlots.remove("strength_number");
        MedicationStrength attribute = new MedicationStrength(jCas);
        if (unit != null) {
          KnowtatorAnnotation.Span unitSpan = unit.getCoveringSpan();
          String unitString = text.substring(unitSpan.begin, unitSpan.end);
          attribute.setUnit(unitString);
        }
        if (number != null) {
          KnowtatorAnnotation.Span numberSpan = number.getCoveringSpan();
          String numberString = text.substring(numberSpan.begin, numberSpan.end);
          attribute.setNumber(numberString);
        }
        attribute.addToIndexes();
        MedicationStrengthModifier modifier = new MedicationStrengthModifier(jCas, coveringSpan.begin, coveringSpan.end);
View Full Code Here

    mention.setPolarity(negation == null
        ? CONST.NE_POLARITY_NEGATION_ABSENT
        : negation == true ? CONST.NE_POLARITY_NEGATION_PRESENT : CONST.NE_POLARITY_NEGATION_ABSENT);

    // add features for conditional, generic, etc.
    KnowtatorAnnotation conditional = annotationSlots.remove("conditional_CU");
    delayedFeatures.add(new DelayedFeatureFromFeature(mention, "conditional", conditional));
    KnowtatorAnnotation generic = annotationSlots.remove("generic_CU");
    delayedFeatures.add(new DelayedFeatureFromFeature(mention, "generic", generic));
    KnowtatorAnnotation historyOf = annotationSlots.remove("historyOf_CU");
    delayedFeatures.add(new DelayedFeatureFromFeature(mention, "historyOf", historyOf));
    KnowtatorAnnotation negationIndicator = annotationSlots.remove("negation_indicator_CU");
    delayedFeatures.add(new DelayedFeatureFromFeature(mention, "polarity", negationIndicator));
    KnowtatorAnnotation subject = annotationSlots.remove("subject_CU");
    delayedFeatures.add(new DelayedFeatureFromFeature(mention, "subject", subject) {
      @Override
      public void setValueFrom(Map<String, ? extends TOP> annotationMap) {
        super.setValueFrom(annotationMap);
        if (mention.getSubject() == null) {
          mention.setSubject(CONST.ATTR_SUBJECT_PATIENT);
        }
      }
    });
    KnowtatorAnnotation uncertainty = annotationSlots.remove("uncertainty_indicator_CU");
    delayedFeatures.add(new DelayedFeatureFromFeature(mention, "uncertainty", uncertainty));

    // convert status as necessary
    String status = stringSlots.remove("Status");
    if (status != null) {
View Full Code Here

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Related Classes of org.apache.ctakes.core.knowtator.KnowtatorAnnotation

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