knowtatorURI));
}
}
if ("Anatomical_site".equals(annotation.type)) {
AnatomicalSiteMention mention = new AnatomicalSiteMention(jCas, coveringSpan.begin, coveringSpan.end);
addIdentifiedAnnotationFeatures(
annotation,
mention,
jCas,
CONST.NE_TYPE_ID_ANATOMICAL_SITE,
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);
modifier.setNormalizedForm(attribute);
modifier.addToIndexes();
idAnnotationMap.put(annotation.id, modifier);
} else if ("Strength number".equals(annotation.type)) {
// already handled in "Strength" above
} else if ("Strength unit".equals(annotation.type)) {
// already handled in "Strength" above
} else if ("device_class".equals(annotation.type)) {
String code = stringSlots.remove("associatedCode");
ProcedureDevice attribute = new ProcedureDevice(jCas);
attribute.setValue(code);
ProcedureDeviceModifier modifier = new ProcedureDeviceModifier(jCas, coveringSpan.begin, coveringSpan.end);
modifier.setNormalizedForm(attribute);
modifier.addToIndexes();
idAnnotationMap.put(annotation.id, modifier);
} else if ("method_class".equals(annotation.type)) {
String code = stringSlots.remove("associatedCode");
ProcedureMethod attribute = new ProcedureMethod(jCas);
attribute.setValue(code);
ProcedureMethodModifier modifier = new ProcedureMethodModifier(jCas, coveringSpan.begin, coveringSpan.end);
modifier.setNormalizedForm(attribute);
modifier.addToIndexes();
idAnnotationMap.put(annotation.id, modifier);
} else if ("severity_class".equals(annotation.type)) {
Severity attribute = new Severity(jCas);
attribute.setValue(stringSlots.remove("severity_normalization"));
attribute.addToIndexes();
SeverityModifier modifier = new SeverityModifier(jCas, coveringSpan.begin, coveringSpan.end);
modifier.setTypeID(CONST.MODIFIER_TYPE_ID_SEVERITY_CLASS);
modifier.setNormalizedForm(attribute);
modifier.addToIndexes();
idAnnotationMap.put(annotation.id, modifier);
} else if ("Date".equals(annotation.type)) {
String month = stringSlots.remove("month");
String day = stringSlots.remove("day");
Date date = new Date(jCas);
date.setMonth(month);
date.setDay(day);
date.addToIndexes();
TimeMention mention = new TimeMention(jCas, coveringSpan.begin, coveringSpan.end);
mention.setDate(date);
mention.addToIndexes();
idAnnotationMap.put(annotation.id, mention);
} else if (eventRelationTypes.contains(annotation.type)) {
// store the ALINK information for later, once all annotations are in the CAS
DelayedRelation relation = new DelayedRelation();