Merative Annotator for Clinical Data Container Edition

Symptoms & Diseases

This annotator identifies symptoms and diseases mentioned in the text. It also identifies related text that describes the symptom or disease.

Configurations

ConfigurationValuesDescription
Library
  • umls.latest
  • umls.2022AA
  • umls.2021AA
  • umls.2020AA (deprecated - will be removed in 2023)
Defines the version of the UMLS library that is used when analyzing unstructured data.

The value umls.latest will reference the latest available version of UMLS within the service. As newer versions of UMLS are made available in the service, umls.latest library configurations will automatically leverage the latest available version of UMLS in the service once available. Declaration of a specific version of UMLS is recommended to avoid undesirable changes in output as newer versions of UMLS are made available within the service. Through declaration of a specific version of UMLS, newer versions of UMLS may be evaluated prior to use in production.

Annotation Types

  • aci.SymptomDiseaseInd

aci.SymptomDiseaseInd

FeatureDescription
beginThe start position of the annotation as a character offset into the text. The smallest possible start position is 0.
endThe end position of the annotation as character offset into the text. The end position points at the first character after the annotation, such that end-begin equals the length of the coveredText.
coveredTextThe text covered by an annotation as a string.
typeaci.SymptomDiseaseInd
dateIndicates the date related to the event. For instance, in a patient’s medical form, this date may indicate the date of surgery, or the date of last diagnosis. The value of date is detected from the date that is nearest to the text that is annotated.
dateInMillisecondsIt is a java.util.Calendar date and is the difference, measured in milliseconds, between the date of the event and midnight, January 1, 1970 UTC.
dateSourceIndicates where in the document or text the date value is identified. For example, sentence is one possible option for dateSource
snomedConceptIdNumerical code provided by the SNOMED dictionaries that represents the symptom or disease.
ccsCodeClinical Classification System (CCS) code is used to categorize the symptom and diseases such that it can be used for further analysis.
hccCodeHierarchical Condition Categories (HCC) code is primarily used by Medicare and Medicaid.
cuiUMLS Concept Unique ID (CUI). CUIs are used to uniquely identify concepts across different UMLS sources. Depending on the source of the symptom/disease information, this value may not be available.
modalityThere are three potential values for this feature: positive, negative, and potential. Positive modality means there is a high probability that the identified text is related to symptoms or diseases. Negative modality means that the identified text is not a symptom or a disease. Potential modality means there is some likelihood that the identified text is related to symptoms or diseases.
loincIdLOINC stands for Logical Observations Identifiers, Names, Codes. The value for this feature comes from UMLS.
nciCodeThe NCI Thesaurus covers vocabulary for cancer-related clinical care, translational and basic research, and public information and administrative activities. The value for this feature comes from UMLS.
meshIdThe MeSH thesaurus is a controlled vocabulary used for indexing, cataloging, and searching for biomedical and health-related information and documents. The value for this feature comes from UMLS.
icd9CodeICD stands for International Classification of Diseases. The number 9 is a revision number for this code set.
icd10CodeICD stands for International Classification of Diseases. The number 10 is a revision number for this code set.
symptomDiseaseSurfaceFormThe covered text that refers to the sympton or disease identified by the annotation. For example, in text He had a persistent cough., the symptom is persistent cough.
symptomDiseaseSurfaceFormNormalizedNameThe normalized term for the sympton or disease. For instance, for the term roll-in shower bench, the normalized form can be shower bench.
sectionSurfaceFormMedical documents have many sections such as patient’s information, previous medical history, family history, etc. The covered text that identifies which section of the document that spans the annotation. The default value of this feature is document.
sectionNormalizedNameThe normalized term for the section.
modifiersModifiers represents text that describes the disease or symptom in more detail or provides additional context.

Modifers

FeatureDescription
typeaci.SiteInd - Identifies the related body site or location.
typeaci.ModifierGroupInd - General modifiers that further describe the symptom or disease such as severe, low, high, or mild.
beginThe start position of the annotation as a character offset into the text. The smallest possible start position is 0.
endThe end position of the annotation as character offset into the text. The end position points at the first character after the annotation, such that end-begin equals the length of the coveredText.
coveredTextThe text covered by an annotation as a string.
typeaci.Measurement - Identifies the cancer grade which can help determine the rate of tumor growth.
gradeValueThe value of the grade.
siteNormalizedNameThe normalized name for the site from UMLS.
compoundWhether this a multi-site term.
FeatureDescription
typeaci.ModifierGroupInd - General modifiers that further describe the symptom or disease such as severe, low, high, or mild.
typeaci.ModifierGroupInd - General modifiers that further describe the symptom or disease such as severe, low, high, or mild.
beginThe start position of the annotation as a character offset into the text. The smallest possible start position is 0.
endThe end position of the annotation as character offset into the text. The end position points at the first character after the annotation, such that end-begin equals the length of the coveredText.
coveredTextThe text covered by an annotation as a string.

Sample Response

Sample response from the symptom disease annotator for the text: He has severe cramping and pain in his left leg due to diabetic neuropathy.

{
"unstructured": [
{
"text": "He has severe cramping and pain in his left leg due to diabetic neuropathy.",
"data": {
"SymptomDiseaseInd": [
{
"type": "aci.SymptomDiseaseInd",
"begin": 7,