Alchemist / Critical Care

Documentation on the data exchange format for HIC Critical Care and the Alchemist ingestion pipeline.

Concept Class

The CONCEPT_CLASS table is a reference table, which includes a list of the classifications used to differentiate Concepts within a given Vocabulary. This reference table is populated with a single record for each Concept Class:

Field Required Type FK Table Description
concept_class_id Yes varchar(20)   A unique key for each class.
concept_class_name Yes varchar(255)   The name describing the Concept Class, e.g. “Clinical Finding”, “Ingredient”, etc.
concept_class_concept_id Yes bigint CONCEPT A foreign key that refers to an identifier in the CONCEPT table for the unique Concept Class the record belongs to.

Conventions

  • There is one record for each Concept Class. Concept Classes are used to create additional structure to the Concepts within each Vocabulary. Some Concept Classes are unique to a Vocabulary (for example “Clinical Finding” in SNOMED), but others can be used across different Vocabularies. The separation of Concepts through Concept Classes can be semantically horizontal (each Class subsumes Concepts of the same hierarchical level, akin to sub-Vocabularies within a Vocabulary) or vertical (each Class subsumes Concepts of a certain kind, going across hierarchical levels). For example, Concept Classes in SNOMED are vertical: The classes “Procedure” and “Clinical Finding” define very granular to very generic Concepts. On the other hand, “Clinical Drug” and “Ingredient” Concept Classes define horizontal layers or strata in the RxNorm vocabulary, which all belong to the same concept of a Drug.
  • The concept_class_id field contains an alphanumerical identifier, that can also be used as the abbreviation of the Concept Class.
  • The concept_class_name field contains the unabbreviated names of the Concept Class.
  • Each Concept Class also has an entry in the Concept table, which is recorded in the concept_class_concept_id field. This is for purposes of creating a closed Information Model, where all entities in the OMOP CDM are covered by unique Concepts.
  • Past versions of the OMOP CDM did not have a separate reference table for all Concept Classes. Also, the content of the old concept_class and the new concept_class_id fields are not always identical. A conversion table can be found here:

    Previous CONCEPT_CLASS Version 5 CONCEPT_CLASS_ID
    Administrative concept Admin Concept
    Admitting Source Admitting Source
    Anatomical Therapeutic Chemical Classification ATC
    Anatomical Therapeutic Chemical Classification ATC
    APC Procedure
    Attribute Attribute
    Biobank Flag Biobank Flag
    Biological function Biological Function
    Body structure Body Structure
    Brand Name Brand Name
    Branded Drug Branded Drug
    Branded Drug Component Branded Drug Comp
    Branded Drug Form Branded Drug Form
    Branded Pack Branded Pack
    CCS_DIAGNOSIS Condition
    CCS_PROCEDURES Procedure
    Chart Availability Chart Availability
    Chemical Structure Chemical Structure
    Clinical Drug Clinical Drug
    Clinical Drug Component Clinical Drug Comp
    Clinical Drug Form Clinical Drug Form
    Clinical finding Clinical Finding
    Clinical Pack Clinical Pack
    Concept Relationship Concept Relationship
    Condition Occurrence Type Condition Occur Type
    Context-dependent category Context-dependent
    CPT-4 Procedure
    Currency Currency
    Death Type Death Type
    Device Type Device Type
    Discharge Disposition Discharge Dispo
    Discharge Status Discharge Status
    Domain Domain
    Dose Form Dose Form
    DRG Diagnostic Category
    Drug Exposure Type Drug Exposure Type
    Drug Interaction Drug Interaction
    Encounter Type Encounter Type
    Enhanced Therapeutic Classification ETC
    Enrollment Basis Enrollment Basis
    Environment or geographical location Location
    Ethnicity Ethnicity
    Event Event
    Gender Gender
    HCPCS Procedure
    Health Care Provider Specialty Provider Specialty
    HES specialty Provider Specialty
    High Level Group Term HLGT
    High Level Term HLT
    Hispanic Hispanic
    ICD-9-Procedure Procedure
    Indication or Contra-indication Ind / CI
    Ingredient Ingredient
    LOINC Code Measurement
    LOINC Multidimensional Classification Meas Class
    Lowest Level Term LLT
    MDC Diagnostic Category
    Measurement Type Meas Type
    Mechanism of Action Mechanism of Action
    Model component Model Comp
    Morphologic abnormality Morph Abnormality
    MS-DRG Diagnostic Category
    Namespace concept Namespace Concept
    Note Type Note Type
    Observable entity Observable Entity
    Observation Period Type Obs Period Type
    Observation Type Observation Type
    OMOP DOI cohort Drug Cohort
    OMOP HOI cohort Condition Cohort
    OPCS-4 Procedure
    Organism Organism
    Patient Status Patient Status
    Pharmaceutical / biologic product Pharma/Biol Product
    Pharmaceutical Preparations Pharma Preparation
    Pharmacokinetics PK
    Pharmacologic Class Pharmacologic Class
    Physical force Physical Force
    Physical object Physical Object
    Physiologic Effect Physiologic Effect
    Place of Service Place of Service
    Preferred Term PT
    Procedure Procedure
    Procedure Occurrence Type Procedure Occur Type
    Qualifier value Qualifier Value
    Race Race
    Record artifact Record Artifact
    Revenue Code Revenue Code
    Sex Gender
    Social context Social Context
    Special concept Special Concept
    Specimen Specimen
    Staging and scales Staging / Scales
    Standardized MedDRA Query SMQ
    Substance Substance
    System Organ Class SOC
    Therapeutic Class Therapeutic Class
    UCUM Unit
    UCUM Canonical Canonical Unit
    UCUM Custom Unit
    UCUM Standard Unit
    Undefined Undefined
    UNKNOWN Undefined
    VA Class Drug Class
    VA Drug Interaction Drug Interaction
    VA Product Drug Product
    Visit Visit
    Visit Type Visit Type