Alchemist / Critical Care

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

Vocabulary

The VOCABULARY table includes a list of the Vocabularies collected from various sources or created de novo by the OMOP community. This reference table is populated with a single record for each Vocabulary source and includes a descriptive name and other associated attributes for the Vocabulary.

Field Required Type FK Table Description
vocabulary_id Yes varchar(20)   A unique identifier for each Vocabulary, such as “ICD9CM”, “SNOMED”, “Visit”.
vocabulary_name Yes varchar(255)   The name describing the vocabulary, for example “International Classification of Diseases, Ninth Revision, Clinical Modification, Volume 1 and 2 (NCHS)”, etc.
vocabulary_reference Yes varchar(255)   External reference to documentation or available download about the vocabulary.
vocabulary_version No varchar(255)   Version of the Vocabulary as indicated in the source.
vocabulary_concept_id Yes bigint CONCEPT A foreign key that refers to a standard concept identifier in the CONCEPT table for the Vocabulary the record belongs to.

Conventions

  • There is one record for each Vocabulary. One Vocabulary source or vendor can issue several Vocabularies, each of them creating their own record in the VOCABULARY table. However, the choice of whether a Vocabulary contains Concepts of different Concept Classes, or when these different classes constitute separate Vocabularies cannot precisely be decided based on the definition of what constitutes a Vocabulary. For example, the ICD-9 Volume 1 and 2 codes (ICD9CM, containing predominantly conditions and some procedures and observations) and the ICD-9 Volume 3 codes (ICD9Proc, containing predominantly procedures) are realized as two different Vocabularies. On the other hand, SNOMED-CT codes of the class Condition and those of the class Procedure are part of one and the same Vocabulary. Please refer to the Standardized Vocabularies specifications for details of each Vocabulary.

  • The vocabulary_id field contains an alphanumerical identifier, that can also be used as the abbreviation of the Vocabulary name.
  • The record with vocabulary_id = 'None' is reserved to contain information regarding the current version of the Entire Standardized Vocabularies.
  • The vocabulary_name field contains the full official name of the Vocabulary, as well as the source or vendor in parenthesis.
  • Each Vocabulary has an entry in the CONCEPT table, which is recorded in the vocabulary_concept_id field. This is for purposes of creating a closed Information Model, where all entities in the OMOP CDM are covered by a unique Concept.

  • In past versions of the VOCABULARY table, the vocabulary_id used to be a numerical value. A conversion table between these old and new IDs is given below:

    Previous VOCABULARY_ID Version 5 VOCABULARY_ID
    0 None
    1 SNOMED
    2 ICD9CM
    3 ICD9Proc
    4 CPT4
    5 HCPCS
    6 LOINC
    7 NDFRT
    8 RxNorm
    9 NDC
    10 GPI
    11 UCUM
    12 Gender
    13 Race
    14 Place of Service
    15 MedDRA
    16 Multum
    17 Read
    18 OXMIS
    19 Indication
    20 ETC
    21 ATC
    22 Multilex
    24 Visit
    28 VA Product
    31 SMQ
    32 VA Class
    33 Cohort
    34 ICD10
    35 ICD10PCS
    36 Drug Type
    37 Condition Type
    38 Procedure Type
    39 Observation Type
    40 DRG
    41 MDC
    42 APC
    43 Revenue Code
    44 Ethnicity
    45 Death Type
    46 Mesh
    47 NUCC
    48 Specialty
    49 LOINC
    50 SPL
    53 Genseqno
    54 CCS
    55 OPCS4
    56 Gemscript
    57 HES Specialty
    58 Note Type
    59 Domain
    60 PCORNet
    61 Obs Period Type
    62 Visit Type
    63 Device Type
    64 Meas Type
    65 Currency
    66 Relationship
    67 Vocabulary
    68 Concept Class
    69 Cohort Type
    70 ICD10CM