ID

35278

Description

OMOP Common Data Model (CDM) Concept The Standardized Vocabularies contains records, or Concepts, that uniquely identify each fundamental unit of meaning used to express clinical information in all domain tables of the CDM. Concepts are derived from vocabularies, which represent clinical information across a domain (e.g. conditions, drugs, procedures) through the use of codes and associated descriptions. Some Concepts are designated Standard Concepts, meaning these Concepts can be used as normative expressions of a clinical entity within the OMOP Common Data Model and within standardized analytics. Each Standard Concept belongs to one domain, which defines the location where the Concept would be expected to occur within data tables of the CDM. Concepts can represent broad categories (like 'Cardiovascular disease'), detailed clinical elements ('Myocardial infarction of the anterolateral wall') or modifying characteristics and attributes that define Concepts at various levels of detail (severity of a disease, associated morphology, etc.). Records in the Standardized Vocabularies tables are derived from national or international vocabularies such as SNOMED-CT, RxNorm, and LOINC, or custom Concepts defined to cover various aspects of observational data analysis. For a detailed description of these vocabularies, their use in the OMOP CDM and their relationships to each other please refer to the specifications. OMOP Common Data Model Specifications Version 6.0 Specifications 11October2018 The Observational Medical Outcomes Partnership (OMOP) was a public-private partnership established to inform the appropriate use of observational healthcare databases for studying the effects of medical products. © 2014 Observational Health Data Sciences and Informatics This work is based on work by the Observational Medical Outcomes Partnership (OMOP) and used under license from the FNIH at http://omop.fnih.org/publiclicense. Version updated on 26.02.2019, from https://github.com/OHDSI/CommonDataModel/wiki/CONCEPT All Concepts are maintained centrally by the CDM and Vocabularies Working Group. Additional concepts can be added, as needed, upon request. A descriptive name for each Concept is stored as the Concept Name as part of the CONCEPT table. Additional names and descriptions for the Concept are stored as Synonyms in the CONCEPT_SYNONYM table. Each Concept is assigned to a Domain. For Standard Concepts, these is always a single Domain. Source Concepts can be composite or coordinated entities, and therefore can belong to more than one Domain. The domain_id field of the record contains the abbreviation of the Domain, or Domain combination. Please refer to the Standardized Vocabularies specification for details of the Domain Assignment. For details of the Vocabularies adopted for use in the OMOP CDM refer to the Standardized Vocabularies specification. Concept Class designation are attributes of Concepts. Each Vocabulary has its own set of permissible Concept Classes, although the same Concept Class can be used by more than one Vocabulary. Depending on the Vocabulary, the Concept Class may categorize Concepts vertically (parallel) or horizontally (hierarchically). See the specification of each vocabulary for details. All logical data elements associated with the various CDM tables (usually in the _type_concept_id field) are called Type Concepts, including defining characteristics, qualifying attributes etc. They are also stored as Concepts in the CONCEPT table. Since they are generated by OMOP, their is no meaningful concept_code. The lifespan of a Concept is recorded through its valid_start_date, valid_end_date and the invalid_reason fields. This allows Concepts to correctly reflect at which point in time were defined. Usually, Concepts get deprecated if their meaning was deemed ambiguous, a duplication of another Concept, or needed revision for scientific reason. For example, drug ingredients get updated when different salt or isomer variants enter the market. Usually, drugs taken off the market do not cause a deprecation by the terminology vendor. Since observational data are valid with respect to the time they are recorded, it is key for the Standardized Vocabularies to provide even obsolete codes and maintain their relationships to other current Concepts.

Link

http://omop.fnih.org/publiclicense

Keywords

Versions (3)
  1. 1/4/17 1/4/17 -
  2. 2/18/19 2/18/19 -
  3. 2/26/19 2/26/19 -
Copyright Holder

Observational Medical Outcomes Partnership (OMOP)

Uploaded on

February 26, 2019

DOI

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License

Creative Commons BY-NC 3.0
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OMOP Common Data Model (CDM) Concept

English

OMOP Common Data Model (CDM) Concept

1 forms  
Concept
Description

Concept

Alias
UMLS CUI-1
C0178566
UMLS CUI-2
C2708733
UMLS CUI-3
C1955348
concept ID
Description

A unique identifier for each concept across all domains. For all Concepts, whether they are custom generated or adopted from published terminologies, a unique numeric identifier concept_id is assigned and used as the key to link all observational data to the corresponding Concept reference data. The concept_id of a Concept is persistent, i.e. stays the same for the same Concept between releases of the Standardized Vocabularies. Values for CONCEPT_IDs generated as part of Standardized Vocabularies will be reserved from 0 to 2,000,000,000. Above this range, CONCEPT_IDs are available for local use and are guaranteed not to clash with future releases of the Standardized Vocabularies.

Data type

integer

Alias
UMLS CUI [1,1]
C0178566
UMLS CUI [1,2]
C1300638
concept name
Description

An unambiguous, meaningful and descriptive name for the concept. (Type varchar(255))

Data type

text

Alias
UMLS CUI [1,1]
C0178566
UMLS CUI [1,2]
C0027365
Domain ID
Description

A foreign key to the DOMAIN table the Concept belongs to. (Type varchar(20))

Data type

text

Alias
UMLS CUI [1,1]
C1883204
UMLS CUI [1,2]
C1300638
Vocabulary ID
Description

A foreign key to the vocabulary table indicating from which source the concept has been adapted. (Type varchar(20))

Data type

text

Alias
UMLS CUI [1,1]
C0042926
UMLS CUI [1,2]
C1300638
Concept class ID
Description

The attribute or concept class of the Concept. Examples are 'Clinical Drug', 'Ingredient', 'Clinical Finding' etc. Concept Class attributes should not be confused with Classification Concepts. These are separate Concepts that have a hierarchical relationship to Standard Concepts or each other, while Concept Classes are unique Vocabulary-specific attributes for each Concept. Standard Concepts (designated as 'S' in the standard_concept field) may appear in CDM tables in all *_concept_id fields, whereas Classification Concepts ('C') should not appear in the CDM data, but participate in the construction of the CONCEPT_ANCESTOR table and can be used to identify Descendants that may appear in the data. See CONCEPT_ANCESTOR table. Non-standard Concepts can only appear in *_source_concept_id fields and are not used in CONCEPT_ANCESTOR table. Please refer to the Standardized Vocabularies specifications for details of the Standard Concept designation. (Type varchar(20))

Data type

text

Alias
UMLS CUI [1,1]
C0178566
UMLS CUI [1,2]
C0456387
UMLS CUI [1,3]
C1300638
Standard concept
Description

This flag determines where a Concept is a Standard Concept, i.e. is used in the data, a Classification Concept, or a non-standard Source Concept. The allowables values are 'S' (Standard Concept) and 'C' (Classification Concept), otherwise the content is NULL. (Type varchar(1))

Data type

text

Alias
UMLS CUI [1,1]
C0034925
UMLS CUI [1,2]
C0178566
Concept code
Description

The concept code represents the identifier of the Concept in the source vocabulary, such as SNOMED-CT concept IDs, RxNorm RXCUIs etc. Note that concept codes are not unique across vocabularies. For Concepts inherited from published terminologies, the source code is retained in the concept_code field and can be used to reference the source vocabulary. (Type varchar(50))

Data type

text

Alias
UMLS CUI [1,1]
C0178566
UMLS CUI [1,2]
C0805701
valid start date
Description

The date when the Concept was first recorded. The default value is 1-Jan-1970, meaning, the Concept has no (known) date of inception. Concepts without a known instantiated date are assigned valid_start_date of '1-Jan-1970'.

Data type

date

Alias
UMLS CUI [1,1]
C0178566
UMLS CUI [1,2]
C2349101
UMLS CUI [1,3]
C0808070
valid end date
Description

The date when the Concept became invalid because it was deleted or superseded (updated) by a new concept. The default value is 31-Dec-2099, meaning, the Concept is valid until it becomes deprecated. Concepts that are not invalid are assigned valid_end_date of '31-Dec-2099'.

Data type

date

Alias
UMLS CUI [1,1]
C0178566
UMLS CUI [1,2]
C2349101
UMLS CUI [1,3]
C0806020
invalid reason
Description

Reason the Concept was invalidated. Possible values are D (deleted), U (replaced with an update) or NULL when valid_end_date has the default value. Deprecated Concepts (with a valid_end_date before the release date of the Standardized Vocabularies) will have a value of 'D' (deprecated without successor) or 'U' (updated). The updated Concepts have a record in the CONCEPT_RELATIONSHIP table indicating their active replacement Concept. (Type varchar(1))

Data type

text

Alias
UMLS CUI [1,1]
C0178566
UMLS CUI [1,2]
C3245471
UMLS CUI [1,3]
C0566251
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Similar models

OMOP Common Data Model (CDM) Concept

1 forms
Name
Type
Description | Question | Decode (Coded Value)
Data type
Alias
Item Group
Concept
C0178566 (UMLS CUI-1)
C2708733 (UMLS CUI-2)
C1955348 (UMLS CUI-3)
concept ID
Item
concept ID
integer
C0178566 (UMLS CUI [1,1])
C1300638 (UMLS CUI [1,2])
concept name
Item
concept name
text
C0178566 (UMLS CUI [1,1])
C0027365 (UMLS CUI [1,2])
Domain ID
Item
Domain ID
text
C1883204 (UMLS CUI [1,1])
C1300638 (UMLS CUI [1,2])
Vocabulary ID
Item
Vocabulary ID
text
C0042926 (UMLS CUI [1,1])
C1300638 (UMLS CUI [1,2])
Concept class ID
Item
Concept class ID
text
C0178566 (UMLS CUI [1,1])
C0456387 (UMLS CUI [1,2])
C1300638 (UMLS CUI [1,3])
Standard concept
Item
Standard concept
text
C0034925 (UMLS CUI [1,1])
C0178566 (UMLS CUI [1,2])
Concept code
Item
Concept code
text
C0178566 (UMLS CUI [1,1])
C0805701 (UMLS CUI [1,2])
valid start date
Item
valid start date
date
C0178566 (UMLS CUI [1,1])
C2349101 (UMLS CUI [1,2])
C0808070 (UMLS CUI [1,3])
valid end date
Item
valid end date
date
C0178566 (UMLS CUI [1,1])
C2349101 (UMLS CUI [1,2])
C0806020 (UMLS CUI [1,3])
invalid reason
Item
invalid reason
text
C0178566 (UMLS CUI [1,1])
C3245471 (UMLS CUI [1,2])
C0566251 (UMLS CUI [1,3])
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