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Updated CONCEPT (markdown)

clairblacketer 2017-06-19 20:13:20 -04:00
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StandardizedVocabularies/CONCEPT.md

@ -9,8 +9,8 @@ Field|Required|Type|Description
:-----|:--------|:----|:-----------
|concept_id|Yes|integer|A unique identifier for each Concept across all domains.|
|concept_name|Yes|varchar(255)|An unambiguous, meaningful and descriptive name for the Concept.|
|domain_id|Yes|varchar(20)|A foreign key to the [DOMAIN](wiki/DOMAIN) table the Concept belongs to.|
|vocabulary_id|Yes|varchar(20)|A foreign key to the [VOCABULARY](wiki/VOCABULARY] table indicating from which source the Concept has been adapted.|
|domain_id|Yes|varchar(20)|A foreign key to the [DOMAIN](https://github.com/OHDSI/CommonDataModel/wiki/DOMAIN) table the Concept belongs to.|
|vocabulary_id|Yes|varchar(20)|A foreign key to the [VOCABULARY](https://github.com/OHDSI/CommonDataModel/wiki/VOCABULARY) table indicating from which source the Concept has been adapted.|
|concept_class_id|Yes|varchar(20)|The attribute or concept class of the Concept. Examples are “Clinical Drug”, “Ingredient”, “Clinical Finding” etc.|
|standard_concept|No|varchar(1)|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.|
|concept_code|Yes|varchar(50)|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.|
@ -23,16 +23,16 @@ Concepts in the Common Data Model are derived from a number of public or proprie
* All Concepts are maintained centrally by the CDM and Vocabularies Working Group. Additional concepts can be added, as needed, upon request.
* 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.
* 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](wiki/CONCEPT_SYNONYM) table.
* 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](https://github.com/OHDSI/CommonDataModel/wiki/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](http://www.ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary) 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.
* 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.
* 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.
* 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](wiki/CONCEPT_ANCESTOR) table and can be used to identify Descendants that may appear in the data. See [CONCEPT_ANCESTOR](wiki/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](http://www.ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary:standard_classification_and_source_concepts) for details of the Standard Concept designation.
* 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](https://github.com/OHDSI/CommonDataModel/wiki/CONCEPT_ANCESTOR) table and can be used to identify Descendants that may appear in the data. See [CONCEPT_ANCESTOR](https://github.com/OHDSI/CommonDataModel/wiki/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](http://www.ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary:standard_classification_and_source_concepts) for details of the Standard Concept designation.
* All logical data elements associated with the various CDM tables (usually in the <domain>_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 .
* Concepts without a known instantiated date are assigned valid_start_date of ‘1-Jan-1970’.
* Concepts that are not invalid are assigned valid_end_date of ‘31-Dec-2099’.
* 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](wiki/CONCEPT_RELATIONSHIP) table indicating their active replacement Concept.
* 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](https://github.com/OHDSI/CommonDataModel/wiki/CONCEPT_RELATIONSHIP) table indicating their active replacement Concept.
* 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.