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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.). | 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 [[http://ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary:introduction|Specifications]]. | + | 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 [[documentation:vocabulary|Specifications]]. |
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* 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. | * 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. | * 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 table. | + | * A descriptive name for each Concept is stored as the Concept name as part of the [[documentation:cdm:concept|CONCEPT]] table. Additional names and descriptions for the Concept are stored as Synonyms in the [[documentation:cdm:concept_synonym|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. | * 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. | ||
* 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. | * 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 <domain>_concept_id fields, whereas Class concepts ('C') should not appear in the CDM data, but participate in the CONCEPT_ANCESTOR and can be used to identify descendants that may very well appear in the data. See [[documentation:cdm:cdm:concept_ancestor]CONCEPT_ANCESTOR table]. Non-standard concepts can only appear in source_concept_id fields and are not used in CONCEPT_ANCESTOR. | + | * Standard Concepts (designated as 'S' in the standard_concept field) may appear in CDM tables in all <domain>_concept_id fields, whereas Class concepts ('C') should not appear in the CDM data, but participate in the construction of the [[documentation:cdm:concept_ancestor|CONCEPT_ANCESTOR]] table and can be used to identify Descendants that may very well appear in the data. See [[documentation:cdm:cdm:concept_ancestor|CONCEPT_ANCESTOR]] table. Non-standard concepts can only appear in source_concept_id fields and are not used in CONCEPT_ANCESTOR table. |
- | * 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. | + | * 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 [[documentation:cdm:concept|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 deprecatd if their meaning was deamed ambigous, a duplication of another Conncept, 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 . | * 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 deprecatd if their meaning was deamed ambigous, a duplication of another Conncept, 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 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’. | + | * 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 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 [[documentation:cdm:concept_ancestor|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. | * 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. | ||
- | ~~DISQUS~~ |