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<br>*Authors: Christian Reich, Patrick Ryan, Rimma Belenkaya, Karthik Natarajan, Clair Blacketer* <br>*Authors: Christian Reich, Patrick Ryan, Rimma Belenkaya, Karthik Natarajan, Clair Blacketer*
<br>***Release date needed*** <br>***Release date needed***
[Back to Table of Contents](Documentation/TableofContents.md) [Back to Table of Contents](https://github.com/OHDSI/CommonDataModel/blob/master/Documentation/TableofContents.md)
<br>[Back to Background](Background.md) <br>[Back to Background](Background.md)
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Notation|Description Notation|Description
--------|----------- --------|-----------
|<entity>_SOURCE_VALUE|Verbatim information from the source data, typically used in ETL to map to CONCEPT_ID, and not to be used by any standard analytics. For example, condition_source_value = 787.02 was the ICD-9 code captured as a diagnosis from the administrative claim| |<entity>_SOURCE_VALUE|Verbatim information from the source data, typically used in ETL to map to CONCEPT_ID, and not to be used by any standard analytics. For example, condition_source_value = 787.02 was the ICD-9 code captured as a diagnosis from the administrative claim|
|<entity>_ID|Unique identifiers for key entities, which can serve as foreign keys to establish relationships across entities For example, person_id uniquely identifies each individual. visit_occurrence_id uniquely identifies a PERSON encounter at a point of care.| |<entity>_ID|Unique identifiers for key entities, which can serve as foreign keys to establish relationships across entities For example, person_id uniquely identifies each individual. visit_occurrence_id uniquely identifies a PERSON encounter at a point of care.|
|<entity>_CONCEPT_ID|Foreign key into the Standardized Vocabularies (i.e. the standard_concept attribute for the corresponding term is true), which serves as the primary basis for all standardized analytics For example, condition_concept_id = 31967 contains reference value for SNOMED concept of Nausea| |<entity>_CONCEPT_ID|Foreign key into the Standardized Vocabularies (i.e. the standard_concept attribute for the corresponding term is true), which serves as the primary basis for all standardized analytics For example, condition_concept_id = 31967 contains reference value for SNOMED concept of Nausea|
|<entity>_SOURCE_CONCEPT_ID|Foreign key into the Standardized Vocabularies representing the concept and terminology used in the source data, when applicable For example, condition_source_concept_id = 35708202 denotes the concept of Nausea in the MedDRA terminology; the analogous condition_concept_id might be 31967, since SNOMED-CT is the Standardized Vocabularies for most clinical diagnoses and findings.| |<entity>_SOURCE_CONCEPT_ID|Foreign key into the Standardized Vocabularies representing the concept and terminology used in the source data, when applicable For example, condition_source_concept_id = 35708202 denotes the concept of Nausea in the MedDRA terminology; the analogous condition_concept_id might be 31967, since SNOMED-CT is the Standardized Vocabularies for most clinical diagnoses and findings.|
|<entity>_TYPE_CONCEPT_ID|Delineates the origin of the source information, standardized within the Standardized Vocabularies For example, drug_type_concept_id can allow analysts to discriminate between Pharmacy dispensing and Prescription written| |<entity>_TYPE_CONCEPT_ID|Delineates the origin of the source information, standardized within the Standardized Vocabularies For example, drug_type_concept_id can allow analysts to discriminate between Pharmacy dispensing and Prescription written|
## Representation of content through Concepts ## Representation of content through Concepts
@ -78,13 +78,13 @@ When processing your data where source value is a reference to a coding scheme c
- If the source code uses alternative formatting (ex. format has removed decimal point from ICD-9 codes), you will need to perform the formatting transformation within the ETL. In this case, you may wish to store the mappings from original codes to source concept ids in the SOURCE_TO_CONCEPT_MAP table. - If the source code uses alternative formatting (ex. format has removed decimal point from ICD-9 codes), you will need to perform the formatting transformation within the ETL. In this case, you may wish to store the mappings from original codes to source concept ids in the SOURCE_TO_CONCEPT_MAP table.
- If the source code is not mappable to a vocabulary term, the source_concept_id field is set to 0 - If the source code is not mappable to a vocabulary term, the source_concept_id field is set to 0
- Use the CONCEPT_RELATIONSHIP table to identify the standard concept_id that corresponds to the source_concept_id in the domain. - Use the CONCEPT_RELATIONSHIP table to identify the standard concept_id that corresponds to the source_concept_id in the domain.
- Each source_concept_id can have 1 or more Standard concept_id mapped to it. Each Standard concept_id belongs to only one primary domain, but when a source concept_id maps to multiple standard concept_ids, it is possible for that source_concept_id to result in records being produced across multiple domains. For example, HCPCS code for infusion of a drug will map to a concept in the procedure domain of the infusion and a different concept in the drug domain for the product infused. It is also possible for one source_concept_id to map to multiple standard concept_ids within the same domain. For example, ICD-9 for viral hepatitis with hepatic coma maps to SNOMED viral hepatitis and a different concept for hepatic coma in which case multiple condition_occurrence records will be generated for the one source value record. - Each source_concept_id can have 1 or more Standard concept_id mapped to it. Each Standard concept_id belongs to only one primary domain, but when a source concept_id maps to multiple standard concept_ids, it is possible for that source_concept_id to result in records being produced across multiple domains. For example, HCPCS code for infusion of a drug will map to a concept in the procedure domain of the infusion and a different concept in the drug domain for the product infused. It is also possible for one source_concept_id to map to multiple standard concept_ids within the same domain. For example, ICD-9 for viral hepatitis with hepatic coma maps to SNOMED viral hepatitis and a different concept for hepatic coma in which case multiple condition_occurrence records will be generated for the one source value record.
- If the source_concept_id is not mappable to any standard concept_id, the concept_id field is set to 0. - If the source_concept_id is not mappable to any standard concept_id, the concept_id field is set to 0.
- Write the data record into table(s) corresponding to the domain of the standard concept_id(s). - Write the data record into table(s) corresponding to the domain of the standard concept_id(s).
- If the source value is mapped to source_concept_id, but the source_concept_id is not mapped to a standard concept_id, then the domain for the data record, and hence it's table location, is determined by the domain_id field of the CONCEPT record the source_concept_id refers to. The standard concept_id is set to 0. - If the source value is mapped to source_concept_id, but the source_concept_id is not mapped to a standard concept_id, then the domain for the data record, and hence it's table location, is determined by the domain_id field of the CONCEPT record the source_concept_id refers to. The standard concept_id is set to 0.
- If the source value cannot be mapped to a source_concept_id or standard concept_id, then direct the data record to the most appropriate CDM domain based on your local knowledge of the intent of the source data and associated value. For example, if the unmappable source_value came from a diagnosis table, then in the absence of other information, you may choose to record that fact in the CONDITION_OCCURRENCE table. - If the source value cannot be mapped to a source_concept_id or standard concept_id, then direct the data record to the most appropriate CDM domain based on your local knowledge of the intent of the source data and associated value. For example, if the unmappable source_value came from a diagnosis table, then in the absence of other information, you may choose to record that fact in the CONDITION_OCCURRENCE table.
Each standard concept_id field has a set of allowable concept_id values. The allowable values are defined by the domain of the concepts. For example, there is a domain concept of Gender, for which there are only two allowable standard concepts of practical use (8507- Male, 8532- Female) and one allowable generic concept to represent a standard notion of no information (concept_id = 0). Each standard concept_id field has a set of allowable concept_id values. The allowable values are defined by the domain of the concepts. For example, there is a domain concept of Gender, for which there are only two allowable standard concepts of practical use (8507- Male, 8532- Female) and one allowable generic concept to represent a standard notion of no information (concept_id = 0).
There is no constraint on allowed concept_ids within the source_concept_id fields. There is no constraint on allowed concept_ids within the source_concept_id fields.