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documentation:cdm:source_to_concept_map [2014/12/29 05:17]
cgreich
documentation:cdm:source_to_concept_map [2017/08/17 15:20]
clairblacketer
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 ===== SOURCE_TO_CONCEPT_MAP table ===== ===== SOURCE_TO_CONCEPT_MAP table =====
 +**The CDM documentation is now being housed on [[https://​github.com/​OHDSI/​CommonDataModel/​wiki|github]]. The most recent release is [[https://​github.com/​OHDSI/​CommonDataModel/​releases/​tag/​v5.2.-bugfix.1|v5.2]]**
  
 The source to concept map table is a legacy data structure within the OMOP Common Data Model, recommended for use in ETL processes to maintain local source codes which are not available as Concepts in the Standardized Vocabularies,​ and to establish mappings for each source code into a Standard Concept as target_concept_ids that can be used to populate the Common Data Model tables. The SOURCE_TO_CONCEPT_MAP table is no longer populated with content within the Standardized Vocabularies published to the OMOP community. ​ The source to concept map table is a legacy data structure within the OMOP Common Data Model, recommended for use in ETL processes to maintain local source codes which are not available as Concepts in the Standardized Vocabularies,​ and to establish mappings for each source code into a Standard Concept as target_concept_ids that can be used to populate the Common Data Model tables. The SOURCE_TO_CONCEPT_MAP table is no longer populated with content within the Standardized Vocabularies published to the OMOP community. ​
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   * This table is no longer used to distribute mapping information between source codes and Standard Concepts for the Standard Vocabularies. Instead, the CONCEPT_RELATIONSHIP table is used for this purpose, using the relationship_id='​Maps to'.   * This table is no longer used to distribute mapping information between source codes and Standard Concepts for the Standard Vocabularies. Instead, the CONCEPT_RELATIONSHIP table is used for this purpose, using the relationship_id='​Maps to'.
   * However, this table can still be used for the translation of local source codes into Standard Concepts.   * However, this table can still be used for the translation of local source codes into Standard Concepts.
 +  * **Note: **This table should not be used to translate source codes to Source Concepts. The source code of a Source Concept is captured in its concept_code field. If the source codes used in a given database do not follow correct formatting the ETL will have to perform this translation. For example, if ICD-9-CM codes are recorded without a dot the ETL will have to perform a lookup function that allows identifying the correct ICD-9-CM Source Concept (with the dot in the concept_code field).
   * The source_concept_id,​ or the combination of the fields source_code and the source_vocabulary_id uniquely identifies the source information. It is the equivalent to the concept_id_1 field in the CONCEPT_RELATIONSHIP table.   * The source_concept_id,​ or the combination of the fields source_code and the source_vocabulary_id uniquely identifies the source information. It is the equivalent to the concept_id_1 field in the CONCEPT_RELATIONSHIP table.
   * If there is no source_concept_id available because the source codes are local and not supported by the Standard Vocabulary, the content of the field is 0 (zero, not null) encoding an undefined concept. However, local Source Concepts are established (concept_id values above 2,​000,​000,​000).   * If there is no source_concept_id available because the source codes are local and not supported by the Standard Vocabulary, the content of the field is 0 (zero, not null) encoding an undefined concept. However, local Source Concepts are established (concept_id values above 2,​000,​000,​000).
documentation/cdm/source_to_concept_map.txt ยท Last modified: 2017/09/25 14:59 by clairblacketer