documentation:cdm:source_to_concept_map
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documentation:cdm:source_to_concept_map [2014/12/29 05:20] cgreich |
documentation:cdm:source_to_concept_map [2017/09/25 14:59] (current) clairblacketer |
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| ===== SOURCE_TO_CONCEPT_MAP table ===== | ===== SOURCE_TO_CONCEPT_MAP table ===== | ||
| + | **THIS IS OUTDATED. All documentation is now on the [[https://github.com/OHDSI/CommonDataModel/wiki|github wiki]]. Please refer there or to the [[projects:workgroups:cdm-wg|CDM working group]] for more information** | ||
| 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 database doesn't follow the correct formatting, the ETL will have to perform this translation. For example, if an ICD-9-CM code in a database is recorded without a dot the ETL will have to perform a lookup function that allows identifying the correct ICD-9-CM Source Concept. | + | * **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.1419830434.txt.gz ยท Last modified: 2014/12/29 05:20 by cgreich
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