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Closes #587

This commit is contained in:
Clair Blacketer 2024-03-28 13:16:30 -04:00
parent 03ce1d5260
commit 6333928fe0
2 changed files with 10 additions and 10 deletions
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8
inst/csv/OMOP_CDMv5.3_Field_Level.csv
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@ -361,10 +361,10 @@ cdm_source,cdm_source_abbreviation,No,varchar(25),The abbreviation of the CDM in
cdm_source,cdm_holder,No,varchar(255),The holder of the CDM instance.,NA,No,No,NA,NA,NA,NA,NA
cdm_source,source_description,No,varchar(MAX),The description of the CDM instance.,NA,No,No,NA,NA,NA,NA,NA
cdm_source,source_documentation_reference,No,varchar(255),NA,NA,No,No,NA,NA,NA,NA,NA
cdm_source,cdm_etl_reference,No,varchar(255),NA,Put the link to the CDM version used.,No,No,NA,NA,NA,NA,NA
cdm_source,source_release_date,No,date,The release date of the source data.,NA,No,No,NA,NA,NA,NA,NA
cdm_source,cdm_release_date,No,date,The release data of the CDM instance.,NA,No,No,NA,NA,NA,NA,NA
cdm_source,cdm_version,No,varchar(10),NA,NA,No,No,NA,NA,NA,NA,NA
cdm_source,cdm_etl_reference,No,varchar(255),NA,Version of the ETL script used. e.g. link to the Git release,No,No,NA,NA,NA,NA,NA
cdm_source,source_release_date,No,date,The date the data was extracted from the source system. In some systems that is the same as the date the ETL was run. Typically the latest even date in the source is on the source_release_date.,NA,No,No,NA,NA,NA,NA,NA
cdm_source,cdm_release_date,No,date,The date the ETL script was completed. Typically this is after the source_release_date.,NA,No,No,NA,NA,NA,NA,NA
cdm_source,cdm_version,No,varchar(10),Version of the OMOP CDM used as string. e.g. v5.4,NA,No,No,NA,NA,NA,NA,NA
cdm_source,vocabulary_version,No,varchar(20),NA,NA,No,No,NA,NA,NA,NA,NA
concept,concept_id,Yes,integer,A unique identifier for each Concept across all domains.,NA,Yes,No,NA,NA,NA,NA,NA
concept,concept_name,Yes,varchar(255),"An unambiguous, meaningful and descriptive name for the Concept.",NA,No,No,NA,NA,NA,NA,NA

1 cdmTableName cdmFieldName isRequired cdmDatatype userGuidance etlConventions isPrimaryKey isForeignKey fkTableName fkFieldName fkDomain fkClass unique DQ identifiers
361 concept_ancestor ancestor_concept_id Yes integer The Concept Id for the higher-level concept that forms the ancestor in the relationship. NA No Yes CONCEPT CONCEPT_ID NA NA NA
362 concept_ancestor descendant_concept_id Yes integer The Concept Id for the lower-level concept that forms the descendant in the relationship. NA No Yes CONCEPT CONCEPT_ID NA NA NA
363 concept_ancestor min_levels_of_separation Yes integer The minimum separation in number of levels of hierarchy between ancestor and descendant concepts. This is an attribute that is used to simplify hierarchic analysis. NA No No NA NA NA NA NA
364 concept_ancestor max_levels_of_separation Yes integer The maximum separation in number of levels of hierarchy between ancestor and descendant concepts. This is an attribute that is used to simplify hierarchic analysis. NA No No NA NA NA NA NA
365 source_to_concept_map source_code Yes varchar(50) The source code being translated into a Standard Concept. NA No No NA NA NA NA NA
366 source_to_concept_map source_concept_id Yes integer A foreign key to the Source Concept that is being translated into a Standard Concept. This is either 0 or should be a number above 2 billion, which are the Concepts reserved for site-specific codes and mappings. No Yes CONCEPT CONCEPT_ID NA NA NA
367 source_to_concept_map source_vocabulary_id Yes varchar(20) A foreign key to the VOCABULARY table defining the vocabulary of the source code that is being translated to a Standard Concept. NA No No NA NA NA NA NA
368 source_to_concept_map source_code_description No varchar(255) An optional description for the source code. This is included as a convenience to compare the description of the source code to the name of the concept. NA No No NA NA NA NA NA
369 source_to_concept_map target_concept_id Yes integer The target Concept to which the source code is being mapped. NA No Yes CONCEPT CONCEPT_ID NA NA NA
370 source_to_concept_map target_vocabulary_id Yes varchar(20) The Vocabulary of the target Concept. NA No Yes VOCABULARY VOCABULARY_ID NA NA NA

12
inst/csv/OMOP_CDMv5.4_Field_Level.csv
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@ -397,12 +397,12 @@ cdm_source,cdm_source_abbreviation,Yes,varchar(25),The abbreviation of the CDM i
cdm_source,cdm_holder,Yes,varchar(255),The holder of the CDM instance.,NA,No,No,NA,NA,NA,NA,NA
cdm_source,source_description,No,varchar(MAX),The description of the CDM instance.,NA,No,No,NA,NA,NA,NA,NA
cdm_source,source_documentation_reference,No,varchar(255),NA,NA,No,No,NA,NA,NA,NA,NA
cdm_source,cdm_etl_reference,No,varchar(255),NA,Put the link to the CDM version used.,No,No,NA,NA,NA,NA,NA
cdm_source,source_release_date,Yes,date,The release date of the source data.,NA,No,No,NA,NA,NA,NA,NA
cdm_source,cdm_release_date,Yes,date,The release data of the CDM instance.,NA,No,No,NA,NA,NA,NA,NA
cdm_source,cdm_version,No,varchar(10),NA,NA,No,No,NA,NA,NA,NA,NA
cdm_source,cdm_version_concept_id,Yes,integer,The Concept Id representing the version of the CDM.,You can find all concepts that represent the CDM versions using the query: SELECT * FROM CONCEPT WHERE VOCABULARY_ID = 'CDM' AND CONCEPT_CLASS = 'CDM',No,Yes,CONCEPT,CONCEPT_ID,NA,NA,NA
cdm_source,vocabulary_version,Yes,varchar(20),NA,You can find the version of your Vocabulary using the query: SELECT vocabulary_version from vocabulary where vocabulary_id = 'None',No,No,NA,NA,NA,NA,NA
cdm_source,cdm_etl_reference,No,varchar(255),NA,Version of the ETL script used. e.g. link to the Git release,No,No,NA,NA,NA,NA,NA
cdm_source,source_release_date,Yes,date,The date the data was extracted from the source system. In some systems that is the same as the date the ETL was run. Typically the latest even date in the source is on the source_release_date.,NA,No,No,NA,NA,NA,NA,NA
cdm_source,cdm_release_date,Yes,date,The date the ETL script was completed. Typically this is after the source_release_date.,NA,No,No,NA,NA,NA,NA,NA
cdm_source,cdm_version,No,varchar(10),Version of the OMOP CDM used as string. e.g. v5.4,NA,No,No,NA,NA,NA,NA,NA
cdm_source,cdm_version_concept_id,Yes,integer,The Concept Id representing the version of the CDM.,You can find all concepts that represent the CDM versions using the query: `SELECT * FROM CONCEPT WHERE VOCABULARY_ID = 'CDM' AND CONCEPT_CLASS = 'CDM'`,No,Yes,CONCEPT,CONCEPT_ID,NA,NA,NA
cdm_source,vocabulary_version,Yes,varchar(20),Version of the OMOP standardised vocabularies loaded,You can find the version of your Vocabulary using the query: `SELECT vocabulary_version from vocabulary where vocabulary_id = 'None'`,No,No,NA,NA,NA,NA,NA
concept,concept_id,Yes,integer,A unique identifier for each Concept across all domains.,NA,Yes,No,NA,NA,NA,NA,NA
concept,concept_name,Yes,varchar(255),"An unambiguous, meaningful and descriptive name for the Concept.",NA,No,No,NA,NA,NA,NA,NA
concept,domain_id,Yes,varchar(20),A foreign key to the [DOMAIN](https://ohdsi.github.io/CommonDataModel/cdm531.html#domain) table the Concept belongs to.,NA,No,Yes,DOMAIN,DOMAIN_ID,NA,NA,NA

1 cdmTableName cdmFieldName isRequired cdmDatatype userGuidance etlConventions isPrimaryKey isForeignKey fkTableName fkFieldName fkDomain fkClass unique DQ identifiers
397 concept_synonym language_concept_id Yes integer NA NA No Yes CONCEPT CONCEPT_ID NA NA NA
398 concept_ancestor ancestor_concept_id Yes integer The Concept Id for the higher-level concept that forms the ancestor in the relationship. NA No Yes CONCEPT CONCEPT_ID NA NA NA
399 concept_ancestor descendant_concept_id Yes integer The Concept Id for the lower-level concept that forms the descendant in the relationship. NA No Yes CONCEPT CONCEPT_ID NA NA NA
400 concept_ancestor min_levels_of_separation Yes integer The minimum separation in number of levels of hierarchy between ancestor and descendant concepts. This is an attribute that is used to simplify hierarchic analysis. NA No No NA NA NA NA NA
401 concept_ancestor max_levels_of_separation Yes integer The maximum separation in number of levels of hierarchy between ancestor and descendant concepts. This is an attribute that is used to simplify hierarchic analysis. NA No No NA NA NA NA NA
402 source_to_concept_map source_code Yes varchar(50) The source code being translated into a Standard Concept. NA No No NA NA NA NA NA
403 source_to_concept_map source_concept_id Yes integer A foreign key to the Source Concept that is being translated into a Standard Concept. This is either 0 or should be a number above 2 billion, which are the Concepts reserved for site-specific codes and mappings. No Yes CONCEPT CONCEPT_ID NA NA NA
404 source_to_concept_map source_vocabulary_id Yes varchar(20) A foreign key to the VOCABULARY table defining the vocabulary of the source code that is being translated to a Standard Concept. NA No No NA NA NA NA NA
405 source_to_concept_map source_code_description No varchar(255) An optional description for the source code. This is included as a convenience to compare the description of the source code to the name of the concept. NA No No NA NA NA NA NA
406 source_to_concept_map target_concept_id Yes integer The target Concept to which the source code is being mapped. NA No Yes CONCEPT CONCEPT_ID NA NA NA
407 source_to_concept_map target_vocabulary_id Yes varchar(20) The Vocabulary of the target Concept. NA No Yes VOCABULARY VOCABULARY_ID NA NA NA
408 source_to_concept_map valid_start_date Yes date The date when the mapping instance was first recorded. NA No No NA NA NA NA NA