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modifier_source_value 

closes #655
This commit is contained in:
Clair Blacketer 2024-04-17 20:54:23 -04:00
parent f114b8d5fd
commit 802d9ee2a3
2 changed files with 2 additions and 2 deletions
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2
inst/csv/OMOP_CDMv5.3_Field_Level.csv
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@ -124,7 +124,7 @@ procedure_occurrence,visit_occurrence_id,No,integer,The visit during which the p
procedure_occurrence,visit_detail_id,No,integer,"The VISIT_DETAIL record during which the Procedure occurred. For example, if the Person was in the ICU at the time of the Procedure the VISIT_OCCURRENCE record would reflect the overall hospital stay and the VISIT_DETAIL record would reflect the ICU stay during the hospital visit.",Same rules apply as for the VISIT_OCCURRENCE_ID.,No,No,VISIT_DETAIL,VISIT_DETAIL_ID,NA,NA,NA procedure_occurrence,visit_detail_id,No,integer,"The VISIT_DETAIL record during which the Procedure occurred. For example, if the Person was in the ICU at the time of the Procedure the VISIT_OCCURRENCE record would reflect the overall hospital stay and the VISIT_DETAIL record would reflect the ICU stay during the hospital visit.",Same rules apply as for the VISIT_OCCURRENCE_ID.,No,No,VISIT_DETAIL,VISIT_DETAIL_ID,NA,NA,NA
procedure_occurrence,procedure_source_value,No,varchar(50),"This field houses the verbatim value from the source data representing the procedure that occurred. For example, this could be an CPT4 or OPCS4 code.",Use this value to look up the source concept id and then map the source concept id to a standard concept id.,No,No,NA,NA,NA,NA,NA procedure_occurrence,procedure_source_value,No,varchar(50),"This field houses the verbatim value from the source data representing the procedure that occurred. For example, this could be an CPT4 or OPCS4 code.",Use this value to look up the source concept id and then map the source concept id to a standard concept id.,No,No,NA,NA,NA,NA,NA
procedure_occurrence,procedure_source_concept_id,No,integer,"This is the concept representing the procedure source value and may not necessarily be standard. This field is discouraged from use in analysis because it is not required to contain Standard Concepts that are used across the OHDSI community, and should only be used when Standard Concepts do not adequately represent the source detail for the Procedure necessary for a given analytic use case. Consider using PROCEDURE_CONCEPT_ID instead to enable standardized analytics that can be consistent across the network.",If the PROCEDURE_SOURCE_VALUE is coded in the source data using an OMOP supported vocabulary put the concept id representing the source value here.,No,No,CONCEPT,CONCEPT_ID,NA,NA,NA procedure_occurrence,procedure_source_concept_id,No,integer,"This is the concept representing the procedure source value and may not necessarily be standard. This field is discouraged from use in analysis because it is not required to contain Standard Concepts that are used across the OHDSI community, and should only be used when Standard Concepts do not adequately represent the source detail for the Procedure necessary for a given analytic use case. Consider using PROCEDURE_CONCEPT_ID instead to enable standardized analytics that can be consistent across the network.",If the PROCEDURE_SOURCE_VALUE is coded in the source data using an OMOP supported vocabulary put the concept id representing the source value here.,No,No,CONCEPT,CONCEPT_ID,NA,NA,NA
procedure_occurrence,modifier_source_value,No,varchar(50),NA,The original modifier code from the source is stored here for reference.,No,No,NA,NA,NA,NA,NA procedure_occurrence,modifier_source_value,No,varchar(50),This field houses the verbatim value from the source data representing the modifier code for the procedure that occurred.,The value stored here is mapped to a MODIFIER_CONCEPT_ID.,No,No,NA,NA,NA,NA,NA
device_exposure,device_exposure_id,Yes,integer,The unique key given to records a person's exposure to a foreign physical object or instrument.,Each instance of an exposure to a foreign object or device present in the source data should be assigned this unique key.,Yes,No,NA,NA,NA,NA,NA device_exposure,device_exposure_id,Yes,integer,The unique key given to records a person's exposure to a foreign physical object or instrument.,Each instance of an exposure to a foreign object or device present in the source data should be assigned this unique key.,Yes,No,NA,NA,NA,NA,NA
device_exposure,person_id,Yes,integer,NA,NA,No,Yes,PERSON,PERSON_ID,NA,NA,NA device_exposure,person_id,Yes,integer,NA,NA,No,Yes,PERSON,PERSON_ID,NA,NA,NA
device_exposure,device_concept_id,Yes,integer,"The DEVICE_CONCEPT_ID field is recommended for primary use in analyses, and must be used for network studies. This is the standard concept mapped from the source concept id which represents a foreign object or instrument the person was exposed to.",The CONCEPT_ID that the DEVICE_SOURCE_VALUE maps to.,No,Yes,CONCEPT,CONCEPT_ID,Device,NA,NA device_exposure,device_concept_id,Yes,integer,"The DEVICE_CONCEPT_ID field is recommended for primary use in analyses, and must be used for network studies. This is the standard concept mapped from the source concept id which represents a foreign object or instrument the person was exposed to.",The CONCEPT_ID that the DEVICE_SOURCE_VALUE maps to.,No,Yes,CONCEPT,CONCEPT_ID,Device,NA,NA

1 cdmTableName cdmFieldName isRequired cdmDatatype userGuidance etlConventions isPrimaryKey isForeignKey fkTableName fkFieldName fkDomain fkClass unique DQ identifiers
124 device_exposure provider_id No integer The Provider associated with device record, e.g. the provider who wrote the prescription or the provider who implanted the device. The ETL may need to make a choice as to which PROVIDER_ID to put here. Based on what is available this may or may not be different than the provider associated with the overall VISIT_OCCURRENCE record. No Yes PROVIDER PROVIDER_ID NA NA NA
125 device_exposure visit_occurrence_id No integer The Visit during which the device was prescribed or given. To populate this field device exposures must be explicitly initiated in the visit. No Yes VISIT_OCCURRENCE VISIT_OCCURRENCE_ID NA NA NA
126 device_exposure visit_detail_id No integer The Visit Detail during which the device was prescribed or given. To populate this field device exposures must be explicitly initiated in the visit detail record. No Yes VISIT_DETAIL VISIT_DETAIL_ID NA NA NA
127 device_exposure device_source_value No varchar(50) This field houses the verbatim value from the source data representing the device exposure that occurred. For example, this could be an NDC or Gemscript code. This code is mapped to a Standard Device Concept in the Standardized Vocabularies and the original code is stored here for reference. No No NA NA NA NA NA
128 device_exposure device_source_concept_id No integer This is the concept representing the device source value and may not necessarily be standard. This field is discouraged from use in analysis because it is not required to contain Standard Concepts that are used across the OHDSI community, and should only be used when Standard Concepts do not adequately represent the source detail for the Device necessary for a given analytic use case. Consider using DEVICE_CONCEPT_ID instead to enable standardized analytics that can be consistent across the network. If the DEVICE_SOURCE_VALUE is coded in the source data using an OMOP supported vocabulary put the concept id representing the source value here. No Yes CONCEPT CONCEPT_ID NA NA NA
129 measurement measurement_id Yes integer The unique key given to a Measurement record for a Person. Refer to the ETL for how duplicate Measurements during the same Visit were handled. Each instance of a measurement present in the source data should be assigned this unique key. In some cases, a person can have multiple records of the same measurement within the same visit. It is valid to keep these duplicates and assign them individual, unique, MEASUREMENT_IDs, though it is up to the ETL how they should be handled. Yes No NA NA NA NA NA
130 measurement person_id Yes integer The PERSON_ID of the Person for whom the Measurement is recorded. This may be a system generated code. NA No Yes PERSON PERSON_ID NA NA NA

2
inst/csv/OMOP_CDMv5.4_Field_Level.csv
View File

@ -126,7 +126,7 @@ procedure_occurrence,visit_occurrence_id,No,integer,The visit during which the p
procedure_occurrence,visit_detail_id,No,integer,"The VISIT_DETAIL record during which the Procedure occurred. For example, if the Person was in the ICU at the time of the Procedure the VISIT_OCCURRENCE record would reflect the overall hospital stay and the VISIT_DETAIL record would reflect the ICU stay during the hospital visit.",Same rules apply as for the VISIT_OCCURRENCE_ID.,No,Yes,VISIT_DETAIL,VISIT_DETAIL_ID,NA,NA,NA procedure_occurrence,visit_detail_id,No,integer,"The VISIT_DETAIL record during which the Procedure occurred. For example, if the Person was in the ICU at the time of the Procedure the VISIT_OCCURRENCE record would reflect the overall hospital stay and the VISIT_DETAIL record would reflect the ICU stay during the hospital visit.",Same rules apply as for the VISIT_OCCURRENCE_ID.,No,Yes,VISIT_DETAIL,VISIT_DETAIL_ID,NA,NA,NA
procedure_occurrence,procedure_source_value,No,varchar(50),"This field houses the verbatim value from the source data representing the procedure that occurred. For example, this could be an CPT4 or OPCS4 code.",Use this value to look up the source concept id and then map the source concept id to a standard concept id.,No,No,NA,NA,NA,NA,NA procedure_occurrence,procedure_source_value,No,varchar(50),"This field houses the verbatim value from the source data representing the procedure that occurred. For example, this could be an CPT4 or OPCS4 code.",Use this value to look up the source concept id and then map the source concept id to a standard concept id.,No,No,NA,NA,NA,NA,NA
procedure_occurrence,procedure_source_concept_id,No,integer,"This is the concept representing the procedure source value and may not necessarily be standard. This field is discouraged from use in analysis because it is not required to contain Standard Concepts that are used across the OHDSI community, and should only be used when Standard Concepts do not adequately represent the source detail for the Procedure necessary for a given analytic use case. Consider using PROCEDURE_CONCEPT_ID instead to enable standardized analytics that can be consistent across the network.",If the PROCEDURE_SOURCE_VALUE is coded in the source data using an OMOP supported vocabulary put the concept id representing the source value here.,No,Yes,CONCEPT,CONCEPT_ID,NA,NA,NA procedure_occurrence,procedure_source_concept_id,No,integer,"This is the concept representing the procedure source value and may not necessarily be standard. This field is discouraged from use in analysis because it is not required to contain Standard Concepts that are used across the OHDSI community, and should only be used when Standard Concepts do not adequately represent the source detail for the Procedure necessary for a given analytic use case. Consider using PROCEDURE_CONCEPT_ID instead to enable standardized analytics that can be consistent across the network.",If the PROCEDURE_SOURCE_VALUE is coded in the source data using an OMOP supported vocabulary put the concept id representing the source value here.,No,Yes,CONCEPT,CONCEPT_ID,NA,NA,NA
procedure_occurrence,modifier_source_value,No,varchar(50),NA,The original modifier code from the source is stored here for reference.,No,No,NA,NA,NA,NA,NA procedure_occurrence,modifier_source_value,No,varchar(50),This field houses the verbatim value from the source data representing the modifier code for the procedure that occurred.,The value stored here is mapped to a MODIFIER_CONCEPT_ID.,No,No,NA,NA,NA,NA,NA
device_exposure,device_exposure_id,Yes,integer,The unique key given to records a person's exposure to a foreign physical object or instrument.,Each instance of an exposure to a foreign object or device present in the source data should be assigned this unique key.,Yes,No,NA,NA,NA,NA,NA device_exposure,device_exposure_id,Yes,integer,The unique key given to records a person's exposure to a foreign physical object or instrument.,Each instance of an exposure to a foreign object or device present in the source data should be assigned this unique key.,Yes,No,NA,NA,NA,NA,NA
device_exposure,person_id,Yes,integer,NA,NA,No,Yes,PERSON,PERSON_ID,NA,NA,NA device_exposure,person_id,Yes,integer,NA,NA,No,Yes,PERSON,PERSON_ID,NA,NA,NA
device_exposure,device_concept_id,Yes,integer,"The DEVICE_CONCEPT_ID field is recommended for primary use in analyses, and must be used for network studies. This is the standard concept mapped from the source concept id which represents a foreign object or instrument the person was exposed to.",The CONCEPT_ID that the DEVICE_SOURCE_VALUE maps to.,No,Yes,CONCEPT,CONCEPT_ID,Device,NA,NA device_exposure,device_concept_id,Yes,integer,"The DEVICE_CONCEPT_ID field is recommended for primary use in analyses, and must be used for network studies. This is the standard concept mapped from the source concept id which represents a foreign object or instrument the person was exposed to.",The CONCEPT_ID that the DEVICE_SOURCE_VALUE maps to.,No,Yes,CONCEPT,CONCEPT_ID,Device,NA,NA

1 cdmTableName cdmFieldName isRequired cdmDatatype userGuidance etlConventions isPrimaryKey isForeignKey fkTableName fkFieldName fkDomain fkClass unique DQ identifiers
126 device_exposure quantity No integer NA NA No No NA NA NA NA NA
127 device_exposure provider_id No integer The Provider associated with device record, e.g. the provider who wrote the prescription or the provider who implanted the device. The ETL may need to make a choice as to which PROVIDER_ID to put here. Based on what is available this may or may not be different than the provider associated with the overall VISIT_OCCURRENCE record. No Yes PROVIDER PROVIDER_ID NA NA NA
128 device_exposure visit_occurrence_id No integer The Visit during which the device was prescribed or given. To populate this field device exposures must be explicitly initiated in the visit. No Yes VISIT_OCCURRENCE VISIT_OCCURRENCE_ID NA NA NA
129 device_exposure visit_detail_id No integer The Visit Detail during which the device was prescribed or given. To populate this field device exposures must be explicitly initiated in the visit detail record. No Yes VISIT_DETAIL VISIT_DETAIL_ID NA NA NA
130 device_exposure device_source_value No varchar(50) This field houses the verbatim value from the source data representing the device exposure that occurred. For example, this could be an NDC or Gemscript code. This code is mapped to a Standard Device Concept in the Standardized Vocabularies and the original code is stored here for reference. No No NA NA NA NA NA
131 device_exposure device_source_concept_id No integer This is the concept representing the device source value and may not necessarily be standard. This field is discouraged from use in analysis because it is not required to contain Standard Concepts that are used across the OHDSI community, and should only be used when Standard Concepts do not adequately represent the source detail for the Device necessary for a given analytic use case. Consider using DEVICE_CONCEPT_ID instead to enable standardized analytics that can be consistent across the network. If the DEVICE_SOURCE_VALUE is coded in the source data using an OMOP supported vocabulary put the concept id representing the source value here. No Yes CONCEPT CONCEPT_ID NA NA NA
132 device_exposure unit_concept_id No integer UNIT_SOURCE_VALUES should be mapped to a Standard Concept in the Unit domain that best represents the unit as given in the source data. There is no standardization requirement for units associated with DEVICE_CONCEPT_IDs, however, it is the responsibility of the ETL to choose the most plausible unit. If the source unit is NULL (applicable to cases when there's no numerical value or when it doesn't require a unit), keep unit_concept_id NULL as well. If there's no mapping of a source unit, populate unit_concept_id with 0. No Yes CONCEPT CONCEPT_ID Unit NA NA