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closes themis #158

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Clair Blacketer 2024-04-29 15:31:25 -04:00
parent 4f96366924
commit 91414a60c1
2 changed files with 2 additions and 2 deletions
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2
inst/csv/OMOP_CDMv5.3_Field_Level.csv
View File

@ -134,7 +134,7 @@ device_exposure,device_exposure_end_date,No,date,"The DEVICE_EXPOSURE_END_DATE d
device_exposure,device_exposure_end_datetime,No,datetime,NA,If a source does not specify datetime the convention is to set the time to midnight (00:00:0000),No,No,NA,NA,NA,NA,NA device_exposure,device_exposure_end_datetime,No,datetime,NA,If a source does not specify datetime the convention is to set the time to midnight (00:00:0000),No,No,NA,NA,NA,NA,NA
device_exposure,device_type_concept_id,Yes,integer,"You can use the TYPE_CONCEPT_ID to denote the provenance of the record, as in whether the record is from administrative claims or EHR.","Choose the drug_type_concept_id that best represents the provenance of the record, for example whether it came from a record of a prescription written or physician administered drug. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=). A more detailed explanation of each Type Concept can be found on the [vocabulary wiki](https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT).",No,Yes,CONCEPT,CONCEPT_ID,Type Concept,NA,NA device_exposure,device_type_concept_id,Yes,integer,"You can use the TYPE_CONCEPT_ID to denote the provenance of the record, as in whether the record is from administrative claims or EHR.","Choose the drug_type_concept_id that best represents the provenance of the record, for example whether it came from a record of a prescription written or physician administered drug. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=). A more detailed explanation of each Type Concept can be found on the [vocabulary wiki](https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT).",No,Yes,CONCEPT,CONCEPT_ID,Type Concept,NA,NA
device_exposure,unique_device_id,No,varchar(50),"This is the Unique Device Identification number for devices regulated by the FDA, if given.","For medical devices that are regulated by the FDA, a Unique Device Identification (UDI) is provided if available in the data source and is recorded in the UNIQUE_DEVICE_ID field.",No,No,NA,NA,NA,NA,NA device_exposure,unique_device_id,No,varchar(50),"This is the Unique Device Identification number for devices regulated by the FDA, if given.","For medical devices that are regulated by the FDA, a Unique Device Identification (UDI) is provided if available in the data source and is recorded in the UNIQUE_DEVICE_ID field.",No,No,NA,NA,NA,NA,NA
device_exposure,quantity,No,integer,NA,NA,No,No,NA,NA,NA,NA,NA device_exposure,quantity,No,integer,NA,"If there is a record of device exposure in the source but no quantity value, then set to 1.",No,No,NA,NA,NA,NA,NA
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 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
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 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
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 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

1 cdmTableName cdmFieldName isRequired cdmDatatype userGuidance etlConventions isPrimaryKey isForeignKey fkTableName fkFieldName fkDomain fkClass unique DQ identifiers
134 measurement measurement_time No varchar(10) NA This is present for backwards compatibility and will be deprecated in an upcoming version. No No NA NA NA NA NA
135 measurement measurement_type_concept_id Yes integer This field can be used to determine the provenance of the Measurement record, as in whether the measurement was from an EHR system, insurance claim, registry, or other sources. Choose the MEASUREMENT_TYPE_CONCEPT_ID that best represents the provenance of the record, for example whether it came from an EHR record or billing claim. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=). A more detailed explanation of each Type Concept can be found on the [vocabulary wiki](https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT). No Yes CONCEPT CONCEPT_ID Type Concept NA NA
136 measurement operator_concept_id No integer The meaning of Concept [4172703](https://athena.ohdsi.org/search-terms/terms/4172703) for '=' is identical to omission of a OPERATOR_CONCEPT_ID value. Since the use of this field is rare, it's important when devising analyses to not to forget testing for the content of this field for values different from =. Operators are <, <=, =, >=, > and these concepts belong to the 'Meas Value Operator' domain. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Meas+Value+Operator&standardConcept=Standard&page=1&pageSize=15&query=). Leave it NULL if there's an exact numeric value given (instead of putting '=') or there's no numeric value at all. No Yes CONCEPT CONCEPT_ID NA NA NA
137 measurement value_as_number No float This is the numerical value of the Result of the Measurement, if available. Note that measurements such as blood pressures will be split into their component parts i.e. one record for systolic, one record for diastolic. [Convention for negative values](https://ohdsi.github.io/Themis/negative_value_as_number.html) No No NA NA NA NA NA
138 measurement value_as_concept_id No integer If the raw data gives a categorial result for measurements those values are captured and mapped to standard concepts in the 'Meas Value' domain. If there is no categorial result in the source data, set VALUE_AS_CONCEPT_ID to NULL, if there is a categorial result in a source data but without mapping, set VALUE_AS_CONCEPT_ID to 0, else map to a CONCEPT_ID. No Yes CONCEPT CONCEPT_ID NA NA NA
139 measurement unit_concept_id No integer At present, there isn't a prescribed unit for individual measurements, such as Hemoglobin A1C, meaning it's not obligatory to express these measurements as a percentage. UNIT_SOURCE_VALUES should be linked to a Standard Concept within the Unit domain that most accurately reflects the unit provided in the source data. If the source data does not include units, set UNIT_CONCEPT_ID to NULL. If units are provided but not mapped, set UNIT_CONCEPT_ID to 0. Otherwise, map the units to a CONCEPT_ID. Remember that units are case-sensitive in vocabulary. No Yes CONCEPT CONCEPT_ID Unit NA NA
140 measurement range_low No float Ranges have the same unit as the VALUE_AS_NUMBER. These ranges are provided by the source and should remain NULL if not given. If reference ranges for upper and lower limit of normal as provided (typically by a laboratory) these are stored in the RANGE_HIGH and RANGE_LOW fields. This should be set to NULL if not provided. No No NA NA NA NA NA

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

@ -137,7 +137,7 @@ device_exposure,device_exposure_end_datetime,No,datetime,NA,If a source does not
device_exposure,device_type_concept_id,Yes,integer,"You can use the TYPE_CONCEPT_ID to denote the provenance of the record, as in whether the record is from administrative claims or EHR.","Choose the drug_type_concept_id that best represents the provenance of the record, for example whether it came from a record of a prescription written or physician administered drug. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=). A more detailed explanation of each Type Concept can be found on the [vocabulary wiki](https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT).",No,Yes,CONCEPT,CONCEPT_ID,Type Concept,NA,NA device_exposure,device_type_concept_id,Yes,integer,"You can use the TYPE_CONCEPT_ID to denote the provenance of the record, as in whether the record is from administrative claims or EHR.","Choose the drug_type_concept_id that best represents the provenance of the record, for example whether it came from a record of a prescription written or physician administered drug. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=). A more detailed explanation of each Type Concept can be found on the [vocabulary wiki](https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT).",No,Yes,CONCEPT,CONCEPT_ID,Type Concept,NA,NA
device_exposure,unique_device_id,No,varchar(255),"This is the Unique Device Identification (UDI-DI) number for devices regulated by the FDA, if given.","For medical devices that are regulated by the FDA, a Unique Device Identification (UDI) is provided if available in the data source and is recorded in the UNIQUE_DEVICE_ID field.",No,No,NA,NA,NA,NA,NA device_exposure,unique_device_id,No,varchar(255),"This is the Unique Device Identification (UDI-DI) number for devices regulated by the FDA, if given.","For medical devices that are regulated by the FDA, a Unique Device Identification (UDI) is provided if available in the data source and is recorded in the UNIQUE_DEVICE_ID field.",No,No,NA,NA,NA,NA,NA
device_exposure,production_id,No,varchar(255),This is the Production Identifier (UDI-PI) portion of the Unique Device Identification.,NA,No,No,NA,NA,NA,NA,NA device_exposure,production_id,No,varchar(255),This is the Production Identifier (UDI-PI) portion of the Unique Device Identification.,NA,No,No,NA,NA,NA,NA,NA
device_exposure,quantity,No,integer,NA,NA,No,No,NA,NA,NA,NA,NA device_exposure,quantity,No,integer,NA,"If there is a record of device exposure in the source but no quantity value, then set to 1.",No,No,NA,NA,NA,NA,NA
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 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
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 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
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 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

1 cdmTableName cdmFieldName isRequired cdmDatatype userGuidance etlConventions isPrimaryKey isForeignKey fkTableName fkFieldName fkDomain fkClass unique DQ identifiers
137 measurement measurement_concept_id Yes integer The MEASUREMENT_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 value which represents a measurement. The CONCEPT_ID that the MEASUREMENT_SOURCE_VALUE maps to. Only records whose source values map to concepts with a domain of Measurement should go in this table. No Yes CONCEPT CONCEPT_ID Measurement NA NA
138 measurement measurement_date Yes date Use this date to determine the date of the measurement. If there are multiple dates in the source data associated with a record such as order_date, draw_date, and result_date, choose the one that is closest to the date the sample was drawn from the patient. No No NA NA NA NA NA
139 measurement measurement_datetime No datetime NA This is not required, though it is in v6. If a source does not specify datetime the convention is to set the time to midnight (00:00:0000) No No NA NA NA NA NA
140 measurement measurement_time No varchar(10) NA This is present for backwards compatibility and will be deprecated in an upcoming version. No No NA NA NA NA NA
141 measurement measurement_type_concept_id Yes integer This field can be used to determine the provenance of the Measurement record, as in whether the measurement was from an EHR system, insurance claim, registry, or other sources. Choose the MEASUREMENT_TYPE_CONCEPT_ID that best represents the provenance of the record, for example whether it came from an EHR record or billing claim. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=). A more detailed explanation of each Type Concept can be found on the [vocabulary wiki](https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT). No Yes CONCEPT CONCEPT_ID Type Concept NA NA
142 measurement operator_concept_id No integer The meaning of Concept [4172703](https://athena.ohdsi.org/search-terms/terms/4172703) for '=' is identical to omission of a OPERATOR_CONCEPT_ID value. Since the use of this field is rare, it's important when devising analyses to not to forget testing for the content of this field for values different from =. Operators are <, <=, =, >=, > and these concepts belong to the 'Meas Value Operator' domain. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Meas+Value+Operator&standardConcept=Standard&page=1&pageSize=15&query=). Leave it NULL if there's an exact numeric value given (instead of putting '=') or there's no numeric value at all. No Yes CONCEPT CONCEPT_ID NA NA NA
143 measurement value_as_number No float This is the numerical value of the Result of the Measurement, if available. Note that measurements such as blood pressures will be split into their component parts i.e. one record for systolic, one record for diastolic. [Convention for negative values](https://ohdsi.github.io/Themis/negative_value_as_number.html) No No NA NA NA NA NA