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OMOP
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closes #672

This commit is contained in:
Clair Blacketer 2024-04-29 09:24:35 -04:00
parent 6eaeab4e6a
commit 6d80bb3f55
2 changed files with 2 additions and 2 deletions
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2
inst/csv/OMOP_CDMv5.3_Field_Level.csv
View File

@ -289,7 +289,7 @@ payer_plan_period,sponsor_concept_id,No,integer,"This field represents the spons
payer_plan_period,sponsor_source_value,No,varchar(50),The Plan sponsor as it appears in the source data.,NA,No,No,NA,NA,NA,NA,NA
payer_plan_period,sponsor_source_concept_id,No,integer,NA,If the source data codes the sponsor in an OMOP supported vocabulary store the concept_id here.,No,Yes,CONCEPT,CONCEPT_ID,NA,NA,NA
payer_plan_period,family_source_value,No,varchar(50),The common identifier for all people (often a family) that covered by the same policy.,Often these are the common digits of the enrollment id of the policy members.,No,No,NA,NA,NA,NA,NA
payer_plan_period,stop_reason_concept_id,No,integer,"This field represents the reason the Person left the Plan, if known.",Map the stop reason directly to a standard CONCEPT_ID. If one does not exists please contact the vocabulary team. There is no global controlled vocabulary available for this information. [Accepted Concepts](http://athena.ohdsi.org/search-terms/terms?domain=Plan+Stop+Reason&standardConcept=Standard&page=1&pageSize=15&query=).,No,Yes,CONCEPT,CONCEPT_ID,NA,NA,NA
payer_plan_period,stop_reason_concept_id,No,integer,"This field represents the reason the Person left the Plan, if known.",Map the stop reason directly to a standard CONCEPT_ID with a domain of 'Plan Stop Reason' ([Accepted Concepts](http://athena.ohdsi.org/search-terms/terms?domain=Plan+Stop+Reason&standardConcept=Standard&page=1&pageSize=15&query=)). If one does not exist visit the [Custom Concepts](https://ohdsi.github.io/CommonDataModel/customConcepts.html) pate for more information.,No,Yes,CONCEPT,CONCEPT_ID,NA,NA,NA
payer_plan_period,stop_reason_source_value,No,varchar(50),The Plan stop reason as it appears in the source data.,NA,No,No,NA,NA,NA,NA,NA
payer_plan_period,stop_reason_source_concept_id,No,integer,NA,If the source data codes the stop reason in an OMOP supported vocabulary store the concept_id here.,No,Yes,CONCEPT,CONCEPT_ID,NA,NA,NA
cost,cost_id,Yes,integer,NA,NA,Yes,No,NA,NA,NA,NA,NA

1 cdmTableName cdmFieldName isRequired cdmDatatype userGuidance etlConventions isPrimaryKey isForeignKey fkTableName fkFieldName fkDomain fkClass unique DQ identifiers
289 drug_era person_id Yes integer NA NA No Yes PERSON PERSON_ID NA NA NA
290 drug_era drug_concept_id Yes integer The drug_concept_id should conform to the concept class 'ingredient' as the drug_era is an era of time where a person is exposed to a particular drug ingredient. NA No Yes CONCEPT CONCEPT_ID Drug Ingredient NA
291 drug_era drug_era_start_date Yes date NA The Drug Era Start Date is the start date of the first Drug Exposure for a given ingredient, with at least 31 days since the previous exposure. No No NA NA NA NA NA
292 drug_era drug_era_end_date Yes date NA The Drug Era End Date is the end date of the last Drug Exposure. The End Date of each Drug Exposure is either taken from the field drug_exposure_end_date or, as it is typically not available, inferred using the following rules: For pharmacy prescription data, the date when the drug was dispensed plus the number of days of supply are used to extrapolate the End Date for the Drug Exposure. Depending on the country-specific healthcare system, this supply information is either explicitly provided in the day_supply field or inferred from package size or similar information. For Procedure Drugs, usually the drug is administered on a single date (i.e., the administration date). A standard Persistence Window of 30 days (gap, slack) is permitted between two subsequent such extrapolated DRUG_EXPOSURE records to be considered to be merged into a single Drug Era. No No NA NA NA NA NA
293 drug_era drug_exposure_count No integer The count of grouped DRUG_EXPOSURE records that were included in the DRUG_ERA row NA No No NA NA NA NA NA
294 drug_era gap_days No integer NA The Gap Days determine how many total drug-free days are observed between all Drug Exposure events that contribute to a DRUG_ERA record. It is assumed that the drugs are "not stockpiled" by the patient, i.e. that if a new drug prescription or refill is observed (a new DRUG_EXPOSURE record is written), the remaining supply from the previous events is abandoned. The difference between Persistence Window and Gap Days is that the former is the maximum drug-free time allowed between two subsequent DRUG_EXPOSURE records, while the latter is the sum of actual drug-free days for the given Drug Era under the above assumption of non-stockpiling. No No NA NA NA NA NA
295 dose_era dose_era_id Yes integer NA NA Yes No NA NA NA NA NA

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

@ -307,7 +307,7 @@ payer_plan_period,sponsor_concept_id,No,integer,"This field represents the spons
payer_plan_period,sponsor_source_value,No,varchar(50),The Plan sponsor as it appears in the source data.,NA,No,No,NA,NA,NA,NA,NA
payer_plan_period,sponsor_source_concept_id,No,integer,NA,If the source data codes the sponsor in an OMOP supported vocabulary store the concept_id here.,No,Yes,CONCEPT,CONCEPT_ID,NA,NA,NA
payer_plan_period,family_source_value,No,varchar(50),The common identifier for all people (often a family) that covered by the same policy.,Often these are the common digits of the enrollment id of the policy members.,No,No,NA,NA,NA,NA,NA
payer_plan_period,stop_reason_concept_id,No,integer,"This field represents the reason the Person left the Plan, if known.",Map the stop reason directly to a standard CONCEPT_ID. If one does not exists please contact the vocabulary team. There is no global controlled vocabulary available for this information. [Accepted Concepts](http://athena.ohdsi.org/search-terms/terms?domain=Plan+Stop+Reason&standardConcept=Standard&page=1&pageSize=15&query=).,No,Yes,CONCEPT,CONCEPT_ID,NA,NA,NA
payer_plan_period,stop_reason_concept_id,No,integer,"This field represents the reason the Person left the Plan, if known.",Map the stop reason directly to a standard CONCEPT_ID with a domain of 'Plan Stop Reason' ([Accepted Concepts](http://athena.ohdsi.org/search-terms/terms?domain=Plan+Stop+Reason&standardConcept=Standard&page=1&pageSize=15&query=)). If one does not exist visit the [Custom Concepts](https://ohdsi.github.io/CommonDataModel/customConcepts.html) pate for more information.,No,Yes,CONCEPT,CONCEPT_ID,NA,NA,NA
payer_plan_period,stop_reason_source_value,No,varchar(50),The Plan stop reason as it appears in the source data.,NA,No,No,NA,NA,NA,NA,NA
payer_plan_period,stop_reason_source_concept_id,No,integer,NA,If the source data codes the stop reason in an OMOP supported vocabulary store the concept_id here.,No,Yes,CONCEPT,CONCEPT_ID,NA,NA,NA
cost,cost_id,Yes,integer,NA,NA,Yes,No,NA,NA,NA,NA,NA

1 cdmTableName cdmFieldName isRequired cdmDatatype userGuidance etlConventions isPrimaryKey isForeignKey fkTableName fkFieldName fkDomain fkClass unique DQ identifiers
307 drug_era person_id Yes integer NA NA No Yes PERSON PERSON_ID NA NA NA
308 drug_era drug_concept_id Yes integer The drug_concept_id should conform to the concept class 'ingredient' as the drug_era is an era of time where a person is exposed to a particular drug ingredient. NA No Yes CONCEPT CONCEPT_ID Drug Ingredient NA
309 drug_era drug_era_start_date Yes date NA The Drug Era Start Date is the start date of the first Drug Exposure for a given ingredient, with at least 31 days since the previous exposure. No No NA NA NA NA NA
310 drug_era drug_era_end_date Yes date NA The Drug Era End Date is the end date of the last Drug Exposure. The End Date of each Drug Exposure is either taken from the field drug_exposure_end_date or, as it is typically not available, inferred using the following rules: For pharmacy prescription data, the date when the drug was dispensed plus the number of days of supply are used to extrapolate the End Date for the Drug Exposure. Depending on the country-specific healthcare system, this supply information is either explicitly provided in the day_supply field or inferred from package size or similar information. For Procedure Drugs, usually the drug is administered on a single date (i.e., the administration date). A standard Persistence Window of 30 days (gap, slack) is permitted between two subsequent such extrapolated DRUG_EXPOSURE records to be considered to be merged into a single Drug Era. No No NA NA NA NA NA
311 drug_era drug_exposure_count No integer The count of grouped DRUG_EXPOSURE records that were included in the DRUG_ERA row NA No No NA NA NA NA NA
312 drug_era gap_days No integer NA The Gap Days determine how many total drug-free days are observed between all Drug Exposure events that contribute to a DRUG_ERA record. It is assumed that the drugs are "not stockpiled" by the patient, i.e. that if a new drug prescription or refill is observed (a new DRUG_EXPOSURE record is written), the remaining supply from the previous events is abandoned. The difference between Persistence Window and Gap Days is that the former is the maximum drug-free time allowed between two subsequent DRUG_EXPOSURE records, while the latter is the sum of actual drug-free days for the given Drug Era under the above assumption of non-stockpiling. No No NA NA NA NA NA
313 dose_era dose_era_id Yes integer NA NA Yes No NA NA NA NA NA