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closes #546

This commit is contained in:
Clair Blacketer 2024-03-28 15:28:11 -04:00
parent 8ed7a3908e
commit 8b74e16ce0
3 changed files with 3 additions and 3 deletions
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2
inst/csv/OMOP_CDMv5.3_Field_Level.csv
View File

@ -322,7 +322,7 @@ drug_era,drug_era_end_date,Yes,date,NA,"The Drug Era End Date is the end date of
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 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). 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 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
drug_era,drug_exposure_count,No,integer,NA,NA,No,No,NA,NA,NA,NA,NA 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
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 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
dose_era,dose_era_id,Yes,integer,NA,NA,Yes,No,NA,NA,NA,NA,NA dose_era,dose_era_id,Yes,integer,NA,NA,Yes,No,NA,NA,NA,NA,NA
dose_era,person_id,Yes,integer,NA,NA,No,Yes,PERSON,PERSON_ID,NA,NA,NA dose_era,person_id,Yes,integer,NA,NA,No,Yes,PERSON,PERSON_ID,NA,NA,NA

1 cdmTableName cdmFieldName isRequired cdmDatatype userGuidance etlConventions isPrimaryKey isForeignKey fkTableName fkFieldName fkDomain fkClass unique DQ identifiers
322 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
323 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
324 cdm_source vocabulary_version No varchar(20) NA NA No No NA NA NA NA NA
325 concept concept_id Yes integer A unique identifier for each Concept across all domains. NA Yes No NA NA NA NA NA
326 concept concept_name Yes varchar(255) An unambiguous, meaningful and descriptive name for the Concept. NA No No NA NA NA NA NA
327 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
328 concept vocabulary_id Yes varchar(20) A foreign key to the [VOCABULARY](https://ohdsi.github.io/CommonDataModel/cdm531.html#vocabulary) table indicating from which source the Concept has been adapted. NA No Yes VOCABULARY VOCABULARY_ID NA NA NA

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

@ -340,7 +340,7 @@ drug_era,drug_era_end_date,Yes,date,NA,"The Drug Era End Date is the end date of
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 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). 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 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
drug_era,drug_exposure_count,No,integer,NA,NA,No,No,NA,NA,NA,NA,NA 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
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 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
dose_era,dose_era_id,Yes,integer,NA,NA,Yes,No,NA,NA,NA,NA,NA dose_era,dose_era_id,Yes,integer,NA,NA,Yes,No,NA,NA,NA,NA,NA
dose_era,person_id,Yes,integer,NA,NA,No,Yes,PERSON,PERSON_ID,NA,NA,NA dose_era,person_id,Yes,integer,NA,NA,No,Yes,PERSON,PERSON_ID,NA,NA,NA

1 cdmTableName cdmFieldName isRequired cdmDatatype userGuidance etlConventions isPrimaryKey isForeignKey fkTableName fkFieldName fkDomain fkClass unique DQ identifiers
340 episode_event event_id Yes integer This field is the primary key of the linked record in the database. For example, if the Episode Event is a Condition Occurrence, then the CONDITION_OCCURRENCE_ID of the linked record goes in this field. Put the primary key of the linked record here. No No NA NA NA NA NA
341 episode_event episode_event_field_concept_id Yes integer This field is the CONCEPT_ID that identifies which table the primary key of the linked record came from. Put the CONCEPT_ID that identifies which table and field the EVENT_ID came from. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?vocabulary=CDM&conceptClass=Field&page=1&pageSize=15&query=) No Yes CONCEPT CONCEPT_ID Metadata NA NA
342 metadata metadata_id Yes integer The unique key given to a Metadata record. Attribute value is auto-generated Yes No NA NA NA NA NA
343 metadata metadata_concept_id Yes integer NA NA No Yes CONCEPT CONCEPT_ID NA NA NA
344 metadata metadata_type_concept_id Yes integer NA NA No Yes CONCEPT CONCEPT_ID NA NA NA
345 metadata name Yes varchar(250) NA NA No No NA NA NA NA NA
346 metadata value_as_string No varchar(250) NA NA No No NA NA NA NA NA

2
inst/csv/OMOP_CDMv6.0_Field_Level.csv
View File

@ -360,7 +360,7 @@ drug_era,drug_era_end_datetime,Yes,datetime,NA,"The Drug Era End Date is the end
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 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). 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 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
drug_era,drug_exposure_count,No,integer,NA,NA,No,No,NA,NA,NA,NA,NA 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
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 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
dose_era,dose_era_id,Yes,bigint,NA,NA,Yes,No,NA,NA,NA,NA,NA dose_era,dose_era_id,Yes,bigint,NA,NA,Yes,No,NA,NA,NA,NA,NA
dose_era,person_id,Yes,bigint,NA,NA,No,Yes,PERSON,PERSON_ID,NA,NA,NA dose_era,person_id,Yes,bigint,NA,NA,No,Yes,PERSON,PERSON_ID,NA,NA,NA

1 cdmTableName cdmFieldName isRequired cdmDatatype userGuidance etlConventions isPrimaryKey isForeignKey fkTableName fkFieldName fkDomain fkClass unique DQ identifiers
360 cdm_source cdm_release_date No date The release data of the CDM instance. NA No No NA NA NA NA NA
361 cdm_source cdm_version No varchar(10) NA NA No No NA NA NA NA NA
362 cdm_source vocabulary_version No varchar(20) NA NA No No NA NA NA NA NA
363 concept concept_id Yes integer A unique identifier for each Concept across all domains. NA Yes No NA NA NA NA NA
364 concept concept_name Yes varchar(255) An unambiguous, meaningful and descriptive name for the Concept. NA No No NA NA NA NA NA
365 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
366 concept vocabulary_id Yes varchar(20) A foreign key to the [VOCABULARY](https://ohdsi.github.io/CommonDataModel/cdm531.html#vocabulary) table indicating from which source the Concept has been adapted. NA No Yes VOCABULARY VOCABULARY_ID NA NA NA