errors in inst/csv/OMOP_CDMv6.0_Field_Level.csv
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Assessment
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- 3/5
- Estimated time
- 1-2 days
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- Issue type
- Bug
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- Mostly clear
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- Domain
- databases
Research direction
Review inst/csv/OMOP_CDMv6.0_Field_Level.csv alongside the v6.0 changes described at the linked Common Data Model page. Check the drug_exposure stop_reason entry and date/datetime requirements in condition_occurrence and drug_exposure, then compare the remaining v6.0 field specifications with the documented changes. Done means all identified v5.4 carryovers are corrected in the CSV.
Written by the indexing model from the issue text.
Description
The csv file that contains the field-level specs for the OMOP CDM v6.0 seems to have some errors in it.
For example:
(1) In the drug_exposure table, the field stop_reason is present, even though it is explained in the user guidance that this field "will be retired in v6.0."
(2) In several tables, the requirements on date/datetimes seems to be reversed. The explanation at https://ohdsi.github.io/CommonDataModel/cdm60.html#Changes_in_v60 is that "DATETIME fields were made mandatory and date fields were made optional." This is true in the spec for some tables (e.g., visit_occurrence), but the opposite is specified for condition_occurrence and drug_exposure.
It looks to me like some of the specs were updated appropriately in this file for v5.4 -> v6.0, but for certain tables, the field-level specs from v5.4 were simply repeated in the file for v6.0 when they should have been changed.
Examples above are not intended to be exhaustive, they are simply a few observations.
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