OHDSI / OHDSI/FeatureExtraction

Drug era/exposure groupings to be more configurable at ATC levels

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Dominant language
R
Stars
74
Forks
63
PR merge metrics
No merged PRs in 30d

Description

It has been noted that the output for Drug groupings (based on ATC classes in the current implementation) is quite limited as:

  1. not all ATC levels are useful - ATC 1 and 2 are too broad and 3 is generally not that useful.
  2. The groupings create a large amount of junk data that can be a challenge to sift through
  3. It is not clear which group the categories correspond to, making it difficult to filter categories

proposed change

Add in options within the default covariate builders for all different grouping levels.
The default useDrugEraGroup can be maintained but, in addition, it would be nice to have

useDrugEraGroupAtc1
useDrugEraGroupAtc2
useDrugEraGroupAtc3
useDrugEraGroupAtc4
useDrugEraGroupAtc5

I expect CohortDiagnostics will only use 3 and 4, with 5 being less useful than the RxNorm ingredient level mapping.

The names of covariates could also be modified to include the ATC level within them, which would make filtering the output more straightforward.

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

The issue points to inst/sql/sql_server/DomainConceptGroup.sql and the default covariate builders. Start by tracing the existing useDrugEraGroup option and how its covariate names are generated. Done means the requested ATC-level grouping options are supported and the resulting categories identify their ATC level, with the existing default preserved.

Written by the indexing model from the issue text.

Assessment

Tech stack
r, sql
Domain
data, database
Issue type
Feature
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
38/100

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