MIMIC-III concept generation in BigQuery/postgres diverged
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Description
The MIMIC-III concepts in BigQuery are generated by the make-concepts.sh script (static link)
The ones in PostgreSQL are generated by either postgres_make_concepts.sh (static link) or postgres_make_concepts_windows.bat (static link).
The latter two queries only generate a subset of the concepts in the first one (particularly the pivot queries are missing). Also, seems like all the scripts may be omitting queries (e.g. I just added dose queries to the BigQuery script in #1183).
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Compare mimic-iii/concepts/make-concepts.sh with postgres_make_concepts.sh and postgres_make_concepts_windows.bat, focusing on the concept queries each generator includes. Review the generated concept set, including the missing pivot queries and the dose queries referenced in #1183. Done means the BigQuery and PostgreSQL generators cover the same intended concepts.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- postgres, shell, sql
- Domain
- databases
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100