SQLite support for mimic-iv
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Description
Prerequisites
- [X ] Put an X between the brackets on this line if you have done all of the following:
- Checked the online documentation: https://mimic.mit.edu/
- Checked that your issue isn't already addressed: https://github.com/MIT-LCP/mimic-code/issues?utf8=%E2%9C%93&q=
Description
Is there a way to import mimic-iv data to SQLite? Just like for mimic-iii? It is much quicker than Postgres SQL.
I have tried to reuse the SQLite code for mimic-iii, but it gives me an error. The reason I think is not all tables have ROW_ID now. Is it possible to have a script for SQLite?
Another question I have is the download version of mimic-iv (https://physionet.org/content/mimiciv/1.0/) seems to have no ED/CXR/NOTE tables available. Just wondering when this can be put online for download?
Thanks
Labels
- mimic-iv
Contributor guide
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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
Start by comparing the existing MIMIC-III SQLite code with the MIMIC-IV schema, focusing on the reported ROW_ID difference. Check the linked PhysioNet MIMIC-IV download for the ED, CXR, and NOTE tables. Done would require a defined SQLite import path for MIMIC-IV and a clear answer about the requested tables.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- sqlite
- Domain
- databases
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100