MIMIC Code v2.3.0

[alistairewj]

This release was built using MIMIC-IV v2.1. The release of this version will update the mimiciv_derived tables to use the latest version of MIMIC-IV on BigQuery, which is currently v2.1.

Change log

General

• Notebook with figures/tables for MIMIC-IV by @alistairewj in Notebook with figures/tables for MIMIC-IV #1364
  • This is used to generate statistics for the paper describing MIMIC-IV (to be published shortly)
• GitHub actions refactor by @alistairewj in GitHub actions refactor #1400
  • Runs a GH action to test concept scripts on demo data in postgresql/mysql
• Updated row validation counts for MIMIC-IV by @nragusa in Updated row validation counts for MIMIC-IV #1425
• Fix bug in calculation of first day GCS by @alistairewj in Fix bug in calculation of first day GCS #1447

Concept mapping

• Add rxnorm concept mapping by @a-chahin in Add rxnorm concept mapping #1312
• Add outputevents concept mapping by @a-chahin in Add outputevents concept mapping #1309
• Update loinc table by @a-chahin in Update loinc table #1310
• Add procedures concept mapping by @a-chahin in Add procedures concept mapping #1308
• Add chartevents concept mapping by @a-chahin in Add chartevents concept mapping #1307

PostgreSQL improvements

• Updated MIMIC-IV-ED psql build scripts to v2.0 by @alistairewj in Update MIMIC-IV-ED psql build scripts to v2.0 #1340
  • PostgreSQL build scripts now work with MIMIC-IV v2.0 and v2.1
• mimic-iv/concepts: fix postgres-make-concepts and minor updates by @schu in mimic-iv/concepts: fix postgres-make-concepts and minor updates #1363
• Include postgres MIMIC-III concepts by @alistairewj in Include postgres MIMIC-III concepts #1448
  • Now the scripts which generate MIMIC-III concepts in PostgreSQL are version controlled, and tested to work.

MySQL improvements

• MIMIC-IV MySQL build script update by @alistairewj in MIMIC-IV MySQL build script update #1341
  • MySQL build scripts now work with MIMIC-IV v2.0 and v2.1.

SQLite improvements

• mimic-iv/buildmimic/sqlite/import.py: replace strip() by @schu in mimic-iv/buildmimic/sqlite/import.py: replace strip() #1360
• mimic-iv/buildmimic/sqlite/README: mention sqlalchemy requirement by @schu in mimic-iv/buildmimic/sqlite/README: mention sqlalchemy requirement #1361
• mimic-iv/buildmimic/sqlite/README: remove "edit step" by @schu in mimic-iv/buildmimic/sqlite/README: remove "edit step" #1362

New Contributors

• @schu made their first contribution in mimic-iv/buildmimic/sqlite/import.py: replace strip() #1360
• @nragusa made their first contribution in Updated row validation counts for MIMIC-IV #1425

Full Changelog

v2.2.1...v2.3.0

---

This discussion was created from the release MIMIC Code v2.3.0.