Releases: MIT-LCP/mimic-code
MIMIC Code v2.4.0
This release was built using MIMIC-IV v2.2. The release of this version will update the mimiciv_derived tables on BigQuery to use MIMIC-IV v2.2.
What's Changed
- Avoid unnecessary dependency on sqlalchemy by @bemoody in #1455
- Add correct indices for mimic-iv-ed postgres by @kiendang in #1403
- feat: Add mimic-iv-note (v2.2) loading of postgres by @DopamineLcy in #1467
- concepts_postgres: updates (on top of
mimiciv_v2.2_updates
) by @schu in #1468 - Update charlson.sql for correct age-adjusted CCI score implementation by @tchang1997 in #1463
- Add missing value for InvasiveVent. by @marceliwac in #1402
- MIMIC-IV v2.2 updates by @alistairewj in #1469
- add crrt to kdigo concept by @aegis301 in #1461
- KDIGO improvements by @alistairewj in #1470
- fix issues 1297 by @yongfanbeta in #1477
- Update row counts in validate scripts for mimic-iv-ed v2.2 by @ZhipengHe in #1476
New Contributors
- @bemoody made their first contribution in #1455
- @DopamineLcy made their first contribution in #1467
- @marceliwac made their first contribution in #1402
- @aegis301 made their first contribution in #1461
- @yongfanbeta made their first contribution in #1477
- @ZhipengHe made their first contribution in #1476
Full Changelog: v2.3.0...v2.4.0
MIMIC Code v2.3.0
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 #1364
- This is used to generate statistics for the paper describing MIMIC-IV (to be published shortly)
- GitHub actions refactor by @alistairewj in #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 #1425
- Fix bug in calculation of first day GCS by @alistairewj in #1447
Concept mapping
- Add rxnorm concept mapping by @a-chahin in #1312
- Add outputevents concept mapping by @a-chahin in #1309
- Update loinc table by @a-chahin in #1310
- Add procedures concept mapping by @a-chahin in #1308
- Add chartevents concept mapping by @a-chahin in #1307
PostgreSQL improvements
- Updated MIMIC-IV-ED psql build scripts to v2.0 by @alistairewj in #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 #1363 - Include postgres MIMIC-III concepts by @alistairewj in #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 #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 #1360 - mimic-iv/buildmimic/sqlite/README: mention sqlalchemy requirement by @schu in #1361
- mimic-iv/buildmimic/sqlite/README: remove "edit step" by @schu in #1362
New Contributors
Full Changelog
MIMIC Code v2.2.1
This release updates the MIMIC Code repository to align with MIMIC-IV v2.0. It also contains many bug fixes.
Change log:
- This version (v2.2.1) fixes a bug in the workflow generating tables on BigQuery occurring in v2.2.0. The rest of the changes below are in comparison to v2.1.1.
- Build MIMIC scripts
- Updated PostgreSQL build scripts for MIMIC-IV v2.0 (#1328, thanks @alexmbennett2)
- Added SQLite build of MIMIC-IV (thanks @armando-fandango) and updated for MIMIC-IV v2.0
- Fixed MySQL build code (thanks @mdsung) and updated for MIMIC-IV v2.0
- Updated DuckDB code to work with MIMIC-IV v2.0
- Concept improvements
- The generation of BigQuery tables by the GitHub action no longer prints rows to the standard output
- Fixed incompatibility of
convert_bigquery_to_postgres.sh
on Mac OS X. The script should run on both Mac OS X and Ubuntu now. - Fixed imputation of cell counts (#1208, thanks @duanxiangjie)
- Added an initial concept mapping of labs to LOINC (thanks @a-chahin). This mapping will continue to be improved in this repository.
- Fixed matching of GCS value with prior value in the last 6 hours (#1248, thanks @prockenschaub)
- Added mapping tables for standard concepts for waveform data (#1321 and #1322, thanks @a-chahin)
Full Changelog: v2.1.1...v2.2.1
MIMIC Code v2.2.0
This release updates the MIMIC Code repository to align with MIMIC-IV v2.0. It also contains many bug fixes.
Change log:
- Build MIMIC scripts
- Updated PostgreSQL build scripts for MIMIC-IV v2.0 (#1328, thanks @alexmbennett2)
- Added SQLite build of MIMIC-IV (thanks @armando-fandango) and updated for MIMIC-IV v2.0
- Fixed MySQL build code (thanks @mdsung) and updated for MIMIC-IV v2.0
- Updated DuckDB code to work with MIMIC-IV v2.0
- Concept improvements
- The generation of BigQuery tables by the GitHub action no longer prints rows to the standard output
- Fixed incompatibility of
convert_bigquery_to_postgres.sh
on Mac OS X. The script should run on both Mac OS X and Ubuntu now. - Fixed imputation of cell counts (#1208, thanks @duanxiangjie)
- Added an initial concept mapping of labs to LOINC (thanks @a-chahin). This mapping will continue to be improved in this repository.
- Fixed matching of GCS value with prior value in the last 6 hours (#1248, thanks @prockenschaub)
- Added mapping tables for standard concepts for waveform data (#1321 and #1322, thanks @a-chahin)
Full Changelog: v2.1.1...v2.2.0
MIMIC Code v2.1.1
This is a bug fix release to ensure concepts are created correctly.
Change log:
- Rather than redirect the GitHub action output to /dev/null, the make concept query now uses
bq query --quiet
. This makes it easier to see where the script fails in the case of an error. - Fix syntax bugs in the norepinephrine / norepinephrine_equivalent_dose / ventilation queries
- Various query changes are carried forward to postgresql scripts (vasoactive, ntprobnp, ventilation)
- Use bg
specimen
in the severity score queries rather thanspecimen_pred
Full Changelog: v2.1.0...v2.1.1
MIMIC Code v2.1.0
This release fixes blood gas and (postgres) vent/oxygen delivery queries, adds the ntprobnp column to the cardiac_marker concept, and improves aux scripts for generating concepts in MIMIC-III.
Change log:
- Allow extra options to be passed to psql calls with MIMIC-III by @juliangilbey in #1195
- A single table aggregating vasoactive agents is now available as
vasoactive_agent
, see #1203 - Include BNP in cardiac markers concept by @pedrogemal in #1204
- Fixed first day blood gas queries to use the specimen data present in labevents rather than a no-longer existing probabilistic prediction of speciment, #1209
- Same PR as above, propagated previous vent/oxygen delivery changes to the postgres scripts and improved tests #1209
Full Changelog: v2.0.0...v2.1.0
MIMIC Code v2.0.0
This is the first release with the new repository organization where all MIMIC related code is located here, including MIMIC-III, MIMIC-IV, MIMIC-IV-ED, and MIMIC-CXR. Many thanks to @briangow for so much effort in doing this reorganization!
Change log:
- A GitHub action workflow now regenerates BigQuery tables for MIMIC-IV upon publish of a release, ensuring BigQuery is synchronized with the latest release of the code.
- Added MIMIC-IV and MIMIC-IV-ED build scripts.
- Added MIMIC-IV and MIMIC-IV-ED concepts.
- Added code for parsing MIMIC-CXR DICOMs (dcm) and deidentified free-text reports (txt) - this is the mimic-iv-cxr subfolder here (the mimic-iv prefix helps clarify this data can be used with MIMIC-IV - i.e. mimic-iv-cxr is synonymous with MIMIC-CXR).
- Added version of MIMIC-IV concepts in the PostgreSQL dialect. These concepts are (mostly) automatically generated using a shell script from the BigQuery syntax.
- Various bug fixes for MIMIC concepts.
MIMIC Code v1.4.2
Changelog:
- Added an example R markdown notebook which uses BigQuery to connect to MIMIC
- Filtered non-IV vancomycin administrations from the vancomycin dosing notebook
- Documentation on a common failure case when building MIMIC
- Added a contributed dplyr tutorial
- Fixed logic in identifying central/arterial lines in metavision
- Adjusted the calculation of UO in KDIGO to look backward; this will result in overestimation of UO and thus fewer AKI cases (before, the estimate was too low and AKI cases were potentially inflated)
- Improve comments in various scripts
MIMIC Code v1.4.1
This is the latest release of the code repository. It contains a number of improvements in the build scripts and many more concepts. This build is for use with MIMIC-III v1.4.
MIMIC-III v1.4
Scripts for building and querying MIMIC-III v1.4