Releases: MIT-LCP/mimic-code
Releases · MIT-LCP/mimic-code
v3.0.1
This release adds a _metadata table which will indicate the version of MIMIC-IV for the BigQuery tables.
_metadata schema: attribute, value. Example query:
select attribute, value
FROM `physionet-data.mimiciv_derived._metadata`Current attribute available:
- mimic_version
- mimic_code_version
- mimic_code_commit_hash
These values are populated automatically for mimiciv_derived on publication of a release.
What's Changed
- Update BigQuery dataset build to use latest gh actions by @alistairewj in #1889
Full Changelog: v3.0.0...v3.0.1
Contributors
alistairewj
Assets 2
v3.0.0
This release is intended to rebuild the derived datasets on BigQuery using v3.1. It also creates a static snapshot for v2.2 which we will keep up in a separate dataset for users of the older data.
As of this release (Apr 22nd, 2025), the mimiciv_derived schema contains derived concepts from MIMIC-IV v3.1.
What's Changed
- Add vital signs mappings for MIMIC-IV v2.0 - SSSOM format by @a-chahin in #1417
- Update row counts in validate scripts for MIMIC-IV v3.1 by @shujuecn in #1856
- Publish action update by @alistairewj in #1886
New Contributors
Full Changelog: v2.5.0...v3.0.0
v2.5.0
MIMIC Code v2.5.0
Major changes
- Linting/formatting SQL files with sqlfluff
- Converting BigQuery syntax SQL to postgres/duckdb using sqlglot
- Improvements in concept queries (thanks everyone for contributing!)
What's Changed
- Add linting of SQL files using sqlfluff by @alistairewj in #1480
- Postgres shell script update by @alistairewj in #1482
- Fixed an error: Line 90, an L is missing, by @lewis738 in #1503
- fix NULL typo at mysql buildmimic-iv load.sql by @asha-ndf in #1502
- Fix gh db build by @alistairewj in #1504
- fix issue 1279 by @yongfanbeta in #1497
- Improvements for duckdb by @alistairewj in #1489
- fix gh actions by @alistairewj in #1506
- Fix norepinephrine in PSQL, tidy vasoactive code by @alistairewj in #1505
- Update load.sql by @trostalski in #1492
- Create view for code_status in MIMIC-IV by @ajb5d in #1291
- fix typo in extraction of diabetes_without_cc by @alistairewj in #1508
- change dir as import_duckdb relies on relative dirs by @alistairewj in #1509
- Streamlining and updating Postgres building process for mimic-iv, mimic-iv-notes, mimic-iv-ed by @stefanhgm in #1537
- fix: MIMIC Note README.md by @aegis301 in #1592
- remove stale/broken docker scripts, see #684 by @alistairewj in #1635
- fixing wrong mimic-iv folder name by @fvillena in #1639
- Fix constraint.sql for mimic-iv-ed PostgreSQL by @SimonUzL in #1659
- Add the 'load_7z.sql' script to enable the loading of 'ed' module dat… by @notwarn in #1656
- Changed column widths to import data without truncating by @KenjiOhtsuka in #1608
- Update code_status.sql by @SichengH in #1676
- fix sapsii and oasis score based on issue 1568 by @yongfanbeta in #1587
- nsaid & acei medication by @Juan-L-Dominguez in #1680
- Add duckdb build/concepts and use SQLGlot to convert BigQuery SQL into other dialects by @alistairewj in #1689
- Add procedures mappings for MIMIC-IV v2.0 - SSSOM format by @a-chahin in #1419
- Fix GitHub CI by using a Python container by @alistairewj in #1783
- Increase admissions language length for postgres schema by @MB-Finski in #1776
- SQLite python improvements by @alistairewj in #1784
- Sqlglot fixes by @alistairewj in #1786
- add validate.sql for mimic-iv-note by @Jin-Zhang-Yaoguang in #1687
- Fix SQLite build using all CSV files by @alistairewj in #1788
- ARBs SQL by @Juan-L-Dominguez in #1690
- Add ARB by @alistairewj in #1789
- fix #1354 by @rustamzh in #1785
- Fix bug: Columns dislocation in the 'emar' table. by @Scott1743 in #1779
- fix: Readme mimic-iv postgres build and concepts links by @chamathpali in #1685
New Contributors
- @lewis738 made their first contribution in #1503
- @asha-ndf made their first contribution in #1502
- @trostalski made their first contribution in #1492
- @fvillena made their first contribution in #1639
- @SimonUzL made their first contribution in #1659
- @notwarn made their first contribution in #1656
- @KenjiOhtsuka made their first contribution in #1608
- @SichengH made their first contribution in #1676
- @Juan-L-Dominguez made their first contribution in #1680
- @MB-Finski made their first contribution in #1776
- @Jin-Zhang-Yaoguang made their first contribution in #1687
- @rustamzh made their first contribution in #1785
- @Scott1743 made their first contribution in #1779
- @chamathpali made their first contribution in #1685
Full Changelog: v2.4.0...v2.5.0
Contributors
alistairewj, KenjiOhtsuka, and 18 other contributors
Assets 2
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
Contributors
schu, alistairewj, and 8 other contributors
Assets 2
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-conceptsand 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.shon 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
Contributors
armando-fandango, prockenschaub, and 4 other contributors
Assets 2
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.shon 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
Contributors
armando-fandango, prockenschaub, and 4 other contributors
Assets 2
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
specimenin 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
Contributors
juliangilbey and pedrogemal
Assets 2
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.
Contributors
briangow