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

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

• @schu made their first contribution in #1360
• @nragusa made their first contribution in #1425

Full Changelog

v2.2.1...v2.3.0

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 than specimen_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.