Mimic Code Versions Save

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 https://github.com/MIT-LCP/mimic-code/pull/1455
• Add correct indices for mimic-iv-ed postgres by @kiendang in https://github.com/MIT-LCP/mimic-code/pull/1403
• feat: Add mimic-iv-note (v2.2) loading of postgres by @DopamineLcy in https://github.com/MIT-LCP/mimic-code/pull/1467
• concepts_postgres: updates (on top of mimiciv_v2.2_updates) by @schu in https://github.com/MIT-LCP/mimic-code/pull/1468
• Update charlson.sql for correct age-adjusted CCI score implementation by @tchang1997 in https://github.com/MIT-LCP/mimic-code/pull/1463
• Add missing value for InvasiveVent. by @marceliwac in https://github.com/MIT-LCP/mimic-code/pull/1402
• MIMIC-IV v2.2 updates by @alistairewj in https://github.com/MIT-LCP/mimic-code/pull/1469
• add crrt to kdigo concept by @aegis301 in https://github.com/MIT-LCP/mimic-code/pull/1461
• KDIGO improvements by @alistairewj in https://github.com/MIT-LCP/mimic-code/pull/1470
• fix issues 1297 by @yongfanbeta in https://github.com/MIT-LCP/mimic-code/pull/1477
• Update row counts in validate scripts for mimic-iv-ed v2.2 by @ZhipengHe in https://github.com/MIT-LCP/mimic-code/pull/1476

New Contributors

• @bemoody made their first contribution in https://github.com/MIT-LCP/mimic-code/pull/1455
• @DopamineLcy made their first contribution in https://github.com/MIT-LCP/mimic-code/pull/1467
• @marceliwac made their first contribution in https://github.com/MIT-LCP/mimic-code/pull/1402
• @aegis301 made their first contribution in https://github.com/MIT-LCP/mimic-code/pull/1461
• @yongfanbeta made their first contribution in https://github.com/MIT-LCP/mimic-code/pull/1477
• @ZhipengHe made their first contribution in https://github.com/MIT-LCP/mimic-code/pull/1476

Full Changelog: https://github.com/MIT-LCP/mimic-code/compare/v2.3.0...v2.4.0

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 https://github.com/MIT-LCP/mimic-code/pull/1364
  • This is used to generate statistics for the paper describing MIMIC-IV (to be published shortly)
• GitHub actions refactor by @alistairewj in https://github.com/MIT-LCP/mimic-code/pull/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 https://github.com/MIT-LCP/mimic-code/pull/1425
• Fix bug in calculation of first day GCS by @alistairewj in https://github.com/MIT-LCP/mimic-code/pull/1447

Concept mapping

• Add rxnorm concept mapping by @a-chahin in https://github.com/MIT-LCP/mimic-code/pull/1312
• Add outputevents concept mapping by @a-chahin in https://github.com/MIT-LCP/mimic-code/pull/1309
• Update loinc table by @a-chahin in https://github.com/MIT-LCP/mimic-code/pull/1310
• Add procedures concept mapping by @a-chahin in https://github.com/MIT-LCP/mimic-code/pull/1308
• Add chartevents concept mapping by @a-chahin in https://github.com/MIT-LCP/mimic-code/pull/1307

PostgreSQL improvements

• Updated MIMIC-IV-ED psql build scripts to v2.0 by @alistairewj in https://github.com/MIT-LCP/mimic-code/pull/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 https://github.com/MIT-LCP/mimic-code/pull/1363
• Include postgres MIMIC-III concepts by @alistairewj in https://github.com/MIT-LCP/mimic-code/pull/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 https://github.com/MIT-LCP/mimic-code/pull/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 https://github.com/MIT-LCP/mimic-code/pull/1360
• mimic-iv/buildmimic/sqlite/README: mention sqlalchemy requirement by @schu in https://github.com/MIT-LCP/mimic-code/pull/1361
• mimic-iv/buildmimic/sqlite/README: remove "edit step" by @schu in https://github.com/MIT-LCP/mimic-code/pull/1362

New Contributors

• @schu made their first contribution in https://github.com/MIT-LCP/mimic-code/pull/1360
• @nragusa made their first contribution in https://github.com/MIT-LCP/mimic-code/pull/1425

Full Changelog

https://github.com/MIT-LCP/mimic-code/compare/v2.2.1...v2.3.0

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: https://github.com/MIT-LCP/mimic-code/compare/v2.1.1...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:

• 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: https://github.com/MIT-LCP/mimic-code/compare/v2.1.1...v2.2.0

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: https://github.com/MIT-LCP/mimic-code/compare/v2.1.0...v2.1.1

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 https://github.com/MIT-LCP/mimic-code/pull/1195
• A single table aggregating vasoactive agents is now available as vasoactive_agent, see https://github.com/MIT-LCP/mimic-code/pull/1203
• Include BNP in cardiac markers concept by @pedrogemal in https://github.com/MIT-LCP/mimic-code/pull/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, https://github.com/MIT-LCP/mimic-code/pull/1209
• Same PR as above, propagated previous vent/oxygen delivery changes to the postgres scripts and improved tests https://github.com/MIT-LCP/mimic-code/pull/1209

Full Changelog: https://github.com/MIT-LCP/mimic-code/compare/v2.0.0...v2.1.0

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.

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

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.

Scripts for building and querying MIMIC-III v1.4