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Releases: MIT-LCP/mimic-code

v2.5.0

26 Aug 12:28
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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

New Contributors

Full Changelog: v2.4.0...v2.5.0

MIMIC Code v2.4.0

04 Feb 00:38
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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

New Contributors

Full Changelog: v2.3.0...v2.4.0

MIMIC Code v2.3.0

15 Dec 21:44
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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

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

v2.2.1...v2.3.0

MIMIC Code v2.2.1

11 Jul 17:06
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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

11 Jul 15:07
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MIMIC Code v2.2.0 Pre-release
Pre-release

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

15 Dec 03:41
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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

15 Dec 02:16
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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

07 Dec 22:01
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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

16 May 15:12
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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

07 Sep 11:57
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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.