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AmsterdamUMCdb Changelog

This changelog documents both the changes to the AmsterdamUMCdb database and the amsterdamumcdb Python package containing tools for working with the database.

[package/v0.3.1] - 2025-01-17

Changed

  • improved dictionary.csv generation
  • re-added some missing functions for OMOP version
  • added better documentation for OMOP tables
  • moved changelog to separate CHANGELOG.md file
  • updated requirements.txt

[package/v0.3.0] - 2024-05-17

Added

  • Support for using AmsterdamUMCdb version 1.5.0 for the 6th ESICM Datathon 2024

Changed

  • The legacy AmsterdamUMCdb format can be used using the legacy=true flag in the package functions.
  • The code for generating ICU scores and the sepsis cohort based on these scores is currently not implemented for version 1.5.0.

[database/v1.5.0] - 2024-05-10

Changed

  • Changed the data model to the OMOP Common Data Model version 5.4 using the AMSTEL repository
  • Improved mapping to standardized vocabularies to >95% coverage for both attributes and categorical values

Security

  • Minor quasi-identifiers, identified during mapping review, were removed from the dataset.

Deprecated

  • Support for the legacy versions (<= v1.0.2) will be dropped after release of AmsterdamUMCdb v2.0.0

[package/v0.2.1] - 2022-11-22

Added

  • unified PostgreSQL and BigQuery processing
  • Added unit tests for the cohorts. Forces pd.Na to be considered False during comparisons.

Fixed

  • Fixed filtering based boolean indexing using np.NaN (pandas default) and pd.NA (used by pandas-gbq since the default is Int64) leading to different results, particularly when finding the complement using negation.

Changed

  • By default, uses only validated data for amsterdamumcdb functions for consistent PostgreSQL and BigQuery results.
  • Removed aggregation in SQL code of Glasgow Coma Scale (GCS) in line with other functions.
  • Update SOFA GCS processing for more accurate scoring
  • Added rounding to 1 decimal for conversions (from kPa to mmHg) in SQL statements
  • Updated deprecated matplotlib style (seaborn-darkgrid)
  • Update engine to SQLAlchemy for official pandas support instead of direct psycopg2 connection
  • Moved code from Jupyter reason_for_admission.ipynb notebook into amsterdamumcdb.cohorts module.

[package/v0.2.0] - 2022-11-02

Added

  • sample cohorts (sepsis-3, mechanical ventilation, shock) in cohorts.py
  • SOFA scoring to scores.py
  • util functions for PostgresSQL to BigQuery translation

Changed

  • moved SQL code from notebooks to separate SQL files

[package/v0.1.5] - 2022-04-27

Added

  • dictionary: as part of the ICUnity project in preparation for the The Dutch ICU Data Warehouse a number of commonly used items have been mapped to LOINC, SNOMED CT or ATC with data in the vocabulary_id, vocabulary_concept_code, vocabulary_concept_name columns.
  • dictionary: UCUM units added

[package/v0.1.4] - 2021-04-23

Fixed

  • fixes binning in outliers_histogram() when all values < 1

[package/v0.1.3] - 2021-05-23

Changed

  • Improves binning in outliers_histogram()

[package/v0.1.2] - 2021-05-20

Changed

  • Allows negative dates in get_fluidbalance()

[package/v0.1.1] - 2021-05-20

Fixed

  • Fixes Google BigQuery Project must be a string error.

[package/v0.1.0] - 2021-04-23

Initial release for ESICM Datathon 2021

[database/v1.0.2] - 2020-02-29

Security

  • Reduces re-identification risk by removing additional quasi-identifiers.

Fixed/Changed

  • admissions: Fixes incorrect labeling of ICU (IC) patients as MCU (MC) patient in the location column of the admissions table.
  • numericitems: Fixes an error in temperature values due to a conversion error from degrees Fahrenheit to Celsius.

[database/v1.0.1] - 2020-01-19

Security

  • Reduces re-identification risk for additional adversary attacks by outlier suppression based on presumed background knowledge.

Fixed/Changed

  • admissions: Uses the more common 'height' for tallness (human height or stature) instead of 'length' in the admissions table (columns: heightgroup, heightsource).

[database/v1.0] - 2019-11-19

First publicly released version of AmsterdamUMCdb.