Fluid Balance Estimation in MIMIC-IV

A re-adaptation of the code found in mimic-iv/concepts/fluid-balance.
Tested on BigQuery, MIMIC-IV version 2.2.

This code generates two tables: fluid_rates and fluid_amounts, reporting respectively rates in ml/hour and amounts in ml for different selected order categories.

Requirements

1. Access to MIMIC-IV. Learn more here.
2. Project ID of a Google Project, make sure to have the necessary IAM permissions to run queries on Big Query.
3. Ensure that the Google SDK is properly installed in your environment with proper authentication.

Important Note: The google account enabled to access the MIMIC-IV must the be same as the one associated with the Google Project.

Installation

Run:

pip install "git+https://github.com/jhn-nt/mimic-iv__fluid-balance.git"

To generate the <your project-id>.mimiciv_derived.fluid_rates and <your project-id>.mimiciv_derived.fluid_amounts tables in your BigQuery, run:

python3 -m mimiciv__fluid_balance -p <your project-id>

You can then access the tables simply from BigQuery:

SELECT *
FROM `<your project-id>.mimiciv_derived.fluid_amounts`
LIMIT 1000

Simply recall that this new table will be built on tour project id and not in physionet-data.

Manual Installation

If you do not have access to a GCP authenticated environment, you can manually add the tables to your Big Query (or any other database).
The procedures to build the tables are defined in mimiciv__fluid_balance/fluid_rates.sql and mimiciv__fluid_balance/fluid_amounts.sql.
The former should be built first.

Acknowledgements

1. Johnson, Alistair, et al. "Mimic-iv." PhysioNet. Available online at: https://physionet. org/content/mimiciv/1.0/(accessed August 23, 2021) (2020).
2. Johnson, Alistair EW, et al. "MIMIC-IV, a freely accessible electronic health record dataset." Scientific data 10.1 (2023): 1.
3. Johnson, Alistair EW, et al. "MIMIC-III, a freely accessible critical care database." Scientific data 3.1 (2016): 1-9.