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Postgres MIMIC Importer

License: MIT Python Version: 3.8plus Code style: black

MIMIC data importer for PostgreSQL.

This repository does not contain any MIMIC data.

Data

The location of the MIMIC is to be set as an environment variable before running docker-compose.

Data Preparation

As MIMIC-IV and MIMIC-IV-ED are separate downloads, please ensure that all data is copied into a single target folder.

The target folder must have the following structure:

.
data
└───mimiciv
    └───<version>
        ├───ed
        ├───hosp
        └───icu

If you do not require MIMIC-IV-ED data to be imported, edit the config.json file to remove the import.

Set the target location

Using the environment variable (default):

Windows

PowerShell:

$env:MIMIC_DATA_PATH = "C:/absolute/path/to/mimic/data"

Command Prompt:

set MIMIC_DATA_PATH=C:/absolute/path/to/mimic/data

Linux

export MIMIC_DATA_PATH=/absolute/path/to/mimic/data

The docker-compose.yaml can be edited to hard code the location:

version: "3"
services:
  mimic_import:
    volumes:
       - /absolute/path/to/mimic/data/:/usr/src/app/data

Compatible Data Versions

MIMIC Dataset Version Compatibility
MIMIC-IV 2.0
MIMIC-IV-ED 2.0
MIMIC-IV 2.2
MIMIC-IV-ED 2.2

Build MIMIC-IV database services

docker-compose build

The service can be started and stopped after being built:

  1. Start the service: docker-compose up
    • Start the service as a background daemon: docker-compose up -d
  2. Stop the service: docker-compose down
  3. Stop the service and remove data: docker-compose down -v

License

MIT License

Copyright (c) 2024 Rudolf J

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.