MIMIC-III database docker container

MIMIC-III is a corpus has 58,976 hospital admission and 2,083,180 had written notes by medical professionals. This repo contains Docker configuration files and a GNU makefile create and control the life cycle of a Postgres database containing the MIMIC-III corpus. The Docker Postgres container is populated with the MIMIC-III corpus using scripts from the MIMIC Code Repository.

Installation

The installation of the database isn't trivial. Even though everything is automated, there is a lot that can go wrong. For this reason, images of the database are available by the author with provided proof you have taking the PhysioNet MIMIC-III training. The steps to install are as follows:

1. Clone this repository: git --recurse-submodules https://github.com/plandes/mimicdb.git
2. Do the PhysioNet MIMIC-III training. Only after you have done this do you have access to the corpus source data.
3. Download the source MIMIC-III data files as the file mimic-iii-clinical-database-1.4.zip to this directory.
4. Install the Postgres client:
   • macOS: brew install libpq
   • Linux: apt install postgresql postgresql-contrib
   • Windows: Installer
5. Install git, Docker, and GNU make
6. Edit the user editable values section of the makefile to make any changes such as the database name, user, or port.
7. Bring up the database Docker container and install the database: make world.

The last step does the following:

1. Decompresses the MIMIC-III data files.
2. Clones the MIMIC Code Repository.
3. Generates passwords in password.txt and sa-password.txt.
4. Uses the MIMIC Code Repository to load the Postgres database with the corpus.
5. Creates the mimic3 database user and grants the user select rights.
6. Shuts down the instance.

Usage

• To start the container: make up
• To stop the container: make down
• To login to the database as a user: make userlogin
• To login to the database as the system administrator: make rootlogin

A bash script could be created to do everything the makefile does very easily. If you do that, please send it to me and I will add it to this repo.

Changelog

An extensive changelog is available here.

License

MIT License

Copyright (c) 2023 Paul Landes