https://github.com/plandes/mimicdb
MIMIC-III database docker container
https://github.com/plandes/mimicdb
biomedical clinical clinical-informatics database mimic mimic-iii
Last synced: 8 months ago
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MIMIC-III database docker container
- Host: GitHub
- URL: https://github.com/plandes/mimicdb
- Owner: plandes
- License: other
- Created: 2023-06-29T21:22:00.000Z (over 2 years ago)
- Default Branch: master
- Last Pushed: 2023-06-30T00:44:12.000Z (over 2 years ago)
- Last Synced: 2025-01-02T04:14:38.088Z (9 months ago)
- Topics: biomedical, clinical, clinical-informatics, database, mimic, mimic-iii
- Language: Makefile
- Homepage:
- Size: 5.86 KB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE.md
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README
# 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`
1. Do the PhysioNet [MIMIC-III training]. Only after you have done this do you
have access to the corpus source data.
1. Download the source [MIMIC-III] data files as the file
`mimic-iii-clinical-database-1.4.zip` to this directory.
1. Install the [Postgres] client:
* macOS: `brew install libpq`
* Linux: `apt install postgresql postgresql-contrib`
* Windows: [Installer](https://www.postgresql.org/download/windows)
1. Install [git], [Docker], and [GNU make]
1. Edit the *user editable values* section of the [makefile] to
make any changes such as the database name, user, or port.
1. 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.
1. Clones the [MIMIC Code Repository].
1. Generates passwords in `password.txt` and `sa-password.txt`.
1. Uses the [MIMIC Code Repository] to load the [Postgres] database with the
corpus.
1. Creates the `mimic3` database user and grants the user `select` rights.
1. 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](CHANGELOG.md).
## License
[MIT License](LICENSE.md)
Copyright (c) 2023 Paul Landes
[Docker]: https://www.docker.com
[git]: https://git-scm.com
[GNU make]: https://www.gnu.org/software/make/
[Postgres]: https://www.postgresql.org
[MIMIC-III]: https://mimic.mit.edu/docs/iii/
[MIMIC-III training]: https://mimic.mit.edu/docs/gettingstarted/
[MIMIC Code Repository]: https://github.com/MIT-LCP/mimic-code.git
[makefile]: ./makefile