https://github.com/plandes/mimicdbsqlite
MIMIC-III SQLite Database Creation
https://github.com/plandes/mimicdbsqlite
medical mimic-iii sqlite sqlite3
Last synced: about 1 month ago
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MIMIC-III SQLite Database Creation
- Host: GitHub
- URL: https://github.com/plandes/mimicdbsqlite
- Owner: plandes
- Created: 2023-08-04T15:35:17.000Z (almost 3 years ago)
- Default Branch: master
- Last Pushed: 2025-07-06T17:35:37.000Z (12 months ago)
- Last Synced: 2025-07-06T18:38:43.683Z (12 months ago)
- Topics: medical, mimic-iii, sqlite, sqlite3
- Language: Shell
- Homepage:
- Size: 5.86 KB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# MIMIC-III SQLite Database Creation
[MIMIC-III] is a corpus has 58,976 hospital admission and 2,083,180 had written
notes by medical professionals. This repo contains an automated build process
that creates an SQLite database (file) populated with the [MIMIC-III] corpus
using scripts from the [MIMIC Code Repository].
## Installation
1. Download the source [MIMIC-III] data files as the file
`mimic-iii-clinical-database-1.4.zip` to this directory.
1. Install [git], and [GNU make].
1. Run the automation process: `make all`. This does the following:
1. Uncompress the `mimic-iii-clinical-database-1.4.zip` of the compressed
CSV MIMIC-III data files.
1. Clones the [MIMIC-III code repository], which has the SQLite DB load
scripts.
1. Loads the database using the [MIMIC-III code repository] scripts.
1. Creates some indexes on some tables such as `NOTEEVENTS`, `ADMISSIONS`
and `PATEINTS`.
1. Create additional indexes to suit your needs. Use the [post configuration
script] as an example.
1. Check for errors and the existence of the `mimic3.sqlite3` SQLite database
file.
1. Optionally clear up disk usage: `make cleanall`.
1. Optionally reduce the SQLite database file by editing and rerunning the
[post configuration script].
[MIMIC-III]: https://mimic.mit.edu/docs/iii/
[SQLite]: https://www.sqlite.org/index.html
[git]: https://git-scm.com
[GNU make]: https://www.gnu.org/software/make/
[MIMIC-III code repository]: https://github.com/MIT-LCP/mimic-code.git
[post configuration script]: ./src/bin/postconfig.sh