https://github.com/plandes/mimicdbsqlite

MIMIC-III SQLite Database Creation
https://github.com/plandes/mimicdbsqlite

medical mimic-iii sqlite sqlite3

Last synced: 9 days ago
JSON representation

MIMIC-III SQLite Database Creation

• Host: GitHub
• URL: https://github.com/plandes/mimicdbsqlite
• Owner: plandes
• Created: 2023-08-04T15:35:17.000Z (over 1 year ago)
• Default Branch: master
• Last Pushed: 2023-08-04T16:41:44.000Z (over 1 year ago)
• Last Synced: 2023-08-31T19:56:36.626Z (about 1 year ago)
• Topics: medical, mimic-iii, sqlite, sqlite3
• Language: Shell
• Homepage:
• Size: 4.88 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

Awesome Lists containing this project

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