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.
2. Install git, and GNU make.
3. 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.
   2. Clones the MIMIC-III code repository, which has the SQLite DB load scripts.
   3. Loads the database using the MIMIC-III code repository scripts.
   4. Creates some indexes on some tables such as NOTEEVENTS, ADMISSIONS and PATEINTS.
4. Create additional indexes to suit your needs. Use the post configuration script as an example.
5. Check for errors and the existence of the mimic3.sqlite3 SQLite database file.
6. Optionally clear up disk usage: make cleanall.
7. Optionally reduce the SQLite database file by editing and rerunning the post configuration script.