Create MIMIC-III in a local Postgres database

Instructions for use

First ensure that Postgres is running on your computer. For installation instructions, see: http://www.postgresql.org/download/

Once Postgres is installed, clone the mimic-code repository into a local directory using the following command:

$ git clone https://github.com/MIT-LCP/mimic-code.git

Change to the buildmimic/postgres/ directory and use make to run the Makefile, which contains instructions for creating MIMIC in a local Postgres database. For instructions on using the Makefile, run the following command:

$ make help

For example, to create MIMIC from a set of zipped CSV files in the "/path/to/data/" directory, run the following command:

$ make mimic datadir="/path/to/data/"

By default, the Makefile uses the following parameters:

• Database name: mimic
• User name: postgres
• Password: postgres
• Schema: mimiciii
• Host: none (defaults to localhost)
• Port: none (defaults to 5432)

If you would like to change any of these parameters, you can do so in the make call:

$ make mimic datadir="/path/to/data/" DBNAME="my_db" DBPASS="my_pass" DBHOST="192.168.0.1"

When using the database be sure to change the default search path to the mimic schema:

# connect to database mimic
$ psql -d mimic
# set default schema to mimiciii
mimic=# SET search_path TO mimiciii;

Troubleshooting

Error creating schema

psql:postgres_create_tables.sql:12: ERROR:  syntax error at or near "NOT"
LINE 1: CREATE SCHEMA IF NOT EXISTS mimiciii;

The IF NOT EXISTS syntax was introduced in PostgreSQL 9.3. Make sure you have the latest PostgreSQL version. While one possible option is to modify the code here to be function under earlier versions, we highly recommend upgrading as most of the code written in this repository uses materialized views (which were introduced in PostgreSQL version 9.4).

NOTICE

NOTICE:  materialized view "XXXXXX" does not exist, skipping

This is normal. By default, the script attempts to delete tables before rebuilding them. If it cannot find the table to delete, it outputs a notice letting the user know.

Stuck on copy

Many users report that the scripts get stuck at the following point:

COPY 58976
COPY 34499
COPY 7567

This is expected. The 4th table is CHARTEVENTS, and this table can take many hours to load. Give it time, and ensure that the computer does not automatically hibernate during this time.

Also note that eventually, the 4th line will read COPY 0. This is expected, see https://github.com/MIT-LCP/mimic-code/issues/182

Other

Please see the issues page to discuss other issues you may be having: https://github.com/MIT-LCP/mimic-code/issues