mimic3

research for MIMIC-III dataset

guide to install

go to data folder and do wget --user YOURUSERNAME --ask-password -A csv.gz -m -p -E -k -K -np -nd https://physionet.org/works/MIMICIIIClinicalDatabase/files/ with YOURUSERNAME is the email you register for mimic3 dataset
install postgresql sudo apt-get install postgresql libpq-dev
install pgadmin4: download wget https://ftp.postgresql.org/pub/pgadmin3/pgadmin4/v1.3/pip/pgadmin4-1.3-py2.py3-none-any.whl and do pip install pgadmin* in your conda environment
make your computer account a superuser for postgres: sudo su - postgres then psql postgres then CREATE USER youraccount;, ALTER USER youraccount superuser;, and CREATE DATABASE mimic3 OWNER youraccount
fork the repo git clone --recursive https://github.com/AM2-Labs/mimic3.git
go the the subfolder cd mimic3/mimic-code/buildmimic/postgres/
create tables psql mimic3 -f postgres_create_tables.sql -U youraccount
import data into tables psql mimic3 -f postgres_load_data_gz.sql -U youraccount -v mimic_data_dir='<path_to_data>'
add indices to database psql mimic3 -f postgres_add_indexes.sql -U your account
add password to your account psql mimic3 then ALTER USER youraccount PASSWORD 'yourpassword' then ALTER USER youraccount nosuperuser;
run pgadmin4: go to your python source folder of pgadmin4 cd PATH/lib/python3.5/site-packages/pgadmin4, do python pgAdmin4.py, and go to the browser http://127.0.0.1:5050
to add database to pgadmin4, right click in Servers -> Create -> Server -> fill name (any name) -> Connection -> host: localhost -> database: mimic3 -> username: youraccount -> pass: yourpassword -> Save