ehr_postgres

Postgres Docker container setup scripts for MIMIC-IV (including ED), MIMIC-III, and eICU datasets.

How-to-use

1. Download EHR data what you want from physionet.
2. Run python --mimic_iv {MIMIC_IV_PATH} --mimic_iv_ed {MIMIC_IV_ED_PATH} --mimic_iii {MIMIC_III_PATH} --eicu {EICU_PATH} to bulid and run docker container.
   • NOTE: You can use each option separately.
   • NOTE: This script automatically removes pre-existing containers and images named ehr_postgres.
3. Run PGPASSWORD=postgres psql -h localhost -p 5432 -U postgres, and enjoy!
   • The database names are mimiciv, mimiciii, eicu.

NOTE

• This script has been tested with the following dataset versions: MIMC-IV v2.2, MIMIC-IV-ED v2.2, MIMIC-III v1.4, and eICU v2.0.
• The whole process takes few hours.
• Each dataset requires approximately 100GB of storage space.