TRExt Workshop DB Setup

Prerequisites

Please ensure either MIMIC-III or MIMIC-IV licensed data is downloaded, these datasets can be found here:

• https://physionet.org/content/mimic-iv-note/2.2/
• https://physionet.org/content/mimiciii/1.4/

Additionally, a small selection of Athena vocab files should be downloaded. It isn't currently confirmed which ones we should use, so pick some such as SNOMED and MeSH for a good start.

Athena vocab files: https://athena.ohdsi.org/search-terms/start

Setup

Required software

• PostgreSQL
• Python >= 3.8

Data file placement

Store your OMOP CDM 5.4 postgresql creation scripts inside the OMOP_5_4_Postgres folder.

Store your MIMIC-4 (discharge.csv) or MIMIC-3 (NOTEEVENTS.csv) data in the mimic_4_data or mimic_3_data folders respectively.

Store your Athena vocab files inside the OMOP_Vocabs folder.

Once completed, your file structure should look similar to this:

Python environment

Python uv was used in this project, however all dependencies can be installed using alternative package managers.

# create virtual environment
uv venv

# activate the venv
source .venv/bin/activate

# sync dependencies
uv sync

DB Configuration

Your PostgreSQL connection string can be set within the .env file.

Running

Run the import python script whilst providing either 3 or 4 for the desired MIMIC version. MIMIC-III Import

python import_mimic_discharge.py 3

MIMIC-IV Import

python import_mimic_discharge.py 4