omop-lite

A small container to get an OMOP CDM Postgres database running quickly.

Drop your data into data/, and run the container.

Environment Variables

You can configure the Docker container using the following environment variables:

• DB_HOST: The hostname of the PostgreSQL database. Default is db.
• DB_PORT: The port number of the PostgreSQL database. Default is 5432.
• DB_USER: The username for the PostgreSQL database. Default is postgres.
• DB_PASSWORD: The password for the PostgreSQL database. Default is password.
• DB_NAME: The name of the PostgreSQL database. Default is omop.
• SCHEMA_NAME: The name of the schema to be created/used in the database. Default is omop.
• DATA_DIR: The directory containing the data CSV files. Default is data.
• SYNTHETIC: Load synthetic data (boolean). Default is false

Usage

docker run -v ./data:/data ghcr.io/health-informatics-uon/omop-lite

# docker-compose.yml
services:
  omop-lite:
    image: ghcr.io/health-informatics-uon/omop-lite
    volumes:
      - ./data:/data
    depends_on:
      - db

  db:
    image: postgres:latest
    environment:
      - POSTGRES_DB=omop
      - POSTGRES_PASSWORD=password
    ports:
      - "5432:5432"

Synthetic Data

If you need synthetic data, some is provided in the synthetic directory. It provides a small amount of data to load quickly. To load the synthetic data, run the container with the SYNTHETIC environment variable set to true.

This data only provides the following tables:

• CONCEPT
• CONDITION_OCCURRENCE
• MEASUREMENT
• OBSERVATION
• PERSON

Bring Your Own Data

You can provide your own data for loading into the tables by placing your files in the data/ directory. This should contain .csv files matching the data tables (DRUG_STRENGTH.csv, CONCEPT.csv, etc.).

To match the vocabulary files from Athena, this data should be tab-separated, but as a .csv file extension.

Setup Script

The setup.sh script included in the Docker image will:

1. Create the schema if it does not already exist.
2. Execute the SQL files to set up the database schema, constraints, and indexes.
3. Load data from the .csv files located in the DATA_DIR.