omop-lite 0.0.15

Get an OMOP CDM database running quickly.

omop-lite

A small container to get an OMOP CDM database running quickly, with support for both PostgreSQL and SQL Server.

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 database. Default is db.
• DB_PORT: The port number of the database. Default is 5432.
• DB_USER: The username for the database. Default is postgres.
• DB_PASSWORD: The password for the database. Default is password.
• DB_NAME: The name of the database. Default is omop.
• DIALECT: The type of database to use. Default is postgresql, but can also be mssql.
• SCHEMA_NAME: The name of the schema to be created/used in the database. Default is public.
• DATA_DIR: The directory containing the data CSV files. Default is data.
• SYNTHETIC: Load synthetic data (boolean). Default is false
• SYNTHETIC_NUMBER: Size of synthetic data, 100 or 1000. Default is 100.
• DELIMITER: The delimiter used to separate data. Default is tab, can also be ,

Usage

Docker

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"

Helm

To install using Helm:

# Add the Helm repository
helm repo add omop-lite https://health-informatics-uon.github.io/omop-lite
helm repo update

# Install the chart
helm install omop-lite omop-lite/omop-lite

The Helm chart deploys OMOP Lite as a Kubernetes Job that creates an OMOP CDM in a database. You can customise the installation using a values file:

# values.yaml
env:
  dbHost: postgres
  dbPort: "5432"
  dbUser: postgres
  dbPassword: postgres
  dbName: omop_helm
  dialect: postgresql
  schemaName: public
  synthetic: "false" 

# Data mounting configuration
data:
  persistentVolumeClaim:
    enabled: true
    create: true
    size: 10Gi
    storageClass: standard
    accessModes:
      - ReadOnlyMany
  
  # Optional: Prepare data from a local directory
  prepare:
    enabled: true
    sourcePath: "/path/to/your/data"  # Path on the node where data is stored

Install with custom values:

helm install omop-lite omop-lite/omop-lite -f values.yaml

Using Your Own Data

To use your own data with the Helm chart:

1. Option 1: Use the built-in data preparation

   • Set data.prepare.enabled: true
   • Set data.prepare.sourcePath to the path on your node where the data is stored
   • The chart will automatically copy your data to the PVC before running the OMOP Lite job

2. Option 2: Manual data preparation

   • Create a PVC (either through the chart or manually)
   • Copy your data to the PVC using kubectl or another method
   • Set data.persistentVolumeClaim.enabled: true and provide the PVC name

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.

• 100 is fake data.
• 1000 is Synthea 1k data.

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. You can override the delimiter with DELIMITER configuration.

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.

Text search OMOP

Full-text search

Adding a tsvector column to the concept table and an index on that column makes full-text search queries on the concept table run much faster. This can be configured by setting FTS_CREATE to be non-empty in the environment.

Vector search

Postgres does vector search too! To enable this on omop-lite, you can compose the compose-omop-ts.yml with

docker compose -f compose-omop-ts.yml

To do this, you need to have embeddings/embeddings.parquet, containing concept_ids and embeddings. This uses pgvector to create an embeddings table.

omop-lite testing

If you're a developer and want to iterate on omop-lite quickly, there's a small subset of the vocabularies sufficient to build in synthetic/. If you wish to test the vector search, there are matching embeddings in embeddings/embeddings.parquet.