OMOP Docker

Aim of this repository

This repository provide DockerFile and docker compose for an OMOP + WebAPI + ATLAS installation. Useful for educational purpose.

How to use

Configuration

The configuration is performed by defining the environment variables in the env file.
The variables are:

Parameter	Description
POSTGRES_USER	Username of the postgres database
POSTGRES_PASSWORD	Password of the postgres database
POSTGRES_DB	Name of the postgres database
CDM_SCHEMA_NAME	Schema for the OMOP CDM database
WEB_API_SCHEMA_NAME	Schema for the WebAPI and Atlas database
TEMP_SCHEMA_NAME	Schema for the temporary tables database
WEBAPI_URL	Expected URL for the WEBAPI with port

Get OMOP vocabularies

The Vocabularies should be Downloaded from ATHENA website and the CSV file copied in the CDM/data/vocabularies folder.
If you want to use your own local Vocabularies files, the expected files are : CONCEPT.csv CONCEPT_ANCESTOR.csv CONCEPT_CLASS.csv CONCEPT_RELATIONSHIP.csv CONCEPT_SYNONYM.csv DOMAIN.csv DRUG_STRENGTH.csv RELATIONSHIP.csv VOCABULARY.csv.
Any missing file will result in an empty corresponding table.
The files should be tabulation separated, containing and header and encoded in UTF-8.

Run the docker

docker compose up

Acces to Atlas and WebAPI

Atlas is located in http://$WEBAPI_URL/atlas, by default: http://localhost:8080/atlas
WebAPI is located in http://$WEBAPI_URL/WebAPI, by default: http://localhost:8080/WebAPI

To do

CDM DockerFile
- Configure the Posgresql database
- Integrate the ATHENA vocabularies in the database
- Data generation (Synthea) according to the environment variable parameters (/!\ Synthea is slow /!)
WebAPI and Atlas DockerFile

alibell/omop_docker