Synthetic Breast Cancer OMOP Database

IMPORTANT: This repository does not contain the synthetic data. You can request the synthetic dataset from here (iknl.nl). Make sure to add OMOP synthetic dataset in the description of the request.

Preliminaries

• Request the synthetic data from here and mention OMOP synthetic dataset in the form.
• Docker installed
• Clone this repository

Initial Setup

1. Place the .csv file you obtained from iknl inside the ./data folder. There is a README.txt in that directory telling you the same.
2. Obtain the necessary vocabulary files from Athena, see the README.txt in the ./init/vocab folder for more information.
3. Verify that the name of your .csv file is identical to the name in the docker-compose.yaml file. If not, change it to the correct name.
4. Navigate to the directory containing the docker-compose.yaml file.
5. Run docker compose up (or docker compose up -d to detach the process from your terminal).
6. Wait for a long time until you see database system is ready to accept connections.
7. Now you have a working OMOP database.

Note: in case you want to have multiple databases running on your machine you can uncomment the db2 section in the docker-compose.yaml file and change the csv path /data/alternative.csv to the correct path. In this case pgadmin is only connected to the first instance. You can manually add this instance to the pgadmin by logging in to the pgadmin interface and adding a new server with the credentials given in the docker-compose.yaml file.

Life Cycle

1. You can stop the database at any time using docker compose down or CRTL+C in case you did not use the -d flag when you started the database.

   ✅ Changes are persistent

   The database is persistently stored on your machine in the pgadmin-data and the postgres-data. So any changes you made in a session are kept.

2. You can start the database any time again using the docker compose up -d command.

3. In case you want to start fresh:

   1. Stop the database: docker compose down
   2. Remove the database files by deleting the pgadmin-data and postgres-data folders
   3. Remove the containers: docker compose rm (when prompted enter yes)

PGAdmin

In order to explore the database in a visual way the pgadmin container is started along with the omop database. If the database is up and running you can access the pgadmin interface through browsing to: http://127.0.0.1:5050 and login with the credentials:

• username: [email protected]
• password: root

✅ Note that these are the pgadmin credentials and not the credentials used to connect to the database

SQL Connection Details

The container binds the internal 5432 to the localhost by default. It is also possible to connect from another Docker container if they are in the same Docker network.

url: 127.0.0.1 from the Docker host or omop if you connect from another container that is the same Docker network port: 5432 user: postgres password: password

Some details to the OMOP CDM:

dbms: postgresql cdm_database: omopcdm_synthetic cdm_schema: omopcdm_synthetic results_schema: results_synthetic

Folder Structure

init/*.sql

All the .sql files in this folder are executed on initialization in numerical order.

1. It first builds the OMOP CDM (creating all schema's, tables) [files: 0xx-*.sql]
2. then it loads a syntetic dataset [files: 1xx-*.sql]
3. it loads the synthetic dataset into the OMOP CDM [files: 2xx-*.sql]

default-server.json

This file makes sure the pgadmin already has the omop database server attached.

pgadmin-data & postgres-data[1,2]

Mount for the pgadmin-data container. This allows for persistent storage even when the container is stopped. Deleting these folders will remove all settings and data from the containers.

docker-compose

container configuration file for the postgres and pgadmin instance