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Create Synthea data and load to OMOP CDM (v5.3.1)

Docker images to (1) generate Synthea data and (2) load Synthea data into OMOP CDM. The goal is to quickly load an OMOP CDM with data for testing and demonstration.

  1. Synthea data is created with the official Synthea builder: https://github.com/synthetichealth/synthea
  2. Data is loaded to OMOP CDM with the ETL-Synthea project developed by OHDSI

Synthea data creation and OMOP ETL version have to be synchronized. The following versions are currently pinned:

image module version
synthea_generate_data synthea 3.2.0
synthea_load_to_omop_cdm r-base 4.2.2
synthea_load_to_omop_cdm Synthea ETL 2.0.0
synthea_load_to_omop_cdm OMOP CDM 5.3

⚠️ For now Postgres and OMOP CDM 5.3 are hard coded, the Synthea ETL repo has early support for OMOP CDM 5.4 but this was not tested.

How to use

Prerequresites

You need a OMOP CDM database with vocabularies.

👉 Guide to set up a simple test OMOP CDM database in Postgres: https://github.com/kaiserpreusse/omop_database

The following environment variables are needed, best practice is to store them in a .env file:

OUTPUT_PATH=Writable local path for output
POSTGRES_PASSWORD=Postgres password
POSTGRES_USER=Postgres user
POSTGRES_HOST=Postgres host
POSTGRES_DB=Postgres database name
POSTGRES_PORT=Postgres port
CDM_SCHEMA=name of CDM schema in OMOP DB (this has to be set up before, with vocabularies)
SYNTHEA_NUM_PATIENTS=Number of patients for synthea

1. Generate Synthea data

Build and run the synthea_generate_data image, e.g. with the provided compose file:

docker-compose -f compose-synthea_generate_data.yml up --build

See the compose file for required ENV variables.

2. Load Synthea data to OMOP CDM

Build and run the synthea_load_to_omop_cdm image, e.g. with the provided compose file.

docker-compose -f compose-synthea_load_to_omop_cdm.yml up --build

See the compose file for required ENV variables.

⚠️ Building the images takes considerable time because R builds a lot of packages from source. Help with this issue would be appreciated.

TODO

  • OMOP CDM v6
    • right now this works with OMOP CDM 5.3.1 only
    • in principle, the ETL-Synthea can also load to OMOP CDM v6