OHDSI Synthea-to-OMOP using SQLMesh

This is a working PoC of the use of SQLMesh to generate on OMOP 5.4 CDM using Synthea synthetic data.

Getting started

1. Clone this repository
2. Create a python virtual environment and activate it
3. Run pip install -r ./requirements.txt
4. Run python ./bootstrap.py. The following steps are executed.
   • Creates a DuckDb database using the information in config.yaml and creates ./data/synthea and ./data/vocab folders.
   • Downloads the latest Synthea 100 sample patients CSV data, and uploads them into the database.
   • Pauses code execution until user downloads/copies the Athena vocabulary data zip file into ./data/vocab and presses Enter to continue
   • Uploads vocabulary into the database.
   • Prints out the table names in the database
5. You are all set to get started. Run sqlmesh ui for next steps.

Please do not hesistate to fork, create a PR, raise an issue or get involved in any other way.

Related projects:

DISCLAIMER: The following are all pre-alpha proof-of-concepts with absolutely no guarantees. In fact, running any of these in your data warehouse without guardrails may try to kill your cat. Read more about guardrails here.

SQLMesh

• SQLMesh Achilles

dbt

• Synthea-to-OMOP - SQLServer
• Synthea-to-OMOP - Databricks
• Synthea-to-OMOP from first principles
• Achilles and DQD with dbt