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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

dbt