[Python] Is there an existing library or tool to convert FHIR JSON Bundles into OMOP CDM...

Discussão em 'Python' iniciado por Stack, Agosto 19, 2025.

  1. Stack

    Stack Membro Participativo

    I am working with a large set of FHIR JSON Bundles (over 1000 files) and want to load them into an OMOP Common Data Model (CDM) database (MySQL).

    Right now, I am writing custom mapping functions resource by resource (e.g., Patient → PERSON, Observation → MEASUREMENT, etc.). However, this is turning out to be very time-consuming and complex.

    Before I proceed further, I would like to know:

    • Is there any existing open-source library, framework, or tool that can directly convert FHIR JSON into OMOP CDM tables?
    • If yes, does it support bulk data ingestion and handle common FHIR resources automatically?
    • If not, are there recommended approaches or partial solutions (e.g., mapping templates, intermediate standards, existing GitHub projects) that can simplify the process instead of building everything from scratch?

    I am mainly using Python and MySQL, but I’m open to other tooling if necessary.

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