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How directly connect my EHR's FHiR APIs to azuree

HrishikeshAshokSagar-4960 20 Reputation points
2025-10-19T09:29:59.7933333+00:00

Hi Team,
I am trying to conenct a EHR's FHiR service through a API which is supported by an client app from the EHR(Athena), I have the client_id, secret_id and scopes/resources. Now I want to pull the data into so that I can analyse,transform using Healthcare Data Solutions in microsoft fabric. But all the topics only include documentation of how to read the data from a FHiR service within Azure or pre-downloaded data.

I am exploring three options:

  1. Azure service to pull data from an external FHIR server, Is there an already existing services within the azure environment that can pull the data from an external EHR's FHIR APIs?
  2. Pull the data through other libraries(e.g FHiR pyrate), I already have a python notebook that does this reliably. In this case how would I run the notebook within the same fabric?
  3. Pull the data manually through other libraries and load into AZure FHIR services and let azure take it over from there.

So the main question is how do I let azure take my credentials of the EHR and handle authentication, data pull and load the data into somewhere in azure.

Azure Health Data Services
Azure Health Data Services
An Azure offering that provides a suite of purpose-built technologies for protected health information in the cloud.
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Answer accepted by question author
  1. Vinodh247 40,056 Reputation points MVP Volunteer Moderator
    2025-10-19T16:07:12.52+00:00

    Hi ,

    Thanks for reaching out to Microsoft Q&A.

    azure does not natively provide a managed service to directly pull data from external EHR FHIR APIs like Athena’s. You have three practical options:

    1. Use Azure API Management + Logic Apps or adf: Configure API Management to securely store your client_id, secret, and handle OAuth2. Then use Logic Apps or Data Factory REST connectors to periodically pull FHIR data into ADLS or Azure Health Data Services (FHIR). This is the most production ready approach.
    2. Use your Python FHIR client within Microsoft Fabric: Run your existing notebook in a Fabric Notebook or Data Pipeline (notebook activity). Store credentials securely in Keyvault and mount them in the notebook. Save the extracted data to a Fabric Lakehouse for further analysis.
    3. Stage in Azure FHIR Service: If you prefer Azure native FHIR handling, first pull via your Python or API workflow, then load it into Azure FHIR Service, letting Azure manage FHIR validation and downstream processing.

    For automation, option 1 (Logic Apps + Keyvault + Health Data Services) is most maintainable and secure.

    Please 'Upvote'(Thumbs-up) and 'Accept' as answer if the reply was helpful. This will be benefitting other community members who face the same issue.

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