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Use FHIR data ingestion in healthcare data solutions (preview)

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[This article is prerelease documentation and is subject to change.]

You can import your Fast Healthcare Interoperability Resources (FHIR) data from the Azure Health Data Services FHIR service to the data lake by using the FHIR data ingestion pipeline. This pipeline stores the raw JSON files in the lake and supports all FHIR R4 resources. Integrating your FHIR data into the lake environment allows you to harness a wealth of clinical, financial (including claims and explanation of benefits), and administrative data. This integration facilitates the development of analytical scenarios tailored for various healthcare needs, such as quality reporting, population health management, clinical research studies, operational reporting, and decision support.

To learn more about the capability and understand how to deploy and configure it, go to:

The capability includes the FHIR export service notebook healthcare#_msft_fhir_export_service that imports data from the Azure FHIR service to OneLake.

Note

If you're using your own FHIR data, you need the FHIR data ingestion capability to run other healthcare data solutions (preview) capabilities. FHIR data ingestion also has a dependency on the Healthcare data foundations capability. Before you deploy FHIR data ingestion and run the pipeline, make sure that you successfully deploy and set up Healthcare data foundations first.

Prerequisites

Before you run the FHIR export service notebook, make sure that you:

  • Complete the setup steps in Use FHIR service if you use Azure Health Data Services as your FHIR data source.
  • Set up the sample data as explained in Deploy sample data if you don't have a FHIR server in your test environment.
  • Deploy the FHIR data ingestion capability in your Fabric workspace.
  • Configure the healthcare#_msft_fhir_export_service notebook as explained in Configure the FHIR export service.

Execute the FHIR export service

To use the FHIR data ingestion pipeline, you can choose one of the following three data ingestion options:

  1. Use the sample data shipped with healthcare data solutions (preview).
  2. Bring your own data to the Fabric lakehouse.
  3. Ingest data using a FHIR service such as Azure Health Data Services.

Note

Using a FHIR service to ingest data only works with first-party Microsoft FHIR services.

The notebook configuration and execution differs for each data ingestion option. Make sure you review the configuration guidance in FHIR data ingestion options.

The pipeline uses the bulk $export operation endpoint in the FHIR service to export FHIR data to a storage container in an Azure Data Lake Storage Gen2 storage account. The FHIRExportService module in the healthcare#_msft_fhir_export_service notebook helps you monitor the status of these export operations.

After you set up the correct configuration for your option, follow these steps to execute the pipeline:

  • On the FHIR data ingestion capability management page, select the healthcare#_msft_fhir_export_service notebook to open it.
  • Review the details in the Configuration management and setup and Run the FHIRExportService sections.
  • Select the Run cell or Run all option to execute the pipeline and wait for the execution to complete.

We recommend that you schedule this notebook job to run every four hours, or as often as you need.

By default, all new Fabric workspaces use the latest Fabric runtime version, which is now Runtime 1.3. However, the solution currently only supports Runtime 1.2.

Hence, after deploying healthcare data solutions (preview) to your workspace, remember to update the default Fabric runtime version to Runtime 1.2 (Apache Spark 3.4 and Delta Lake 2.4) before executing any of the pipelines or notebooks. If not, your notebook executions can fail. For more information, see Reset Spark runtime version in the Fabric workspace.