How to integrate Metabase with FHIR Data

Metabase is an open source data visualization tool that allows users to create interactive dashboards. When paired with CData Connect Cloud, users can easily create visualizations and dashboards linked to live FHIR data. This article describes how to connect to FHIR and build a simple visualization using FHIR data.

CData Connect provides a pure cloud-to-cloud interface for FHIR, allowing you to easily integrate with live FHIR data in Metabase — without replicating the data. Connect looks exactly like a SQL Server database to Metabase and uses optimized data processing out of the box to push all supported SQL operations (filters, JOINs, etc) directly to FHIR, leveraging server-side processing to quickly return FHIR data.

Configure FHIR Connectivity for Metabase

Connectivity to FHIR from Metabase is made possible through CData Connect Cloud. To work with FHIR data from Metabase, we start by creating and configuring a FHIR connection.

1. Log into Connect Cloud, click Connections and click Add Connection
2. Select "FHIR" from the Add Connection panel
3. Enter the necessary authentication properties to connect to FHIR.

   Set URL to the Service Base URL of the FHIR server. This is the address where the resources are defined in the FHIR server you would like to connect to. Set ConnectionType to a supported connection type. Set ContentType to the format of your documents. Set AuthScheme based on the authentication requirements for your FHIR server.

   Generic, Azure-based, AWS-based, and Google-based FHIR server implementations are supported.

   Sample Service Base URLs

   • Generic: http://my_fhir_server/r4b/
   • Azure: https://MY_AZURE_FHIR.azurehealthcareapis.com/
   • AWS: https://healthlake.REGION.amazonaws.com/datastore/DATASTORE_ID/r4/
   • Google: https://healthcare.googleapis.com/v1/projects/PROJECT_ID/locations/LOCATION/datasets/DATASET_ID/fhirStores/FHIR_STORE_ID/fhir/

   Generic FHIR Instances

   The product supports connections to custom instances of FHIR. Authentication to custom FHIR servers is handled via OAuth (read more about OAuth in the Help documentation. Before you can connect to custom FHIR instances, you must set ConnectionType to Generic.

4. Click Create & Test
5. Navigate to the Permissions tab in the Add FHIR Connection page and update the User-based permissions.

Add a Personal Access Token

If you are connecting from a service, application, platform, or framework that does not support OAuth authentication, you can create a Personal Access Token (PAT) to use for authentication. Best practices would dictate that you create a separate PAT for each service, to maintain granularity of access.

1. Click on your username at the top right of the Connect Cloud app and click User Profile.
2. On the User Profile page, scroll down to the Personal Access Tokens section and click Create PAT.
3. Give your PAT a name and click Create.
4. The personal access token is only visible at creation, so be sure to copy it and store it securely for future use.

With the connection configured, you are ready to connect to FHIR data from Metabase.

Connect to CData Connect from Metabase

After creating the virtual database, navigate to your Metabase instance. Use the SQL Server interface to connect to Connect Cloud.

1. Navigate to the administration screen (Settings -> Admin) and click "Add Database" from the "Databases" tab
2. Configure the connection to Connect Cloud and click "Save"
   • Database type: Select "SQL Server"
   • Name: Name the connection (e.g. "FHIR (Connect Cloud)")
   • Host: tds.cdata.com
   • Port: 14333
   • Database name: The name of the connection you just created (e.g. FHIR1)
   • Username: A Connect Cloud username (e.g. user@mydomain.com)
   • Password: The PAT for the above Connect Cloud user
   • Click to Use a secure connection (SSL)

Execute FHIR Data with Metabase

Once you configure the connection to Connect Cloud, you can query FHIR and build visualizations.

1. Use the "Write SQL" tool to retrieve the FHIR data
2. Write a SQL query based on the FHIR connection in CData Connect Cloud, e.g.
   
   

   SELECT Id, [name-use] FROM Patient WHERE [address-city] = 'New York'

3. Navigate to the "Visualization" screen, choose a visualization, and configure the visualization

More Information & Free Trial

At this point, you have built a simple visualization from FHIR data in Metabase. You can continue to work with live FHIR data in Metabase just like you would any SQL Server database. For more information on creating a live connection to FHIR (and more than 100 other data sources), visit the Connect Cloud page. Sign up for a free trial and start working with live FHIR data in Metabase today.