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 AI, 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 AI. To work with FHIR data from Metabase, we start by creating and configuring a FHIR connection.

1. Log into Connect AI, click Sources, and then click Add Connection
👁 Adding a Connection

2. Select "FHIR" from the Add Connection panel
👁 Selecting a data source

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.

   👁 Configuring a connection (Salesforce is shown)
   
4. Click Save & Test
5. Navigate to the Permissions tab in the Add FHIR Connection page and update the User-based permissions. 👁 Updating permissions
   

Add a Personal Access Token

When connecting to Connect AI through the REST API, the OData API, or the Virtual SQL Server, a Personal Access Token (PAT) is used to authenticate the connection to Connect AI. It is best practice to create a separate PAT for each service to maintain granularity of access.

1. Click on the Gear icon () at the top right of the Connect AI app to open the settings page.
2. On the Settings page, go to the Access Tokens section and click Create PAT.
3. Give the PAT a name and click Create. 👁 Creating a new PAT
   
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 and a PAT generated, you are ready to connect to FHIR data from Metabase.

Connect to CData Connect AI from Metabase

After creating the connection in Connect AI, navigate to your Metabase instance. Use the SQL Server interface to connect to Connect AI.

1. Navigate to the administration screen (Settings -> Admin) and click "Add Database" from the "Databases" tab 👁 Adding a new database connection to Metabase.
   
2. Configure the connection to Connect AI and click "Save"
   • Database type: Select "SQL Server"
   • Name: Name the connection (e.g. "FHIR (Connect AI)")
   • Host: tds.cdata.com
   • Port: 14333
   • Database name: The name of the connection you just created (e.g. FHIR1)
   • Username: A Connect AI username (e.g. [email protected])
   • Password: The PAT previously created
   • Click to Use a secure connection (SSL)
   👁 Configuring the connection to Connect AI.
   

Execute FHIR Data with Metabase

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

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

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

   👁 Collected data (Salesforce is shown).
   
3. Navigate to the "Visualization" screen, choose a visualization, and configure the visualization 👁 Collected data (Salesforce is shown).
   

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 AI page. Sign up for a free trial and start working with live FHIR data in Metabase today.