Integrate Live FHIR Data into Amazon SageMaker Canvas with RDS

Amazon SageMaker Canvas is a no-code machine learning platform that lets you generate predictions, prepare data, and build models without writing code. When paired with CData Connect AI, you get instant, cloud-to-cloud access to FHIR data for building custom machine-learning models, predicting customer churn, generating texts, building chatbots, and more. This article shows how to connect to Connect AI from Amazon SageMaker Canvas using the RDS connector and integrate live FHIR data into your ML model deployments.

CData Connect AI provides a pure SQL, cloud-to-cloud interface for FHIR, allowing you to easily integrate with live FHIR data in Amazon SageMaker Canvas — without replicating the data. CData Connect AI looks exactly like a SQL Server database to Amazon SageMaker Canvas 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 Amazon SageMaker Canvas

Connectivity to FHIR from Amazon SageMaker Canvas is made possible through CData Connect AI. To work with FHIR data from Amazon SageMaker Canvas, 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 Amazon SageMaker Canvas.

Connecting to CData Connect AI from Amazon SageMaker Canvas

With the connection in CData Connect AI configured, you are ready to integrate live FHIR data into Amazon SageMaker Canvas using its RDS connector.

1. Select a domain and user profile in Amazon SageMaker Canvas and click on "Open Canvas". 👁 Open SageMaker Canvas application
   
2. Once the Canvas application opens, navigate to the left panel, and select "My models". 👁 Select My models
   
3. Click on "Create new model" in the My models screen.
4. Specify a Model name in Create new model window and select a Problem type. Click on "Create". 👁 Create a new model
   
5. Once the model version gets created, click on "Create dataset" in the Select dataset tab. 👁 Select a dataset
   
6. In the Create a tabular dataset window, add a "Dataset name" and click on "Create". 👁 Create a tabular dataset
   
7. Click on the "Data Source" drop-down and search for or navigate to the RDS connector and click on " Add Connection". 👁 Select RDS connector
   
8. In the Add a new RDS connection window, set the following properties:
   
   
   • Connection Name: a relevant connection name
   • Set Engine type to sqlserver-web
   • Set Port to 14333
   • Set Address as tds.cdata.com
   • Set Username to a Connect AI user (e.g. [email protected])
   • Set Password to the PAT for the above user
   • Set Database name the FHIR connection (e.g., FHIR1) 👁 Create an RDS connection
     
9. Click on "Create connection".

Integrating FHIR Data into Amazon SageMaker Canvas

With the connection to Connect AI configured in the RDS, you are ready to integrate live FHIR data into your Amazon SageMaker Canvas dataset.

1. In the tabular dataset created in RDS with FHIR data, search for the FHIR connection configured on Connect AI in the search bar or from the list of connections. 👁 Search for the FHIR connection
   
2. Select the table of your choice from FHIR, drag and drop it into the canvas on the right. 👁 Select a table of your choice
   
3. You can create workflows by joining any number of tables from the FHIR connection (as shown below). Click on "Create dataset". 👁 Create the workflow and the dataset
   
4. Once the dataset is created, click on "Select dataset" to build your model. 👁 Select the dataset to build a model
   👁 Build a model from the dataset
   
5. Perform analysis, generate prediction, and deploy the model.

At this point, you have access to live FHIR data in Amazon SageMaker that you can utilize to build custom ML models to generate predictive business insights and grow your organization.

SQL Access to FHIR Data from Cloud Applications

Now you have a direct connection to live FHIR data from Amazon SageMaker Canvas. You can create more connections, datasets, and predictive models to drive business — all without replicating FHIR data.

To get real-time data access to hundreds of SaaS, Big Data, and NoSQL sources directly from your cloud applications, see the CData Connect AI.