FHIR^® Bulk Data Workshop

National Institutes of Health (NIH), Office of the Director (OD), Office of Data Science Strategy (ODSS)

June 13, 2023

FHIR® is the registered trademark of Health Level Seven International (HL7). Use of the FHIR trademark does not constitute an HL7 endorsement of this workshop.

FHIR Bulk Data workflow

1. Get an access token from the FHIR server
2. Request: GET https://fhir.example.org/Group/[id]/$export
3. Receive the requested FHIR data (“NDJSON” format)

FHIR Bulk Data workflow

Step 1: Get an access token from the FHIR server

1. Create a key set for the client application (what we are making)
2. Register public key with the server
3. Authorize bulk data connection (SMART Backend Services OAuth)

FHIR Bulk Data workflow

Step 2: Retrieving a Bulk Data export

1. Make a Bulk Data kick-off request
2. Request the status of the export

FHIR Bulk Data workflow

Step 3: Receive the requested FHIR data (“NDJSON” format)

1. Download the NDJSON files
2. Load them into the destination environment (in our case, Python + Pandas)

Additional resources

• http://purl.org/fhir-for-research/web

• Google Colab notebook showing how to load FHIR Bulk Data into a SQL (SQLite) database