DbGaP FHIR API Docs

This is the documentation repository for the dbGaP FHIR API. (API base URL)

dbGaP is the Database of Genotypes and Phenotypes.
FHIR is HL7's REST API standard for transmission of electronic health record data.

• Quickstart
• Obtaining a Task-Specific Token for Controlled Data
• Notebooks
• 2024 Pilot Server for URECA(phs002921) and UDN(phs001232)

Prerequisites

You should already have a basic understanding of FHIR - especially before working through the Notebooks. The notebooks are based on the FHIR Exercises repo from the NIH Office of Data Sharing Strategy (ODSS).

For the Notebooks, you should also understand how Notebooks work and Pandas dataframes.

Issues

If you have a query that returns after 20 seconds with an error like the following:

{
  "error": {
    "status": 500,
    "message": "error forwarding request",
    "api-key": "192.168.0.1"
  }
}

Then you probably hit a 20-second timeout. Removing sorting, simplifying your query, or including fewer sub-queries in a batch can sometimes help.

For other issues please see the Issues list in this GitHub repository.

Privacy

The example code in this repository does not collect user data or send it to NCBI. However, using the code to access our FHIR servers will send data to NCBI. To learn more about how we handle that data, see the "NCBI Website and Data Usage Policies and Disclaimers" page.

Contact

The dbGaP FHIR API is provided by NCBI. Please contact us with any questions.

dbGaP FHIR is under active development; suggestions for features and data are welcome.