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README.md

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OVERVIEW

This pilot directory will have the sample code to access the dbGaP pilot FHIR servers. There are 3 pilot FHIR servers.

  1. FHIR API service for ICAC/URECA at https://dbgap-api.ncbi.nlm.nih.gov/fhir-jpa-pilot1/x1/metadata for dbGaP datasets "Whole Genome Sequencing in the Inner City Asthma Consortium (ICAC) Cohorts".

    • Please see phs002921 for study details.
    • You need NIH Data Access approval to access this study. Please follow instructions to request access.
    • Once your Data Access Request (DAR) is approved, you can access this study's data both from the dbGaP website and from this pilot FHIR API server.
    • With you DAR approval, you can get the FHIR API authorization token at dbGaP power user portal and scroll-down to click on "Task specific token".

  2. FHIR API service for UDN at https://dbgap-api.ncbi.nlm.nih.gov/fhir-jpa-pilot2/x1/metadata for dbGaP datasets "Clinical and Genetic Evaluation of Individuals with Undiagnosed Disorders through the Undiagnosed Diseases Network (UDN)".

    • Please see phs001232 for study details.
    • You need NIH Data Access approval to access this study. Please follow instructions to request access.
    • Once your Data Access Request (DAR) is approved, you can access this study's data both from the dbGaP website and from this pilot FHIR API server.
    • With you DAR approval, you can get the FHIR API authorization token at dbGaP power user portal and scroll-down to click on "Task specific token".

  3. 📌 Important note on data security If you have approved access and are using URECA data at fhir-jpa-pilot1 or UDN data at fhir-jpa-pilot2, note that the sample code output csv files contain "controlled-access" data. Please only save the files in secure computing environment which is allowed to have controlled data.

  4. Open-access test FHIR server for those without Data Access approval but who would like to explore how to programmatically access dbGaP data with the FHIR API. This test server with synthetic data is at https://dbgap-api.ncbi.nlm.nih.gov/fhir-jpa-pilot/x1/metadata.

📌 Note: Please note that if you are using CAVATICA to access, make sure to enable "Allow Network Access" in the Project setting.