FHIR UC3: UDN phenotype structuring in FHIR for Kids First interoperability

[cottonva]

Platforms involved: NCBI/SRA/dbGaP & Kids First
Scientific Lead: Lisa Bastarache
Platform Lead: Anne Deslattes Mays @adeslatt + Allison Heath, Meen Chul Kim
One pager description: (what research question to be answered, plan of data use and analysis) https://github.com/NIH-NCPI/NCPI_use_case_tracker/blob/main/one_pagers/FHIRUC3.OnePagerDetails.md
and
https://github.com/NIH-NCPI/NCPI_use_case_tracker/blob/main/one_pagers/UC10_InteroperabilityUDN.md
Use Case: Enable researchers to pull phenotype data from Kids First FHIR server and dbGaP FHIR server together in one cloud-based workspace for combined analysis without downloading and uploading data. User will run workflows and other analysis to help solve pediatric undiagnosed UDN cases using variants represented in Kids First childhood cancer and/or structural birth defects datasets.
Funding resources: ODSS supplement to Kids First DRC and funded DATA Scholar

#10

[avillach]

UDN clinical and genomic data is accessible via PIC-SURE API
Here are examples in R and Python on how to SEARCH and RETRIEVE UDN clinical and Genomic data
https://github.com/hms-dbmi/Access-to-Data-using-PIC-SURE-API/tree/master/NIH_Undiagnosed_Diseases_Network

[linikujp]

@avillach do you suggest that the group could call PIC-SURE API to retrieve data and pull into CAVATICA workspace?

[cottonva]

@linikujp - I think we are open to discussing, but that would negate one goal of this exercise with is to test NCBI's FHIR-RAS integration and applicability to other dbGaP/SRA use cases.

[linikujp]

related issues:
NIH-NCPI/ncpi-fhir-ig#43
NIH-NCPI/ncpi-fhir-ig#42
NIH-NCPI/ncpi-fhir-ig#41
NIH-NCPI/ncpi-fhir-ig#40
NIH-NCPI/ncpi-fhir-ig#39

[linikujp]

UDN ResearchStudy in dbGaP FHIR API: https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/ResearchStudy/phs001232

[bwalsh]

Additional related issue
NIH-NCPI/ncpi-fhir-ig#44