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NIH-NCPI / NCPI_use_case_tracker

This repo is for tracking NCPI interoperability use cases.
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FHIR UC3: UDN phenotype structuring in FHIR for Kids First interoperability #18

Open cottonva opened 3 years ago

cottonva commented 3 years ago

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

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avillach commented 3 years ago

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 commented 3 years ago

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

cottonva commented 3 years ago

@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 commented 3 years ago

related issues: https://github.com/NIH-NCPI/ncpi-fhir-ig/issues/43 https://github.com/NIH-NCPI/ncpi-fhir-ig/issues/42 https://github.com/NIH-NCPI/ncpi-fhir-ig/issues/41 https://github.com/NIH-NCPI/ncpi-fhir-ig/issues/40 https://github.com/NIH-NCPI/ncpi-fhir-ig/issues/39

linikujp commented 3 years ago

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

bwalsh commented 2 years ago

Additional related issue https://github.com/NIH-NCPI/ncpi-fhir-ig/issues/44