UC 10. SRA & Kids First DRC for Kids First & UDN co-analysis

[NoopDog]

Status: ACTIVE
Platform contact; TBD
Researcher contact: TBD (will ask Matt Wheeler)
Next steps: requires moving BAM files into AWS hot storage at SRA for DRS accessibility. This use case also relies on RAS.
Dataset: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001232.v3.p2

[cottonva]

Update:

Status: NCBI actively moving all files (BAMs) to hot AWS/SRA storage. Files become immediately accessible to DRS as they are moved into S3. Next steps: Seven Bridges development work to obtain RAS passports, present them to NCBI/SRA DRS server to access files in CAVATICA workspaces.
Platform contact: Michele Mattioni and Kurt Rodarmer
Researcher contact: Lisa Bastarache
Dataset: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001232.v3.p2
Use Case: Enable researchers to pull genomic data files from Kids First and SRA 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.
One pager description: https://github.com/NIH-NCPI/NCPI_use_case_tracker/blob/main/one_pagers/UC10_InteroperabilityUDN.md
NCPI use case link: https://github.com/NIH-NCPI/NCPI_use_case_tracker/issues
Funding resources: Kids First DRC parent award

Next steps:

• Genomic data: requires moving BAM files into AWS hot storage at SRA for DRS accessibility. NCBI ready to test RAS (requires v1.1) to achieve co-analysis of Kids First and UDN data in CAVATICA.

• Phenotypic data: leverage dbGaP on FHIR for users to access data from CAVATICA for analysis? Work with NCBI to prioritize UDN data for dbGaP on FHIR? Waiting for feedback from NCBI regarding RAS-FHIR integration, requirements. Assess FHIR structuring with NCPI FHIR Working Group? See separate FHIR ticket.

[cottonva]

https://github.com/NIH-Auth-Services/CIT-IAM-RAS/issues/56

[jackDiGi]

@mattions, I think we are very close to getting full approval from RAS, once the tabletop tests are done - can you please confirm here?

[mattions]

Yes -- that is correct

[ianfore]

Issues were discussed in this GA4GH Connect session about how the files in NCBI managed AWS storage are accessed/transferred by the Cavatica platform and how

Assignment by the platform of new DRS ids to objects that already have DRS ids surfaces in this use case.
The issue should be addressed.

The RAS issues have been addressed on the requisite servers for some time. The use of those services, along with others relevant to the use case have been explored.

• Passport and clearing house use for access to the dataset has been verified
• Compute on the data accessed via a DRS provided URL has been verified using a placeholder tool (samtools)
• Query of controlled access phenotype attributes. FHIR version requires exploration and implementation.

The specific notebook for this has not been shared due to its controlled access content. The notebooks differs from this one only in that it uses controlled access data. The server calls used are identical other than that they include the passport required for authorization.