Minutes 2024-10-04 – R Submissions Working Group

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Administrative Updates

The working group welcomed Terry Christiani, the new executive director for the R Consortium. We are greatly appreciate the important leadership provided by Joseph Rickert, the previous director. More information can be found on this R Consortium Blog post.

The submissins pilot 4 (web-assembly version) was transferred on September 20, 2024 successfully and received by the FDA reviewers through the eCTD gateway transfer. The news was also shared in this announcement post on the R Consortium blog.
Hye Soo informed that their internal reviewer computers required an update to R version 4.4.1 to match the version used in the pilot submission. She also verified that there were no issues in rendering the Shiny application with the web-assembly method of execution.
A small issue with column labels being switched on Primary Table was identified (a legacy issue that unfortunately was carried forward from an earlier version of the Pilot 1 output). While this is not a critical issue for the scope of pilot 4, Ben Straub shared how leveraging continuous integration / continuous deployment (CI/CD) for verifying the integrity of the data and outputs could be helpful.
The full review of the submission is ongoing.
Eric Nantz shared that the Docker container version of Pilot 4 is undergoing additional testing with the working group, and the goal is to have a transfer to the FDA reviewers in November (exact timing TBD).
Communication with the Nature journal on a potential manuscript is ongoing. Michael Kane noted that additional journals such as the Journal of Statistical Software are another possibility for sharing the concepts of web-assembly in clinical submissions.

Joel Laxamana shared the ADRG Phuse working group established quarterly meetings starting on October 16.
Initial steps involve identifying all of the pieces required for an ADRG, and how can templates be enhanced using the learnings from previous open-source efforts such as the Pilot submissions.
Additional members from the submmissions working group will be invited to future discussions after the initial brainstorming of high-level ideas.

The Repositories Working Group is continuing their efforts to deliver a reproducible environment structure in which each organization can adopt to fit their needs.
It was recommended to invite Doug Kelkoff to a future submissions WG meeting to stay updated with their efforts

The previous pilot submissions have been successful with the higher-level goals of demonstrating open-source software including R is a viable method for producing the typical submission deliverables.
However, the mock clinical data sets and collection of outputs are a much smaller scale than a typical clinical submission which routinely involve many data sets and clinical TFLs.
Bringing members outside of this core group to lead a realistic pilot submission grouup could be valuable in many fronts.
Paul Schutte shared that there isn’t a cononical data set applicable to the life sciences space in the way that widely-known data sets such as iris and more recently Palmer Penguins.
With the lack of public de-identified clinical data sets on the scale of the typical submission, creating these realistic sets via robust simulation could be a path forward.
Action item: Create a subgroup of those interested in this effort.
Sources such as Project Datasphere are a way to obtain ADAM data sets involving treatment and standard of care data sets (with many oncology studies). One must request access before data are shared.

The group is interested in learning more on the current progress of the Dataset-JSON effort.
Mike Stakhouse will share more information on the {datasetjson} package in the next submissions working group meeting.