Manager Call 2020-09-16

• Present:
• Regrets:

Agenda

Projects updates

GAF 2.2 (#4h) and GPAD/GPI 2.0 (#4i)(Kimberly)

• When do we want to make an announcement to the user community?
  • This seems dependent upon a firm date for switchover - do we have that?
  • We should also supply a test file for developers and include its location in the announcement.
  • MGI and WB are nearly ready with their files; based on 2020-09-15 annotation call, other groups are coming along
  • Propose a meeting between David, Kimberly, Helen, Penelope, and Alex to discuss UniProt files wrt timing of new file release and relations used
  • Expect that we will need to continue to provide support (questions, clarifications) to groups as we get closer to the switchover

Ongoing projects updates

• Noctua Imports (#3a)
  • MGI/Wormbase imports
    • Dustin has a new import on his USC server where David and Kimberly can check models for a select number (15-20) of genes, but code is still using GPAD 1.2 for import. Upshot: this will allow us to check the current state of the import rules for any errors, but does not reflect what the final import will include, e.g. annotation metadata
  • GPAD/GPI 2.0
  • Minerva and GPAD output
    • We need to schedule a virtual working meeting to focus on the GO-CAM GPAD output. Proposal: David and Kimberly create an agenda so we can schedule a meeting knowing what specific work needs to get done, and then find a good time for everyone. This meeting will required Ben, Jim, and Seth. Also Eric? Dustin?
• Legacy data (#6)

Pascale, Laurent-Philippe

• 1. gp2protein, gp2RNA files, gpi files: Any preferences for keeping/dropping them ?
  • gp2protein, gp2RNA: https://github.com/geneontology/archive-reconstruction/issues/3
  • gpi: https://github.com/geneontology/archive-reconstruction/issues/2
• 2. File names: what about users citing old filenames ? see https://github.com/geneontology/archive-reconstruction/issues/1#issuecomment-680121448
• 3. Folder structure: can we avoid repetition in folder names ? see https://github.com/geneontology/archive-reconstruction/issues/1#issuecomment-680122454 . How do we plan for future changes ? For instance if annotation files are created for species rather than groups (this would also be a breaking change for Zenodo).
• 4. File browser: use the AWS S3 of the archive (https://geneontology-tmp.s3.amazonaws.com/index.html) for both current & release.geneontology.org ?
• 5. Do we store this archive only on release.geneontology.org or do we store it also on Zenodo *now* ? Pros: Zenodo is here for "always" and free, AWS S3 could be turned off (eg if cost not paid); Cons: everything in Zenodo would have a DOI and it could easily discourage any changes to the archive folder hierarchy / file names (situation we are in)
• Noctua (#3e)
  • ui implementations
    • bug fixes
      • Ongoing; Tremayne is submitting some PRs to noctua-dev for testing
      • Adding: connect to existing nodes; re-use of fields in a given model
    • ART
      • Tremayne has a prototype that David and Kimberly can test. The prototype has much of the desired functionality but is not yet employing the necessary functionality from minerva which will be developed later when Ben is available to work on that.

https://github.com/geneontology/noctua-annotation-review/issues/21

• • testing and release framework
  • Minerva support for noctua
• Pipeline (ongoing) (#4a)
• Pathways2GO paper (#1bi)