Projects update meeting 2024-02-14

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Attendees

  • Members: Kimberly, Pascale, Seth, Suzi, Jim, Huaiyu, Paul, Chris, Cynthia
  • Present:

Discussion topics

GOC meeting

  • Agenda & logistics
  • May 21-23 (Tues-Thurs)
  • Monday May 20th: users meeting
  • Friday May 24th: Managers' meeting?
  • Group dinner Tuesday
  • Group outing: Thursday from lunch time: picnic at the Botanical Garden

Active projects

SGD Noctua migration

Pipeline status

No snapshot/release for > 2 weeks; should we do a snapshot/release without the SGD data to make new data available?

Noctua Form UI improvement

Paul, Kimberly, Tremayne

  • Minimal changes to prevent exposing the GO-CAM model from users in the Form version of Noctua
  • Move Project to Active?
  • On dev server
    • First pass is on noctua-dev; Kimberly is testing
    • BLOCKER: We need to make a decision about how standard 'contributes to' annotations will be modeled
      • Gene-centric annotations from MGI, SGD, etc. were brought in using GP -> contributes to -> MF
      • For GO-CAMs, though, we have talked about using two statements: protein-containing complex -> 'has part' -> GP AND MF -> enabled by -> protein-containing complex to infer GP -> contributes to -> MF in GPAD output
      • What should the standard annotation form do?

Noctua form improvement specs

Kimberly

  • List of 'selected' UI changes from discussion with curators
  • Other high priority functionality (for example, metadata for curators to describe models as GO-CAM versus standard annotation)

Document and test devops documentation for GO services

Status, expected closing date of project

Discussion points

Potential Noctual meeting & Software developers meeting

Shared gdoc/notebook for stats gathering for progress reports

  • Seth: I spent more time remembering how I did something than doing it

https://docs.google.com/document/d/19U_bSs8UjtTB-dLRH85vZM15yWcT1QHwUYFhlgtfROo/edit

Constrain ECO in GO

  • https://github.com/geneontology/noctua/issues/856
  • We asked curators about ECO on the annotation call and some groups do use some of the more granular codes.
    • Xenbase - more granular IMP codes
    • CACAO - easier for students to use the more granular, methods-specific evidence
  • Is different use of ECO causing issues for users right now?
  • Can we propose a future project to review our use of ECO codes?

Standardize isoform descriptions?

UniProt uses P12345-x; MGI uses PRO IDs; thus is causing apparent 'duplicate' annotations https://github.com/geneontology/go-site/issues/2043#issuecomment-1865209874

MDBD Evaluation

Projects status


Discussion topics