Projects update meeting 2024-02-14

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

• import timeline; file and data location review
  (from convo w/dustin about order of operations moving forward)
• Requires (?): Add feature or workflow to produce both inferred and non-inferred GPADs
• Next step:
  • Check if the problems can be located to a few terms, for which we can change logical definition or make other ontology changes

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?
  • I moved the project to Active: https://github.com/geneontology/project-management/issues/87. (Kimberly)
• 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)
  • Project and list of tasks: where is this?
    • https://github.com/orgs/geneontology/projects/148

Document and test devops documentation for GO services

Status, expected closing date of project

Discussion points

Potential Noctual meeting & Software developers meeting

• Noctua face-to-face: https://docs.google.com/document/d/1zo-k6-VJ4nDb0EDW8e9L5QpSXXBB0akRxsIx9z57wyM/edit
• Software face-to-face: https://docs.google.com/document/d/1sM3kdvMhRfSl6M84PWpoH0NaaqWf9ZPrgP4-xMIo_zo/edit

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

• Collab notebook: https://colab.research.google.com/drive/1BhjsacipBPDCAEk84O-r5JHqRUbw3Fgz#scrollTo=ZWtNO2K7QjS_

Projects status

• https://github.com/geneontology/project-management/issues/85