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
- 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?
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
- 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