Projects update meeting 2022-08-17: Difference between revisions
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== Xenbase load into Noctua== | == Xenbase load into Noctua== | ||
* Alliance moving forward with direct upstream ingest | * Alliance moving forward with direct upstream ingest | ||
* PAINT data is now included in the XenBase files: | * PAINT data is now included in the GO XenBase release files: | ||
** https://github.com/geneontology/go-site/issues/1434#issuecomment-1204407177 | ** https://github.com/geneontology/go-site/issues/1434#issuecomment-1204407177 | ||
** https://github.com/geneontology/go-site/issues/1889#issuecomment-1204404759 | ** https://github.com/geneontology/go-site/issues/1889#issuecomment-1204404759 |
Revision as of 20:37, 16 August 2022
Attendees
- Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia
- Present:
- Regrets:
Announcements
GOC meeting
- Oct 11-13 at CalTech; a mix of in-person and remote
- 'Skeleton' agenda is here: https://docs.google.com/document/d/1YdM-RRosNJh1i4w4MLCF5lGfRrFIv7EqyNhEQD_QL0M/edit#heading=h.uediktlm7wwz
- Suggestions for discussion topics are welcome
Discussion items
Ontology summary emails missed during 3 days
https://github.com/geneontology/go-site/issues/1891
Xenbase load into Noctua
- Alliance moving forward with direct upstream ingest
- PAINT data is now included in the GO XenBase release files:
- However Malcolm mentions unmapped IDs (from PAINT to XenBase?) -> can this be fixed??
Timeline for SGD and WB import into Noctua
- Proposal: prioritize this work for mid-October after the GOC meeting with the aim of completing by the end of 2022
- Need to coordinate SGD, WB, UniProt, and GO developer and curator time
- AI: Need to elaborate a list of tasks + person responsible + detailed timeline (similar to what MGI did)
- AI: who needs to participate: Kimberly, Suzi, Alex, Seth, Dustin, Shuai, Juancarlos
142 species and which species we can annotate in Noctua
https://github.com/geneontology/noctua-landing-page/issues/87
Projects soon ready to be closed
Google drive move
https://github.com/orgs/geneontology/projects/90
- Suzy to report on status & check on other people
- Chris to move his files
- Do we need to add any documentation (since we said documentation should be part of all projects) - would be worth it to write how we organize files, etc
- Plan to end by the end of July
Model copy
- Status
- Curator-facing documentation, first draft done: https://docs.google.com/document/d/17qlOwSOov-hTKt1wxcyhF1M0XzfQG-r2N6RmhaNj2-E/edit
- Do we need developer documentation?
SynGO Updates
- Is the next task documentation?
- Seth: we need a new project to determine load/testing in the future
Loading MGI non-mouse annoations into Protein2GO
Status
MOU draft
- https://docs.google.com/document/d/1T1yW4dPaztjTJIkDPLBi3ob_-IGiqkP-kvGscprYijY/edit#
- update contributors list: http://geneontology.org/docs/go-consortium/
- unify with: http://geneontology.org/docs/annotation-contributors/
- http://geneontology.org/docs/collaborations/
Can this be automated from the yaml?
- CHRIS: YES!!!!
- NEXT
- Make a list of the various contributing groups and their status
- Make a Google form so people can 'sign'
- Set up some reminder system so we check every year or so whether groups are stil active (especially those that don't attend the meetings)
Noctua enhancements and bug fixes
- This project is now completed and closed.
- Next possible Noctua project when Tremayne returns: align AE relations between ShEx and Noctua form and VPE?
Ontology updates in Minerva / Noctua
Status
- All tickets done
- Need to add curator-facing documentation
- Documentation has been added to the Noctua outage SOP
Visual Pathway Editor
- Last tickets need testing/closing
- Documentation needs to be completed
Yeast Pathways
- Dustin
Ongoing projects
Alliance software support
Is this active?
Relations to link MFs
- Kimberly (PO), David, Pascale, Paul T (PI)
- Aim to clarify use of relations to link MFs. This work may also entail creating new relations in RO. The deliverables are: a set of relations to links MFs, exemplar models and explanations, documentation, and a strategy for harmonizing existing relations with new guidelines.
- We need to establish regular meeting times again.
[GO-CAM Enrichment]
Explore GO-CAM enrichment with PaulS's summer student Nick. PI: Chris (PaulS) PO: Kimberly TL: Dustin Other: Kimberly, Jim, Dustin
GO API refactor
Sierra
Software essential and proactive maintenance
Ongoing data QC and pipeline maintenance
To prioritize
Loading widgets into AmiGO
- Preliminary work indicates that this is not too much work
- Before we drop the pathway widget in AmiGO, we should first fix: https://github.com/geneontology/api-gorest-2021/issues/6
- no blockers for dropping in ribbon
- do we want to use the AGR slim?
What's next? How high of a priority is this?
- Need to decide exactly what we want - needs have a proper project and propose some specs and deliverables (and PI, PO, TL)
Potential priorities short list
To schedule for a future call
- Paper planning: Chris and Nomi
- Review API refactor project - Sierra
- Review [1] Yeast Pathways project - Dustin