Projects update meeting 2022-03-30
Attendees
- Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia
- Present: David, Pascale, Seth, Suzi, Huaiyu,
- Regrets: Chris, Cynthia, Kimberly
Announcements
- Preparing GOC meeting: start planning the agenda: https://docs.google.com/document/d/1q1_OfUz-EZvw28WJhDnbuNUGFAZz-21-uynNybdJcqg/edit
- Fall meeting in Baltimore?
Discussion points
- David is asking whether GO central will become the 'main provider' of mouse data - however
- MGI loaded in Noctua
- Pipeline also pick up a Reminders File from MGI (P2GO + IEAs and other loads)
Follow up from last meeting
- Google drive move
- Query owner:me in the 'LEGACY Gene Ontology -use Shared Drive' to make sure all files have been moved
- Looks like few files are left ?? https://drive.google.com/drive/search?q=parent:0B8kRPmmvPJU3dFhhcWhTSmlUcDA%20owner:
QC & Pipeline and Essential software maintenance
Anything to report? what resources are needed until the next release stats?
- Release for removing regulates closure ready to go
- Next MGI will be included in Noctua (final import)
- We will wait until the MGI data is fully imported to trigger a new release, to avoid too many parallel tasks for Seth and Dustin
Project updates
New visual editor
Ready to deploy?
NEO load of Swiss-Prot reviewed sequences
- Status - Seth
- Project description needs to be updated
PLANNED Old Shallow Model Copy GH project
Status - Jim
GPAD output
Review specs
Yeast Pathways
Status - Dustin
Ontology
Jamboree next week about single step processes: https://github.com/geneontology/go-ontology/projects/26
Next week
Update annotation documentation
Chris: Present Diataxis as a possible tool to do documentation
MGI import into Noctua
MGI import into Noctua Expect to be completed
Noctua updates
Noctua 2021 & Noctua 2020 Expect to be merged
Currently active projects
Project name | Link to GH project | Resources: PI, PO, TL, Other resources | Next review | Follow up review | Aligned with Matrix? | Notes |
---|---|---|---|---|---|---|
Software improvement | ||||||
Finalize AmiGO default relation change (Aim 3) | AmiGO default relation GH project | PI: Chris, PO:Chris, TL: Seth, Others: Seth | 2022-03-30 | Yes | To review and close after the next release. Webpage on relations need improvement (Chris, Pascale) | |
Software improvements : GO API | GO API | PI: Chris, PO:??, TL: Seth, Others: Sierra | Review status 2022-04-20 | Yes | Will review at the end of April to see the status of the project | |
Software improvements : pipeline cleanup | PLANNING Pipeline cleanup | PI: Chris, PO:??, TL: Seth, Others: Seth, Dustin, Sujay? | Review specs & scope 2022-04-20 | Yes | Planned for April | |
Alliance software support | Alliance software support | PI: , PO:??, TL: Seth, Others: | 2022-03-23 | No | ||
Noctua improvement and maintenance | Noctua 2021 & Noctua 2020 | PI: Paul , PO: Kimberly, TL: Seth, Others: Tremayne, Jim | 2022-03-23 | 2022-04-05 | No | |
GO_REFs | GO_REFs | PI: Chris, PO: Chris, TL: Seth, Others: Sujay, some of Sierra | 2022-04-20 | Yes | ||
Ongoing data QC and pipeline maintenance | Ongoing data QC and pipeline maintenance | PI: Chris, PO:Pascale, TL: Seth, Others: Seth, Dustin, Sujay, Jim? | Ad hoc if there is a big bug | Yes | ||
Essential software maintenance | Essential software maintenance | PI: Chris, PO:Pascale, TL: Seth, Others: Seth, Dustin, Sujay, Jim? | Ad hoc if there is a big bug | Yes | ||
Remove some main roadblocks for GO-CAM models curation (Aim 2) | ||||||
NEO load of new sequences | NEO load GH project | PI: Chris, PO: Pascale , TL:, Seth Others: Sujay | 2022-03-30 | Yes | Seth will look into a strategy - week of March 16th | |
New visual editor (Tremayne) -> ready to push to Noctua dev? | Visual Pathway editor GH project | PI: Paul, PO: Paul, TL:, Others: Tremayne | 2022-03-23 | Yes | Ready for release to prod? Present at a future annotation call - or GOC meeting | |
Model copy | PLANNED Old Shallow Model Copy GH project | PI: Paul, PO: Kimberly, TL: Jim, Others: Tremayne | 2022-03-30 - Review status | Yes | Aim to present at GOC meeting (or announce work is ongoing) | |
Noctua output | GPAD output | PI: Chris, PO: Kimberly, TL:?, Others: Jim | 2022-03-30 - Review specs | +/- : Planned for March, but project not yet defined or resourced | David will split into 3 projects: (1) GPAD for MOD imports (done); (2) remove redundancy in exports (high priority); (3) problems with complicated models | |
Simple version of automation of Noctua updates | Noctua updates | PI: Chris, PO: TBD, TL: Seth, Others: | 2022-03-30 - Review status | Yes | ||
Complete MOD imports (Aim 2) | ||||||
MOD imports | MGI - WB - SGD | PI: Chris, PO: Kimberly, TL: Seth, Others: David, Suzi, Dustin | 2022-03-23 | 2022-04-05 MGI done? | No | |
Annotation Extension Relation Review | Annotation Extension Relation Review | PI: , PO: Kimberly, TL: , Others: David, Dustin, Pascale | TBD - after some projects are closed | |||
Integrate YeastPathways in GO Cam | Yeast Pathways | PI: Paul, PO: , TL: Dustin, Others: | 2022-03-30 | No | ||
Ontology (Aim 1) | ||||||
Phylogenetic taxon constraints | TC GH project - ontology repo | PI: Paul, PO: Pascale, TL: Jim, Others: | 2022-04-20 | Yes | ||
Outreach/usability (Aim 3) | ||||||
Switch to “species” for download outputs | PLANNED Improved Downloads ???? | PI: , PO:, TL:, Others: | 2022-03-23 - Review specs | No | ||
Manage users more actively (+ all contributing groups, in particular those not attending GOC and annotation calls) | PI: Mike , PO: Suzi, TL:, Others: | 2022-04-xx before the GOC meeting | No | |||
Noctua training material | Noctua training Project | PI: Mike , PO: Suzi, TL: NA, Others: David | 2022-04-20 | Yes | After/around the ZFIN training session | |
Other projects | ||||||