Projects update meeting 2022-03-30

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Attendees

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

Main tasks - Jan-July 2022

Announcements

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

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