Projects update meeting 2022-04-20

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


Project updates

Completed projects?

Task Matrix

Main tasks - Jan-July 2022 Needs updating for April

Ongoing projects status

Google drive move

Seth, Suzi: status

Ongoing data QC and pipeline maintenance

  • AspGD being taken off line- will now load from GOA:
  • EXP Annotations by AspGD
    • (3434) Aspergillus nidulans FGSC A4
    • (981) Aspergillus fumigatus
    • (431) Aspergillus niger CBS 513.88
    • (354) Aspergillus oryzae RIB40
  • status:

Ontology single step BP jamboree week of 2022-04-04

Noctua Training

  • Training session with ZFIN curators, Thursday, April 14th (David, Kimberly)

Shallow Model Copy

Alliance software support

Need to define PI, deliverables, resource





PLANNING Pipeline cleanup


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
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: 2022-04-06 No
Noctua improvement and maintenance Noctua 2021 & Noctua 2020 PI: Paul , PO: Kimberly, TL: Seth, Others: Tremayne, Jim 2022-04-05 Close? 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 2022-04-06 Yes Close?
New visual editor (Tremayne) -> ready push to Noctua prod? Visual Pathway editor GH project PI: Paul, PO: Paul, TL:, Others: Tremayne 2022-04-05 Close? Yes Missing documentation
Model copy PLANNED Old Shallow Model Copy GH project PI: Paul, PO: Kimberly, TL: Jim, Others: Tremayne 2022-04-20 - Review status Yes Aim to present at GOC meeting (or announce work is ongoing)
Simple version of automation of Noctua updates Noctua updates PI: Chris, PO: TBD, TL: Seth, Others: 2022-04-06 - Close? Yes
Complete MOD imports (Aim 2)
MOD imports MGI - WB - SGD PI: Chris, PO: Kimberly, TL: Seth, Others: David, Suzi, Dustin 2022-04-05 - MGI close? 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: 2022-04-06 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)
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
Projects to prioritize
Switch to “species” for download outputs PLANNED Improved Downloads ???? PI: , PO:, TL:, Others: 2022-03-23 - Review specs No
Noctua output PLANNING GPAD outputs- Complex Models and Redundancy Filtering PI: Chris, PO: Kimberly, TL:?, Others: Jim 2022-04-20 - Review specs
Next Noctua tasks
ECO-GO Alignment ECO-GO Alignment
GO rules, including missing valid rules from the report
Other projects

Future topic/project


  • What stats do we want to track, what do we need? Thinking grants, official reports, etc.
    • End-of-year summary stats for users, downloads?
    • Coming from consideration of log retention (policy) for some systems
    • This has been pretty ad hoc; do we want/need more structure with this?
    • Straw proposal: yearly roll of S3 logs, tooling to make extraction and use easier (need a policy of some kind)