Projects update meeting 2022-02-16

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


David & Kimberly out next Wednesday

Finalize GOC meeting date


  • Tuesday April 26 to Thursday April 28, 7AM-11AM Pacific time
  • Virtual meeting (with possibility of local nodes)
  • SAB in the fall (may be uncoupled form GOC meeting?)

Projects update

Procedure for project management

  • From the broader grant aims, PIs/managers select a list of ACTIVE projects
  • Active projects have a PI, PO, TL, and necessary resources
  • Active projects have a Project in GitHub with a set list of tasks (tickets).
  • The list of tasks is reviewed with the entire team (including PI and PO) to define/restrict the scope of the project. A 'future' project may be created for longer-term tasks.
  • Tasks can be added/removed in the course of a project, but it is expected that major changes and addition of time-consuming tasks are reviewed with the PI/PO and to approve the new scope.
  • Because it is difficult to estimate a delivery date, projects are reviewed every 6-8 weeks, sooner if needed (or upon completion).

Current active projects: (adapted from Paul's list and from Seth's matrix)

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 2022-02-16  2022-03-02 or 2022-03-16 Yes To review and close after the next release
Software improvements (to prioritize between API or pipeline) ++ Seth: specify (Seth would like to remove unneeded code) PLANNING Pipeline cleanup & PLANNING GO API PI: Chris, PO:??, TL: Seth, Others: Seth, Dustin, Sujay? 2022-02-23 - Review specs Needs to be better specified
 Alliance software support  Alliance software support  PI: , PO:??, TL: Seth, Others:  No
Noctua improvement and maintenance Noctua 2021 & Noctua 2020 PI: Paul , PO: Kimberly, TL: Seth, Others: Tremayne, Jim No
Ongoing data QC and pipeline maintenance Ongoing data QC and pipeline maintenance PI: Chris, PO:Pascale, TL: Seth, Others: Seth, Dustin, Sujay, Jim? 2022-02-23 - Review project status Not applicable
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? Not applicable
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 2022-03-16 Yes
New visual editor (Tremayne) -> ready to push to Noctua dev? Visual Pathway editor GH project PI: Paul, PO: Paul, TL:, Others: Tremayne 2022-03-02 Yes Software call: OK to move to development; Need to define plan for next phase: testing, which bugs/features need to be fixed/added
Model copy PLANNED Old Shallow Model Copy GH project PI: Paul, PO: Kimberly, TL: Jim, Others: Tremayne 2022-03-02 - Review specs No - was supposed to be Feb
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
Simple version of automation of Noctua updates (planned) PI: Chris, PO: TBD, TL: Seth, Others: 2022-02-23 - Review specs No
Complete MOD imports (Aim 2)
Define specific remaining tasks for MOD imports + choose priorities for this period To be created - MGI - WB - SGD PI: Chris, PO: Kimberly, TL: Seth, Others: David, Suzi, Dustin 2022-03-23 No
 Annotation Extension Relation Review  Annotation Extension Relation Review  PI: , PO: Kimberly, TL: , Others: David, Dustin, Pascale      
 Integrate YeastPathways in GO Cam  Yeast Pathways  PI: Paul, PO: , TL: Dustin, Others:     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
Outreach - collect teaching materials in Google drive? 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-xx before the GOC meeting No
Other projects

Annotation of protein-containing complexes in Noctua

  • There is a new bug with entering Complex Portal IDs as enablers in Noctua Form
    • This was introduced with a change in how protein-containing complexes are typed, and thus affected what is available in the autocomplete
    • Current workaround is to use the 'Add Individual' functionality in the graph editor
  • This and other issues that have arisen regarding annotating to complexes in Noctua made us realize we need to review current practice
    • Can SGD curators meet the week of March 7th to let us know how they annotate complexes
  • Note that we don't currently have a mechanism to derive and export complex annotations onto individual genes
  • Also note that we are not up to the standards of IMEX/ComplexPortal for creation of complexes, so we have a parallel, albeit probably less stringent, way of assigning genes to complexes