Projects update meeting 2022-09-28

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Attendees

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

GOC meeting

  • The week after next (Oct 11-13)
  • The following week will be a no GO calls week (week of Sept 17th)


Priorities until the end of the year

Pascale - I have updated the ‘main tasks’ document: https://docs.google.com/document/d/17ikwodMNC_xwEGZhBre_tilw4Fd8NI1IWZ8KxefSPBU/edit (I realize that Sept is almost over, but this is a mix of a proposal and placeholder and actual ongoing projects)

where we list on which project we are each working on. This is based on the proposed priorities here: https://docs.google.com/document/d/1TrxTZMRMAS0BCektM79nqvcZq8R3PXEMVWd_CbW-RfI

Look at the list of project and (a) add any missing project you are working on or (b) remove projects you are not working on (these can also be moved to later in the year) Entering your % effort on the project for this period


Projects update

Annotation Extension Relations in Noctua

Model Copy

  • Sent link to documentation to Leyla, Suzi, Patrick, and Sylvain (currently on vacation)
  • Made one revision based on feedback from Suzi
  • Good to go?
  • Check on plans for GOC meeting

SGD and WB Migration to Noctua

  • We have confirmation from Alex that mid-October will work for him
  • Move forward with this after the GOC meeting
  • Petra is going to talk with the dictyBase team about possibly joining us

Ongoing Noctua bug fix project?

  • We should probably have a project for this when there are bug fixes that need to be addressed asap
  • It'd be good to keep track of the work

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 Ongoing - schedule next review + estimate date of completion
Ongoing - GO releases QC GO releases QC PI:?? , PO: Pascale , TL: Seth , Others:        
Alliance software support Alliance software support PI: , PO:??, TL: Seth, Others:
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)
Noctua Visual editor (Tremayne) - V1.0 done Visual Pathway editor GH project PI: Paul, PO: Paul, TL:, Others: Tremayne 1 open ticket
Model copy PLANNED Old Shallow Model Copy GH project PI: Paul, PO: Kimberly, TL: Jim, Others: Tremayne Documentation was sent to Leyla, Suzi, Patrick, and Sylvain for comments; updated based on input from Suzi
Relations to link MFs ACTIVE: relations to link MFs PI: Paul, PO: Kimberly, TL: Others: David, Pascale, Chris, Jim Presented to ontology group on Monday, 9/19 - will move forward with RO editorial work and curator documentation
Annotation Extension Relations in Noctua ACTIVE: Annotation Extension Relations in Noctua PI: Paul , PO: Kimberly, TL: Seth , Others: David, Jim Need clarification on scope of project
Complete MOD imports (Aim 2)
WB and SGD MOD imports WB - SGD PI: Chris, PO: Kimberly, TL: Seth, Others: David, Suzi, Dustin Scheduled for mid-october
Integrate YeastPathways in GO Cam Yeast Pathways PI: Paul, PO: , TL: Dustin, Others:
Ontology (Aim 1)
Improve ontology design patterns GH project - ontology repo PI: Chris, PO: Pascale, TL: Jim, Others: Had a summer camp - Sept 6-9th; some improvements and cleaning done, much work remains
Multiorganism processes GH project - ontology repo PI: ??, PO: Pascale, TL: Jim, Others: Summer camp - Sept 19th-22nd; some improvements and cleaning done, much work remains
Transcription, non-coding RNA, chromatin processes refactoring Transcription refactor  Biweekly call - on hold for a few weeks (group members working on other projects)
Boomer - to align GO and RHEA Boomer  10 open tickets
Outreach/usability (Aim 3)
PI: , PO: , TL: , Others:
Projects to prioritize
Software & pipeline issues & improvement
Software improvements : pipeline cleanup PLANNING Pipeline cleanup PI: Chris, PO:??, TL: Seth, Others: Seth, Dustin, Sujay?
Switch to “species” for download outputs PLANNED Improved Downloads ???? PI: , PO:, TL:, Others:
ECO-GO Alignment ECO-GO Alignment
Remove some main roadblocks for GO-CAM models curation (Aim 2)
Noctua output PLANNING GPAD outputs- Complex Models and Redundancy Filtering PI: Chris, PO: Kimberly, TL:?, Others: Jim
Noctua training material Noctua training Project PI: Mike , PO: Suzi, TL: NA, Others: David Develop new training materials based on MGI and ZFIN training?
Annotation Extension Relation Review Annotation Extension Relation Review PI: , PO: Kimberly, TL: , Others: David, Dustin, Pascale
Ontology (Aim 1)
Phylogenetic taxon constraints TC GH project - ontology repo PI: Paul, PO: Pascale, TL: Jim, Others:
Other projects

Priorities

Today we discuss the next GO priorities based on this document: https://docs.google.com/document/d/1TrxTZMRMAS0BCektM79nqvcZq8R3PXEMVWd_CbW-RfI/edit#