Projects update meeting 2022-09-28
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
- Need clarification on scope of project - Kimberly
- Project Specifications
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#