Projects update meeting 2022-05-25: Difference between revisions
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** First successful run on Thursday, April 14th | ** First successful run on Thursday, April 14th | ||
** Did not run the ontology updates on Thursday, April 28th, due to the EMAPA-UBERON issue | ** Did not run the ontology updates on Thursday, April 28th, due to the EMAPA-UBERON issue | ||
** | ** May 12th maintenance outage - no ontology updates | ||
** May 26th maintenance outage (tomorrow) - ontology updates, but not relations (outstanding question about models with both directly regulates and regulates relations) | |||
*** https://github.com/geneontology/noctua-models/blob/master/migrations/replace_relations.tsv | *** https://github.com/geneontology/noctua-models/blob/master/migrations/replace_relations.tsv | ||
*** [https://github.com/geneontology/minerva/issues/392#issuecomment-1111019005 Checklist for updating relations] | *** [https://github.com/geneontology/minerva/issues/392#issuecomment-1111019005 Checklist for updating relations] |
Revision as of 10:35, 25 May 2022
Attendees
- Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia
- Present:
- Regrets: David
Reminder
We will have our 'priorities' discussion next week, hopefully everyone can be present.
Discussion
New groups (and groups in general): it would be nice to have guidelines as to what is a group, when to create a new group Decision from last week: We will add a parent field to groups and ensure every group other than GOC has a parent
Review and finalize + present at the next annotation call?
GitHub Projects
Update status for projects: https://github.com/orgs/geneontology/projects Are they Active, Planning, On Hold, or Closed?
Projects nearing completion
- Noctua 2021 (3 tickets left)
- Work on these tickets was pushed to noctua-dev
- Testing: 2 fixed, 1 still broken
- Visual Pathway editor v1.0: Documentation done - the project can probably be closed and a new one opened (to be confirmed with Paul T)
- Wish list from Swiss-Prot/next tasks:
- https://github.com/geneontology/noctua/issues/771 issue with 'is small molecule activator'
- RNA molecules display:
- RNA molecule reasoner problem (fixed?): https://github.com/geneontology/noctua/issues/760
- Wish list from Swiss-Prot/next tasks:
- Simple version of Noctua updates
- First successful run on Thursday, April 14th
- Did not run the ontology updates on Thursday, April 28th, due to the EMAPA-UBERON issue
- May 12th maintenance outage - no ontology updates
- May 26th maintenance outage (tomorrow) - ontology updates, but not relations (outstanding question about models with both directly regulates and regulates relations)
- Increase number of annotable entities in Noctua / NEO
- Note that Debbie Siegele has asked for addition of phage proteins
- Patrick Masson also did not find all entities, see Some IDs we expect are not found in Noctua
- Google drive move: @cmungall @huaiyumi @vanaukenk @thomaspd still have unmoved files
- Looks like many files are still not moved
- What is the plan for meeting presentations?
New projects
Review specs and scope
Task Matrix
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 | Yes | Project continues in May - schedule next review + estimate date of completion | ||
Software improvements : pipeline cleanup | PLANNING Pipeline cleanup | PI: Chris, PO:??, TL: Seth, Others: Seth, Dustin, Sujay? | Status still Planning | |||
Alliance software support | Alliance software support | PI: , PO:??, TL: Seth, Others: | ||||
Noctua improvement and maintenance | Noctua 2021 | PI: Paul , PO: Kimberly, TL: Seth, Others: Tremayne, Jim | ||||
GO_REFs | GO_REFs | PI: Chris, PO: Chris, TL: Seth, Others: Sujay, some of Sierra | Was supposed to end in April; make new estimate of time needed | |||
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 | ||||
Noctua Visual editor (Tremayne) - V1.0 done | Visual Pathway editor GH project | PI: Paul, PO: Paul, TL:, Others: Tremayne | Yes | Need to complete documentation (Pascale + Kimberly, David, Paul, Patrick proof read) | ||
Model copy | PLANNED Old Shallow Model Copy GH project | PI: Paul, PO: Kimberly, TL: Jim, Others: Tremayne | Yes ? | Is this Jim's next priority? | ||
Simple version of automation of Noctua updates | Noctua updates | PI: Chris, PO: TBD, TL: Seth, Others: | ||||
Complete MOD imports (Aim 2) | ||||||
MOD imports | MGI - WB - SGD | PI: Chris, PO: Kimberly, TL: Seth, Others: David, Suzi, Dustin | ||||
Integrate YeastPathways in GO Cam | Yeast Pathways | PI: Paul, PO: , TL: Dustin, Others: | ||||
Ontology (Aim 1) | ||||||
PI: , PO: , TL: , Others: | ||||||
Outreach/usability (Aim 3) | ||||||
PI: , PO: , TL: , Others: | ||||||
Projects to prioritize | ||||||
Switch to “species” for download outputs | PLANNED Improved Downloads ???? | PI: , PO:, TL:, Others: | ||||
Noctua output | PLANNING GPAD outputs- Complex Models and Redundancy Filtering | PI: Chris, PO: Kimberly, TL:?, Others: Jim | ||||
Next Noctua tasks | ||||||
Annotation Extension Relation Review | Annotation Extension Relation Review | PI: , PO: Kimberly, TL: , Others: David, Dustin, Pascale | ||||
ECO-GO Alignment | ECO-GO Alignment | |||||
GO rules, including missing valid rules from the report | ||||||
Phylogenetic taxon constraints | TC GH project - ontology repo | PI: Paul, PO: Pascale, TL: Jim, Others: | ||||
Noctua training material | Noctua training Project | PI: Mike , PO: Suzi, TL: NA, Others: David | Develop new training materials based on MGI and ZFIN training | |||
Other projects |