Projects update meeting 2022-03-02

From GO Wiki
Revision as of 09:12, 3 March 2022 by Pascale (talk | contribs) (→‎Currently active projects:)
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to navigation Jump to search

Attendees

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

Projects updates

Noctua Visual Editor

Visual Pathway editor GH project Paul: status, next tasks, timeline to move to production

Noctua Updates

Model copy

PLANNED Old Shallow Model Copy GH project

  • PI: Paul, PO: Kimberly, TL: Jim, Others: Tremayne
  • A summary from the (long) existing ticket:
    • Implement a 'shallow copy'.
    • Shallow copy = Everything (ontology terms, relations, enablers, extensions) is copied. See Paul's comment
    • We will NOT copy evidence and other metadata.
    • A DerivedFrom tag will capture, at the model level, the originating model id.
    • The new model will only have the copier as contributor.
    • A default title, 'copy of x', where x is the original model title will be added.
    • All copied models will initially have state = development.
    • Technical issues still to be decided. See Seth's comment:
      • A way forward here to restart would be to re-evaluate the two paths forward: an examination of the changes needed to the client copier (and dusting of the interface to test it) and balancing that against the amount of work if the same was to be done in minerva.

Status Automated Ontology Updates in Noctua/Minerva

https://github.com/orgs/geneontology/projects/87

  • PI: Chris (@cmungall) PO: TBD TL: Seth Others: Jim

Loading Beetle data

Suzi - Can Dustin do that?

Adding 'has part' annotations in GO pipeline

Pascale - annoying for ontology(ie, for GO terms that have 'has part' terms, we'd like these to be asserted since they are not in the hierarchy by default) -> can this be added to the pipeline improvement project? https://github.com/geneontology/go-ontology/issues/19721 See issue comment and next item https://github.com/geneontology/pipeline/issues/130


Review current work

Main Tasks

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
Finalize AmiGO default relation change (Aim 3) AmiGO default relation GH project PI: Chris, PO:Chris, TL: Seth, Others: Seth 2022-02-16 2022-03-16 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 2022-03-02 2022-03-16 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. Needs a more "formal" tech doc (as opposed to the current user-oriented one).
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) Noctua updates 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