Projects update meeting 2022-03-02: Difference between revisions

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===Model copy===
===Model copy===
[https://github.com/orgs/geneontology/projects/80 PLANNED Old Shallow Model Copy GH project]
[https://github.com/orgs/geneontology/projects/80 PLANNED Old Shallow Model Copy GH project]
* '''PI: Paul''', '''PO: Kimberly''', '''TL: Jim''', '''Others:''' Tremayne  
* '''PI: Paul''', '''PO: Kimberly''', '''TL: Jim''', '''Others:''' Tremayne
*From the (long) existing ticket:
**We've agreed to move forward with a 'shallow copy' functionality.
**Shallow copy = ontology terms and relations are copied in full, but genes (and other enablers), evidence, and other metadata are not copied to the new model. **Inputs and Outputs, if not genes or gene products, should also be copied over as well as contextual information, e.g. cells and tissues types.
**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.


===Status Automated Ontology Updates in Noctua/Minerva===
===Status Automated Ontology Updates in Noctua/Minerva===

Revision as of 18:11, 1 March 2022

Attendees

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

Projects updates

Noctua Visual Editor

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

Model copy

PLANNED Old Shallow Model Copy GH project

  • PI: Paul, PO: Kimberly, TL: Jim, Others: Tremayne
  • From the (long) existing ticket:
    • We've agreed to move forward with a 'shallow copy' functionality.
    • Shallow copy = ontology terms and relations are copied in full, but genes (and other enablers), evidence, and other metadata are not copied to the new model. **Inputs and Outputs, if not genes or gene products, should also be copied over as well as contextual information, e.g. cells and tissues types.
    • 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.

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 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