Projects update meeting 2022-03-16: Difference between revisions

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


==Projects updates==
=Announcements=
* Moving the GO google drive https://drive.google.com/drive/folders/0ABiscjZCrxjUUk9PVA
* Preparing GOC meeting


==Projects updates==
==Projects updates==
===Finalize AmiGO default relation change  (Aim 3)===
===Finalize AmiGO default relation change  (Aim 3)===
Should be completed with the (Feb) March release: [https://github.com/orgs/geneontology/projects/68 AmiGO default relation GH project]
* Should be completed with the (Feb) March release: [https://github.com/orgs/geneontology/projects/68 AmiGO default relation GH project]
* links to the relations page - needs improvement (Chris, Pascale if needed)


===NEO load of new sequences ===
===NEO load of new sequences ===
Status and next steps: [https://github.com/orgs/geneontology/projects/79 NEO load GH project]
Status and next steps: [https://github.com/geneontology/neo/issues/82 NEO load SP reviewed entries]


===Simple version of automation of Noctua updates (planned)===
===Simple version of automation of Noctua updates (planned)===
Are the specs finalized? [https://github.com/orgs/geneontology/projects/87 Noctua updates]
Are the specs finalized? [https://github.com/orgs/geneontology/projects/87 Noctua updates]
Yes, Jim is working on this
===Moving the wiki===
* Seth
* Scheduled for next week - Monday/Tuesday (March 21/22)
* Seth will send an announcement by the end of this week
===Noctua Training===
* David - MGI curators were trained last week
* Kimberly planning a training for ZFIN curators by the end of the month. The documentation will be made more general


===Review current work===
===Review current work===
[https://docs.google.com/document/d/1r3aWGjyz2nXNpyzETPO-ah276HQDc1ClNs57Cm6Nwv0/edit Main Tasks]
[https://docs.google.com/document/d/1r3aWGjyz2nXNpyzETPO-ah276HQDc1ClNs57Cm6Nwv0/edit Main Tasks]
===[https://github.com/orgs/geneontology/projects/88 GOREFS]===
Objective:
* contains all of the GO_REF data in a single machine-usable metadata file (location TBD)
* Compiles on action to a static page in geneontology.github.io for delivery to geneontology.org
==Follow up from last meeting==
===Noctua Visual Editor===
* [https://github.com/orgs/geneontology/projects/84 Visual Pathway editor GH project]
* Status & next steps
===Noctua Updates===
* https://github.com/orgs/geneontology/projects/65
* Plan is to merge next week (week of 2022-03-07)
* New project (smaller) should be created for next work.
* Plan a date for the review of the next project (scope definition)
===Model copy===
* [https://github.com/orgs/geneontology/projects/80 PLANNED Old Shallow Model Copy GH project]
* Specs finalized? Plan was to finalize on 2022-03-03 Technical call
* Need to plan a start date and a review date
* Aim to present at GOC meeting
===Status Automated Ontology Updates in Noctua/Minerva===
* https://github.com/orgs/geneontology/projects/87
* Specs finalized?
* Resources attributed?
* Need to plan a review date
===New tasks/Projects===
* [https://github.com/geneontology/noctua-form/issues/175 Move all SheX compliant relations to the form], even if some will be changed later (Kimberly, Tremayne): project or ticket in next Noctua improvements?
* [https://github.com/orgs/geneontology/projects/90 Google drive move] (Pascale, Suzi, others later) -- CAN WE DISCUSS THIS FIRST??  https://github.com/geneontology/go-site/issues/1813
* [https://github.com/orgs/geneontology/projects/89 Annotation documentation] (Pascale, Patrick, others later)


=== Currently active projects:===
=== Currently active projects:===
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| [https://github.com/orgs/geneontology/projects/86 PLANNING Pipeline cleanup] & [https://github.com/orgs/geneontology/projects/85 PLANNING GO API]
| [https://github.com/orgs/geneontology/projects/86 PLANNING Pipeline cleanup] & [https://github.com/orgs/geneontology/projects/85 PLANNING GO API]
| '''PI:''' Chris, '''PO:'''??, '''TL:''' Seth, '''Others:''' Seth, Dustin, Sujay?
| '''PI:''' Chris, '''PO:'''??, '''TL:''' Seth, '''Others:''' Seth, Dustin, Sujay?
| (Spec reviewed  2022-02-23)
| Spec reviewed  2022-02-23
| Yes
| 2022-04-20
|  
|  
| Needs to be better specified
|
|-
|-
| Alliance software support
| Alliance software support
Line 75: Line 121:
| [https://github.com/orgs/geneontology/projects/69 Essential software maintenance]
| [https://github.com/orgs/geneontology/projects/69 Essential software maintenance]
| '''PI:''' Chris, '''PO:'''Pascale, '''TL:''' Seth, '''Others:''' Seth, Dustin, Sujay, Jim?  
| '''PI:''' Chris, '''PO:'''Pascale, '''TL:''' Seth, '''Others:''' Seth, Dustin, Sujay, Jim?  
| Ad hoc if there is a big bug?
| Ad hoc if there is a big bug
|  
|  
| Not applicable
| Not applicable

Latest revision as of 00:49, 17 March 2022

Attendees

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

Announcements

Projects updates

Finalize AmiGO default relation change (Aim 3)

NEO load of new sequences

Status and next steps: NEO load SP reviewed entries

Simple version of automation of Noctua updates (planned)

Are the specs finalized? Noctua updates Yes, Jim is working on this

Moving the wiki

  • Seth
  • Scheduled for next week - Monday/Tuesday (March 21/22)
  • Seth will send an announcement by the end of this week

Noctua Training

  • David - MGI curators were trained last week
  • Kimberly planning a training for ZFIN curators by the end of the month. The documentation will be made more general

Review current work

Main Tasks

GOREFS

Objective:

  • contains all of the GO_REF data in a single machine-usable metadata file (location TBD)
  • Compiles on action to a static page in geneontology.github.io for delivery to geneontology.org

Follow up from last meeting

Noctua Visual Editor

Noctua Updates

Model copy

Status Automated Ontology Updates in Noctua/Minerva

New tasks/Projects

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 2022-03-16 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? Spec reviewed 2022-02-23 Yes 2022-04-20
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? 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: 2022-03-16 - 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