Projects update meeting 2022-03-23: 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, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Cynthia
* Regrets:  
* Regrets: Paul
 
[https://docs.google.com/document/d/1r3aWGjyz2nXNpyzETPO-ah276HQDc1ClNs57Cm6Nwv0/edit Main tasks - Jan-July 2022]


=Announcements=
=Announcements=
* Preparing GOC meeting: start planning the agenda
* Preparing GOC meeting: start planning the agenda: https://drive.google.com/drive/folders/1Y5DfKpQu4tGxDmJaH-nHDDNkFy5x-w6B


== Follow up from last meeting==
== Follow up from last meeting==
* wiki move
* wiki move (this is it)
* [http://wiki.geneontology.org/index.php/Projects_update_meeting_2022-03-16#Model_copy Google drive move]
* [http://wiki.geneontology.org/index.php/Projects_update_meeting_2022-03-16#Model_copy Google drive move]


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===Alliance software support===
===Alliance software support===
Seth
Seth
[https://github.com/orgs/geneontology/projects/76 Alliance software support]
[https://github.com/orgs/geneontology/projects/76 Alliance software support] (noting split with https://github.com/orgs/geneontology/projects/92)


===Noctua improvement and maintenance===
===Noctua improvement and maintenance===
*  Status and next steps
*  Status and next steps
** [https://github.com/orgs/geneontology/projects/65 Noctua 2021]  
** [https://github.com/orgs/geneontology/projects/65 Noctua 2021]  
** [https://github.com/orgs/geneontology/projects/46 Noctua 2020]
** [https://github.com/orgs/geneontology/projects/46 Noctua 2020] - reviewed remaining outstanding tickets and closed project as of 2022-03-18
*** Two tickets moved to neo project
*** Two tickets moved to current project - done
*** Two put back into repos for future discussion
 
===MOD imports===
* Review projects, decide what's in scope
* [https://github.com/orgs/geneontology/projects/58 MGI] - [https://github.com/orgs/geneontology/projects/59 WB] - [https://github.com/orgs/geneontology/projects/61 SGD]
 
===New visual editor===
Ready to deploy?
 
===QC & Pipeline and Essential software maintenance===
Release last week (March 16th); anything to report?what resources are needed until the next release stats?
 
===Update annotation documentation===
* [https://github.com/orgs/geneontology/projects/89 Update annotation documentation]
Pascale -> would like to wait until the wiki and the G drive are moved
 
===New projects to create===
* Manager new users more actively (+ all contributing groups, in particular those not attending GOC and annotation calls)


== Currently active projects==
== Currently active projects==
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| [https://github.com/orgs/geneontology/projects/65 Noctua 2021] & [https://github.com/orgs/geneontology/projects/46 Noctua 2020]
| [https://github.com/orgs/geneontology/projects/65 Noctua 2021] & [https://github.com/orgs/geneontology/projects/46 Noctua 2020]
| '''PI: '''Paul , '''PO:''' Kimberly, '''TL:''' Seth, '''Others:'''  Tremayne, Jim
| '''PI: '''Paul , '''PO:''' Kimberly, '''TL:''' Seth, '''Others:'''  Tremayne, Jim
|  
| 2022-03-23
|  
|  
| No  
| No  
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|-
|-
| GO_REFs
| GO_REFs
| [GO_REFs]
| [https://github.com/orgs/geneontology/projects/88 GO_REFs]
| '''PI:''' Chris, '''PO:''', '''TL:''' Seth, '''Others:''' Sujay,
| '''PI:''' Chris, '''PO:''' Chris, '''TL:''' Seth, '''Others:''' Sujay, some of Sierra
| 2022-04-20
| 2022-04-20
|  
|  
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| [https://github.com/orgs/geneontology/projects/62 Ongoing data QC and pipeline maintenance]
| [https://github.com/orgs/geneontology/projects/62 Ongoing data QC and pipeline 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
|  
|  
| Yes
| Yes
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|  
|  
| +/- : Planned for March, but project not yet defined or resourced
| +/- : Planned for March, but project not yet defined or resourced
|
| David will split into 3 projects: (1) GPAD for MOD imports (done); (2) remove redundancy in exports (high priority); (3) problems with complicated models
|-
|-
|  Simple version of automation of Noctua updates (planned)
|  Simple version of automation of Noctua updates (planned)
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|  
|  
| Yes
| Yes
|
|  
|-
|-
! colspan="7" | Complete MOD imports (Aim 2)
! colspan="7" | Complete MOD imports (Aim 2)
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| [https://github.com/orgs/geneontology/projects/67 Annotation Extension Relation Review]
| [https://github.com/orgs/geneontology/projects/67 Annotation Extension Relation Review]
| '''PI:''' , '''PO:''' Kimberly, '''TL:''' , '''Others:''' David, Dustin, Pascale
| '''PI:''' , '''PO:''' Kimberly, '''TL:''' , '''Others:''' David, Dustin, Pascale
|  
| TBD - after some projects are closed
|  
|  
|  
|  
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| [https://github.com/orgs/geneontology/projects/77 Yeast Pathways]
| [https://github.com/orgs/geneontology/projects/77 Yeast Pathways]
| '''PI:''' Paul, '''PO:''' , '''TL:''' Dustin, '''Others:'''  
| '''PI:''' Paul, '''PO:''' , '''TL:''' Dustin, '''Others:'''  
|  
| 2022-03-20
|  
|  
| No
| No
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| [https://github.com/orgs/geneontology/projects/83 Noctua training Project]
| [https://github.com/orgs/geneontology/projects/83 Noctua training Project]
| '''PI:''' Mike , '''PO:''' Suzi, '''TL:''' NA, '''Others:''' David
| '''PI:''' Mike , '''PO:''' Suzi, '''TL:''' NA, '''Others:''' David
| 2022-03-30
| 2022-04-20
|
|
| Yes
| Yes

Latest revision as of 03:30, 29 March 2022

Attendees

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

Main tasks - Jan-July 2022

Announcements

Follow up from last meeting

Project updates

Alliance software support

Seth Alliance software support (noting split with https://github.com/orgs/geneontology/projects/92)

Noctua improvement and maintenance

  • Status and next steps
    • Noctua 2021
    • Noctua 2020 - reviewed remaining outstanding tickets and closed project as of 2022-03-18
      • Two tickets moved to neo project
      • Two tickets moved to current project - done
      • Two put back into repos for future discussion

MOD imports

  • Review projects, decide what's in scope
  • MGI - WB - SGD

New visual editor

Ready to deploy?

QC & Pipeline and Essential software maintenance

Release last week (March 16th); anything to report?what resources are needed until the next release stats?

Update annotation documentation

Pascale -> would like to wait until the wiki and the G drive are moved

New projects to create

  • Manager new users more actively (+ all contributing groups, in particular those not attending GOC and annotation calls)

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 2022-03-30 Yes To review and close after the next release. Webpage on relations need improvement (Chris, Pascale)
Software improvements : GO API GO API PI: Chris, PO:??, TL: Seth, Others: Sierra Review status 2022-04-20 Yes Will review at the end of April to see the status of the project
Software improvements : pipeline cleanup PLANNING Pipeline cleanup PI: Chris, PO:??, TL: Seth, Others: Seth, Dustin, Sujay? Review specs & scope 2022-04-20 Yes Planned for April
Alliance software support Alliance software support PI: , PO:??, TL: Seth, Others: 2022-03-23 No
Noctua improvement and maintenance Noctua 2021 & Noctua 2020 PI: Paul , PO: Kimberly, TL: Seth, Others: Tremayne, Jim 2022-03-23 No
GO_REFs GO_REFs PI: Chris, PO: Chris, TL: Seth, Others: Sujay, some of Sierra 2022-04-20 Yes
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 2022-03-30 Yes Seth will look into a strategy - week of March 16th
New visual editor (Tremayne) -> ready to push to Noctua dev? Visual Pathway editor GH project PI: Paul, PO: Paul, TL:, Others: Tremayne 2022-03-23 Yes Ready for release to prod? Present at March 22 annotation call
Model copy PLANNED Old Shallow Model Copy GH project PI: Paul, PO: Kimberly, TL: Jim, Others: Tremayne 2022-03-30 - Review status Yes Aim to present at GOC meeting (or announce work is ongoing)
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 David will split into 3 projects: (1) GPAD for MOD imports (done); (2) remove redundancy in exports (high priority); (3) problems with complicated models
Simple version of automation of Noctua updates (planned) Noctua updates PI: Chris, PO: TBD, TL: Seth, Others: 2022-03-30 - Review status Yes
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 TBD - after some projects are closed
Integrate YeastPathways in GO Cam Yeast Pathways PI: Paul, PO: , TL: Dustin, Others: 2022-03-20 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 2022-04-20 Yes After/around the ZFIN training session
Other projects