Projects update meeting 2022-04-20: Difference between revisions

From GO Wiki
Jump to navigation Jump to search
 
(14 intermediate revisions by 2 users not shown)
Line 1: Line 1:
= Attendees =
= Attendees =


* Members:  
* Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia
* Present:  
* Present: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Chris, Cynthia
* Regrets:  
* Regrets:
 
=Announcements=
* Preparing GOC meeting: finalize the agenda: https://docs.google.com/document/d/1q1_OfUz-EZvw28WJhDnbuNUGFAZz-21-uynNybdJcqg/edit
* Fall meeting in Baltimore  - either week of Oct. 10-14 or Oct. 17-21; is everyone available on these dates?
 
=Project updates=
 
==Completed projects?==
* [https://github.com/orgs/geneontology/projects/68 AmiGO default relation GH project] - still need to update http://geneontology.org/docs/ontology-relations/ DONE - Project closed
* [https://github.com/orgs/geneontology/projects/65 Noctua 2021] (3 tickets left) - status:
* [https://github.com/orgs/geneontology/projects/84 Visual Pathway editor v1.0] - status: on prod; need to finish documentation
* [https://github.com/orgs/geneontology/projects/87 Simple version of Noctua updates] - status:
* [https://github.com/orgs/geneontology/projects/79 Increase number of annotable entities in Noctua / NEO] - close ? 1 ticket still open
 
==Task Matrix==
[https://docs.google.com/document/d/1r3aWGjyz2nXNpyzETPO-ah276HQDc1ClNs57Cm6Nwv0/edit Main tasks - Jan-July 2022]
Needs updating for April
 
==Ongoing projects status==
 
===[https://github.com/geneontology/go-site/issues/1813 Google drive move]===
Seth, Suzi: status
 
===[https://github.com/orgs/geneontology/projects/62 Ongoing data QC and pipeline maintenance]===
* AspGD being taken off line- will now load from GOA:
** either like the 'other' uniprot species, ie, only manual annotations
** or could load the complete file from https://www.ebi.ac.uk/GOA/proteomes
* EXP Annotations by AspGD
** (3434) Aspergillus nidulans FGSC A4
** (981) Aspergillus fumigatus
** (431) Aspergillus niger CBS 513.88
** (354) Aspergillus oryzae RIB40
 
* status:
 
===[https://github.com/geneontology/go-ontology/projects/26 Ontology single step BP jamboree week of 2022-04-04]===
 
===[https://github.com/orgs/geneontology/projects/83 Noctua Training]===
* Training session with ZFIN curators, Thursday, April 14th (David, Kimberly)
 
===[https://github.com/orgs/geneontology/projects/80 Shallow Model Copy]===
 
===[https://github.com/orgs/geneontology/projects/76 Alliance software support]===
Need to define PI, deliverables, resource
 
===[https://github.com/orgs/geneontology/projects/88 GO_REFs]===
Status:
 
===[https://github.com/orgs/geneontology/projects/85 GO API] ===
Status:
 
===[https://github.com/orgs/geneontology/projects/86 PLANNING Pipeline cleanup] ===
Status:
 
== Currently active projects==
{| class="wikitable sortable"
! Project name
! Link to GH project
! Resources: PI, PO, TL, Other resources
! Next review
! Follow up review
! Aligned with Matrix?
! Notes
|-
! colspan="7" | Software improvement
|-
|  Software improvements : GO API
| [https://github.com/orgs/geneontology/projects/85 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
| [https://github.com/orgs/geneontology/projects/86 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
| [https://github.com/orgs/geneontology/projects/76 Alliance software support]
| '''PI:''' , '''PO:'''??, '''TL:''' Seth, '''Others:'''
| 2022-04-06
|
| No
|
|-
| Noctua improvement and maintenance
| [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
| 2022-04-05 Close?
|
| No
|
|-
| GO_REFs
| [https://github.com/orgs/geneontology/projects/88 GO_REFs]
| '''PI:''' Chris, '''PO:''' Chris, '''TL:''' Seth, '''Others:''' Sujay, some of Sierra
| 2022-04-20
|
| Yes
|
|-
|  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?
| Ad hoc if there is a big bug
|
| Yes
|
|-
| Essential software maintenance
| [https://github.com/orgs/geneontology/projects/69 Essential software maintenance]
| '''PI:''' Chris, '''PO:'''Pascale, '''TL:''' Seth, '''Others:''' Seth, Dustin, Sujay, Jim?
| Ad hoc if there is a big bug
|
| Yes
|
|-
! colspan="7" | Remove some main roadblocks for GO-CAM models curation (Aim 2)
|-
| NEO load of new sequences
| [https://github.com/orgs/geneontology/projects/79 NEO load GH project]
| '''PI: Chris''', '''PO:''' Pascale ''', TL:''', Seth '''Others:''' Sujay
| 2022-04-06
|
| Yes
| Close?
|-
|  New visual editor (Tremayne) -> ready push to Noctua prod?
| [https://github.com/orgs/geneontology/projects/84 Visual Pathway editor GH project]
| '''PI:''' Paul, '''PO:''' Paul, '''TL:''', '''Others:''' Tremayne
| 2022-04-05 Close?
|
| Yes
| Missing documentation
|-
| Model copy
| [https://github.com/orgs/geneontology/projects/80 PLANNED Old Shallow Model Copy GH project]
| '''PI: Paul''', '''PO: Kimberly''', '''TL: Jim''', '''Others:''' Tremayne
| 2022-04-20 -  Review status
|
| Yes
| Aim to present at GOC meeting (or announce work is ongoing)
|-
|  Simple version of automation of Noctua updates
| [https://github.com/orgs/geneontology/projects/87 Noctua updates]
| '''PI: ''' Chris, '''PO:''' TBD, '''TL:''' Seth, '''Others:'''
| 2022-04-06 -  Close?
|
| Yes
|
|-
! colspan="7" | Complete MOD imports (Aim 2)
|-
|  MOD imports
| [https://github.com/orgs/geneontology/projects/58 MGI] - [https://github.com/orgs/geneontology/projects/59 WB] - [https://github.com/orgs/geneontology/projects/61 SGD]
| '''PI:''' Chris, '''PO:''' Kimberly, '''TL:''' Seth, '''Others:''' David, Suzi, Dustin
| 2022-04-05 - MGI close?
|
| No
|
|-
| Annotation Extension Relation Review
| [https://github.com/orgs/geneontology/projects/67 Annotation Extension Relation Review]
| '''PI:''' , '''PO:''' Kimberly, '''TL:''' , '''Others:''' David, Dustin, Pascale
| TBD - after some projects are closed
|
|
|
|-
| Integrate YeastPathways  in GO Cam
| [https://github.com/orgs/geneontology/projects/77 Yeast Pathways]
| '''PI:''' Paul, '''PO:''' , '''TL:''' Dustin, '''Others:'''
| 2022-04-06
|
| No
|
|-
! colspan="7" | Ontology (Aim 1)
|-
|  Phylogenetic taxon constraints
| [https://github.com/orgs/geneontology/projects/71 TC GH project - ontology repo]
| '''PI:''' Paul, '''PO:''' Pascale, '''TL:''' Jim, '''Others:'''
| 2022-04-20
|
| Yes
|
|-
! colspan="7" | Outreach/usability (Aim 3)
|-
| Manage users more actively (+ all contributing groups, in particular those not attending GOC and annotation calls)
|
| '''PI:''' Mike , '''PO:''' Suzi, '''TL:''', '''Others:'''
| 2022-04-xx before the GOC meeting
|
| No
|
|-
| Noctua training material
| [https://github.com/orgs/geneontology/projects/83 Noctua training Project]
| '''PI:''' Mike , '''PO:''' Suzi, '''TL:''' NA, '''Others:''' David
| 2022-04-20
|
| Yes
| After/around the ZFIN training session
|-
! colspan="7" | Projects to prioritize
|-
|  Switch to “species” for download outputs
| [https://github.com/orgs/geneontology/projects/57 PLANNED Improved Downloads] ????
|  '''PI:''' , '''PO:''', '''TL:''', '''Others:'''
| 2022-03-23 - Review specs
|
| No
|
|-
|  Noctua output
| [https://github.com/orgs/geneontology/projects/91 PLANNING GPAD outputs- Complex Models and Redundancy Filtering ]
| '''PI:''' Chris, '''PO:''' Kimberly, '''TL:'''?, '''Others:''' Jim
| 2022-04-20 -  Review specs
|
|
|-
| Next Noctua tasks
|
|
|
|
|
|-
| ECO-GO Alignment
| [https://github.com/orgs/geneontology/projects/72 ECO-GO Alignment]
|
|
|
|
|
|-
| GO rules, including missing valid rules from the report
|
|
|
|
|
|-
! colspan="7" | Other projects
|-
|}


=Future topic/project=
=Future topic/project=
 
Seth


* What stats do we want to track, what do we need? Thinking grants, official reports, etc.
* What stats do we want to track, what do we need? Thinking grants, official reports, etc.
Line 12: Line 265:
** Coming from consideration of log retention (policy) for some systems
** Coming from consideration of log retention (policy) for some systems
** This has been pretty ad hoc; do we want/need more structure with this?
** This has been pretty ad hoc; do we want/need more structure with this?
** Straw proposal: yearly roll of S3 logs, tooling to make extraction and use easier (need a policy of some kind)


[[Category: GO Managers Meetings]]
[[Category: GO Managers Meetings]]

Latest revision as of 03:23, 3 May 2022

Attendees

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

Announcements

Project updates

Completed projects?

Task Matrix

Main tasks - Jan-July 2022 Needs updating for April

Ongoing projects status

Google drive move

Seth, Suzi: status

Ongoing data QC and pipeline maintenance

  • AspGD being taken off line- will now load from GOA:
  • EXP Annotations by AspGD
    • (3434) Aspergillus nidulans FGSC A4
    • (981) Aspergillus fumigatus
    • (431) Aspergillus niger CBS 513.88
    • (354) Aspergillus oryzae RIB40
  • status:

Ontology single step BP jamboree week of 2022-04-04

Noctua Training

  • Training session with ZFIN curators, Thursday, April 14th (David, Kimberly)

Shallow Model Copy

Alliance software support

Need to define PI, deliverables, resource

GO_REFs

Status:

GO API

Status:

PLANNING Pipeline cleanup

Status:

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 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: 2022-04-06 No
Noctua improvement and maintenance Noctua 2021 & Noctua 2020 PI: Paul , PO: Kimberly, TL: Seth, Others: Tremayne, Jim 2022-04-05 Close? 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 2022-04-06 Yes Close?
New visual editor (Tremayne) -> ready push to Noctua prod? Visual Pathway editor GH project PI: Paul, PO: Paul, TL:, Others: Tremayne 2022-04-05 Close? Yes Missing documentation
Model copy PLANNED Old Shallow Model Copy GH project PI: Paul, PO: Kimberly, TL: Jim, Others: Tremayne 2022-04-20 - Review status Yes Aim to present at GOC meeting (or announce work is ongoing)
Simple version of automation of Noctua updates Noctua updates PI: Chris, PO: TBD, TL: Seth, Others: 2022-04-06 - Close? Yes
Complete MOD imports (Aim 2)
MOD imports MGI - WB - SGD PI: Chris, PO: Kimberly, TL: Seth, Others: David, Suzi, Dustin 2022-04-05 - MGI close? 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: 2022-04-06 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)
Manage users more actively (+ all contributing groups, in particular those not attending GOC and annotation calls) 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
Projects to prioritize
Switch to “species” for download outputs PLANNED Improved Downloads ???? PI: , PO:, TL:, Others: 2022-03-23 - Review specs No
Noctua output PLANNING GPAD outputs- Complex Models and Redundancy Filtering PI: Chris, PO: Kimberly, TL:?, Others: Jim 2022-04-20 - Review specs
Next Noctua tasks
ECO-GO Alignment ECO-GO Alignment
GO rules, including missing valid rules from the report
Other projects

Future topic/project

Seth

  • What stats do we want to track, what do we need? Thinking grants, official reports, etc.
    • End-of-year summary stats for users, downloads?
    • Coming from consideration of log retention (policy) for some systems
    • This has been pretty ad hoc; do we want/need more structure with this?
    • Straw proposal: yearly roll of S3 logs, tooling to make extraction and use easier (need a policy of some kind)