Projects update meeting 2022-04-20: 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, Chris, Cynthia | ||
* Regrets: | * Regrets: | ||
=Announcements= | =Announcements= | ||
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Needs updating for April | Needs updating for April | ||
==Google drive move== | ==Ongoing projects status== | ||
===[https://github.com/geneontology/go-site/issues/1813 Google drive move]=== | |||
Seth, Suzi: status | 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= |
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
- 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?
- AmiGO default relation GH project - still need to update http://geneontology.org/docs/ontology-relations/ DONE - Project closed
- Noctua 2021 (3 tickets left) - status:
- Visual Pathway editor v1.0 - status: on prod; need to finish documentation
- Simple version of Noctua updates - status:
- Increase number of annotable entities in Noctua / NEO - close ? 1 ticket still open
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:
- 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:
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)