Projects update meeting 2022-04-06: 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: avid, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia | ||
* Regrets: | * Regrets: | ||
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==Completed projects?== | ==Completed projects?== | ||
* [https://github.com/orgs/geneontology/projects/58 MGI import into Noctua] for mouse annotations | * [https://github.com/orgs/geneontology/projects/58 MGI import into Noctua] for mouse annotations - OK CLOSED | ||
* [https://github.com/orgs/geneontology/projects/52 GO-CAM GPAD Output for MOD imported annotations] OK CLOSED | * [https://github.com/orgs/geneontology/projects/52 GO-CAM GPAD Output for MOD imported annotations] OK CLOSED | ||
* [https://github.com/orgs/geneontology/projects/68 AmiGO default relation GH project] - still need to update http://geneontology.org/docs/ontology-relations/ | * [https://github.com/orgs/geneontology/projects/68 AmiGO default relation GH project] - still need to update http://geneontology.org/docs/ontology-relations/ | ||
* [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] (3 tickets left) & [https://github.com/orgs/geneontology/projects/46 Noctua 2020] (closed) | ||
* [https://github.com/orgs/geneontology/projects/84 Visual Pathway editor v1.0] | * [https://github.com/orgs/geneontology/projects/84 Visual Pathway editor v1.0] | ||
* [https://github.com/orgs/geneontology/projects/87 Simple version of Noctua updates] | * [https://github.com/orgs/geneontology/projects/87 Simple version of Noctua updates] | ||
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==Project status== | ==Project status== | ||
===[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]=== | ||
* 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 | |||
===[https://github.com/orgs/geneontology/projects/79 NEO load of Swiss-Prot reviewed entries]=== | ===[https://github.com/orgs/geneontology/projects/79 NEO load of Swiss-Prot reviewed entries]=== | ||
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Need to define PI, deliverables, resource | Need to define PI, deliverables, resource | ||
===[https://github.com/geneontology/go-ontology/projects/26 Ontology single BP jamboree this week]=== | ===[https://github.com/geneontology/go-ontology/projects/26 Ontology single step BP jamboree this week]=== | ||
Monday - Thursday | Monday - Thursday | ||
===[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/80 Shallow Model Copy]=== | ||
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|- | |- | ||
| Noctua output | | Noctua output | ||
| [https://github.com/orgs/geneontology/projects/ | | [https://github.com/orgs/geneontology/projects/91 PLANNING GPAD outputs- Complex Models and Redundancy Filtering ] | ||
| '''PI:''' Chris, '''PO:''' Kimberly, '''TL:'''?, '''Others:''' Jim | | '''PI:''' Chris, '''PO:''' Kimberly, '''TL:'''?, '''Others:''' Jim | ||
| 2022-04-20 - Review specs | | 2022-04-20 - Review specs | ||
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| | | | ||
|- | |- | ||
| | | ECO-GO Alignment | ||
| | | [https://github.com/orgs/geneontology/projects/72 ECO-GO Alignment] | ||
| | | | ||
| | | |
Latest revision as of 01:38, 20 April 2022
Attendees
- Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia
- Present: avid, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia
- Regrets:
Announcements
- Preparing GOC meeting: start planning the agenda: https://docs.google.com/document/d/1q1_OfUz-EZvw28WJhDnbuNUGFAZz-21-uynNybdJcqg/edit
- Fall meeting in Baltimore?
- Pascale off next week
Google drive move
- Google drive move
- Query owner:me in the 'LEGACY Gene Ontology -use Shared Drive' to make sure all files have been moved
- Looks like quite a few files are left https://drive.google.com/drive/search?q=parent:0B8kRPmmvPJU3dFhhcWhTSmlUcDA%20owner:
Project updates
Task Matrix
Main tasks - Jan-July 2022 Needs updating for April
Completed projects?
- MGI import into Noctua for mouse annotations - OK CLOSED
- GO-CAM GPAD Output for MOD imported annotations OK CLOSED
- AmiGO default relation GH project - still need to update http://geneontology.org/docs/ontology-relations/
- Noctua 2021 (3 tickets left) & Noctua 2020 (closed)
- Visual Pathway editor v1.0
- Simple version of Noctua updates
Project 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
NEO load of Swiss-Prot reviewed entries
Blocking for Swiss-Prot curators to make models
Alliance software support
Need to define PI, deliverables, resource
Ontology single step BP jamboree this week
Monday - Thursday
Noctua Training
- Training session with ZFIN curators, Thursday, April 14th (David, Kimberly)
Shallow Model Copy
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 | 2022-04-06 Close? | 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: | 2022-04-06 | 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 | Seth will look into a strategy - week of March 16th | |
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 | Ready for release to prod? Present at a future annotation call - or GOC meeting | |
Model copy | PLANNED Old Shallow Model Copy GH project | PI: Paul, PO: Kimberly, TL: Jim, Others: Tremayne | 2022-04-05 - 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 | |||||
Other projects |