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 | ||
== | =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/ | 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== | ==Follow up from last meeting== | ||
Line 36: | Line 53: | ||
* Specs finalized? Plan was to finalize on 2022-03-03 Technical call | * Specs finalized? Plan was to finalize on 2022-03-03 Technical call | ||
* Need to plan a start date and a review date | * Need to plan a start date and a review date | ||
* Aim to present at GOC meeting | |||
===Status Automated Ontology Updates in Noctua/Minerva=== | ===Status Automated Ontology Updates in Noctua/Minerva=== | ||
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===New tasks/Projects=== | ===New tasks/Projects=== | ||
* 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/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? | ||
* Google drive move (Pascale, Suzi, others later) | * [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 | ||
* Annotation documentation (Pascale, Patrick, others later) | * [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 | ||
| Yes | |||
| 2022-04-20 | |||
| | | | ||
|- | |- | ||
| Alliance software support | | Alliance software support |
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
- Moving the GO google drive https://drive.google.com/drive/folders/0ABiscjZCrxjUUk9PVA
- Preparing GOC meeting
Projects updates
Finalize AmiGO default relation change (Aim 3)
- Should be completed with the (Feb) March release: AmiGO default relation GH project
- links to the relations page - needs improvement (Chris, Pascale if needed)
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
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
- 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
- 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
- Move all SheX compliant relations to the form, even if some will be changed later (Kimberly, Tremayne): project or ticket in next Noctua improvements?
- Google drive move (Pascale, Suzi, others later) -- CAN WE DISCUSS THIS FIRST?? https://github.com/geneontology/go-site/issues/1813
- Annotation documentation (Pascale, Patrick, others later)
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 | ||||||