Projects update meeting 2022-03-02
- Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia
- Present: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia
Noctua Visual Editor
Visual Pathway editor GH project Paul: status, next tasks, timeline to move to production
- Testing on production (beta) Tremayne's latest PR: https://github.com/geneontology/noctua-form/pull/167
- Aiming to move to production by end of this week/early next week
- PI: Paul, PO: Kimberly, TL: Jim, Others: Tremayne
- A summary from the (long) existing ticket:
- Implement a 'shallow copy'.
- Shallow copy = Everything (ontology terms, relations, enablers, extensions) is copied. See Paul's comment
- We will NOT copy evidence and other metadata.
- A DerivedFrom tag will capture, at the model level, the originating model id.
- The new model will only have the copier as contributor.
- A default title, 'copy of x', where x is the original model title will be added.
- All copied models will initially have state = development.
- Technical issues still to be decided. See Seth's comment:
- A way forward here to restart would be to re-evaluate the two paths forward: an examination of the changes needed to the client copier (and dusting of the interface to test it) and balancing that against the amount of work if the same was to be done in minerva.
Status Automated Ontology Updates in Noctua/Minerva
- PI: Chris (@cmungall) PO: TBD TL: Seth Others: Jim
Loading Beetle data
Suzi - Can Dustin do that?
Adding 'has part' annotations in GO pipeline
Pascale - annoying for ontology(ie, for GO terms that have 'has part' terms, we'd like these to be asserted since they are not in the hierarchy by default) -> can this be added to the pipeline improvement project? https://github.com/geneontology/go-ontology/issues/19721 See issue comment and next item https://github.com/geneontology/pipeline/issues/130
Review current work
Currently active projects:
|Project name||Link to GH project||Resources: PI, PO, TL, Other resources||Next review||Follow up review||Aligned with Matrix?||Notes|
|Finalize AmiGO default relation change (Aim 3)||AmiGO default relation GH project||PI: Chris, PO:Chris, TL: Seth, Others: Seth||2022-02-16||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?||2022-02-23 - Review specs||Needs to be better specified|
|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||2022-03-02||2022-03-16||No|
|Ongoing data QC and pipeline maintenance||Ongoing data QC and pipeline maintenance||PI: Chris, PO:Pascale, TL: Seth, Others: Seth, Dustin, Sujay, Jim?||2022-02-23 - Review project status||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:||2022-02-23 - 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|