Manager Call 2020-07-22

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Agenda

  • Agenda: Seth
  • Minutes: Pascale
  • Present: Suzi, Laurent, Pascale, David, Judy, Huaiyu, Kimberly, PaulT



Users question

https://github.com/geneontology/helpdesk/issues/269

Paul will answer - Suzi will forward to the user

Projects update

https://docs.google.com/document/d/1URLkEQBewlzD-NVAjbPLWD5Gu-5xq0RysTrm1GMbuiM/edit#

Stats

Seth? (Laurent-Philippe's tasks are completed?) Almost ready to be integrated - didn't make the July release (yesterday) Discussion: To be discussed on the software call Thursday.


Pipeline (#4)

d. 142 species Laurent-Philippe sent the list of 204 species with > 1000 annotations - Paul, Huaiyu, Pascale to check which to integrate? Discussion: Paul: the 204 species include non-EXP; will set up a separate call -> Pascale and Paul off line - looking at EXP data, only A. fumigatus and rainbow trout has > 1000 EXP annotations. Asked Marc Feuermann if A. fumigatus would be useful to have. Trout have many 'response to' annotations, probably would not provide much useful primary annotations.

Legacy data

Laurent-Philippe Will try to use the SVN archive

Additional taxon constraints

(Pascale) Jim estimates that to integrate new taxon constraints that Paul proposes, and check if they are conflicting or redundant would take 2-3 days Paul/Seth: Add as a secondary priority

Ontology

Design patterns (Pascale): would like to clean up the repo, and get Jim (?) to help link terms to the appropriate design patterns, so that new children would be created with the correct design pattern. Pascale: will check with Jim what we could do to improve this and how much time it might take

Moving groups to Noctua (#3)

Kimberly has a GPAD file with full history and looking into loading this David is working on GPAD/GPI 2.0 files

GO pipeline solidified / Infrastructure / DevOps (#4)

Discussion: Seth: nothing to report Had no time to work on the pipeline Pascale asked if we could pay for any services to make the pipeline more efficient. Seth: Nothing on the main pipeline, but the Travis checks (go-ontology) perhaps. We need to check

GO-CAM content

i. List of BP to annotate ii. Annotation jamboree(s)

-> Do we want to schedule that ? Or are there Noctua features required first ? - Kimberly generated a list of pathways for C elegans - Kimberly: We *could* schedule a jamboree for the fall, but she is concerned that we have many questions about how to model certain things (namely, activity-regulating processes) - Kimberly will ask at the next annotation call to see who would be interested in attending, and will schedule a date


GO-CAMs from existing pathway resources

Ben is writing the paper


Creating GMT files

https://github.com/geneontology/go-site/issues/1536 Does this needs to be added in the priorities ?


GPAD/GPI

Would like to formalize groups’ review of the specifications and ask groups to sign off their review on a github ticket. Would give groups until September 1st, but after that no changes would be allowed for 2.0.