Manager Call 2020-08-05

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Agenda

  • Agenda: Laurent-Philippe
  • Minutes: David
  • Present: SuziA, Chris, Laurent-Philippe, Huaiyu, Seth, David

GO Baltimore

Basic page created with google doc to start filling agenda: http://wiki.geneontology.org/index.php/October_2020_Remote_GOC_Meeting_Logistics

Format: 3 half days like in May ? Yes

User meeting: nothing prepared for the moment. Do we want one ? There was nothing in mind.

From last meeting, users preference were:

- enrichment analysis

- data access and integration

- hands-on, jupyter notebooks

- ontology

- curation

If it is up to a general audience, then we can customize it however we want. What do we want to communicate to a broader audience? Laurent-Philippe will contact Michelle.

GO-CAM Jamboree

  • Proposal to have a GO-CAM curation jamboree sometime this fall
  • How critical will it be to have Noctua on a more secure production footing by this time?

Not sure yet before or after GO meeting. Possible concern with the fire season.

Name: GO-CAMboree ?

GPAD/GPI

  • There is a discussion about possibly duplicating effort by asking groups to submit a GPI file to GO and a BGI file to the Alliance.
    • Stacia raised the issue of possibly overlapping goals here on a GO annotation call some time ago.
    • Should we re-visit this and discuss aligning these files more closely? Could one file be derived from the other?
    • Should these types of files be moving towards a more ontological representation of entities? We'd ultimately like to do that with annotatable entities in GO.
    • What would the development costs be for everyone to make changes?
    • Need to communicate our thoughts/decision on this to the Alliance PIs
  • 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.

Also how to include xrefs (eg gp2protein, gp2rna) in GPI files.

The GPI format is superceding these. This is already in the format for the GPI.

Data Visualization Workshop at ECCB

Any update on register as a group ? Assign someone ?

https://bionetvisa.github.io

Laurent-Philippe will go and report back to the group.

GO COVID-19

Update ? New GPI ingested ? Patrick annotations ?


The GPI file has been recurated. It has a single entry for all annotatable entries. Chris will make a ticket to pick up the new file. https://github.com/geneontology/neo/issues/60

Projects update

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


Legacy data

Laurent-Philippe

100 releases generated over the last 8 years from SVN

Waiting for CVS / backup of archive.geneontology.org (eg MySQL)

GH repository to keep track of development & share comments/issues: https://github.com/geneontology/archive-reconstruction

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

ART

Specs here to discuss: https://docs.google.com/document/d/1iaqE1xEhvgT0OxfF8YUN36Gii962mQQ-ouTlP8OppGM/edit#heading=h.gx5r3bwu5gee Converging on something stable with general approval

GO pipeline solidified / Infrastructure / DevOps (#4)

Discussion on taxon constraints ? Anything else to report ?

Jim is working on this. Eric is addressing a bug.

GO release

Some issues:

GO-CAM content

-> 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