Manager Call 2019-03-27

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Agenda

  • Agenda: Pascale
  • Minutes: Laurent-Philippe


Cambridge GOC Agenda

Start to firm up the agenda for GO meeting:

https://docs.google.com/document/d/1QiqfZ5eAwmljqt5Fh0Ooi1Pd-HKgMSGsYC_wx6-UEPY/edit

Discuss next week whether to present the model copy at this meeting.

Discussion points

March release status

There was a discrepancy in March between the data available in AmiGO (Feb 2nd) and in zenodo (2019-03-10) Discuss next week when Seth is back

PURLs from the public website

PURLs for the ontology need to point to 'current' rather than 'snapshot' -> https://github.com/geneontology/go-site/issues/873 When will we do that ?

It's done. Moving the snapshot links to the wiki (http://wiki.geneontology.org/index.php/Release_Pipeline)

Discussion points

Carried over from previous agendas:

Fate of "unmanaged" external2go files

https://github.com/geneontology/go-ontology/issues/16989

  • Ontology group would like to archived them since we don't have the resources to maintain them and no one is maintaining these (e.g. mips is deprecated).

Must list which projects are not maintained anymore, and at least simplify the list. Waiting from Paul review. It seems tigr will be maintained by NCBI.

external2go svn link: http://viewvc.geneontology.org/viewvc/GO-SVN/trunk/external2go/

Also looking at "Genome Properties" for GO mappings. Chris will put some slides on this for microbial annotations, possibly another grant to have sufficient resources.

Note that there has been a discussion of why the Reactome file hasn't been updated. https://github.com/geneontology/go-site/issues/1031

New IEAs (not InterPro2GO)

https://github.com/geneontology/helpdesk/issues/195

We decided earlier to not accept IEAs from outside groups, as all sequences would be run through the dependable InterPro2GO after uploading- but this group/method *seems* like they have more accurate annotations and higher coverage.

SynGO import

Long discussion last week - What's the next step ?

GPAD/GPI Specs

  • We were going to set up a call - has it be scheduled?
    • Chris was going to review current specs, particularly wrt SO/MSO
  • Discuss expanding the gpi file to include other entities used in annotation, particularly the With/From field. e.g. variation IDs, RNAi experiment IDs, etc.
    • This has come up in discussions with several curation groups, including MGI, WB, and Zfin
    • How does the GO gpi file work fit in with Alliance data files?
    • Not all GO contributors are part of the Alliance, but it would be nice to have standardized file formats for other entities.

New topics

  • We need an SOP for how to handle annotation (or other?) files that have pipeline-blocking errors that can be fixed by GO
    • Is it okay to fix these errors?
    • If yes, then is it okay to point to a GO version of the file in the source URL in the datasets.yaml file until the source file is fixed?
  • Seth to visit MGI in July? Do we have the funds to bring Seth out so he can sit with the software engineer at MGI who handles all of our loads? If we are going to create the uber-gafs at the GOC it would be nice for him to learn the ins and outs of what we do.
  • Should Kimberly and David plan to go to visit Jim some time this spring to focus on the GPAD outputs generated from GO-CAM models?

Minutes

See above notes.


Present

Chris, Pascale, David, Kimberly, Huaiyu, Laurent-Philippe, Suzi, Paul