Manager Call 2020-04-15

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Revision as of 04:36, 15 April 2020 by David (talk | contribs) (XenBase onboarding)

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Agenda

  • Agenda: Pascale
  • Minutes: Laurent-Philippe
  • Present:
  • Regrets:

May Consortium Meetings

  • We are within a month of the May consortium meetings
  • Need to start firming up the agenda so people can start planning their schedules and working on presentations

Update on actions from last call

GAF2.2

DECISIONS:

  • Time line: 4 months?
  • Actions:
  1. Pascale/Seth: Write formal specs documentation
  2. Kimberly, David, Laurent-Phlippe: Write usage notes: aim in 2 weeks: Draft of announcement and usage notes
  3. Kimberly, David, Laurent-Phlippe: Write some FAQs: what is the impact; why are we doing this ? Clarify the way a gene is related to a GO term
  4. Send notice
  5. Eric/Seth Adjust scripts
  6. Paul's group: Adjust enrichment tools

XenBase onboarding

ACTIONS

  • Seth will ask Malcom for his files, this will allow to test his pipeline
  • Kimberly and David will continue training XenBase curators, they will join the call
  • Jim is adding the Xenopus anatomy to the imports

Discussion topics

Topics not discussed on last call

GO grant highlights and vision

Google doc with abridged grant with vision sections highlighted: https://docs.google.com/document/d/1t_Ube-ngprwBhyoKh5lDgtYYoQztl3yV1ETcfxrpquk

GOLr search

Collect current issues (eg genes that can not be found) to start improving it

Component for GO annotations in journals

Considering 1) easy to integrate web component and 2) current covid situation where submerged by literature difficult to mine retrospectively, try again to propose a very lightweight tool, probably optional, but that would allow an author to provide (gene, function) associations while submitting. Best journals to try ? biorxiv ?


Pathway Genome Databases and the Alliance

See Chris' email

  • Explore bringing in other existing curated pathways in a similar way that we did for Reactome
  • Follow-up to Alliance call with Peter K. two weeks ago?

ECO and IEAs

In GPAD we mandate use of ECO over evidence codes. However, have we properly evaluated ECO for its use here? There is a massive mismatch in the GO meaning of IEA and the mapped term in ECO, see

Users versus group-contacts.yaml

https://github.com/geneontology/go-site/blob/master/metadata/group-contacts.csv https://github.com/geneontology/go-site/blob/master/metadata/groups.yaml

See discussion in https://github.com/geneontology/go-site/pull/1447

  • users contain all users, including people not on the project anymore
  • Not sure where affiliations come from for eg Cath Brooksbank listed as GO_central).
  • users does not have GH handles
  • group-contacts includes only active members
  • 'Expertise' should like people's expertise or role (developer/curator)

-> How do we want to use those two files moving forward ? Do we need two files ?

Publications

  • Val's matrix paper is available as a draft
  • Authors have reviewed and made comments
  • Do the GO PIs (besides Chris who is last author) also need to read?