Manager Call 2020-04-08

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Agenda

  • Agenda: Seth
  • Minutes: Pascale
  • Present: Pascale, Seth, Judy, Chris, Kimberly, David, Huaiyu, Laurent-Philippe, Paul T,
  • Regrets:

Discussion points

GAF2.2 relations qualifiers

Kimberly and Pascale drafted specs: https://github.com/geneontology/go-annotation/issues/2917

  • What's the next step ?
    • Seth: figure out timeline
  • Will we support both files to load from the MODs ?
  • Will we produce both files, so people don't need to adjust parsers if they don't have the resources
    • Chris: No - we will give a warning a long time in advance, and switch on a given date
    • LP points out some tools are not maintained, so nobody would be able to update their parsers
    • Seth: it would be very confusing to have both files available
    • Chris: we need documentation for programmers
    • Chris: how long it it going to take up to make this information consistent and useful ?
      • David: MGI switched to 'causally upstream of or within' - so for a long time this will not be very informative.
      • Kimberly: this will vary on a group-by-group basis
      • Paul: We can explain the differences between groups, and we can explain that for enrichment analysis we can split genes that are more or less direct: can have an option to include or exclude indirect annotations. This would not be available for all groups until they sort out their annotations.

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
  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. * Draft Google doc
  4. Send notice
  5. Eric/Seth Adjust scripts
  6. Paul's group: Adjust enrichment tools

MGI and WB Imports

Status updates

  • WB
    • Alex will work on preparing a test GPAD file with annotation history for WB - hopes to have it on the GOA ftp site soon
  • MGI
  • Done contributors in the properties field
  • Next: created by/created date
  • Harold has modified the former MGI curators
  • David still cleaning up tons of annotations that have ShEx violations
  • Seth: no the software side: fixing some stuff for GPAD/GPI

Xenbase

  • Xenbase only annotates in Noctua. Would like to get their annotations from GO central.
  • High priority for Xenbase, they would like to consume annotations from us
  • What is the priority for us ?
  • Kimberly and David spent 2 hours last week training them; they will do that again next week. They don't know how long these meetings will carry on.
    • Paul: how much is this costing us ? Can we merge those calls into the annotation call ? To make this more efficient.
    • David: trying to get them up to speed and aim to stop the calls soon.
    • Kimberly: makes sense to move those 1:1 discussions to the annotation calls.
  • Should we switch to encouraging groups to annotate in a process-centric manner ? (The answer was not extremely clear - Pascale added to the PI call)


  • Seth: Getting XenBase in is nice because it gives us a test bed
  • Paul says we can just spot check annotations
  • Chris: maybe is it worth it to delay imports to make sure that the XenBase annotations are good and the documentation is useful
  • Paul: this is very useful, also for the grant AND for the collaboration with Alliance; can we think of a way to make this most efficient ?
  • David: this is exactly what they have been doing; only creating simple annotations.
  • Malcolm already attends Judy's meeting, TO-DO: invite him (and/or xenbase reps) to GO-annotation calls. Need to make sure XB maintains own annotations, is in line with GO SOPs.

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

GO Covid page & banner

http://geneontology.org OK ?

  • Yes - ready to go
  • LP proposes to write a short letter to editor/ or something like this
  • Patrick is able to use viral entries - no chains yet but this should be coming soon.

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?