Manager Call 2020-03-04

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Agenda

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

Discussion points

Caltech f2f, 24-28 Feb

Summary

  • One deliverable from the meeting was GPAD/GPI 2.0 specs.
  • A Google doc with the proposed changes and some comments is available for people to review.
  • There are a few points where we still need a final decision (marked in red).
    • Will we allow >1 reference? Yes, this is the most practical decision.
    • Dates/times ok as specified in the document? Answer:yes
    • For annotation identifiers in the initial import, should we enforce that the identifier prefix be in the db-xref.yaml? These will need to be in the yaml file if the identifiers will persist. Seth thinks they should since they won't be replaced with GO annotation identifiers.
    • Are the new headers ok: Yes
    • For ECO codes in the properties, if they persist we will need to perform a check.
    • For entity types in the GPI, do we want to require groups to go to protein coding gene or non-encoding RNA encoding gene? To what level do we want to require people to annotate? We will require ncRNA and not allow transcript. Otherwise we will follow the existing document.
  • Kimberly will present this on Tuesday's annotation call.

GO meeting Paris

Page ready to be shared: http://wiki.geneontology.org/index.php/2020_Paris_GOC_Meeting_Logistics Registration here: https://www.eventbrite.com/e/gene-ontology-main-meeting-tickets-97870099101

  • People should start registering for the meeting. But there were questions about cancellations.

Pasteur: bioinformatics hub to be cited as co-organizer of the GO User Meeting.

Discussion

Noctua/NEO

  • Loading UniProt Viral + bacterial GPI: This came up again from the multi-organism working group. They want to start making GO-CAM models. Can the loading of the GPI file be prioritized and assigned?

Paper identifying missing 'is_a' relations

David https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaa106/5739437

Some missing relations are not: is it a version problem ? or maybe they aren't using the inferred version of the ontology ?

Is there any missing link that could be useful for the ontology ?

Non-GO editors people making PR in the ontology tracker

https://github.com/geneontology/go-ontology/issues/17091


Isn't our policy that *only* GO editors work on the ontology ? Or do we want to allow some other users to make PRs?