Annotation Conf. Call 2019-02-12

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Meeting URL

  • Please see the GO's Google calendar.
  • Contact Kimberly if you do not have access.

Agenda

GOC Meeting, Cambridge, UK

  • Thursday, April 11th and Friday, April 12th
  • 1/2 day shorter than our usual meetings
  • Logistics
  • Agenda - start Google doc?

New GOC Website

  • Congrats to all who worked on getting the new GOC website out to production
  • Any additional comments, feedback, questions?

Annotation Pipeline

  • Annotation reports on snapshot, current
  • Any comments, feedback, questions?

Ontology Requests

  • Ontology editors are collaborating with the Rhea database to align GO and Rhea (and Reactome).
  • For enzymatic activities, please check for an existing Rhea reaction xref and add to your request.

References for GO Annotations

GOC Progress Report

  • Reminder about PMC submission for all articles associated with the GOC grant progress report

GOC Hackathon - Berkeley, January 28th - February 1st

  • Working meeting held in Berkeley to develop SOP for importing a MOD's worth of GO annotation into Noctua as gene-centric GO-CAMs
  • Details on the outcome of this meeting will be presented on next week's GO-CAM call

Minutes

  • On call: Barbara, Chris, David, Dmitry, Dustin, Edith, Giulia, Helen, Harold, Karen, Kevin M, Kimberly, Li, Michele, Midori, Monika, Patrick N, Rob, Sabrina, Shur-Jen, Seth, Stacia, Suzi A, Tanya, Laurent-Philippe, Petra

GOC Meeting, Cambridge, UK

  • Hotel bloc available thru March 1st, so please reserve now if you need a room
  • Meeting is Thursday and Friday, but Saturday could be reserved for working groups, if needed - please think about this!
  • Registration fees will likely be <100 pounds and Val will look into coordinating payment through her department (otherwise - cash payment at the meeting)

GOC Website

  • Please check funding and contributors list for each group
  • Report any other issues on the github helpdesk repo

Ontology Requests - Enzymatic Activities

  • When requesting a new enzymatic activity term, please check the Rhea database for an appropriate xref and include that with your request
  • Please also always include a PMID or other accession/identifier for a reference
  • You can search Rhea using an EC
  • Rhea is very comprehensive and detailed, but if you believe that the enzymatic activity you're looking for is not included, you can request a new entry from Rhea

Curating Preprints in bioRxiv

  • Good discussion on the pros/cons of curating preprints, especially those found in bioRxiv
  • Although most groups would not choose to do this right now, we concluded that if a curator feels strongly that there is valuable information in a bioRxiv preprint, they may curate that paper
  • Proposed SOP (to be presented on manager's call for final approval):
    • Curator should determine that the preprint is the only published source of the data and that the data is of high quality
    • GO annotations can be made as usual, citing the unique accession of the preprint
    • If and when the preprint appears as a peer-reviewed publication, the curator needs to review the paper again, perhaps in collaboration with the authors, to make certain that the annotations are still correct
    • Existing and/or new annotations from the paper will then be updated to cite the accession for the peer-reviewed paper

Other Reference Related Topics

  • We discussed how groups handle retracted papers - all annotations associated with retracted papers need to be removed
  • Papers where the conclusions may have been over-interpreted or where more recent data has clarified the role or activity of genes - these annotations should be reviewed and removed if no longer accurate
  • We still need an effective mechanism for keeping track of papers that should not be (re-)annotated once the data in the paper has been shown to be incorrect
  • Could we get a handle on how many papers curated for GO have subsequently been shown to have incorrect information?
    • Could we compare older annotation files with new files to see which references have been removed?