Annotation Conf. Call 2017-08-08

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Meeting URL

Agenda

Ontology Report

Signaling Project

  • Update on progress to date, github tickets
    • Wnt - Giulia, Helen, Kimberly
    • MAPK - David H. and Sabrina
      • Examining gene products annotated to the process with no experimental support for known MFs
      • Thinking about how to define the beginning and parts of the pathway
    • Ca2+ Signaling
      • Fertilization - Penelope
    • GPCR - Pascale, Petra
      • Some ontology tickets have been addressed
      • Needs global annotation review
      • Needs GO-CAM model
    • Reminder - discussion on specific github tickets, not on project page

Minutes

  • On call: David H., Harold, Helen, Kevin, Kimberly, Li, Liz, Midori, Moni, Pascale, Penelope, Rob, Sabrina, Sage, Shur-Jen, Stan, Suzi, Terry, Val, Stacia

Ontology Report

Check Annotations

  • SUMO protease annotations may be too generic https://github.com/geneontology/go-ontology/issues/13941
    • Annotations to SUMO protease terms may be able to be deepened to one of the two more specific SUMO protease terms (endopeptidase or isopeptidase)
    • Gene products annotated are listed on the github ticket

GO Slims

  • GOC slim ticket https://github.com/geneontology/go-ontology/issues/13996
    • Mary will use her algorithmic method, but the output slim will need review from GOC member groups
    • Val's matrix tool can be a good tool for checking redundancy in the slim
      • Will also address whether the chosen terms are too high level to be useful
  • AI: Document the methodologies used to create and analyze slims
  • AI: Supply list of GO IDs used for GO slims (make new github ticket)
    • Supply ID - Name pairs
  • Modification to AGR slim
    • Confirm that all AGR member groups are okay with current version of GO AGR slim
    • Doug had suggested including additional bins for:
      • Genes not mapped to any term in the slim (other)
        • It can be very difficult to try to map all genes to a slim term - you want to have biologically meaningful term selection without including terms that are too high level or too specific
      • Genes not annotated to any term at all
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