Annotation Conf. Call 2017-08-08

From GO Wiki
Jump to navigation Jump to search
The printable version is no longer supported and may have rendering errors. Please update your browser bookmarks and please use the default browser print function instead.

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., George, Harold, Helen, Kevin, Kimberly, Li, Liz, Midori, Moni, Pascale, Paul T., Penelope, Petra, Rob, Sabrina, Sage, Shur-Jen, Stacia, Stan, Suzi, Terry, Tom, Val

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
      • Can also help address whether the chosen terms are too high level to be useful
  • 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:
    • Co-annotation can be used to capture information when a combined term in the ontology cannot be made
    • Analysis can help determine when there might need to be work done on the ontology (e.g. missing relations) or on the annotations (e.g. cytoplasm annotations -> cytosol annotations)
    • Note that in the AGR display, the labels may need to be adapted to be more biologist friendly
    • Can we have some outside review of the labels?

Action Items

  • AI: Document the methodologies used to create and analyze slims
  • AI: Supply list of GO ID - Name pairs used for GO slims (new github ticket - https://github.com/geneontology/go-ontology/pull/14031)
  • AI: Get feedback from users on GO slim term labels
    • Pascale will send out the list

Signaling Project

  • Wnt - Giulia, Helen, Kimberly
  • MAPK - David H., Sabrina
    • Examining genes for MAPK pathway +/- MF support
    • Looking at gene products potentially upstream/downstream
  • Ca2+ Signaling - Penelope
    • Still needs an ontology editor
  • GPCR - Pascale, Petra
    • Have downloaded annotations, but still need to review them
    • Have created a generic GO-CAM model
      • A few templates already existed - link to model 0000200, 0000466, 0000486
      • Is the heterotrimeric G protein cycle term needed?
      • How much detail should be included about the functions of the members of the pathway?
      • If there is more than one way to represent a pathway, how should we choose which way to annotate?
Retrieved from "https://wiki.geneontology.org/index.php?title=Annotation_Conf._Call_2017-08-08&oldid=64742"