Annotation Conf. Call 2022-02-01

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Agenda and Minutes

Meetings and Announcements


  • Regularly scheduled Noctua outages:
    • Thursday, February 10th
    • Thursday, February 24th

Ontology and Annotation Issues


  • Overall goal:
    • Use a core set of relations in the ontology and annotation
    • Capture the biologically relevant inputs in a clear, consistent way
  • Discuss work needed to update 'transports or maintains localization of' -> 'has primary input'

Ontology Terms

Aging miniproject

(Proposed by Val) This became a higher priority last week because there will be a NSF workshop in Florida this week about microbial annotation, and one possible outcome is the increase in automatic/text-mining-based annotation, and phenotypes are often misannoatated by these tools. Val mentions function prediction people working with fission yeast researchers making predictions to ageing. All they are probably doing really is extrapolating phenotypes like this: (an ageing phenotype, already has 415 annotation) and inferences from other species to the GO term "ageing". (which as far as we know is just 'cells survive longer under starvation before they die) it's just knockouts which increase viability (mainly those that attenuate growth like genes involved in TOR signalling and translation or carbohydrate utilization.

It is difficult for to say these predictions are invalid if GO has such terms.


  • Features added:
    • Alliance Pathway Preview workbench
      • Example Alliance GO-CAM Display
      • What models get displayed?
      • Defaults to display models with two or more consecutive causal relations between MFs, e.g. positively regulates
        • Ongoing discussion and work with the Alliance Pathways working group and the GO software team to refine this


  • On call: Bob, Chris, David, Deborah, Dustin, Edith, Giulia, Harold, Helen, Jodi, Karen, Kimberly, Li, Malcolm, Pascale, Patrick, Rahi, Raymond, Rob, Stacia, Suzi, Tanya, Petra, Seth, Val