Annotation Conf. Call 2020-01-28

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Agenda and Minutes

  • Present: Bob, Chris, David, Edith, Giulia, Harold, Helen, Karen, Kimberly, Laurent-Philippe, Li, Midori, Pascale, Penelope, Sabrina, Seth, Stacia, Stan, Suzi, Tanya

Annotation Calls

  • We will meet weekly on Tuesdays at 8am PST.
  • Will no longer make the distinction between annotation and GO-CAM/Noctua calls.

Noctua

  • Noctua will be updated later today to make the new Noctua form the default version of the form.
  • Please let us know if you experience any trouble with Noctua after the update, or have questions on how to use the form.
  • Documentation is here: http://wiki.geneontology.org/index.php/Noctua

Annotation Relations

  • Goal is to review use of relations across annotations (standard and GO-CAM) and the ontology to ensure consistency wherever possible
  • Relation to discuss this week:
    • 'activated by'
    • https://github.com/geneontology/go-annotation/issues/2718
    • 'activated by' had been defined as a relation used to identify a chemical substance that increases the activity of the gene product
    • Going forward, though, the aims are to:
      • model regulatory events in terms of activities enabled by gene products (this implies that we have some knowledge of the regulatory mechanism)
      • capture bona fide regulatory molecules (what is being 'sensed'), but not cofactors such as ions or coenzymes
        • experiments that determine an enzyme's ion specificity, for example, would not be annotated
    • For standard annotation, an example is:
      • GeneProduct 1 'enables' small molecule binding (GO:0036094) 'has_input' (some chemical), 'directly_positively_regulates' molecular function
      • GeneProduct 1 'enables' molecular function
    • Sample GO-CAM model: http://noctua.geneontology.org/editor/graph/gomodel:5db9c9a500000296
    • Note that, in some cases, we have MF terms that capture what curators may have been trying to capture with 'activated by', e.g. calcium-activated potassium channel activity (GO:0015269)
      • Ontology editors could discuss these types of terms and making sure we are consistent with term creation and labels
  • Much discussion on the sample GO-CAM model for annotating the effects of small molecules on the activity of gene products.
  • Some of the key issues raised and possible actions:
    • Use of 'small molecule binding' or child terms for annotation
      • This has been an outstanding issue in GO for some time, but looking at the estrogen receptor model brings it to the forefront again
      • We need guidelines on when curators should capture these binding annotations
      • If the binding is annotated, then we also need guidelines on when curators should request new pre-composed terms vs when they should annotate to a parent binding term and use the 'has input' extension to capture the actual small molecule being bound
      • The ontology editors will discuss this issue and get back to curators with a decision