Annotation Conf. Call 2020-01-28: Difference between revisions

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**'activated by'
**'activated by'
**https://github.com/geneontology/go-annotation/issues/2718
**https://github.com/geneontology/go-annotation/issues/2718
**'activated by' had been used to identify a chemical substance that increases the activity of the gene product
**'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:  
**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)
***model regulatory events in terms of activities enabled by gene products (this implies that we have some knowledge of the regulatory mechanism)

Revision as of 11:07, 28 January 2020

Agenda and Minutes

  • Present:

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, it will typically look like this:
      • GeneProduct 1 'enables' binding (GO:0005488) '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)