Annotation Conf. Call 2019-11-19

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Agenda

Progress Reports

  • Reminder: due mid-December
  • Annotation Group Template
  • GO will generate annotation stats

Annotation Extension Relations

'activated by' and 'inhibited by'

  • If the chemical or molecular entity performing the activation or inhibition acts directly on the gene product by binding to it and is believed to be an endogenous regulator:
    • remove the 'activated by' or 'inhibited by' annotation extension
    • create a new 'binding' annotation with an annotation extension of: 'directly positively regulates' or 'directly negatively regulates' the regulated activity of the gene product
  • If the annotation is to a binding term, and the extension is 'activated by' the chemical or molecular entity bound:
    • remove the 'activated by' annotation extension and replace with 'has input'
    • the annotations will be used in the future to create or check the logical definitions in the ontology
  • If the inhibitor acts by competitively binding to an entity required for the activity of another gene product:
    • proposal: the activity of the inhibitor (upstream) 'directly negatively regulates' the activity of the downstream gene product
    • Examples (with standard annotations):
      • Two DNA-binding transcription factors that compete for overlapping regulatory sequences
        • TF-A enables 'regulatory region binding' directly negatively regulates 'regulatory region binding'
      • A gene product that binds and sequesters an enzyme substrate
      • Inhibitor A 'enables' 'substrate binding' directly negatively regulates 'catalytic activity'
      • A decoy receptor that binds and sequesters a ligand
        • decoy receptor 'enables' ligand binding directly negatively regulates 'receptor activity'
        • secreted frizzled-related proteins

Noctua Form 2.0 Demo

Minutes

  • Present: