Annotation Conf. Call 2019-11-19

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 'directly negatively regulates' the activity of the other gene product
  • Examples:
    • Two DNA-binding transcription factors that compete for overlapping regulatory sequences
    • A gene product that binds and sequesters an enzyme substrate
    • A decoy receptor that binds and sequesters a ligand
      • secreted frizzled-related proteins

• Spreadsheet for activated_by: https://docs.google.com/spreadsheets/d/1bUQ7uSHaLbr8uvYu04Jbmr76bn-ja01hJxbcGnx-U6I/edit#gid=0
• Spreadsheet for inhibited_by: https://docs.google.com/spreadsheets/d/17SV7E7MUlJzyfc5c8DKss2yqPAIgXIXN1xMXNioWc-U/edit#gid=0

Noctua Form 2.0 Demo

• Demonstration of the newly redesigned Noctua curation form

Minutes

• Present: