Annotation Conf. Call 2019-11-19: Difference between revisions

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= Minutes =
= Minutes =
*Present: Bill, Colin, David H, Dave F, Dmitry, Doug, Dustin, Giulia, Harold, Karen, Kimberly, Leyla, Li, Midori, Niels, Patrick, Penelope, Petra, Rob, Ruth, Pascale, Sabrina, Seth, Shur-Jen, Stacia, Stan, Tanya
*Present: Bill, Bob, Colin, David H, Dave F, Dmitry, Doug, Dustin, Giulia, Harold, Karen, Kimberly, Leyla, Li, Midori, Niels, Patrick, Penelope, Petra, Rob, Ruth, Pascale, Sabrina, Seth, Shur-Jen, Stacia, Stan, Tanya




[[Category:Annotation Working Group]]
[[Category:Annotation Working Group]]

Revision as of 12:03, 19 November 2019

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
    • Example:
      • GP enables
  • 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
    • Example:
      • GP enables '(1->3)-beta-D-glucan binding' has input '(1->3)-beta-D-glucan'
    • the annotations can be used in the future to create or check term logical definitions in the ontology
  • If the inhibitor acts by competitively binding to an entity required for the activity of another gene product:
    • The activity of the inhibitor (upstream) 'directly negatively regulates' the activity of the next (downstream) gene product
    • Examples (with standard annotations):
      • Two DNA-binding transcription factors that compete for overlapping regulatory sequences
        • TF-A enables 'RNA polymerase II regulatory region sequence-specific DNA binding' directly negatively regulates 'RNA polymerase II regulatory region sequence-specific DNA binding'
      • A gene product that binds and sequesters an enzyme's substrate
      • Inhibitor enables 'protein binding' directly negatively regulates 'catalytic activity'
      • A decoy receptor that binds and sequesters a ligand
        • Decoy receptor enables 'protein binding' directly negatively regulates 'receptor activity'
          • secreted frizzled-related proteins

Noctua Form 2.0 Demo

Minutes

  • Present: Bill, Bob, Colin, David H, Dave F, Dmitry, Doug, Dustin, Giulia, Harold, Karen, Kimberly, Leyla, Li, Midori, Niels, Patrick, Penelope, Petra, Rob, Ruth, Pascale, Sabrina, Seth, Shur-Jen, Stacia, Stan, Tanya