Annotation Conf. Call 2019-11-19

From GO Wiki
Jump to: navigation, search

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, Suzi A, Tanya

Progress Reports

  • Annotation groups should copy and complete the template (linked above)
  • Include all FTEs working on GO, even if not paid by the grant
  • Annotation stats will be produced by the GOC pipeline scripts, but it would be good if curators review them
  • Groups should fill out other sections, e.g. annotation strategy, publications, highlights (e.g. web display, special annotation projects)

Annotation Extension Relations

'activated by' and 'inhibited by'

  • Re-annotation of standard annotations using these relations for extensions should focus on the relevant activities and their causal relation
  • Curators should also focus on the relevant regulatory activities where the mechanism for the regulation is known
  • If the mechanism is not known, we would no longer capture this information in a GO annotation
  • We will review/add some more examples to the documentation and curators should bring these examples to annotation calls for discussion
    • Midori asked about enzymes that require a metal ion in order to function; if these are considered co-factors we would not be annotating that information

Noctua Form 2.0 Demo

  • Noctua Form 2.0 will be going into production soon, so we had a demo of its new functionality and workflow
  • We'll send an email out to curators when the form is officially in production
  • Please provide feedback on the geneontology/noctua-form github tracker

Next Annotation Call

  • We will have our next call on Tuesday, November 26th