Annotation Conf. Call 2020-02-04

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Agenda and Minutes

  • Present: David, Dmitry, Edith, Giulia, Harold, Helen, Karen, Kimberly, Li, Midori, Patrick, Rob, Ruth, Sabrina, Seth, Stacia, Suzi A, Tanya, Tremayne

Annotation Calls

  • We will meet weekly on Tuesdays at 8am PST.
  • Will no longer make the distinction between annotation and GO-CAM/Noctua calls.


  • Noctua is now updated 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:
  • Thank you to the MGI curators and to Sabrina for their feedback

Annotation Relations

  • Goal is to review use of relations across annotations (standard and GO-CAM) and the ontology to ensure consistency wherever possible
  • Relation discussed this week:

Follow-Up Discussion with Ontology Editors

Chemical Entity Binding Terms

  • Question from last week's call: should curators request new pre-composed binding terms for binding chemical entities, or should they use 'binding' has_input 'ChEBI term'?
  • Ontology editors discussed this on their weekly call yesterday and the decision is:
    • Going forward, curators are asked to annotate to 'binding' and use the 'has input' extension to capture the chemical entity
    • Future work will evaluate existing 'binding' terms in the ontology and decide which should stay and also the criteria for instantiating new 'binding' terms
    • As an annotation group, we will also continue to evaluate what 'binding' annotations are appropriate for GO and why
    • Most groups can make annotation extensions in their current tools; if not, Noctua is available for groups to use partially or fully

Molecular Function Regulators

  • One of the inferred annotations generated from the proposed nuclear receptor model was that of molecular function regulator (GO:0098772)
  • Molecular function regulator
    • Textual definition: A molecular function that modulates the activity of a gene product or complex. Examples include enzyme regulators and channel regulators.
    • Logical definition: molecular function AND ('directly regulates' some molecular function)
    • Any upstream MF that directly regulates a downstream MF will be inferred to be a 'molecular function regulator' by the reasoner
    • Two issues from last week's call:
      • Was the model of nuclear receptor activity correct?
        • The idea was to try to model cases where curators used the 'activated by' extension relation, but in the case of nuclear receptors the premise that the ligand binding 'activates' the transcription factor activity may not actually be the correct way to think about this compound function
        • Ontology editors are currently reviewing how compound functions like 'nuclear receptor' are logically defined
        • Also reviewing 'molecular function regulator' as a class in the ontology - is it still useful?
      • 'directly' in 'directly regulates' = direct physical interaction
        • reasoning rule behind-the-scenes that generates the resulting 'protein binding' annotation based on this meaning of 'directly'
        • keeping the rule for now, but may reevaluate in the future
    • Note that we have the ability to refine what is export in the GPAD file, even if those annotations are created via reasoning
      • This is an option for retaining the logical definitions in the ontology and the intended meaning of the relations without necessarily outputting 'standard' annotations that groups may not want to display