Annotation Conf. Call 2017-01-24

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Bluejeans URL

https://bluejeans.com/993661940

Agenda

GO Meeting Reminder

github Tickets

LEGO Models

MGI - David and Karen

Model: PMID-12771146-KRC

Paper: The tyrosine kinase Pyk2 regulates Arf1 activity by phosphorylation and inhibition of the Arf-GTPase-activating protein ASAP1.

WB - Kimberly

Model: Regulation of HIF-1 under normoxic conditions

Paper: C. elegans EGL-9 and mammalian homologs define a family of dioxygenases that regulate HIF by prolyl hydroxylation.

  • Questions:
    • How to annotate the role of substrates and co-factors wrt the hydroxylase activity of EGL-9?
      • Capturing the protein substrate, HIF-1.
      • Other players: O2, Fe2+, 2-oxoglutarate
    • To what extent do we want to tease out the different molecular functions of complex members?
      • VCB complex: pVHL, elongin B, elongin C, cullin-2 (Cul2), and Rbx1

Minutes

  • On call: Barbara, David H., David OS, Edith, George, Giulia, Harold, Helen, Karen, Li, Midori, Moni, Paola, Pascale, Paul T., Petra, Rachael, Ruth, Sabrina, Stacia, Stan, Tanya, Terry, Val

GO Meeting

  • Need more info on attendees so we can plan - will talk with Pankaj

Biocurator Meeting

  • February 17th - deadline for poster abstract and early registration
  • Stanford - end of March

github Ticket on New Qualifiers

  • Proposal to add more qualifiers for BP annotation
  • Need to review the use of these and have very clear documentation on their usage
  • causally upstream of or within may be useful for annotating results of phenotypic analysis
  • There may be different ways of annotating regulation, but we will want to standardize what we use
  • Think about how we can provide separate sets of annotations to users by employing these qualifiers
  • Curators will need to re-examine existing annotations to determine what the correct qualifier will be
    • Can we be clever about this, e.g. using evidence codes to help guide what qualifier is used?

LEGO Models

David and Karen

  • Two points:
    • How deep do we drill down with respect to evidence codes in a LEGO model?
    • How do we annotate models when information comes form more than one species?
  • Highlights:
    • MGI using PRO IDs for modified forms of a protein
    • Human protein annotated with three specific pieces of evidence to support kinase activity
      • Output in GPAD is three separate lines - one for each piece of evidence
    • MGI has decided, however, to instead select the one GO evidence code that supports the annotation
      • This will result in just one line of evidence in the GPAD file
    • Pascale - SIB is using these more granular evidence codes in their internal curation practices
    • In the case of these three evidence codes, two map to IDA and one didn't
    • Karen - don't really want three lines of evidence when the inference is really based on the summation of the three
    • Paul T. - can we still trace back to the PubMed ID?
    • David H. - yes
    • Tanya - if we were going to also add IMP, should that be a new annoton?
    • David H. - no, you can just add the additional evidence onto the same assertion?
  • Mouse protein is annotated to kinase activity with ISO evidence code, based on the human annotation
  • Should the human annotation be included in the same model, or can it be included in the same model?
  • Easier for curator to put the annotation in the same model
  • Karen - do we need to make strict rules on this?
  • Pascale - in terms of data model, thought we wanted just one model per species
  • Paul T. - this should be okay with the data model; curators will need to decide what they want as a curation unit
  • David H. - within an annoton, though, we're NOT mixing species
  • Species are kept together, but evidence may be based on orthology
  • Ruth - nice to include all of the evidence in one canvas to help track down the evidence
  • David H. - could scrolling over the evidence 'E' in the mouse model, somehow highlight the human annotation from which it's derived
  • Paul T. - could we harness the Excel sheet concept here?