Annotation Conf. Call 2017-01-24: Difference between revisions

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*Two points:
*Two points:
**How deep do we drill down with respect to evidence codes in a LEGO model?
**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?


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

Revision as of 12:18, 24 January 2017

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

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?