Annotation Conf. Call 2017-01-24

Bluejeans URL

https://bluejeans.com/993661940

Agenda

GO Meeting Reminder

• Corvallis, Oregon - June 1-3rd, Noctua Workshop - June 4th, Reactome Workshop - June 5th
• Meeting Registration Site
• Meeting Agenda

github Tickets

• New qualifiers for biological process
  • Will be discussed on the February 14th annotation call, but please look at the ticket and comment there, if needed.

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?