Annotation Conf. Call 2017-04-25

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Bluejeans URL

https://bluejeans.com/993661940

Agenda

GOC Meeting, Corvallis, Oregon, June 1-3 (plus workshops June 4-5), 2017

Noctua Models

  • Annotation of activities that change the 'state' of an entity and the processes that depend on that state.

Histone acetylation/deacetylation

Setd5 is essential for mammalian development and the co-transcriptional regulation of histone acetylation.

RNA polyadenylation/deadenylation

Inhibition of telomerase RNA decay rescues telomerase deficiency caused by dyskerin or PARN defects.

Minutes

  • On call: Chris G., Chris M., Edith, Emily, George, Giulia, Harold, Helen, Jim, Karen, Kevin, Kimberly, Li, Marek, Midori, Olivia, Pascale, Paul T., Penelope, Petra, Sabrina, Sage, Stacia, Stan, Tanya, Terry, Val

GO Meeting

  • Please double-check the table, especially wrt the GO dinner.
  • Also, please look over the agenda, and add items if there's something you want to be discussed that's not already there. Also, give an indication of how long you think the discussion might take.

Noctua Models Discussion - 'States' of Molecules

Acetylation/Deacetylation

  • Do activities with opposite effects regulate one another?
    • Not necessarily; they just affect the state of the molecule they are acting upon (i.e., the input)?
  • Question about using IMP evidence for inferring regulation of an activity
    • What is the reason that the HDAC activity is affected in the Set5D knockdown?
      • Is the Set5 protein acting as a methyltransferase?
    • One other possibility would be to include the negative regulation of the histone deacetylation process but not the negative regulation of histone deacetylase activity
      • Instead use the relation 'causally upstream of, negative effect'
  • This model also speaks to the ontology issue of whether we're going to remove one-step biological processes
  • Another key issue here is what information can be gleaned from a single paper vs what is more generally known about the entities studied
  • Another issue is how we annotate protein complexes
    • Would the preferred annotation instead be to histone deacetylase complex binding?
    • Is this protein complex a stable molecular machine that has a function? That should be the guiding principle for adding a complex.
  • Both acetylation and deacetylation are okay as covalent chromatin modification child terms in the ontology.

Adenylation/Deadenylation

  • Used 'directly provides input for' relation
    • Caveat: do we know that there is no enzymatic activity in between the two? If not, should be then use a less granular relation, e.g. 'causally upstream of'?
  • Discussion of metabolic pathway vs regulatory pathway?
    • If activities are required for synthesizing molecules that are then acted upon by downstream pathways, is that just biosynthesis or is there a degree of regulation there?
  • What is the overall process being modeled?
    • Either protein complex maturation/assembly or protein complex activity
  • Will add the next steps and try to determine which activities are part_of the next steps, which activities might regulate those steps.
  • Will also follow up to determine if PAPD5 is the transcription-coupled poly(A) polymerase or is a separate poly(A) polymerase activity