Annotation Conf. Call 2017-05-23

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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

Minutes

  • On call: Bob, Dave F, David H, Harold, Helen, Karen, Kimberly, Li, Moni, Pascale, Petra, Sabrina, Shur-Jen, Stan, Suzi, Tanya

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

  • Please review the agenda

Noctua Models

  • Petra presented a model for exocyst-mediated contractile vacuole discharge in Dicty
  • Export GPAD link from Model menu in Noctua now using the most up-to-date reasoner (note that GAF is currently not available)
  • Use of 'adjacent to' relation - this relation is used to qualify the relation between two things (e.g. cellular components), not between a process and a thing (component)
    • 'adjacent to' entry in RO from Ontology Lookup Service
    • In the model, we want to say that the regulation occurs in the part of the cytosol that is adjacent to the contractile vacuole membrane
    • We do this by going to the View menu and exploding the view (evidence folded or all) and then make the appropriate connection between the two CC terms
    • When we return to the folded view, then you see that the cytosol is removed from the original individual and is now a separate individual so that it can be specifically linked to contractile vacuole membrane
  • Use of 'enabled by' relation - this relation is used between an entity and a Molecular Function (not an entity and a Biological Process)
    • Curators need to make sure that they are articulating exactly which MF is linked to a specific BP
  • Protein binding MF annotations
    • Is the same protein binding individual appropriate as 'part of' each successive BP?
    • Here, the curators needs to decide whether the evidence supports that the protein binding is 'part of' each process.
      • Is Rab8A bound to the same protein throughout? Any other changes?
    • Need to check the GPAD output for representation of Rab8A as 'part of' a process that is 'causally upstream of' a set of other processes
    • With the MF refactoring, will this type of protein binding annotation still be used?
      • In the MF refactoring, protein binding will generally be considered a mechanism to achieve a biological outcome, e.g. sequestration
      • An update on the MF refactoring is scheduled for the Corvallis meeting.
      • For protein binding annotations like this, we will want to make sure that there is an appropriate MF term to describe what Rab8A's activity is
    • Is an annotation to protein complex binding more appropriate for this model?
  • If you don't know what the relevant MF for an entity is, create a generic MF annotation in your Noctua model
    • We need to discuss what evidence should be put on the generic MF annotation
    • Note that the annotation extension information attached to the generic MF annotation may be quite useful to users
  • For each gene product in a model, think of representing it as an annoton, i.e. an MF 'enabled by' a GP; that MF 'occurs in' a CC; and that MF has a causal relation to a BP
    • The causal relations may be 'part of', 'causally upstream of', 'causally upstream of or within', etc.
  • How will the CC contextual information for contractile vacuole discharge be represented in the GPAD?
    • Probably as an annotation extension - but curators should check their GPAD annotations!
  • Annotations to the exocyst complex
    • Right now this is in the model as an independent annotation
    • What is the appropriate MF for the exocyst complex?
  • What are the desired annotations for Noctua?
    • Any annotations can be made
  • Curators would really like context-dependent relation selection
  • Curators would also like to have a human readable (i.e. including term names, gene names, etc.) GPAD for QC