GO-CAM July 12th, 2017

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Zoom URL

https://stanford.zoom.us/j/679970729

Agenda

Update on Proposal for a Tabular Editing Interface

https://github.com/geneontology/noctua/issues/461

Priority list

Minutes

  • On call: David H, Harold, Jim, Karen, Kevin, Kimberly, Pascale, Sabrina, Sage, Seth, Stacia, Terry
  • Regrets: Chris

Software Updates

Update on Proposal for a Tabular Editing Interface

  • Hoping to port over a spreadsheet-like interface from IncaTools project
    • Being used currently for editing DOS-DPs
    • Needs to be able to communicate with minerva
  • Part of the AGR project
    • Three-week time frame (funding) for Noctua development
  • Idea is to have a more P2GO-like, user friendly, intuitive annotation interface
  • Simple design idea is to provide columns that match the fields of a GO annotation
  • Will need input from curators familiar with the P2GO interface
  • One question is whether the table editor should be write only or read-write
    • Feedback so far is that, in the long run, curators would like read-write (i.e. full editing capability)
  • What will be the relation between editing preformed in the graphical interface and the information stored in the table editor?
  • Note that not all models will conform to a design pattern

Priority List

Viewing annotations in GPAD format

Handling evidence properly

  • No progress to report this week

Handling groups as output in the GPAD file

  • Minerva needs to be updated so that users groups, as recorded in the users.yaml file, is included in the annotation output

Creating biological processes to generate regulation annotations

  • Needs more context, examples in documentation
  • See model 00366
  • Creating a regulatory relationship between an MF and a BP currently requires creating an intervening regulatory BP
    • This is because an MF that regulates a process must always be part of some regulatory process
    • You will not get an annotation to a regulation BP term without adding the intervening regulatory BP

Getting Correct Annotation Extensions

  • See model 001088
  • The cell type information needed to be moved from MF to terminal BP in the model to get the desired annotation extensions in the GPAD output
  • Need to be clear on what occurs_in means wrt modifying a BO
  • Saying that a BP occurs_in a CC means that that entire process occurs there
  • Is this consistent with how the occurs_in extension was used in conventional annotation?
  • More general question - how should anatomical and CC terms be used to qualify organism-level processes?
  • Action Item: We need a list of all of the relations and property chains and how they resolve.

Curators should evaluate their workflow for areas where we can improve efficiency - high priority

  • Submit tickets in geneontology/noctua
  • What's the development timeline here?
  • Note that many of these changes involve changing the fundamental graphics tool kit underlying the front end of Noctua - this will be a big endeavor

Import existing CC and BP annotations

  • The Cellular Component Companion exists
  • Accessed via clicking on the green box and scrolling down to 'Other operations'

Documentation

  • Google doc exists, but we still need updated SOPs for the mechanics of using the tool
  • Annotation guidelines, annotation philosophy still need fleshing out
  • One idea is to have an annotation documentation jamboree