Noctua Technical Call 2018-06-27

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Meeting URL

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

Meeting Time Change

  • To give the West Coast a break from the 8am GO meetings, we are thinking of changing the time of this meeting.
  • How about 11am/2pm on Wednesdays?

Meeting Scope

  • We'd like to define the scope of this meeting better
  • Discussion of biological models will be the focus of the Tuesday calls; this call will be technical in nature
  • What's the best use of our time on this call?
    • possibility: less frequent calls
    • possibility: break into more specific subgroups or "hack" groups

Agenda

Internals

  • From 5/23 meeting:
  • refactoring
  • stack alignment
    • common widgets/UI
  • paying down debt
  • functional parity
    • live updates
    • login and groups across clients and workbenches

Annotation

  • If there is plan to just have an update minerva API, preferably batch update just like currently adding multiple entities at the same time. Altering the individual class expression on that low level is very error-prone. For example I just found out, changing the term and evidence is 2 separate processes. (Tremayne)
  • Editing ('conventional' and GO-CAM)
    • Tremayne working on an editing interface
    • Curators can search for gene/gene product ID, GO term, Reference
    • Matches will then be presented in a form view for editing with links to a model, if applicable
  • Model cloning

Error checks

  • The Form to use Reasoner or centralised checker through API to check for errors. I think Noctua Form error checking was for 1.0 release. It depends heavily on golr and different way than Reasoner. I think we should have one definition of an model activity (algorithm wise). Bcz there will be cases where the graph says there is an error and Form doesn't catch it then. (Tremayne)
  • Incorporating annotation rules into Noctua
    • Some annotation errors are flagged in the form editor
    • Others may need to get checked during the release pipeline
      • Curators may wish use lines from GPAD file in order to retrieve the correct model id if they want to edit starting from a model URL

Landing Page

  • I have a particularly blocking issue with NEO and URIs that prevents me to correctly display the name of genes when browsing the models. (Laurent-Philippe)
  • Model searching (production)
  • Model titles - need guidelines
    • This issue is still outstanding, but is maybe not as big an issue now that we can search over more terms, additional metadata, etc.
  • Different landing pages for public vs curators?

Model Seeding

  • From GAFs
  • From Reactome

Relations

  • Reconcile CC annotation relations with CC ontology relations
  • Use of has_input vs has_participant for binding annotations
  • David, Pascale, and Kimberly reviewing all relations used in GO and their documentation

Templates

GPAD Outputs

  • Protein complexes
    • This will need to be one of the high priority tasks for the working group (see below)
    • Emergent functions will need to be handled differently from functions where one of the subunits actually enables the activity of the complex
  • Annotation extension relations white list
    • How do we want to handle this?
    • Do groups want to see all possible extensions and then filter at their respective MODs?
    • If we do that, are there any possibilities for inconsistent display between MODs and AmiGO?

Text Mining

  • TPC integration into form
    • Will draw up requirements for this and hope to make progress before and/or during the late August hackathon at USC

Minutes

  • On call: David, Dmitry, Dustin, Jim, Karen, Kimberly, Laurent-Philippe, Sabrina, Sandy L, Suzi A, Tremayne, Seth (late)