Difference between revisions of "GO-CAM Conference Call - 2019-04-23"

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** We need to make sure that the current work-flow at each of the MODs can still be achieved using Noctua, in addition to having the capabilities of creating more expressive GO annotations  
** We need to make sure that the current work-flow at each of the MODs can still be achieved using Noctua, in addition to having the capabilities of creating more expressive GO annotations  
Present: Pascale, Judy, Chris, Seth, Suzi, Kimberly, Huaiyu, David
==GO Conference Calls==
* Only the calls in the week after the GOC meeting will be canceled.
* Applies to all the GO calls, but not alliance calls.
* This will be announced at the October GO meeting. Suzi will put a note in the agenda.
==GO meeting recap==
* There is a google doc with action items compiled by Pascale. See the link above.
* They are assigned to individuals.
* Will discuss with each group. Some discussing points are in the agenda for this call.
* David: The March release was delayed by MGI.
* Seth: Probably needs more resources to fix issues
* Chris asked whether it is possible to add Dustin to help on the release pipeline. Huaiyu explained that Dustin is currently working on three parallel projects, and it would be helpful to know exactly the tasks (either long-term or short-term). Will continue the discussion offline.
* Landing page is slow loading - Seth: this is a know issue.
* Seth: If it is slow using the editing tool, it is an issue. Should report if this happens.
* The slowness is in comparison with the production. Kimberly experienced the problem of taking a minute or so to add an evidence. Will report if this happens again, and Seth agrees to look into the problem.

Latest revision as of 11:23, 24 April 2019

Call Information

  • See GO's Google calendar for Zoom URL
  • email Kimberly if you need access to the GO's Google calendar


Follow-up from Cambridge GOC Meeting

Gitter for go-annotation

  • Reminder that we will be trying to use gitter as an informal chat room for GO annotation questions
  • https://gitter.im/geneontology/go-annotation
    • login with your github account
  • This doesn't replace github/go-annotation or formal documentation on the wiki, but is meant to be a place to ask questions or share ideas
  • We will monitor the conversations to make sure that key issues are elevated appropriately

Annotation Imports

Naming Models

  • Follow-up from breakout discussion at the Cambridge meeting
  • Model titles are currently visible on the Noctua landing page as well as on the public GO-CAM site for production models only
  • Current naming practice:
    • MOD imports - by MOD gene ID, e.g. WB:WBGene00004732 or MGI:MGI:101757
    • SynGO imports - gene/gene product name, GO aspect, number (?)
    • Manual models:
      • Production, Development (in progress, test)
      • No convention - gene names, species, pmids, mod paper ids, curator initials, paper titles, biological processes, model ids, etc., or combinations of these
        • The diverse titles arose partly out of a desire for curators to easily find production and development models they'd made
        • Do we all agree that this is not optimal and standardized model titles is desirable?
  • Do models need informative, human readable titles?
    • If yes, how should they be generated?
      • Proposal from Cambridge meeting:
        • Use controlled vocabularies and lists to generate consistent model titles
          • Manual or auto-generated?
          • Current tool behavior - a model can't be saved unless it has a title
          • Could a temporary title (e.g. model id) be generated for saving and then curators could construct a model title from a drop-down list of terms and entities present in the completed model?
            • Key points:
              • Aiming for organism-specific models of biological processes - BP terms would thus get preference for naming?
                • Other key information: anatomy and/or cell type, life stage, species
              • Annotations not yet part of a larger process would be added to the gene-specific model?
  • What should curator workflow be when starting to annotate?
    • Search existing models for possible matches?
      • This requires searches on development, as well as production, models

New Noctua "Workbenches"

Noctua Form

Relations Editor

Annotation Review Tool


  • On call: David, Dustin, Edith, Harold, Karen, Kevin, Kimberly, Marie-Claire, Monika, Paul T., Petra, Rob, Sabrina, Seth, Stacia, Tanya, Tremayne

Gitter for go-annotation

  • Chat room available for GO curators to ask questions and share ideas
  • Curators are encouraged to login and participate

Annotation Imports

  • Dustin has begun to implement rules for importing 'has regulation target' annotation extensions
  • David and Kimberly are QCing the resulting models for accuracy
  • 'has regulation target' annotation extensions were not always clear, so if we can establish better rules for capturing targets of regulatory processes, then we can implement those into conventional annotations as well
  • Use of the chained relations, e.g. regulates_o_enabled_by, may ultimately be better for clearly capturing the object of regulation

Naming Models

  • We discussed considerations for naming models
    • There are currently three different types of model names: MOD imports (gene ids), SynGO imports (gene, aspect, internal id), and manually assigned titles
  • Does it matter what we name them?
    • Right now, models names are used, in part, to search for models that curators have made
    • Implementation of better search interfaces for curators should alleviate the need to put model metadata in the model title
    • Users and curators may have different needs, so perhaps the name of a model may ultimately matter more to GO users who are browsing models than to curators?
    • The Annotation Review Tool provides much more search functionality for models than is currently available and also allows editing within that interface. We will demo this on a future GO-CAM call.
    • One good suggestion from the Cambridge meeting was to name models as if you were composing a title for a review article.
  • Can we just use machine-generated titles?
    • Maybe, but we'd need to explore how these would be created.
    • Machine-generated titles would remove the naming burden from curators, but we'd still like to have informative model titles for browsing.
  • We will follow-up with individual groups to determine what are some of the barriers to using Noctua
    • Incorporation of real-time annotation rules and error reports are two things curators really like to have
    • We need to make sure that the current work-flow at each of the MODs can still be achieved using Noctua, in addition to having the capabilities of creating more expressive GO annotations