Manager Call 2017-04-05

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Cilia GO paper

June Consortium Meeting

  • Agenda

Curation Tools


  • Future status of Protein2GO as a curation tool


  • Development priorities
    • Review github tickets
    • GPAD outputs and implications for overall workflow


  • New editors are all now using Protege and Github for ontology commits
  • Is there a possibility for advanced training/meeting of ontology editors this summer?
    • More training in OWL
    • Understanding the Import Pipeline and Various QC checks
    • Creation of Noctua templates
    • Logical definitions

Contact person for contributing groups

Pascale: I cam across annotations by PAMGO and JCVI. I contacted Michelle Giglio - noone seems to be responsible for these annotations anymore. I suggest that we (GOC) take over the ownership of these annotations, so we can clean them as necessary. More generally, we should define rules for 'active contributors'. For example:

  • updating annotations at least one yearly
  • having a person that monitors GH (and responds to queries)
  • etc ?
  • If these conditions are not met the GOC would reserve the right to exclude or 'own' the annotations (the "assigned by" information would be retained, but we would have the ability to edit the annotations).
  • Also, there should be a rule with respect to disputes that never get responses - a certain period by which the 'disputer' can act on his/her suggestion if the 'disputee' does not answer.


  • On call: David, Huaiyu, Judy, Kimberly, Moni, Pascale

Cilia Paper

  • One paper from Paola to review, one coming from Karen

June Meeting

  • Start reviewing agenda for meeting
  • Probably a smaller meeting this time, only maybe ~25-30 people

Curation Tools


  • Maria's email earlier this week to let everyone know that there isn't support for new features or development
  • Exploring other possible funding avenues


  • Still needs some development, particularly for the more complex models
    • Evidence for complex models still is not quite correct
  • Can use Noctua for simpler annotations and get a GPAD out
  • Can't make NOT annotations in Noctua
  • Can get all GPADs for a group
    • Some challenges here, though, wrt non-MOD IDs
  • Need to review tickets, priorities, blocker issues

*AI:Reinstitute Noctua calls - Kimberly will send email to go managers list


  • David tracking new editors time in order to decide how to distribute tickets
  • Propose second, advanced training workshop for this summer
    • Would work on OWL, logical definitions, import pipelines, Noctua templates, integration with design patterns

Contacts for Curation Groups

  • Some annotation groups are now gone (no longer annotating)
  • Therefore, can't dispute annotations and have no mechanism to update or change them, if needed
  • Judy - analogous to nomenclature issues
  • Need to have a mechanism for tracking the status better
    • github go-annotation tracker for annotation disputes
    • can we have some GOC superuser status in Protein2GO that allows GO curators to update annotations
  • Some groups like JCVI, PAMGO no longer annotate - can GOC take control of these experimental annotations

*AI:Add this issue to the June meeting agenda.

  • Need proposal and mechanism. - David and Pascale
  • Give curators a set amount of time to update annotations, and if after that time there is no change, the disputing curator can make the change