Annotation Conf. Call 2016-10-11

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Bluejeans URL:



Next GOC Meeting - USC, Los Angeles, CA, November 4-6, 2016

  • Link to a registration form is now available for the USC Meeting on the Meeting Logistics Page.
  • Register for meeting and dinner, just dinner, just meeting.
  • No registration fee for the Noctua workshop.

Contributing Group Information

  • Paul T. sent out an email earlier today asking groups to check their information on the list of GO contributors:
  • Paul is also requesting additional information about groups
  • Please check the website and send Paul the additional information he's requesting

Outstanding github Tickets - Ontology Requests - SOP for Annotation Calls

  • There are sometimes ontology request issues on github that curators would like to bring forward for discussion on annotation calls
  • To make sure these discussions are maximally useful, we'd like to ask that the initiating curator and the assigned ontology developer agree on a date to discuss the issue and then prepare some brief background material so that everyone on the call can understand the context of the ontology request
  • If specific feedback from other groups is desired, it'd be good to give advance notice via these annotation calls
  • To be discussed on 2015-10-25: NTR: maintenance of differentiated cell state
  • NTR: Endosomal membrane tubulation - recently updated, please see github ticket
  • membrane tubulation/curvature - recently updated, please see github ticket

LEGO Model for dictyBase Annotation Consistency Exercise


  • On call (please add your name if I missed it): Alice, Edith, George, Giulia, Helen, Moni, Paola, Paul T., Penelope, Petra, Sabrina, Shur-Jen, Stan, Suzi

Contributing Group Information

  • Please send Paul T. contributor group information - this includes current annotators and support staff, as well as past contributors going back to the beginning of your group's affiliation with the GOC

Outstanding github Tickets - Ontology Requests - SOP for Annotation Calls

  • When needed, we can discuss specific github ontology request tickets on the annotation calls
  • The ticket originator and assigned ontology developer should coordinate to find a suitable time to present the issue and let David and Kimberly know so they can coordinate the agenda
  • When presenting, please give enough background to allow everyone to understand the context of the issue
  • If you desire feedback or input from a specific group, let them know ahead of time
  • We will try to schedule these discussions at least two weeks out so people have plenty of time to review the issue

LEGO Model for dictyBase Annotation Consistency Exercise

  • Petra and Paul reviewed the LEGO model for the dictyBase annotation consistency exercise
  • Model highlights the molecular activities of each of the gene products described in the paper
  • Each of these activities is part of the process of chemotaxis to cAMP
  • Complex molecular activities, such as for the GPCR, can be expressed by including sub-activities, e.g., cAMP binding
    • This allows more detailed curation of the molecular mechanism by which a function is executed
  • The model allows curators to show how smaller processes, such as the small GTPase-mediated signal transduction, is part of the larger process of chemotaxis to cAMP
  • The regulatory relationship between the GTPase and the cytoskeletal reorganization terms is used because there is background information to support that the GTPase plays a controlling role in these processes (although the mechanism is not currently included in this model)
    • However, if curators were not comfortable choosing the regulatory relation for a model, then they can choose the less granular parent relation of causally upstream of or within (soon will also have the option to include the directionality, i.e., positive or negative of this relation)
  • Suggestions for model display:
    • Gene or gene product names could be displayed more prominently at the very top of the annoton to make them more distinguishable from other information in the annoton
    • Gene or gene product names might also be color-coded to allow people to readily assess all of the activities of a given entity in the model
    • The brown background color for the enabled_by information in the annoton makes it hard to read the gene or gene product name - not enough contrast