LEGO October 31, 2016

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Bluejeans URL - MEETING TIME: 8:00am PST


Software Updates

  • Replacing persona login system
  • Minerva

Models Review

  • David OS: Modeling a complex molecular function in Noctua - the NMDA receptor
  • Kimberly VA: Modeling organization of anatomical structures - dendrite branching
    • Annotation Issues:
      • The model depicts a three-protein complex ligand consisting of one secreted protein and two membrane-bound proteins
        • The receptor binding activity occurs in the extracellular space between two cells/tissues
        • Making the assertion that the receptor binding activity occurs in the extracellular space will generate a CC annotation to 'extracellular space' which is not an annotation curators would typically make
        • One possible solution: split the protein complex out into its respective members and annotate the occurs_in relation separately, i.e. the secreted component's activity occurs_in the extracellular region while the membrane-bound ligands' activities occurs in the plasma membrane?
      • This is another example of activities that are part_of one process that is causally_upstream_of another process, i.e. dendrite guidance upstream of thigmotaxis, or more generally, creating proper neuron morphology in order to effect a given behavior
  • Templates
    • Using PANTHER IDS to capture types of entities

Noctua Workshop - November 7th

  • Participants: ~14 new, ~9 with experience
  • Agenda
  • Goals
    • Logins for all participants
    • Basic tool functions
      • Creating individuals
      • Linking individuals
      • Adding evidence
      • Naming and saving models
    • Hands-on modeling


  • On call: Barbara, Chris, Giulia, Helen, Jim, Kimberly, Midori, Paul T., Sabrina, Stacia

Software Updates

  • Seth working on adding user groups to user metadata
  • Jim experimenting with inferences in GO graph store to generate GAF/GPAD annotations
  • Persona login system is being replaced with OF2 system because persona will no longer be supported by Mozilla as of November 30th
    • Login will still be linked to orcid via the users.yaml file

Models Review

  • David OS emailed slides of his LEGO models of complex molecular functions
    • We missed the presentation due to asynchronous daylight savings in UK and US - Sorry, David!
  • Kimberly presented a model of a three-member protein complex that serves as a ligand
    • Two of the complex members are membrane-bound proteins in one cell type, while the other is a secreted protein from another cell type
    • How best to describe where the activity of the ligand occurs? Extracellular space? External side of plasma membrane?
    • What, if any, CC annotations would be generated for the individual members of the ligand complex from the property chains?
  • Would like to have PANTHER family IDs added to NEO to be able to refer to types of proteins in LEGO templates
    • Chris, Paul will discuss how to do this
  • Barbara would like to annotate mature mouse miRNAs in LEGO models, but needs IDs for these
    • Currently using the MGI gene IDs for the genes encoding the miRNAs
    • Emailed Judy, David to see what MGI's plans for representing mature miRNAs in NEO are
    • Judy looking into it

Noctua Workshop on Monday, November 7th

  • May need to initially split out into two groups - curators relatively new to Noctua and curators with more experience
  • Feedback from Stacia - keep examples simple; it is easy to get overwhelmed with the possibilities for annotating in Noctua
    • Need to show some very simple annotons, how to create them, and how they can be linked to one another to build a model up from scratch