LEGO October 31, 2016
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Bluejeans URL - MEETING TIME: 8:00am PST
https://bluejeans.com/969313231
Agenda
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
- The model depicts a three-protein complex ligand consisting of one secreted protein and two membrane-bound proteins
- Annotation Issues:
- 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
Minutes
- 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