LEGO October 5, 2016

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Bluejeans URL - NOTE NEW MEETING TIME: 8:00am PST

https://bluejeans.com/969313231

Agenda

Review LEGO Model from 2016-09-26 Annotation Consistency Exercise

GPI Files

Ontology requests based on models

  • For both the Dicty model and a model that Kimberly is making, there are likely changes to the structure of the ontology. We should start keeping track of ontology improvements that are due to LEGO modeling and refer to models in ontology requests.

MGI Noctua Annotations

  • The MGI annotations in production Noctua models will be loaded into the MGI production database this Wednesday.

Minutes

  • On call: Barbara, Chris, David H, David OS, Elena, Helen, Kimberly, Jim, Moni, Paul T., Petra, Sabrina, Seth, Stacia, Suzi

Review LEGO Model from 2016-09-26 Annotation Consistency Exercise

  • dictyBase paper - linking GPCR signaling pathway and Ras pathway for response to cAMP
  • Note that the GTPase activity in this model is represented by the two activities of RapA - GTP binding and GDP binding
  • However, the GTP binding is not actually RapA activity, but RapA is bound by GTP when it accomplishes its function, which is to positively regulate cytoskeletal reorganization
  • Think about maximizing the readability and reproducibility
  • Shouldn't all the generic parts of GEF activity be encoded in the ontology? It seems like a big waste of effort to have to add these details every time someone build a LEGO model.
  • We also need to think about how to best represent the functions of the GPCR and the Gbeta/gamma entities; these need to be clear in the ontology definitions.
  • directly_activates and directly_inhibits are being defined as relations that imply a direct physical interaction
  • Would a regulates relation be more appropriate between the activities and the process of chemotaxis? Where does a process of taxis begin and end?
    • If the taxis term refers to the specific stimulus, then the taxis BP would include detection of the stimulus through to the movement towards or away from the stimulus.
  • How does the GPCR signaling pathway fit into this model? How does the Ras signaling pathway fit into this model?
    • Neither of these terms appear in the graph.
    • We could add the part_of relations between the activities and the appropriate signaling pathway terms.
  • To annotate aspects of the biology that are not directly shown in the paper, curators could make TAS annotations.
    • It would also be nice to be able to import BP and CC annotations from existing annotation, though.
  • This model illustrates some of the spotty representation of these activities and processes in the ontoogy.
    • Noctua isn't really an ontology editor, but when making a template it would be nice to be able to feed that back to the ontology editors.
    • Or, the ontology editors provide the templates for the curators to use to fill in details of specific instances of the biology represented in the template.
  • We could continue to discuss this on the annotation calls.

Ontology requests based on models

  • For both the Dicty model and a model that Kimberly is making, there are likely changes to the structure of the ontology. We should start keeping track of ontology improvements that are due to LEGO modeling and refer to models in ontology requests.
  • For example:
    • response to cAMP is not part of chemotaxis to cAMP
    • thermotaxis is not an is a thermosensory behavior
  • New ontology term requests would benefit from Noctua model representation