LEGO December 1, 2014

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Present: Rama, Kimberly, Chris, David, Huaiyu, PaulT, Suzi

  • Noctua system is ready for model building
  • Model should be able to add Evidence at all levels (the function, location, relationship), add multiple evidences/papers for each entity as well.
  • Once we enter a gene product ID/UniProt ID of a protein/enabler, it would be nice to be able to pull existing annotations from the GAF and allow the curator to pick an existing evidence. This will make sure the two systems are kind of in-sync.
  • In the context of the Pho80-85 pathway that Rama showed (http://go-genkisugi.rhcloud.com/seed/model/gomodel:sgd-536d71c50000004) Kimberly asked about how we define complexes: active entities in a complex. You are linking activities. Pho80-85 is a constitutive complex (inference). Pho81 association with pho80-85 complex is transient. In high phosphate Pho81p is not around so you won’t notice that association. You separate out the function when you model.
  • Chris_ Inferencing/reasoning will add the bits of the complex (cyclin and kinase activity). Look at additional papers and add more data and see if there is a
  • if there are holes in the model can we prompt the user to provide evidence.
  • how to express the ambiguity in one model? The tool should be able to allow that functionality.
  • if there are genuinely separate views then there should be separate models. This has to be on a case to case basis.