GO-CAM Conference Call - 2019-05-21

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Call Information

  • See GO's Google calendar for Zoom URL
  • email Kimberly if you need access to the GO's Google calendar


Annotation Imports

  • Status update on MGI and WB annotation imports
    • Implemented imports of With/From
    • Re-visiting the rule for modeling BP 'regulation of MF' with has_regulation_target extension
    • Additional annotation extensions coming on board
  • Track issues on github/gocamgen

Modeling Questions


  • On call: Dmitry, Dustin, Edith, Elena, Giulia, Harold, Helen, Jim B, Karen C, Kevin M, Kimberly, Laurent-Philippe, Li, Marie-Claire, Monica, Pascale, Petra, Sabrina, Seth, Stacia, Suzi A, Tanya

Annotation Imports

  • David and KImberly assessing annotations to BP 'regulation of molecular function' and children that use 'has_regulation_target' extension to see if these could all be modeled just with MFs
  • Continue to check new AE models as they come on board

Modeling Questions

  • caspy2/caspb zebrafish model
    • Each MF, including binding terms, need to be annotated with an enabled_by relation when the entity is known
  • caspy2/caspb zebrafish and ire1-er-upr c. elegans models
  • We discussed the utility of MF and BP terms related to multimerization in both GO-CAM models and conventional annotation
  • Multimerization can be a necessary step before execution of an MF, e.g. receptor tyrosine kinases
  • However, are annotations to multimerization MF and BP terms critical for GO-CAM models? Do they add anything on their own as conventional annotations?
  • Molecular-level details may be interesting to biologists that want to know every step in a pathway, but this brings challenges for curation and display
  • Is regulation of multimerization more important to capture?
  • For curation, do we want to capture these experimental observations, even if it's not yet clear how they fit into the overall biological process
    • Capturing all information while reading a paper is more efficient than trying to go back and make annotations from previously curated papers
  • For display, it could be useful to have different views of a model (one with the details, one with just the essential, or main, functions) and allow users to toggle between them
    • We would want to have specifications for what details would be hidden
  • We should continue this discussion since it impacts curation decisions more broadly