GO-CAM Conference Call - 2019-05-21

Call Information

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

Agenda

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

• From Sabrina on go-annotation gitter:
  • "caspy2 binds directly to lipopolysaccharide, resulting in caspy2 oligomerization, which is critical for pyroptosis" ([https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6076302 PMID:30076291})
  • I started a GOCAM model, but I am not sure it is correct
  • Summary figure from paper

• Related question on modeling activities that influence dimerization state of another protein
  • Role of heat shock proteins in initiating C. elegans IRE1-ER UPR
  • See: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6423427/figure/F3/

Minutes

• 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