GO-CAM Working Group Call 2018-09-25: Difference between revisions

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***Enzymatic modification of a substrate  
***Enzymatic modification of a substrate  
*Relations Ontology working group (broader than just GO) that is also considering [https://github.com/oborel/obo-relations/issues/244 how to model participants in an MF] and [https://github.com/oborel/obo-relations/issues/171 documentation of has_input and child relations]
*Relations Ontology working group (broader than just GO) that is also considering [https://github.com/oborel/obo-relations/issues/244 how to model participants in an MF] and [https://github.com/oborel/obo-relations/issues/171 documentation of has_input and child relations]
== Relations between BPs and Input(s) ==
*Adding the same input to an MF and BP of which that MF is a part
*Is this necessary?  Does is add anything to the model?
*The resulting AEs for the process then have two references to the input, one captured with the asserted 'has input' and the other with the inferred 'has participant'.


= Minutes =
= Minutes =

Revision as of 11:38, 24 September 2018

Meeting URL

https://stanford.zoom.us/j/976175422

Agenda

Evidence Codes in Noctua

  • Decision: leave evidence codes as is in Noctua
  • Will we continue to use full ECO
  • Autocomplete searches perform best when searching on first word in term label, e.g. 'direct' or 'mutant'

Relations between MF and Input(s)

  • How did this discussion start?
  • 'has input' vs 'has direct input'
  • In GO-CAM models, we are using 'has input' for capturing the objects of MFs
  • This is different from conventional annotation where curators sometimes made a distinction between 'has direct input' and 'has input'
  • Proposal: replace 'has direct input' with 'has inpu't; obsolete 'has direct input'
  • Need to review has_input annotations to remove any extensions that are inconsistent with GO-CAM usage, i.e. an indirect or unknown proximity for an input
  • Seth retrieved, as of 2018-07-31, all MF annotations that use has_input in annotation extensions.
  • Use cases to discuss:
    • Enzyme-substrate
      • Enzymatic modification of a substrate
  • Relations Ontology working group (broader than just GO) that is also considering how to model participants in an MF and documentation of has_input and child relations

Relations between BPs and Input(s)

  • Adding the same input to an MF and BP of which that MF is a part
  • Is this necessary? Does is add anything to the model?
  • The resulting AEs for the process then have two references to the input, one captured with the asserted 'has input' and the other with the inferred 'has participant'.

Minutes

  • On call: