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

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(Created page with "= 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 EC...")
 
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== Relations between MF and Input(s) ==
== Relations between MF and Input(s) ==
*has_input vs has_direct_input
*'has input' vs 'has direct input'
*Proposal: replace has_direct_input with has_input; obsolete 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
*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, [https://drive.google.com/drive/folders/1TlwrEM2KjAzxIYiCGg0_oicMOYfhiGou all MF annotations] that use has_input in annotation extensions.
*Seth retrieved, as of 2018-07-31, [https://drive.google.com/drive/folders/1TlwrEM2KjAzxIYiCGg0_oicMOYfhiGou all MF annotations] that use has_input in annotation extensions.
**Initial review:
*Use cases to discuss:
***used to capture a regulatory effect, e.g. protein kinase activator activity, when it was not known whether the effect was direct or indirect (e.g. expression of protein or complex X increases the activity of Y)
**Enzyme-substrate  
***used to capture a regulatory subunit whose presence is necessary for the activity to occur (e.g. cyclin-dependent protein kinase)
***Enzymatic modification of a substrate
***used to capture an enzymatic activity when it was not known if the effect on a substrate was direct or indirect (e.g. caspase-dependent but not known if it was the caspase mutated)
***used to capture an enzymatic substrate where there wasn't also a direct binding assay in the paper (e.g. testing possible chemical substrates for glucuronysyltransferase activity)
***used to capture metal ion-dependence of protein binding (e.g. Ca2+-dependent protein binding)
***used (correctly) to capture the physiologically relevant input in a binding reaction (i.e. cross-species experiment where with/from captures experimental binding partner and AE the relevant binding partner)
*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]


Revision as of 10:19, 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)

  • '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

Minutes

  • On call:
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