GO-CAM Working Group Call 2018-09-25

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'

Modeling Transcription

• Modeling when regulation of transcription is direct vs indirect (or unknown)
• http://noctua.geneontology.org/editor/graph/gomodel:5a5fc23a00000137

Input(s)

Direct Regulation

• Add target of regulation to both the transcription factor and the regulation of transcription process
• Use the 'has input' relation for both MF and BP
• GPAD output currently exports both to the BP (one asserted, one inferred), but we want to filter the GPAD output to only export the most granular relation and value
• See: https://github.com/geneontology/minerva/issues/205

Annotation Review for 'has input' vs 'has direct input'

• • We were reviewing a transcription model and discussing how/where to capture inputs of MFs and BPs.
• '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: