GO-CAM Working Group Call 2018-09-25

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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

Input(s)

Direct Regulation

  • Add input to both the transcription factor activity and the positive (or negative) regulation of transcription process
  • Use the 'has input' relation
  • Connect the positive (or negative) regulation of transcription process to the function of the affected gene using the 'casually upstream of, positive (or negative) effect'
  • 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

indirect or Unknown Regulation

  • In this case, do not add an input to the MF or BP, but use the same causal relation, 'causally upstream of, positive (or negative) effect', between the regulation of transcription process term and the function of the gene whose activity is affected

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

Minutes

  • On call: Chris G., Chris M, Dustin, Edith, Kevin M, Kimberly, Laurent-Philippe, Li, Liz, Marie-Claire, Pascale, Paul T, Penelope, Petra, Rob, Ruth, Sabrina, Seth, Stacia, Stan, Suzi A, Tanya

Modeling Transcription

Input(s)

Direct Regulation

  • Add input to both the transcription factor activity and the positive (or negative) regulation of transcription process using the 'has input' relation
  • Connect the positive (or negative) regulation of transcription process to the function of the affected gene using the 'casually upstream of, positive (or negative) effect'
  • Next call: we will discuss the use of has_input when the input is the same for both the MF and the BP
  • See: https://github.com/geneontology/minerva/issues/205

indirect or Unknown Regulation

  • We discussed at length how to model cases where the precise causal mechanism whereby a transcription factor affects the expression of a gene is not known
  • Agreed upon:
    • If the paper does not support a direct regulatory relationship, then curators should not put the affected gene as an input to the transcription factor
  • Still under discussion:
    • How to accurately represent the relation between the TF and the regulatory process that controls the expression of the affected gene
      • Option 1: Make a part_of relation between the TF activity and a 'regulation of transcription' BP term and then a 'causally upstream of positive (or negative) effect' relation between the 'regulation of transcription' BP term and the MF of the affected gene
      • Option 2: Make a 'causally upstream of or within' relation between the TF activity and a 'positive (or negative) regulation of transcription' BP that has the affected gene captured with 'has input'
      • Option 3: Discussed on a previous call, not favored, but listed here for the sake of completeness - Make a 'part of' relation between the TF activity and a 'regulation of transcription' BP, then a 'causally upstream of or within' relation between the 'regulation of transcription' BP and a 'regulation of gene expression' BP, and finally a 'causally upstream of, positive (or negative) effect' between the 'regulation of gene expression' BP and the MF of the affected gene