GO-CAM Conference Call - 2019-02-19

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Meeting URL

  • Please see the GO's Google calendar
  • Contact Kimberly if you do not have access to the GO calendar


Recap of Berkeley Hackathon

Documentation on Google Drive

Importing MOD annotations into Noctua: Basics

  • Which MODs to start?
    • MGI and WB
  • Which annotations?
    • Generally, all manual annotations assigned by MGI or WB
    • This can be customized, e.g. specific evidence codes, for a given MOD at the time of import
  • How will annotations be modeled?
    • Dustin and Ben are working on the conversion code
    • One gene's annotations = one GO-CAM model
      • Other alternatives we considered:
        • one paper = one GO-CAM (spreads potentially similar annotations and evidence out amongst many different models, harder to review and QC)
        • one "organismal" process = one GO-CAM (although ultimately where we'd like to go, for this initial phase, a one gene = one GO-CAM model is probably easier to review and QC)
  • Input file is GPAD
    • Allows for expanded set of gp2term relations and annotation properties, e.g. contributor
  • Annotations will not be 'transformed' at all upon import, i.e. what's in the file is what will be imported
  • Iterative process, each round of imports is available on noctua-dev

Modeling Conventional Annotations as GO-CAMs: Rules

Molecular Function

  • [GP] <- enabled_by [MF]
  • [GP] contributes_to -> [MF]

Cellular Component

  • [GP] part_of -> [CC]
  • [GP] colocalizes_with -> [CC]

Biological Process

  • Relation between MF and BP will be taken from existing gp2term relations in the GPAD. For example:
    • For existing GP 'involved in' BP:
      • [GP] <-enabled_by (GO:0003674 molecular_function) part_of-> BP
    • For existing GP 'acts upstream of or within' BP:
      • [GP] <-enabled_by (GO:0003674 molecular_function) causally_upstream_of_or_within -> BP


  • Will import one reference ID in order of preference:
    • PMID
    • GO_REF
    • doi
    • MOD paper id

With/From Field

  • github ticket on modeling multiple values in the With/From field in OWL, i.e. commas and/or pipes
  • For now, import as strings?
  • Future project may be to develop and use OWL Union and Intersection to represent what is meant by commas and/or pipes in the With/From field

Annotation Extensions

  • Working with Dustin and Paul to devise a set of rules to convert existing annotation extensions to GO-CAM
  • [https://docs.google.com/spreadsheets/d/1AEAj39mxQnBsuccIxWhpjiFKcdCJLw6uIa1eXiAG1Hs Google spreadsheet of annotation extensions for which the meaning and/or conversion needs to be clarified
  • This is currently where the bulk of the curator work is being done
    • For example, has_regulation_target extensions need to be modeled for GO-CAM


  • On call: David, Dmitry, Dustin, Edith, Giulia, Harold, Karen, Kevin, Kimberly, Laurent-Philippe, Li, Pascale, Patrick, Paul T., Sabrina, Seth, Shur-Jen, Stacia, Suzi A, Tanya