Annotation Conf. Call 2020-12-15

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Agenda and Minutes


Spring GO Meeting

GO-CAM Jamboree

  • REMINDER: please send Paul and/or me your best estimate on how much time it took you to create a model, or begin to create a model, with any additional thoughts on your individual experience. This feedback is being collated into a Google doc for the purposes of the grant renewal.
  • GO-CAM office hours next week?

Meeting-less Weeks

  • We are going to experiment with one meeting-less week a month (second week of the month).
  • Next meeting-less week will be January 10th - 16th
  • People are encouraged, though, to get in direct touch if they have pressing questions or continue to use the github trackers.

GAF 2.2 and GPAD/GPI 2.0

  • Discussion with groups about their current status with creating GAF 2.2 files
  • Internal Protein2GO users need to tell Alex their group's preferred default gp2term relations:

Internal Protein2GO Users - Default Relations Communicated to Alex

Group Contact Decision (Y or N)
dictyBase Petra Y
FlyBase Helen Y
SGD Suzi emailed 2020-12-15
UCL Ruth Y
UniProt Penelope, Sylvain Y
WormBase Kimberly Y

  • Note that the specifications were updated to give guidelines on what relation to use with annotations to the root nodes:
    • Biological Process -> involved_in
    • Molecular Function -> enables
    • Cellular Component -> is_active_in
  • Achieving synchronicity amongst groups wrt applying gp2term relations in a GAF 2.2 file. Note that this is distinct from harmonizing on using the same relations for gp2term for the same, or similar, annotations amongst different curation groups.
  • Each annotation group should be applying their gp2term relations in accordance with the GAF 2.2 file specifications and their annotation practices, as well as the guidelines for root node annotation relations.
  • Alex (UniProt - GOA) and Dustin (PAINT) are joining the call today to provide more information about the annotations from their groups/pipelines as these two annotations sources are a common upstream for many annotation groups.
    • PAINT test files -
      • PAINT files use for default:
        • Biological Process -> involved_in
        • Molecular Function -> enables
        • Cellular Component -> is_active_in (for non-protein-containing complex terms)
        • Cellular Component -> part_of (for protein-containing complex terms)
      • Also use:
        • Molecular Function -> contributes_to
        • Cellular Component -> colocalizes_with
  • External2GO mappings
    • InterPro
    • SPKW
    • SUBC
    • UniRule
    • EC
  • Sequence-based annotation transfer and gp2term relations
    • Curators can update a gp2term relation from a less to a more specific relation upon review for a sequence-based (e.g. ISS, ISO) annotation
    • Consider a centralized reporting system when this happens to feed back to the group that made the original annotation
  • Other outstanding issues/questions?
    • Working group in the new year (2021) to draft proposals for harmonizing gp2term relations for specific gene family - GO term associations

Annotation Issues

Capturing interacting taxon

  • Currently, a second taxa is just captured in a separate field in the GAF (Taxon, pipe separated when more than one) or GPAD (Interacting taxon) with no relation.
  • Proposal: capture dual taxon information using the annotation extension field and a 'has input' relation
  • Questions:
    • Does everyone who uses the existing Taxon or Interacting taxon fields for dual taxon annotations also use annotation extensions?
      • Number from UniProt (Protein2GO):
        • UniProt 1749
        • WB 157
        • CAFA 67
        • ParkinsonsUK-UCL 28
        • ARUK-UCL 23
        • BHF-UCL 21
        • DIBU 3
        • GO_Central 1
        • MTBBASE 1
      • Other groups?
    • Would this apply to all children of interspecies interaction between organisms?


  • On call: Colin, David, Dmitry, Dustin, Harold, Helen, Karen, Kimberly, Li, Malcolm, Midori, Pascale, Patrick, Penelope, Petra, Robert, Sabrina, Seth