Annotation Conf. Call 2020-06-23

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Agenda and Minutes

ChEBI Roles

  • Ontology editing and annotation review updates from Karen Christie

github trackers

GAF 2.2 and GPAD/GPI 2.0

  • Check in to see if there is any additional feedback from groups

GAF 2.2

  • Naming: we won't be changing anything about naming the GAF files, but will need to communicate to users what the change is, i.e. the qualifier field is now mandatory and allowed values have increased
  • There will be a check for the actual relation label used and non-compliant annotations will be flagged/removed - need to confirm what the action will be


  • Wrt the timing and synchronicity of the GAF 2.2 and GPAD/GPI 2.0 changes, we will try to allow a period between the GOC release and when the new files are ingested so we can address any issues before the next release
  • Groups will have to account for some possible asynchronicity in managing their local imports, but the file format should be in the header of each file so the expected format can be dealt with there
  • Berkeley will have parsing scripts available to share and can otherwise assist in helping groups with the transition

Post-meeting action items

  • Transcription annotation review
    • Almost done with review of human TF annotations (almost 10% of the human genome!)
    • Once human review is finished and updates to PANTHER families have percolated through the pipeline, review of other organism annotations can begin
    • Ruth will also have, in the future, a list of human dbTFs as a resource
  • Use of 'contributes to'
    • Following up meeting last Thursday (2020-06-4) to discuss next steps
    • There will be some annotation review coming, with updated documentation
    • One outstanding question is if groups have used an AE with MF annotations to capture that the MF 'occurs in' a protein-containing complex (using either a GO CC term or a Complex Portal accession)
      • It'd be helpful to know how much this has happened as this practice is no longer consistent with representation in GO-CAM
  • Use of 'colocalizes with'
    • We will re-visit this qualifier as well, since there are still some annotations that need review

MOD imports into Noctua

  • Working on GPAD 2.0 files
  • Working on modeling annotation metadata, comments
    • Internal comments with be ingested, but not added to production files available to our users


  • On call: Birgit, Bob, Chris, Colin, David, Dustin, Edith, Giulia, Harold, Helen, Karen, Kimberly, Laurent-Philippe, Li, Malcolm, Midori, Pascale, Penelope, Petra, Rob, Ruth, Sabrina, Seth, Shirin, Stacia, Stan, Val, Suzi, Tanya