Annotation Conf. Call 2020-06-23

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Agenda and Minutes

ChEBI Roles

  • Ontology editing and annotation review updates from Karen Christie
  • We discussed annotation to terms that refer to chemicals that can have drug roles
  • These types of terms are not handled optimally in the ontology and so we don't give users consistent information
  • Karen presented use cases and recommendations for re-annotating gene products that have been associated with these terms
    • Gene products can be annotated to a more general term that encompasses the appropriate chemical classification, with specific chemical entities captured in annotation extensions
    • Curators need to keep in mind, though, that they should always be annotating to the 'normal', evolved, relevant biology; particularly, when annotating the MF, think about what normal biological process that MF is part of
  • There was some concern that by removing these terms, we're removing potentially valuable information for our users, but it's not clear that researchers who want this type of information use GO to get it
    • There may be other resources, e.g. PharmGKB or CTD (Comparative Toxicogenomics Database), that do a more comprehensive job of capturing this information
  • On future calls, we will address: 1) annotating binding (use of With/From and AEs), and 2) response to terms that refer to chemicals with drug role

github trackers

  • Daily digest emails have been deprecated
  • Review github monitoring options to make sure everyone can monitor issues effectively
  • We discussed various ways curators can keep track of github issues
    • digest emails
    • optimizing watch settings in github
    • sorting issues in github
  • A number of people (~10) voiced support for reviving the github email digests
  • Several other people (~4-5) were fine with checking issues in github
  • The software group will need to put some resources onto making this happen as part of the overall pipeline
  • Will discuss on this week's manager's call to confirm availability of resources for this.

GAF 2.2 and GPAD/GPI 2.0

  • Check in to see if there is any additional feedback from groups
  • PLEASE review the specs with your developers and provide feedback
  • The plan is still to switch to the new file formats by the end of 2020

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