Annotation Conf. Call 2024-01-30

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Agenda and Minutes

Meetings and Announcements


  • Next regularly scheduled Noctua outage:

GO Release Pipeline

  • January release on the 17th
  • #release-pipeline Slack channel for updates


Updating 'has input' and 'has output' extension relations to 'has primary input' and 'has primary output'

  • RO has relations to distinguish between different types of inputs and outputs to BPs and MFs
  • In GO annotation, we generally want to capture just the primary inputs and outputs, i.e. the entity whose transformation is the main goal of the process or function.
    • For example, the protein that is a substrate of a kinase or the main chemical that is modified during a metabolic process.
  • The GO ontology has already been updated to reflect this.
  • Protein2GO will need to be updated.
  • Noctua will need to be updated.

ECO codes

  • Do any groups use more granular ECO codes than the traditional three-letter codes for manual annotation?

Automatic replacements for 'x signaling involved in y' BPs

  • Replace annotations with 'x signaling' and an annotation extension of part_of 'y'
  • Request from Ruth (seems like the table below illustrates what she would like):
    • Please could I just say that when I have been revising the of 'x signaling involved in y' BP annotations it has been very helpful to be able to see the parent terms for each term so that I can see what parent annotations to create and what to add to the AE field. So although I have got a lot of these to do I would really appreciate being given a list of the annotations to revise before these are all obsoleted. Or perhaps it would be easier to provide a list of the terms plus their parent terms, so that I can look these up.
  • Feedback from Antonia and Malcolm:
    • Annotations should be made directly to both the signaling term and the 'involved in' term; the latter shouldn't just be an extension on the signaling term
    • In Noctua, even when curators update the annotation to the signaling term plus a 'part of' extension, as long as the original term exists in the ontology, the reasoner will also create an annotation to the compound term

GO-CAM and Noctua

  • Update on new standard annotation UI:
    • Tremayne has prototype - now on noctua-dev
    • Jim is working on rules for adding metadata to all existing Noctua 'models' that would distinguish those that are fully standard annotation 'compliant' from those that have one or more annotations that are not, e.g. include what would be the equivalent of a nested annotation extension or what would be considered a causal model
    • Why do we want this? We want to give curators information on what 'models' can be fully manipulated in a table/form interface vs those models that should be manipulated in the VPE or graph editor


Ongoing Projects



  • On call: Antonia, Colin, Deborah, Dmitry, Dustin, Edith, Giulia, Helen, Kimberly, Leonore, Li, Malcolm, Mary, Pascale, Patrick, Petra, Raymond, Rob, Rossana, Seth, Sridhar, Stan, Steven, Suzi, Val