Annotation Conf. Call 2024-02-20

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Agenda and Minutes

Meetings and Announcements

Noctua

  • Next regularly scheduled Noctua outage:

Next In-Person Consortium Meeting

GO Release Pipeline

  • February release.....
  • #release-pipeline Slack channel for updates

Annotation

Unfolding annotation extensions - BP 'part of' BP

  • One common annotation extension is the statement that a BP is 'part of' another BP
    • For example:
      • 'x signaling pathway' part of 'y developmental process'
      • 'response to x stimulus' part of 'y behavior'
  • Because part of is transitive, annotations that state a GP is involved in the first BP, are also saying that the GP is involved in the second BP
  • The GPAD output from Noctua models makes separate 'involved in' annotations to the first and second BPs
  • Protein2GO, however, isn't doing that automatically right now; curators would have to make the second BP annotation separately (double work)
  • Proposal: to align the two curation tools, there is a proposal to 'unfold' these types of annotations in Protein2GO automatically
  • Is everyone okay with that?

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

  • List of 'currency chemicals' via Reactome to aid in curation
  • 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.
    • Some discussion about what curation options should be available for standard annotation UI vs GO-CAM modeling UI (VPE)

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

Ontology

Ongoing Projects

Signaling

Attendees

  • On call: Antonia, Deborah, Dustin, Giulia, Jodi, Karen, Kimberly, Li, Leonore, Malcolm, Mary, Pascale, Patrick, Petra, Raymond, Rob, Rossana, Seth, Sierra, Sridhar, Steven, Suzi, Val, Victoria