Projects update meeting 2024-06-26

Attendees

• Members: Chris, Kimberly, Pascale, Seth, Suzi, Jim, Huaiyu, Paul, Cynthia
• Present: Chris, Huaiyu, Jim, Kimberly, Pascale, Paul, Seth, Suzi, Tremayne
• Regrets:

Noctua Standard Annotation Form

• Implement dual-taxon annotations in standard annotation form
  • Noctua - dual taxon annotations are captured as an annotation extension to the appropriate BP, e.g. has_input:NCBITaxon652611
  • The ShEx already accounts for this
  • GPAD output will convert this information and place it in the Interacting taxon field
  • https://github.com/geneontology/noctua-standard-annotations/issues/24
  • https://github.com/geneontology/minerva/issues/545

• Multiple annotation extensions
  • Tremayne is investigating how to implement this on the form
  • https://github.com/geneontology/noctua-standard-annotations/issues/20

• Allow curators to clear the annotation extension relation and object field
  • https://github.com/geneontology/noctua-standard-annotations/issues/21

• Non-conformant GPAD models
  • Mostly correctly identifies process-centric GO-CAMs, but there are some exceptions, mainly from the MGI gene-centric imported models
    • Two main issues:
      • Nested annotation extensions, e.g. 'part of' anatomical chains
      • Translated chained annotation extension relations, e.g. regulates_o_occurs_in
  • Proposal from MGI:
    • Leave the current models as is, but add a metadata tag to alert curators that some annotations may not be displayed in full in the new form
    • When we migrate these standard annotations to a different database/storage, flatten the anatomical chains as they were before, but leave behind the translated chain relations, as these were attempts to capture more context and were annotated correctly at the time they were made. Perhaps future work could consolidate these translated annotations to one or more common models based on the BP terms used.
  • Another possible option - create a new RO relation, e.g. 'regulates process that occurs in' and move these annotations into a different database when the time comes.
  • Still need to add the metadata to the models and do the work to update that metadata after curated edits, in case the status changes.
  • Curator/group-specific feedback to fix any models that need fixing.
  • https://github.com/geneontology/go-shapes/issues/306
  • https://github.com/geneontology/go-shapes/pull/307

• Populating root node annotations
  • https://github.com/geneontology/noctua-standard-annotations/issues/22

• Adding a standard annotation form icon to the Noctua landing page
  • https://github.com/geneontology/noctua-standard-annotations/issues/16