Projects stand up meeting 2021-10-27

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  • Present:
  • Regrets:
  • Managers: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris


Discussion points

  • Alliance all hands: next meeting is early December; is there anything GO wants to present?
  • Chris: suggestion pathway widget
  • Kimberly; maybe present future plans?

Priorities & objectives for remainder of 2021

API redesign

  • Right now we have multiple little APIs all over the place.
  • Main GO API, Noctua API and xx
  1.  Modernize API
  2.  Integrate GO-CAM API
  • AI Chris and Seth: will write up objective for project - what can be done in 1st month, and resources needed

Technical debt / refactoring

  • Projects to be defined - this may fit within other projects

Test units


  • Technical
    • Wrap up outstanding curator request tickets in current project
      • Resources needed: Tremayne (full time for xx time); Kimberly, Seth, Jim
      • Will focus on fixing issues that create bad data and closing issues that are almost done
    • Implement annotation and model copy
      • Shallow model copy: Resources needed: Dustin + Kimberly
      • Annotation copy: Tremayne has a prototype
    • Clean up bad or incorrect data highest priority
      • Ontology terms
      • Relations
      • Evidence codes
    • Noctua visual editor:
      • Resources needed: Tremayne 1 month (November 2021 ??) + Paul T
  • Documentation/Guidelines
    • Annotation extension usage
    • Process-specific guidelines
      • Signaling pathways
      • Metabolism
      • Gene expression
    • Improve error reports when running the ShEx (that appear when running the reasoner)
      • Resources needed: David, Kimberly, Jim, Seth

MOD imports

  • Import annotation sets from Protein2GO (SGD and WB)
    • Resources: Dustin, Kimberly
  • Resolve outstanding GPAD output issues
    • Resources: Jim, Kimberly
  • Put WB fully into production?
  • Create roadmap for annotation data exchange amongst all relevant resources
    • Meeting today with GOA, FlyBase, wormbase, SGD to discuss dataflow


  • Boomer + Reports by Anne: errors in GO-RHEA mappings
  • ChEBI Roles: AI set up a jamboree to finish?
  • Other projects
    • transcription:
      • epigenetic processes, miRNA, and related
      • biological processes
    • multiorganism processes:
      • remove MF in BP (modulation of host x activity)
      • fix high level terms to make browsing more logical
    • Obsolete single step processes
    • Implement design patterns
  • Immunology/immune system processes + cytokine production terms


  • Peter got a grant for this project
  • There will be a meeting with people internal to the group

ECO-GO alignment


New Panther release in PAINT in early spring 2022

New Taxon constraints

  • Some terms need logical definitions
  • usage of occurs_in for inferences would add a number of constraints
  • AI set up a jamboree to complete taxon constraints?

GOC meeting follow up

Project updates

Clean up Google drive, calendar, and GH to remove part project members

Asynchrony issues in the release pipeline

Other priorities