Projects stand up meeting 2021-10-27

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Attendees

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

Announcements

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

Noctua

  • 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

Ontology

  • 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

Reactome2GO

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

ECO-GO alignment

PAINT

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

https://github.com/orgs/geneontology/people

Asynchrony issues in the release pipeline

https://github.com/geneontology/go-site/issues/1742

Other priorities

https://docs.google.com/spreadsheets/d/19-i43w0mGQdFYmKXqskVIgrDO-pVTWo1YgjaWa5PI1o/edit#gid=1697332900