Projects stand up meeting 2021-10-27

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

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

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

• Summary metrics workshop: https://docs.google.com/document/d/15tBWdDNQuw9IdfDKk0pxpuDjfrnW3vT-xKnwO8_c1D0/edit#
  • API redesign would facilitate this
  • AI set up a meeting to discuss which of these metrics we'd like to use
• Summary subsets workshop
• DONE Implementation documentation workshop suggestions - will discuss at the next annotation call

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