Projects stand up meeting 2021-11-03

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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? 

Switching default to isa-part-of closure in amigo

  • do we proceed?

2021 progress reports

What is needed and when?

  • Need to ask Paul whether this is due for the last cycle of the grant
  • Pascale : will create a new doc for this

Japonicus db

  • Now in Metadata as a MOD, loaded by Val and Midori
  • We have no formal process for integrating new MODs; how do we decide to 'accept' a new MOD?
  • Picked up by the pipeline process; we now have a new source in the public release
  • New MODs also have entries in the stats
  • What are other implications?


  • METADATA should also have tickets, not just PRs
  • Internal SOP:
    • people would propose species, and the GOC agrees (or not) to include the species our data set
    • if this has not been done, maybe we revert the merge? until things have been decided
    • also need to document all changes that need to be made, for eg in the stats
    • Action Item improve external SOP
    • Action Item add GH ticket template with check list

Priorities & objectives for remainder of 2021

API redesign

Chris, Seth, were to define objectives for the project Right now - only fixes; only Sierra for now


  • 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 last Wed with GOA, FlyBase, wormbase, SGD to discuss dataflow, will meet again today
      • 5 main things to address:
        • Alex is importing Noctua GPAD in P2GO, but this doesn't seem to be working, he is investigating
        • Patrick and Sylvain from SP are making GO-CAM, but these are 'development', so not exported
        • How do GO annotations get into Alliance? Probably this just needs documentation
          • ---> This gets in by the GO Monthly release
        • Inferred annotations generated by reasoning: people dont know what gets generated and output; inferences generated not always useful. Needs to look into this more closely, as part of the large GPAD output discussion
        • Redundant annotations

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?


  • Pascale contacted by Gerard Manning to classify protein kinases
  • GO helpdesk contacted by TEMTIA, ( annotating epithelial and mesenchymal cellular phenotypes (email 21 October 2021)
    • Chris and Mike also interested to join
    • Opportunities to work with experts to improve the ontology and annotations
  • 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

ECO-GO alignment

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