Ontology meeting 2021-11-01

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  • Group members: Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, Sierra, David, Chris, Paul
  • Present:
  • Regrets: Paul, Tanya


Agenda

Primary input/output versus input and output in the ontology versus in annotations

See example 2: http://wiki.geneontology.org/index.php/Annotation_Extension_Relation:has_output#2._Specifying_the_product_of_a_biosynthetic_process

We ask people to annotate as if the were using 'has primary output'; can the annotations be treated as if the used 'has primary output' in the reasoner, so that we could potentially 'deepen' annotations if appropriate?

  • Concern (Kimberly) having differences between what is in the ontology versus what curators do
  • Chris proposes to use 'has primary input' in annotations, and align ontology to match that for example in 'binding' and 'kinase activity' and other terms currently using 'has input'
  • Steps:
    • Makes changes to annotation editors: has input -> has primary input
    • Update GO_REL to include has primary input/ has primary output
    • Fix design patterns
    • Apply design patterns
    • Generate rules to make sure design patterns are applied in ontology
    • Show logical definitions to curators
    • Noctua menus should prefill relations from DP
    • Show Logical definitions in AmiGO and QuickGO
    • Update annotations to the correct relations + how do we decide what is the primary input if people have used more than one input

alternative proposal:

  • keep using has input, this means the same as what we currently use as 'has primary input', use 'has participant' for other reaction participants

ATP-dependent activity- again

https://github.com/geneontology/go-annotation/issues/3963


Subsets

Discussion:

  • Should we have parent/children terms in the subset:
    • Redundant terms: https://github.com/geneontology/go-ontology/issues/22276
    • Depends on the application; for ribbon display we want to avoid; for gene grouping this may make sense
    • We could consider 2 levels - one general level and if there are too many annotations, a second level of slim terms, as if it were chapters and subchapters


Signaling issues encountered in subset workshop

https://github.com/geneontology/go-ontology/issues/22273 Need to invite Helen and Val to a meeting to explain the proposal


New taxon constraints project

https://github.com/orgs/geneontology/projects/71

Decision on ChEBI update?

https://github.com/geneontology/go-ontology/pull/22092

  • AI from last week: Harold and Pascale to write to Alan, Anneticket
  • See PR - Harold will write to CHeBI and request the 8 categories mentioned by Alan

Other Business

https://github.com/geneontology/go-ontology/projects/1

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