Ontology meeting 2022-05-16

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

'provisional' EC xrefs

Kristian' answer: 

  Preliminary EC numbers are unique like the complete ones. When they are turned into real EC numbers they are transferred. So you can safely use them in GO, there is no ambiguity, especially if you provide a link to enzyme.expasy.org.

NAD/NADP issue

Clarified guidelines again with Harold: see https://github.com/geneontology/go-ontology/issues/23235 GO:0004448 isocitrate dehydrogenase activity is the parent for NAD and NADP versions; in this case it seems the enzymes are specific for either cofactors.

  • The parent GO:0004448 isocitrate dehydrogenase activity was flagged as 'do not annotate'
  • xrefs are only added to the specific children that describe the specific reaction
  • def xref was changed to GO:curators since it represents a grouping class, there is no paper describing the general case (and especially no db)
  • Added doc under Ontology_Development#Ontology_editing_principles -> Principles_for_catalytic_activity_terms
    • could this have gone in the design patterns directly?
      • Chris: yes, not every design pattern needs to be defined by genera and a differentia
      • Jim: if we dont have the genera and a differentia we cannot tag them automatically
      • Chris: we can tag them manually or some other way that distinguishes them
    • Feel free to add to this section or to propose new areas where we could have guidelines

Other points

Jim:

Editors discussion tickets

Harold

Pascale: subclasses calculated by Protégé not the same as those requested by user

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