Ontology meeting 2021-09-20

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

Announcements

Agenda

Aims for GOC meeting - Oct 12-14

Suggestions https://docs.google.com/document/d/15_TIWfnu2X_3CVzdcou14PyV4Ff8F9Hz8WSASi1bsaE/edit#


New Taxon constraints

https://github.com/geneontology/go-ontology/issues/16298

Multiorganism processes

Current pattern is

  • 'modulation of process of other organism'
    • 'modulation of process of other organism involved in symbiotic interaction'
      • 'modulation by symbiont of host process'
      • 'modulation by host of symbiont process'

+ suppression/induction children

Issues are : - structure is complex - forces to create 2 independent branches for (intra-organism) symbionts and others (snakes, frogs, etc) - not always very relevant, usually by knowing the pair of organisms you know the relationship - there is probably a better way to capture this information, using context (extensions) that would represent inter-organism relation(host/symbiont, prey/predator, etc) - proposal would be to collapse all terms to “modulation/suppression/induction of x in another organism”

MF regulator activity

As we (try to) remove BPs of type 'regulation of MF', people are asking for 'x regulator activity', but in many cases it is not clear whether it is true regulation, or just that the protein is 'required for' the activity (whatever that might mean) see NTR: tRNA ligase activator activity, citing PMID:30943413

Protein-containing complex localization & protein localization

Inconsistent 'design patterns'

Amino acid conjugates

https://github.com/geneontology/go-ontology/issues/22096


Ontology editors documentation


Imports PRs

  • Someone please take a quick look at CHEBI and CL PRs

Other Business

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