Ontology meeting 2021-09-27

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



GOC meeting - Oct 12-14

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

Suggestion to have a group discussion (breakout?) with people developing external ontologies to discuss expectations, semantic equivalence, etc

New Taxon constraints

https://github.com/geneontology/go-ontology/issues/16298 Any new item to review?

methotrexate terms

Obsoletion proposal for methotrexate terms Quick summary from Karen

The issue to discuss is the fact that the term “response to methotrexate” is imported into the Experimental Factor Ontology (EFO) and used by curators at the Genome-Wide Association Studies (GWAS) catalog, and how to proceed, whether to continue doing what was agreed upon 5 years ago:

place them in the do_not_manually_annotate subset, and add a definition comment "Note that this term is in the subset of terms that should not be used for direct manual annotation of gene products. It was created to be used for cross-referencing by other ontologies. Direct annotations to this term may be amended during annotation QC."

OR If GO still wish to go ahead and obsolete GO:0031427 'response to methotrexate', the alternative option for EFO would be to mint a new EFO term with the same meaning, use it to replace the GO term, and alert GWAS curators

=> DECISION: Notify annotators and people using GO (external ontologies) way in advance (6-12 months) of the upcoming obsoletions, and proceed, at least for 'response to drug' and other non-endogenous chemicals

Multiorganism processes

Two issues

1. 'symbiont regulation of host processes' terms

right now some (but not all) link to the 'normal' process, for example (made up), 'inhibition of host transcription' could have in its subclasses or LD, 'negatively regulates some transcription, DNA templated'

2. 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


Ontology editors documentation

Imports PRs

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

Other Business