Ontology meeting 2021-08-30

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

Announcement

No calls next 2 weeks - labor day + no GO calls week

Agenda

Aims for GOC meeting - Oct 12-14

Suggestions

• documentation
• finish roles??
• RHEA
  • Boomer tickets; finish fixing ?
  • Anne - obsoleted RHEA terms
  • present some strategy for moving forward
  • metrics: how many mappings do we have, how many are missing (GO-> RHEA // RHEA -> GO : aim to map all RHEA terms with annotations; even if that means mapping to a higher level RHEA mapping
  • additional mappings from RHEA: Metacyc/KEGG ?
• transcription refactoring update
• updates in QC and procedures

Report on transcription workshop last week

Colin, Val, Pascale, Ruth, Helen https://docs.google.com/document/d/1dO04FTcWBkWBQaBYJLjmkTTDZvEJTSezXaK9c--RTFU/edit#heading=h.can1sflfx9fi

Make sure unintended inferences don't appear in go-gaf (and maybe go-lego)

https://github.com/geneontology/go-ontology/issues/22051

Ontology editors documentation

• Review new term creation documentation: Guidelines_for_new_Molecular_Functions and Principles_for_creating_a_GO_term
• Review cross-reference documentation: Guidelines_for_'database_cross_references'_and_'definition_database_cross_references'
• Review protein binding term documentation http://wiki.geneontology.org/index.php/Guidelines_for_new_Binding_terms
• Optional: Review Chris's slides on aligning editor/contributor docs across all of OBO: https://docs.google.com/presentation/d/1YyWYSetDML3nhNgMUmcrsw80Xx1Uf1n1dWI-A20PMa8/edit#slide=id.p

• NAD/NADP: do we keep a grouping term even if all annotations can be classified to NAD or NADP-dependent? for eg GO:0003845 11-beta-hydroxysteroid dehydrogenase [NAD(P) activity] - all known enzymes have known specificity, see review ticket
  • added 'do not annotate'
  • DECISION (last call): This is what we will do
  • Need to add to documentation

Imports PRs

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

Other Business

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

amphiregulin production ticket: https://github.com/geneontology/go-ontology/issues/21878 Ontology editors call:

• We would like to describe the biological process - maybe the term label is convenient, but it's not a process in the GO sense
• It's OK to have 'gene expression' of x but we dont think it's a good idea to name these classes