Ontology meeting 2021-12-06

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



Discussion points

Decision on ChEBI update?

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

  • Action Item Harold
    • Create new top level CHEBI ticket to ask why these 3 compounds (succinate, fumarate, tyrosine) are now being classified as lipids - but the 'functional chain' of lipid is very, very short in these case, this is counter-inituitive; can you explain why this is the case?
    • Would like clarification on what is a structural derivative
 See https://github.com/ebi-chebi/ChEBI/issues/4176#issuecomment-984226590 for response thus far
  • We think removing the relationship to a lipid for fumaric acid by ChEBI will fix the tyrosine issue (
   tyrosine catabolic process to fumarate SubClassOf lipid biosynthetic process). 
  • Succinate is still an issue
    • Rerun the imports, excluding the relation 'structural derivative of'
  • Note from Harold: Chebi has informed me that fumaric acid, succinic acid, and malonic acid have had the lipid links removed; this will appear in the Jan 1 release of CHEBI.

Design patterns

Implemented in ontology

Protein-complex organization/assembly/disassembly

Problem with relations used in logical definition https://github.com/geneontology/go-ontology/issues/22488

Other Business