Ontology meeting 2023-12-11

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  • Group members: Pascale, Raymond, Edith, Val, Jim, Tanya, Kimberly, Peter, Chris, Paul
  • Present: Pascale, Raymond, Edith, Val, Jim, Tanya, Kimberly, Peter, Chris,
  • Regrets: Paul


Discussion points

User feedback

Peter - Specific items:

  • partly retract rude comments about commercial users who quietly put our material behind paywalls.
  • point out the need to sweep annotations for this sort of noise. Not so bad – they flagged about 15 papers out of the 37,000 we have used over the past 20 years.
  • See also GORULE-0000022 - implementation on hold until we figure out how to load external files or query external APIs during the pipeline run

Def and synonym cross-references

EC and RHEA are sometimes used in def xref, and EC if often used in synonym xref. This is really tedious to update when the EC or RHEA IDs change.

Can we change this to, for example: GOC:EC and GOC:RHEA, and only maintain the actual cross references in xrefs?

Example 

 [Term]
id: GO:0018819
name: lactoyl-CoA dehydratase activity
namespace: molecular_function
def: "Catalysis of the reaction: lactoyl-CoA = acryloyl-CoA + H2O." [EC:4.2.1.54, RHEA:34691]
synonym: "acrylyl coenzyme A hydratase activity" RELATED [EC:4.2.1.54]
synonym: "lactoyl coenzyme A dehydratase activity" RELATED [EC:4.2.1.54]
synonym: "lactoyl-CoA hydro-lyase (acryloyl-CoA-forming)" RELATED [EC:4.2.1.54]
synonym: "lactoyl-CoA hydro-lyase activity" RELATED [EC:4.2.1.54]
synonym: "lactyl CoA dehydratase activity" RELATED [EC:4.2.1.54]
synonym: "lactyl-coenzyme A dehydrase activity" RELATED [EC:4.2.1.54]
xref: EC:4.2.1.54
xref: MetaCyc:LACTOYL-COA-DEHYDRATASE-RXN
xref: MetaCyc:RXN-781
xref: RHEA:34691
xref: UM-BBD_reactionID:r0086
  • Discussion we will implement a check to make sure synonyms are in synch

AmiGO now showing reaction participants

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