TPV: acyl CoA is under nucleotide metabolism

[ValWood]

Does anyone know why
GO:0071616 JSON
acyl-CoA biosynthetic process

is under purine ribonucleotide metabolic process ?

[deustp01]

Because one of the components of coenzyme A is a purine ribonucleotide. Now, the process for synthesizing acyl-CoA's starts with fatty acids, coenzyme A, and ATP, =so in the same way that acyl-CoA biosynthetic process is not under fatty acid metabolic process, it ought to be possible to keep it from being under purine ribonucleotide metabolic process.

See coenzyme A (CHEBI:15346) is a adenosine 3',5'-bisphosphate (CHEBI:37240)

[pgaudet]

This is what the reasoner says (do you know how to use that?)

But I dont see that in chebi
https://www.ebi.ac.uk/chebi/chebiOntology.do?chebiId=CHEBI:58342&treeView=true#vizualisation

[pgaudet]

[deustp01]

But I dont see that in chebi

I copied that line from the ChEBI ontology / outgoing section on the main page for coenzyme A (CHEBI:15346) Indeed, I do not see this parentage assertion in the expanded ontology. Am I missing somethingin how ontology views are organized?

[ukemi]

Are you sure it's not an asserted subclass?

[ukemi]

I just checked. It's not.

[ValWood]

Assigned to @pgaudet as I don't know how to fix this

[ValWood]

I meant to add, you can assign back to me with instructions, is it a CHEBI issue?

[deustp01]

It is a ChEBI problem. Acyl-CoA has no nucleotide parent, BUT acyl-CoA(4−) (CHEBI:58342) is a acyl-CoA oxoanion (CHEBI:58946) and acyl-CoA (CHEBI:17984) is a adenosine 3',5'-bisphosphate (CHEBI:37240). Fiendishly clever, those gaps in parentage!

[pgaudet]

@ValWood Can you please open a ticket in the ChEBI tracker and ask them to change the relationships?

acyl-CoA (CHEBI:17984)
should not be is_a adenosine 3',5'-bisphosphate (CHEBI:37240) (but I am not sure what the correct relation is)

Thanks, Pascale

[ValWood]

ebi-chebi/ChEBI#4503