Missing parent: GO:0006568 tryptophan metabolic process GO:0006549 isoleucine metabolic process

[ValWood]

• GO term ID and label for which you request a new superclass

• New superclass (parent) suggested

GO:0006568    tryptophan metabolic process GO:0006549 isoleucine metabolic process add GO:0170039 proteinogenic amino acid metabolic process

• Reference(s), if appropriate PMID:nnnnnnn

[pgaudet]

It seems like the ChEBI amino acids under proteinogenic amino acid are not the pH7.3 forms:

@cmungall I suppose we need to ask ChEBI to change this?

[deustp01]

Looking at the first few items on the list, the ChEBI default form of L-amino acid has no ionized groups, exactly like the Wikipedia representation, a fairly common textbook representation. In my small sample, ChEBI goes on to list all the physiologically relevant charged forms of each amino acid as is_a children of this non-ionized one, so it's not clear that correct information is lost. And what is the exact form of an L-amino acid (or strictly, an aminoacyl-tRNA?) at the point it is recruited to be incorporated into a protein?

My opinion is that all the changes that @cmungall has been arguing for in the organization of the ChEBI amino acid ontology and in the text definitions of specific terms (e.g., flagging the one that is predominant at pH 7.3) will make this specific small fix unnecessary, so we should go for the main goal, the larger reorganization.

[pgaudet]

But they do have CHEBI:57719 'D-tryptophan zwitterion' - this should be proteogenic, shouldn't it?

[pgaudet]

My opinion is that all the changes that @cmungall has been arguing for in the organization of the ChEBI amino acid ontology and in the text definitions of specific terms (e.g., flagging the one that is predominant at pH 7.3) will make this specific small fix unnecessary, so we should go for the main goal, the larger reorganization.

and meanwhile why do we do ? assert anything missing from ChEBI ?

[deustp01]

and meanwhile what do we do ?

I'm worried that continuing to make ad hoc patches on a broken structure wastes a lot of GO time and does not solve the problem - not unlike the rationale for the many clean-up and rationalization exercises now underway in the BP and MF ontologies.

[pgaudet]

Right me too!! And ChEBI has been slow to make large changes. I was hoping they would make a smaller change about this set of terms (proteinogenic aa) quicker...

[ValWood]

This would be a small change with a big effect. Having a term for proteinogenic amino acid metabolism, it seems strange not to have all of the protein aminogenic amino acids as subclasses. We were trying to use the proteinogenic term to pull out the genes for the pathways we wanted to model first which was how I noticed this.

But now we know its a problem, I am not in any particular hurry for a fix (we can easily work around this), but we need the tickets tp check that the issues are eventually resolved. I'm happy if they are labelled "pending_CHEBI_Changes" as long as the changes are requested and actioned.