Clean up amino acid metabolic process grouping terms

[edwong57]

Elisabeth Coudert from RHEA suggested that these are not useful grouping terms and should be cleaned up/obsoleted

GO:0009069 serine family amino acid metabolic process
GO:0009078 pyruvate family amino acid metabolic process
GO:0009066 aspartate family amino acid metabolic process
GO:0009064 glutamine family amino acid metabolic process
GO:0000820 regulation of glutamine family amino acid metabolic process
GO:1902221 erythrose 4-phosphate/phosphoenolpyruvate family amino acid metabolic process
& the corresponding biosynthetic/catabolic processes

[deustp01]

not useful grouping terms

Hmmm. Quick searches suggest that diverse workers do find this grouping / classification strategy useful, e.g., "The aspartate pathway is responsible for the biosynthesis of lysine, threonine, isoleucine, and methionine in most plants and microorganisms."; CHEBI:26463 - pyruvate family amino acid. And these usages correspond to metabolic functional similarities among the members of each family. What specifically is said to make them UNuseful?

[edwong57]

@deustp01, good question. @pgaudet, can you clarify with more details? Did she have specific suggestions?

[cmungall]

This is an interesting one in that the CHEBI grouping is basically recapitulating what we should be representing with pathways:

id: CHEBI:22658
name: aspartate family amino acid
def: "An L-alpha-amino acid which is L-aspartic acid or any of the essential amino acids biosynthesised from it (asparagine, lysine, methionine, threonine and isoleucine). A closed class." []

MetaCyc has the concept of a superpathway for this:

It may seem nuanced but the grouping is by the pathway and not the chemical classification

this actually makes a difference because, the superpathway doesn't include alternatives ways of making L-methionine

In GO, this pathways is included
https://amigo.geneontology.org/amigo/term/GO:0009067

I would argue the pathway-centric way is more useful than the pathway-derived-chemical-class

But I think this is complex and I am happy for my comments to be parked in another issue, and for us to preserve the family grouping for now.

We should at the least make this do-not-annotate.

[pgaudet]

Thanks everyone for a feedback. The term label 'aspartate family amino acid xx process' is not very clear.
It's also a bit unusual that we group synthesis pathways be the common precursor, but why not. This would be a case where 'has primary input' would be relevant in the logical definition.

How about aligning with MetaCyc?

• change label 'GO:0009067 aspartate family amino acid biosynthetic process' to 'aspartate-derived amino acid biosynthetic process' (or even oxaloacetate-derived), or something along those lines
  Metacyc:

This superpathway integrates the biosynthesis of several compounds that are derived from the central metabolite oxaloacetate, an intermediate of the

• it seems the catabolic process and therefore metabolic process are not relevant

Thanks, Pascale

[cmungall]

I agree with both points from @pgaudet

[deustp01]

Here's the textbook basis for the classification into families, from an online version of the 5th edition of the Stryer textbook. Use the analytical list of topics down the left side of the page to get to "24. The Biosynthesis of Amino Acids", open it, choose "24.2 Amino acids are made ...", to find:

The pathways for the biosynthesis of amino acids are diverse. However, they have an important common feature: their carbon skeletons come from intermediates of glycolysis, the pentose phosphate pathway, or the citric acid cycle. On the basis of these starting materials, amino acids can be grouped into six biosynthetic families (Figure 24.7).

Read on to find the defining features of each.

[edwong57]

Thanks for that resource, @deustp01

[pgaudet]

For reference:

[pgaudet]

Human essential/non-essential amino acids

See also: https://jasbsci.biomedcentral.com/articles/10.1186/2049-1891-5-34

Amino acids (AA) are building blocks for proteins and must be present in cells for synthesis of polypeptides [1]. The carbon skeletons of eleven of these AA (namely cysteine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, tyrosine, and valine) are not synthesized from non-AA molecules in cells of any animals [2]. Therefore, they are classified as nutritionally essential AA (EAA) and must be included in diets for nonruminants to maintain physiological functions of cells, tissues, and the whole body [3, 4]. This assumes particular importance for the small intestine because its basal membrane lacks an ability to take up a nutritionally significant quantity of all AA, except for glutamine, from the arterial circulation [5, 6].