Obsoletion: [GO term] disaccharide catabolic process (GO:0046352)

[ValWood]

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

disaccharides are glycosides, so should disaccharide catabolic process (GO:0046352) be a descendant of GO:0016139 | glycoside catabolic process

I am picking up a mapping where I have an annotation to melibiose catabolic process

[hdrabkin]

Hmm I notice that glycoside catabolic process has no children at all. at first glance I would think there should be others @deustp01 what do you think (chebi tree view does not include sucrose but does include sucrose derivatives

[deustp01]

sucrose (CHEBI:17992) is_a glycosyl glycoside (CHEBI:24407) is_a disaccharide (CHEBI:36233) but there is no is_a linkage of glycosyl glycoside (CHEBI:24407) to glycoside (CHEBI:24400) in ChEBI, as far as I can tell.

So I'm lost.

Maybe we have stumbled on a gap in the ChEBI ontology, or maybe glycosides, despite having monosaccharide components must also have components that are not conventional otherwise unmodified monosaccharides so molecules like sucrose, lactose, maltose and the like are not glycosides? The Wikipedia definition for glycoside (and accompanying picture), for what it's worth, is consistent with this (and also consistent with sucrose derivatives but not sucrose itself being children of glycoside): "In chemistry, a glycoside is a molecule in which a sugar is bound to another functional group via a glycosidic bond]. Glycosides play numerous important roles in living organisms. Many plants store chemicals in the form of inactive glycosides."

[ValWood]

Let me know if I need to request a CHEBI link.

[hdrabkin]

Carbohydrates Robert J. Ouellette, J. David Rawn, in Organic Chemistry Study Guide, 2015 26.8 Disaccharides Disaccharides are glycosides formed from two monosaccharides that can be either aldoses or ketoses. I'll contact CHEBI.

[ValWood]

I can't see anything on the CHEBI tracker so https://github.com/ebi-chebi/ChEBI/issues/4438 I'll take this one.

[ValWood]

Feedback from CHEBI

I contacted Gerard Moss, author of 2-carb (IUPAC recommendations on the nomenclature of carbohydrates - https://iupac.qmul.ac.uk/2carb/). He raised this issue with the carbohydrate group and they do not think that dissacharides are glycosides. They are currently working on a glossary of carbohydrate terms for the gold book and their current revised definition for glycoside is:

glycosides: Mixed acetals resulting from the attachment of a glycosyl group to a non-acyl group RO– [and chalcogen replacements thereof (RS–, RSe–)].

I also read 2-Carb-36.2 (https://iupac.qmul.ac.uk/2carb/36.html) where it states that disaccharides without a free hemiacetal group are named as glycosyl glycosides whereas the ones that have a free hemiacetal group are named as glycosylglycose.

[deustp01]

sucrose (CHEBI:17992) is_a glycosyl glycoside (CHEBI:24407) is_a disaccharide (CHEBI:36233) but there is no is_a linkage of glycosyl glycoside (CHEBI:24407) to glycoside (CHEBI:24400) in ChEBI, as far as I can tell.

So I'm lost.

OK. I am still lost, but if ChEBI people are now working on this, I'm happy to defer to whatever conclusion they reach.

[ValWood]

From what I gathered, it seems that some, but not all disaccharides are glycosides? I wasn't sure either, so I already asked this as a follow-up question.

I wondered if there would be a sub-branch of disaccharides (without a free hemiacetal group), that could have the glycoside parent?

[pgaudet]

Hi @ValWood

Maybe 'GO:0016139 | glycoside catabolic process' and the more general metabolic process terms should not be in GO? is this a useful biological grouping term?

It seems to have created confusion, it looks like some Glycosylases (https://enzyme.expasy.org/EC/3.2.-.- ) are annotated to glycoside catabolic process

According to wikipedia: https://en.wikipedia.org/wiki/Glycosylase:

Glycosylases (EC 3.2) are enzymes that hydrolyze glycosyl compounds"

and a glycosyl is

a univalent free radical or substituent structure obtained by removing the hydroxyl (−OH) group from the hemiacetal (−CH(OH)O−) group found in the cyclic form of a monosaccharide and, by extension, of a lower oligosaccharide

However this seems different from glycoside as defined by ChEBI: A glycosyl compound resulting from the attachment of a glycosyl group to a non-acyl group RO‒, RS‒, RSe‒, etc.

I would propose to obsolete

• GO:0016137 glycoside metabolic process
• GO:0016138 glycoside biosynthetic process
• GO:0016139 glycoside catabolic process

What do you think ?

[ValWood]

I agree, they probably aren't helpful groupings and they add confusion