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ebi-chebi / ChEBI

Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds.
https://www.ebi.ac.uk/chebi
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CHEBI:79346 anionic ganglioside is missing a link to ganglioside #4535

Open alanbridge opened 2 months ago

alanbridge commented 2 months ago

Hi Adnan,

hope you are doing well.

We have dozens if not more classes of anionic gangliosides in ChEBI and Rhea; but these are not currently classified as gangliosides, nor lipids. This issue impacts the ontology based search in Rhea:

https://www.rhea-db.org/rhea?query=chebi%3Aganglioside - 179 reactions involving a compound named ganglioside versus https://www.rhea-db.org/rhea?query=CHEBI%3A28892 - only 6 reactions involving a compound classed as a ganglioside

Could we start to address this by adding a relation between the two?

CHEBI:79346 anionic ganglioside is_a CHEBI:28892 ganglioside

Other suggestions welcome - thank you.

All the best, Alan

CC @aimol

aimol commented 2 months ago

I have added the relation CHEBI:79346 anionic ganglioside is_a CHEBI:28892 ganglioside in the Ontology, I hope it is accepted!

amalik01 commented 2 months ago

Hi @alanbridge

This is an inherent problem in ChEBI and there is no quick solution to this. Neutral compounds have a completely different hierarchy compared to their ionized counterparts. For example, in ChEBI we have amino-acid anions and amino-acid cations and they are not classified as amino acids via their hierarchy. Instead, a conjugate acid/base relationship is used to define the relationship between amino acids (which have net charge = 0) and their cation/anions.

I have now added a conjugate acid/base relationship between ganglioside and anionic ganglioside.