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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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Check CHEBI:57930 #4250

Open amorgat opened 2 years ago

amorgat commented 2 years ago

Hi Adnan,

I relaized that querying Rhea with CHEBI:58043 and CHEBI:57930 and CHEBI:61557 gives unexpected results (i.e. I found reactions for deoxyribonucleotides): https://www.rhea-db.org/rhea?query=chebi%3A57930+chebi%3A58043+chebi%3A61557

CHEBI:58043 / CHEBI:17188 nucleoside 5'-monophosphate have the 2D structure of ribonucleoside 5'-monophosphate CHEBI:57930 / CHEBI:16862 nucleoside 5'-diphosphate have the 2D structure of ribonucleoside 5'-diphosphate CHEBI:61557 / CHEBI:58104 / CHEBI:17326 nucleoside 5'-triphosphate have the 2D structure of ribonucleoside 5'-triphosphate

Please would you update the name and definitions accordingly to the 2D structure and check the is-a relationships?

Cheers, Anne

amalik01 commented 2 years ago

Hi Anne,

I've realized that we have separate entries for ribonucleoside 5'-monophosphate (CHEBI:37010), diphosphate (CHEBI:37075) and triphosphate (CHEBI:37076). I am not exactly sure why generic chemical structures have been added to the nucleoside phosphates (nucleoside 5'-monophosphate, diphosphate and triphosphate) since the ChEBI name does not specifiy whether the sugar moiety is ribose or deoxyribose. Either the above entries which you mentioned have to be merged or completely separated. Are you free anytime next week to discuss this over a skype call?