migrate CHEBI terms to pH 7.3 subset

[balhoff]

I'm trying to update the pH 7.3 mapping list in #23567, but the update reveals some terms used in GO that aren't currently in the pH 7.3 list, and don't have mappings there:

• phytochromobilin -> changed in the ontology; the correct ph7.3 term was alread in the imports file -> added CHEBI_169942 ## kaempferol 3-O-β-D-glucoside(1−)
• kaempferol 3-O-beta-D-glucoside
• kainic acid -> added CHEBI_156548 ## kainate(1−)
• noradrenaline -> changed to CHEBI_72587 ## (R)-noradrenaline (was already in chebi imports)
• bacitracin A -> Added CHEBI_184381 ## bacitracin A zwitterion to chebi imports
• suramin -> added CHEBI_180911 ## suramin(6−)

[balhoff]

I think this was the case with the previous version of the file, so I'm not sure why these weren't flagged before.

[pgaudet]

Hi @balhoff

CHEBI:26116 phytochromobilin and CHEBI:33569 noradrenaline were not in the CHEBI imports; can they be removed from the other file where this data is coming from, to avoid we use these by mistake in the future?

Thanks, Pascale

[pgaudet]

For kaempferol 3-O-beta-D-glucoside I dont know how to find the corresponding pH 7.3 - @kaxelsen can you help ?

Thanks, Pascale

[kaxelsen]

Go to www.rhea-db.org and search for the CHEBI ID of the compound you have (here CHEBI:30200) or for the compound name (kaempferol 3-O-beta-D-glucoside)
https://www.rhea-db.org/rhea?query=kaempferol+3-O-beta-D-glucoside.
Choose one of the reactions and scroll down to "reaction participants". Here you will see the compound we use is CHEBI:169942

[deustp01]

Go to www.rhea-db.org and search for the CHEBI ID of the compound you have (here CHEBI:30200) or for the compound name (kaempferol 3-O-beta-D-glucoside)
https://www.rhea-db.org/rhea?query=kaempferol+3-O-beta-D-glucoside.
Choose one of the reactions and scroll down to "reaction participants". Here you will see the compound we use is CHEBI:169942

Possible scaling and mapping issue (and possibly also a digression here) - my anecdotal sense, from working to align hundreds of Reactome reactions with their pH 7.3 RHEA counterparts, is that the correctly charged ChEBI instance often (maybe 10% of the time) lacks any comment to indicate that it is the predominant microspecies at pH 7.3. I can indeed check the various ChEBI instances to identify the one that is associated with RHEA reactions but that is slow. It would make our checking and new-curation work easier and more reliable if this information were reliably present in ChEBI entries.

[balhoff]

@pgaudet we've still got a GO term phytochromobilin metabolic process referencing phytochromobilin.