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#17 Polybasic acids
It's sometimes very cumbersome to describe relationships within the ontology between polybasic acids and their associated bases, specifically if we have to concoct a whole series of anions all differing by a difference in charge of one unit. This is exemplified rather nicely by pentetic acid (CHEBI:35739) where we have had to create entries for all the anionic species up to pentetate(5-). More common are the di- and tri-carboxylic acids where occasionally I have taken a short cut, e.g. for 3-oxoadipic acid (CHEBI:37440) I have allowed is_conjugate_acid/base relationships with 3-oxoadipate(2-) (CHEBI:15775). [If we were to create an entry for adipate(1-), on which end of the molecule would the charge reside? Also, as the number of acid groups in a molecule increases, the number of combinations possible for where the charges may be positioned increases dramatically.]
I think we could get round the problem (if indeed we all agree that it is a problem) by adding a qualifying statement to paragraph 5.3.3 of the User Manual (which describes the "is_conjugate_base_of" and "is_conjugate_acid_of" relationships). Something along the following lines might be appropriate:
"For the purposes of accommodating polybasic acids within this ontology, the normal definition of a conjugate acid–base pair is extended to include charge differences between the acid and base entities of greater than one unit."
But would this be pushing the boundaries a bit too far? The Gold Book very definitely refers to the species within a conjugate acid-base pair having a difference in charge of one unit. Any opinions?
Marcus
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Thus we have to introduce a new relationship into ChEBI, viz.
"is alloprote of" -- see the "Feature Request"
http://sourceforge.net/tracker/index.php?func=detail&aid=1706413&group_id=125463&atid=702611