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Metabolomic publications and databases use different database identifiers or even trivial names which disable queries across databases or between studies. The best way to annotate metabolites is by chemical structures, encoded by the International Chemical Identifier code (InChI) or InChIKey.
(Wohlgemuth et al., 2010) The Chemical Translation Service--a web-based tool to improve standardization of metabolomic reports. Bioinformatics.