Metabolites in SBML models in BiGG database contain annotations for providing additional information on other identifiers such as KEGG cpds. However, in some cases for each metabolite there exists more than one KEGG ID. Some cases are justified as some metabolites in BiGG have L and D forms in KEGG. Three other cases including H2O, H2O2 and hydrogen, associate with several KEGG compounds, which seems a bit peculiar (considering that C00001 stands uniquely for water in KEGG).
One the other hand, HMR database and RECON 2 (Thiele lab.) provide only one single KEGG ID for each metabolite. Why is that?
Furthermore, taking a look at reactions these metabolites participate in, the problem will worsen. HMR provides reaction equivalences between BiGG and KEGG reactions; however, it is not clear how such equivalences are valid when there are more than "one" KEGG ID for each metabolite in BiGG.
Dropping any hint about this situation is warmly appreciated!
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