If I have a large list of human genes, and a large list of human metabolites (with KEGG and HMDB IDs), what is the best way to determine if any of these genes and metabolites have a known biological relationship?
ie, suppose metabolite XXX is a byproduct of fatty acid metabolism, which gene YYY is involved in. That would be interesting and I would like a way to flag these relationships.
I am certain all the information I need is in an existing database, I just am not sure how to go about such a query. These data are all currently stored as flat files.