This tools maps metabolite names from a CSV file in a format produced by a particular assay and tries to map them to KEGG Compound IDs via the Human Metabolite Database and some further manual curation.
Download the "All Metabolites" file from HMDB at http://www.hmdb.ca/downloads .
Unzip it into the input directory to obtain hmdb_metabolites.xml (1.6GB).
python map_metabolites.py input/data.csv > output/mapping.csv