Summary: 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. We have implemented a web-based Chemical Translation Service that performs batch conversions of the most common compound identifiers, including CAS, CHEBI, compound formulas, Human Metabolome Database HMDB, InChI, InChIKey, IUPAC name, KEGG, LipidMaps, PubChem CID+SID, SMILES and chemical synonym names. Batch conversion downloads of 1410 CIDs are performed in 2.5 min. Structures are automatically displayed.
Implementation: The software was implemented in Groovy and JAVA, the web frontend was implemented in GRAILS and the database used was PostgreSQL.
Availability: The source code and an online web interface are freely available. Chemical Translation Service (CTS): http://cts.fiehnlab.ucdavis.edu
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