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. 2010 Oct 15;26(20):2647-8.
doi: 10.1093/bioinformatics/btq476. Epub 2010 Sep 9.

The Chemical Translation Service--a web-based tool to improve standardization of metabolomic reports

Gert Wohlgemuth  1 , Pradeep Kumar Haldiya, Egon Willighagen, Tobias Kind, Oliver Fiehn
Affiliations

The Chemical Translation Service--a web-based tool to improve standardization of metabolomic reports

Gert Wohlgemuth et al. Bioinformatics. .

Abstract

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

Contact: ofiehn@ucdavis.edu

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References

    1. Kind T, et al. How large is the metabolome? A critical analysis of data exchange practices in chemistry. PLoS One. 2009;4 Article No: e5440. - PMC - PubMed
    1. Redestig H, et al. Consolidating metabolite identifiers to enable contextual and multi-platform metabolomics data analysis. BMC Bioinformatics. 2010;11:214. - PMC - PubMed
    1. Sitzmann M. NCI/CADD Chemical Identifier Resolver. 2009 Available at http://cactus.nci.nih.gov/chemical/structure (last accessed date May 9, 2010)
    1. Sreekumar A, et al. Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 2009;457:910–914. - PMC - PubMed
    1. Sumner LW, et al. Proposed minimum reporting standards for chemical analysis. Metabolomics. 2007;3:211–221. - PMC - PubMed

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