The chemical translation service-a web-based tool to improve standardization of metabolomic reports

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

Research output: Contribution to journalArticle

53 Citations (Scopus)

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.

Original languageEnglish (US)
Article numberbtq476
Pages (from-to)2647-2648
Number of pages2
JournalBioinformatics
Volume26
Issue number20
DOIs
StatePublished - Sep 9 2010

Fingerprint

Metabolomics
Standardization
Web-based
Databases
Names
Batch
Sudden Infant Death
Metabolome
Metabolites
Publications
Trivial
Software
Query

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computational Theory and Mathematics
  • Computer Science Applications
  • Computational Mathematics
  • Statistics and Probability
  • Medicine(all)

Cite this

Wohlgemuth, G., Haldiya, P. K., Willighagen, E., Kind, T., & Fiehn, O. (2010). The chemical translation service-a web-based tool to improve standardization of metabolomic reports. Bioinformatics, 26(20), 2647-2648. [btq476]. https://doi.org/10.1093/bioinformatics/btq476

The chemical translation service-a web-based tool to improve standardization of metabolomic reports. / Wohlgemuth, Gert; Haldiya, Pradeep Kumar; Willighagen, Egon; Kind, Tobias; Fiehn, Oliver.

In: Bioinformatics, Vol. 26, No. 20, btq476, 09.09.2010, p. 2647-2648.

Research output: Contribution to journalArticle

Wohlgemuth, G, Haldiya, PK, Willighagen, E, Kind, T & Fiehn, O 2010, 'The chemical translation service-a web-based tool to improve standardization of metabolomic reports', Bioinformatics, vol. 26, no. 20, btq476, pp. 2647-2648. https://doi.org/10.1093/bioinformatics/btq476
Wohlgemuth, Gert ; Haldiya, Pradeep Kumar ; Willighagen, Egon ; Kind, Tobias ; Fiehn, Oliver. / The chemical translation service-a web-based tool to improve standardization of metabolomic reports. In: Bioinformatics. 2010 ; Vol. 26, No. 20. pp. 2647-2648.
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