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

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 InChIKe...

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Autores principales: Wohlgemuth, Gert, Haldiya, Pradeep Kumar, Willighagen, Egon, Kind, Tobias, Fiehn, Oliver
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2010
Materias:
Applications Note
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2951090/
https://www.ncbi.nlm.nih.gov/pubmed/20829444
http://dx.doi.org/10.1093/bioinformatics/btq476
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author Wohlgemuth, Gert
Haldiya, Pradeep Kumar
Willighagen, Egon
Kind, Tobias
Fiehn, Oliver
author_facet Wohlgemuth, Gert
Haldiya, Pradeep Kumar
Willighagen, Egon
Kind, Tobias
Fiehn, Oliver
author_sort Wohlgemuth, Gert
collection PubMed
description 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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spelling pubmed-29510902010-10-08 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 Bioinformatics Applications Note 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 Oxford University Press 2010-10-15 2010-09-09 /pmc/articles/PMC2951090/ /pubmed/20829444 http://dx.doi.org/10.1093/bioinformatics/btq476 Text en © The Author(s) 2010. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Note
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
title The Chemical Translation Service—a web-based tool to improve standardization of metabolomic reports
title_full The Chemical Translation Service—a web-based tool to improve standardization of metabolomic reports
title_fullStr The Chemical Translation Service—a web-based tool to improve standardization of metabolomic reports
title_full_unstemmed The Chemical Translation Service—a web-based tool to improve standardization of metabolomic reports
title_short The Chemical Translation Service—a web-based tool to improve standardization of metabolomic reports
title_sort chemical translation service—a web-based tool to improve standardization of metabolomic reports
topic Applications Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2951090/
https://www.ncbi.nlm.nih.gov/pubmed/20829444
http://dx.doi.org/10.1093/bioinformatics/btq476
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