ORAL PRESENTATION Open Access Computational metabolomics–a field at the boundaries of cheminformatics and bioinformatics Christoph Steinbeck * , Stefan Kuhn, Kalai Vanii Jayaseelan, Pablo Moreno From 6th German Conference on Chemoinformatics, GCC 2010 Goslar, Germany. 7-9 November 2010 Metabolomics studies the occurrence and change of concentrations of small molecular weight chemical compounds (metabolites) in organisms, organs, tissues, cells and ultimately cell compartments in the context of environmental changes, disease or other boundary con- ditions. It does this by means of spectroscopic and chro- matographic techniques and by observing at once not only a few but all compounds visible to the particular technique used. As such, it is not only the third large Omics area of research next to Genomics and Proteo- mics, but also a field at the boundary between chemistry and biology, helping to answer biological questions using analytical chemistry and cheminformatics techniques. This talk gives an overview about the field of Metabo- lomics and the challenges we face with respect to com- puting, informatics as well as chemical information aspects of metabolomics, including the analysis of metabolomics experiments, metabolomics databases, computer-assisted structure elucidation of metabolites and more. We give examples from our own research where we have for instance used machine learning techniques to predict NMR spectra of biological metabolites and applied those in computer-assisted structure elucidation systems for metabolites [1-3] – a classical area of cheminformatics which is now seeing a renaissance in the context of metabolomics. We further outline the data- collection challenges currently being address by the development of the MetaboLights database in our group at the European Bioinformatics Institute. Published: 19 April 2011 References 1. Kuhn S, Egert B, Neumann S, Steinbeck C: Building blocks for automated elucidation of metabolites: Machine learning methods for NMR. BMC Bioinformatics 2008, 9:400. 2. Kuhn S, Murray-Rust P, Lancashire RJ, Rzepa H, Helmus T, Steinbeck C, Willighagen E: Chemical Markup, XML, and the World Wide Web: CMLSpect, an XML vocabulary for spectral data. J Chem Inf Comput Sci 2007, 47:2015-2034. 3. Steinbeck C, Kuhn S: NMRShiftDB - compound identification and structure elucidation support through a free community-build web database. Phytochemistry 2004, 65:2711-2717. doi:10.1186/1758-2946-3-S1-O6 Cite this article as: Steinbeck et al.: Computational metabolomics–a field at the boundaries of cheminformatics and bioinformatics. Journal of Cheminformatics 2011 3(Suppl 1):O6. Open access provides opportunities to our colleagues in other parts of the globe, by allowing anyone to view the content free of charge. Publish with ChemistryCentral and every scientist can read your work free of charge W. Jeffery Hurst, The Hershey Company. available free of charge to the entire scientific community peer reviewed and published immediately upon acceptance cited in PubMed and archived on PubMed Central yours you keep the copyright Submit your manuscript here: http://www.chemistrycentral.com/manuscript/ * Correspondence: [email protected] Cheminformatics and Metabolism Group, European Bioinformatics Institute (EBI), Cambridge, CB10 1SD, UK Steinbeck et al. Journal of Cheminformatics 2011, 3(Suppl 1):O6 http://www.jcheminf.com/content/3/S1/O6 © 2011 Steinbeck et al; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Page 1: Computational metabolomics – a field at the boundaries of cheminformatics and bioinformatics

ORAL PRESENTATION Open Access

Computational metabolomics–a field at theboundaries of cheminformatics andbioinformaticsChristoph Steinbeck*, Stefan Kuhn, Kalai Vanii Jayaseelan, Pablo Moreno

From 6th German Conference on Chemoinformatics, GCC 2010Goslar, Germany. 7-9 November 2010

Metabolomics studies the occurrence and change ofconcentrations of small molecular weight chemical com-pounds (metabolites) in organisms, organs, tissues, cellsand ultimately cell compartments in the context ofenvironmental changes, disease or other boundary con-ditions. It does this by means of spectroscopic and chro-matographic techniques and by observing at once notonly a few but all compounds visible to the particulartechnique used. As such, it is not only the third largeOmics area of research next to Genomics and Proteo-mics, but also a field at the boundary between chemistryand biology, helping to answer biological questionsusing analytical chemistry and cheminformaticstechniques.This talk gives an overview about the field of Metabo-

lomics and the challenges we face with respect to com-puting, informatics as well as chemical informationaspects of metabolomics, including the analysis of meta-bolomics experiments, metabolomics databases, compu-ter-assisted structure elucidation of metabolites andmore. We give examples from our own research wherewe have for instance used machine learning techniquesto predict NMR spectra of biological metabolites andapplied those in computer-assisted structure elucidationsystems for metabolites [1-3] – a classical area of che-minformatics which is now seeing a renaissance in thecontext of metabolomics. We further outline the data-collection challenges currently being address by thedevelopment of the MetaboLights database in our groupat the European Bioinformatics Institute.

Published: 19 April 2011

References1. Kuhn S, Egert B, Neumann S, Steinbeck C: Building blocks for automated

elucidation of metabolites: Machine learning methods for NMR. BMCBioinformatics 2008, 9:400.

2. Kuhn S, Murray-Rust P, Lancashire RJ, Rzepa H, Helmus T, Steinbeck C,Willighagen E: Chemical Markup, XML, and the World Wide Web:CMLSpect, an XML vocabulary for spectral data. J Chem Inf Comput Sci2007, 47:2015-2034.

3. Steinbeck C, Kuhn S: NMRShiftDB - compound identification andstructure elucidation support through a free community-build webdatabase. Phytochemistry 2004, 65:2711-2717.

doi:10.1186/1758-2946-3-S1-O6Cite this article as: Steinbeck et al.: Computational metabolomics–a fieldat the boundaries of cheminformatics and bioinformatics. Journal ofCheminformatics 2011 3(Suppl 1):O6.

Open access provides opportunities to our colleagues in other parts of the globe, by allowing

anyone to view the content free of charge.

Publish with ChemistryCentral and everyscientist can read your work free of charge

W. Jeffery Hurst, The Hershey Company.

available free of charge to the entire scientific communitypeer reviewed and published immediately upon acceptancecited in PubMed and archived on PubMed Centralyours you keep the copyright

Submit your manuscript here:http://www.chemistrycentral.com/manuscript/

* Correspondence: [email protected] and Metabolism Group, European Bioinformatics Institute(EBI), Cambridge, CB10 1SD, UK

Steinbeck et al. Journal of Cheminformatics 2011, 3(Suppl 1):O6http://www.jcheminf.com/content/3/S1/O6

© 2011 Steinbeck et al; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the CreativeCommons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, andreproduction in any medium, provided the original work is properly cited.

http://www.ncbi.nlm.nih.gov/pubmed/18817546?dopt=Abstract

http://www.ncbi.nlm.nih.gov/pubmed/15464159?dopt=Abstract

mailto:[email protected]

http://creativecommons.org/licenses/by/2.0