Abstract
Chemical proteomics is concerned with the identification of protein targets interacting with small molecules. Hence, the availability of a high quality and free resource storing small molecules is essential for the future development of the field. The Chemical Entities of Biological Interest (ChEBI) database is one such database. The scope of ChEBI includes any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity. These entities in question are either products of nature or synthetic products used to intervene in the processes of living organisms. In addition, ChEBI contains a chemical ontology which relates the small molecules with each other thereby making it easier for users to discover data. The ontology also describes the biological roles that the small molecules are active in. The ChEBI database also provides a central reference point in which to access a variety of bioinformatics data points such as pathways and their biochemical reactions; expression data; protein sequence and structures.
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References
de Matos, P., Alcantara, R., Dekker, A., Ennis, M., Hastings, J., Haug, K., Spiteri, I., Turner, S., and Steinbeck, C. (2010) Chemical Entities of Biological Interest: an update, Nucl. Acids Res. 38, D249–254.
ChEMBL DB. http://www.ebi.ac.uk/chembldb. Accessed 1 March 2010.
Symyx CTFile formats. http://www.symyx.com/solutions/white_papers/ctfile_formats.jsp. Accessed 1 March 2010.
Stein, S. E., Heller, S. R., and Tchekhovskoi, D. (2003) An Open Standard for Chemical Structure Representation - The IUPAC Chemical Identifier, International Chemical Information Conference, 131–143.
Weininger, D., Weininger, A., and Weininger, J. L. (1989) SMILES. 2. Algorithm for generation of unique SMILES notation, Journal of Chemical Information and Computer Sciences 29, 97–101.
CiteXplore database. http://www.ebi.ac.uk/citexplore. Accessed 1 March 2010.
Studer, R., Benjamins, V. R., and Fensel, D. (1998) Knowledge engineering: Principles and methods, Data & Knowledge Engineering 25, 161–197.
Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., Harris, M. A., Hill, D. P., Issel-Tarver, L., Kasarskis, A., Lewis, S., Matese, J. C., Richardson, J. E., Ringwald, M., Rubin, G. M., and Sherlock, G. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium, Nature Genetics 25, 25–29.
Kanehisa, M., and Goto, S. (2000) KEGG: Kyoto Encyclopedia of Genes and Genomes, Nucl. Acids Res. 28, 27–30.
Fleischmann, A., Darsow, M., Degtyarenko, K., Fleischmann, W., Boyce, S., Axelsen, K., Bairoch, A., Schomburg, D., Tipton, K., and Apweiler, R. (2004) IntEnz, the integrated relational enzyme database, Nucl. Acids Res. 32, D434–437.
Schober, D., Smith, B., Lewis, S., Kusnierczyk, W., Lomax, J., Mungall, C., Taylor, C., Serra, P., and Sansone, S. (2009) Survey-based naming conventions for use in OBO Foundry ontology development, BMC Bioinformatics 10, 125.
Steinbeck, C., and Kuhn, S. (2004) NMRShiftDB - compound identification and structure elucidation support through a free community-built web database, Phytochemistry 65, 2711–2717.
Wang, Y., Xiao, J., Suzek, T., Zhang, J., Wang, J., and Bryant, S. (2009) PubChem: a public information system for analyzing bioactivities of small molecules, Nucl. Acids Res. 37, W623–633.
Rijnbeek, M., and Steinbeck, C. (2009) OrChem - An open source chemistry search engine for Oracle(R), Journal of Cheminformatics 1, 17.
Krause, S., Willighagen, E., and Steinbeck, C. JChemPaint - Using the Collaborative Forces of the Internet to Develop a Free Editor for 2D Chemical Structures, Molecules, 93–98.
Tanimoto TT (1957) IBM Internal Report.
Cote, R., Jones, P., Apweiler, R., and Hermjakob, H. (2006) The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries, BMC Bioinformatics 7, 97.
ChEBI Web Services. http://www.ebi.ac.uk/chebi/webServices.do
Murray-Rust, P., Rzepa, H., and Wright, M. (2001) Development of chemical markup language (CML) as a system for handling complex chemical content, New J. Chem. 25, 618–634.
ChEBI Downloads. http://www.ebi.ac.uk/chebi/downloadsForward.do. Accessed 1 March 2010.
Spjuth, O., Helmus, T., Willighagen, E., Kuhn, S., Eklund, M., Wagener, J., Rust, P., Steinbeck, C., and Wikberg, J. (2007) Bioclipse: an open source workbench for chemo- and bioinformatics, BMC Bioinformatics 8, 59.
Steinbeck, C., Hoppe, C., Kuhn, S., Floris, M., Guha, R., and Willighagen, E. (2006) Recent Developments of the Chemistry Development Kit (CDK) - An Open-Source Java Library for Chemo- and Bioinformatics, Current Pharmaceutical Design 12, 2111–2120(2110).
Day-Richter, J., Harris, M., Haendel, M., The Gene Ontology, O. B. O., and Lewis, S. (2007) OBO-Edit an ontology editor for biologists, Bioinformatics 23, 2198–2200.
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de Matos, P., Adams, N., Hastings, J., Moreno, P., Steinbeck, C. (2012). A Database for Chemical Proteomics: ChEBI. In: Drewes, G., Bantscheff, M. (eds) Chemical Proteomics. Methods in Molecular Biology, vol 803. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-364-6_19
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DOI: https://doi.org/10.1007/978-1-61779-364-6_19
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