Abstract
Simulating networks of biochemical reactions require reliable kinetic data. In order to facilitate the access to such kinetic data we have developed SABIO-RK, a curated database with information about biochemical reactions and their kinetic properties. The data are manually extracted from literature and verified by curators, concerning standards, formats and controlled vocabularies. This process is supported by tools in a semi-automatic manner. SABIO-RK contains and merges information about reactions such as reactants and modifiers, organism, tissue and cellular location, as well as the kinetic properties of the reactions. The type of the kinetic mechanism, modes of inhibition or activation, and corresponding rate equations are presented together with their parameters and measured values, specifying the experimental conditions under which these were determined. Links to other databases enable the user to gather further information and to refer to the original publication. Information about reactions and their kinetic data can be exported to an SBML file, allowing users to employ the information as the basis for their simulation models.
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References
Schomburg, I., Chang, A., Ebeling, C., Gremse, M., Heldt, C., Huhn, G., Schomburg, D.: BRENDA, the enzyme database: updates and major new developments. Nucleic Acids Res. 32, 431–433 (2004)
Bairoch, A., Apweiler, R., Wu, C.H., Barker, W.C., Boeckmann, B., Ferro, S., Gasteiger, E., Huang, H., Lopez, R., Magrane, M., Martin, M.J., Natale, D.A., O’Donovan, C., Redaschi, N., Yeh, L.S.: The Universal Protein Resource (UniProt). Nucleic Acids Res. 33, 154–159 (2005)
Le Novere, N., Bornstein, B., Broicher, A., Courtot, M., Donizelli, M., Dharuri, H., Li, L., Sauro, H., Schilstra, M., Shapiro, B., Snoep, J.L., Hucka, M.: BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Res. 34, 689–691 (2006)
Hucka, M., Finney, A., Sauro, H.M., Bolouri, H., Doyle, J.C., Kitano, H., Arkin, A.P., Bornstein, B.J., Bray, D., Cornish-Bowden, A., Cuellar, A.A., Dronov, S., Gilles, E.D., Ginkel, M., Gor, V., Goryanin, I.I., Hedley, W.J., Hodgman, T.C., Hofmeyr, J.H., Hunter, P.J., Juty, N.S., Kasberger, J.L., Kremling, A., Kummer, U., Le Novere, N., Loew, L.M., Lucio, D., Mendes, P., Minch, E., Mjolsness, E.D., Nakayama, Y., Nelson, M.R., Nielsen, P.F., Sakurada, T., Schaff, J.C., Shapiro, B.E., Shimizu, T.S., Spence, H.D., Stelling, J., Takahashi, K., Tomita, M., Wagner, J., Wang, J.: The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19, 524–531 (2003)
Rojas, I., Bernardi, L., Ratsch, E., Kania, R., Wittig, U., Saric, J.: A database system for the analysis of biochemical pathways. In Silico Biol. 2, p. 7 (2002)
Kanehisa, M., Goto, S., Hattori, M., Aoki-Kinoshita, K.F., Itoh, M., Kawashima, S., Katayama, T., Araki, M., Hirakawa, M.: From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res. 7, 354–357 (2006)
NCBI Taxonomy, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Taxonomy
PubMed, http://www.pubmed.gov
Anstein, S., Kremer, G., Reyle, U.: Identifying and Classifying Terms in the Life Sciences: The Case of Chemical Terminology. In: Proceedings of the Fifth International Conference on Language Resources and Evaluation (LREC) (to appear, 2006)
Weininger, D.: SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules. J. Chem. Inf. Comput. Sci. 28, 31–36 (1988)
International System of Units (SI), http://www.bipm.fr/en/si/
Wittig, U., Weidemann, A., Kania, R., Peiss, C., Rojas, I.: Classification of chemical compounds to support complex queries in a pathway database. Comp. Funct. Genom. 5, 156–162 (2004)
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Wittig, U. et al. (2006). SABIO-RK: Integration and Curation of Reaction Kinetics Data. In: Leser, U., Naumann, F., Eckman, B. (eds) Data Integration in the Life Sciences. DILS 2006. Lecture Notes in Computer Science(), vol 4075. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11799511_9
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DOI: https://doi.org/10.1007/11799511_9
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-36593-8
Online ISBN: 978-3-540-36595-2
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