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The Amine System Project: Systems Biology in Practice

  • Ismael Navas-Delgado
  • Raúl Montañez
  • Miguel Ángel Medina
  • José Luis Urdiales
  • José F. Aldana
  • Francisca Sánchez-Jiménez
Part of the Studies in Computational Intelligence book series (SCI, volume 94)

Summary

In this chapter we present an architecture for the development of Semantic Web applications, and the way it is applied to build an application for Systems Biology. Our working plan is designed to built an ontology-based system with connected biomodules that could be globally analysed, as far as possible. Supported by the advantages of the Semantic Web, we can keep the objective to work on the way to obtain an automated form to integrate both information and tools in our system.

Key words

Semantic Web Systems Biology Semantic Mediation Amine 

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References

  1. 1.
    Rodríguez-Caso, C. and Solé, R. (2006) Networks in cell biology, Fundamentals of Data Mining in Genomics and Proteomics, W. Dubitzky, M. Granzow, and D. Berrar, Eds. Kluwer Academic Publishers, vol. in press.Google Scholar
  2. 2.
    Kitano, H. (2002) Systems biology: a brief overview, Science, vol. 295, no. 5560, pp. 1662–1664, 1095–9203 (Electronic) Journal Article Review.CrossRefGoogle Scholar
  3. 3.
    Medina, M.A, Urdiales, J.L., Matés, J.M., Núñez de Castro, I. and Sánchez-Jiménez, F. (1991) Diamines interfere with the transport of l-ornithine in ehrlich-cell plasma-membrane vesicles, Biochem J, vol. 280 ( Pt 3), pp. 825–827, 0264–6021 (Print) Journal Article.Google Scholar
  4. 4.
    Engel, N., Olmo, M.T., Coleman, C.S., Medina, M.A., Pegg, A.E. and Sánchez-Jiménez, F. (1996) Experimental evidence for structure-activity features in common between mammalian histidine decarboxylase and ornithine decarboxy-lase, Biochem J, vol. 320 ( Pt 2), pp. 365–368, 0264–6021 (Print) Journal Article.Google Scholar
  5. 5.
    Fajardo, I., Urdiales, J.L., Medina, M.A. and Sánchez-Jiménez, F. (2001) Effects of phorbol ester and dexamethasone treatment on histidine decarboxylase and ornithine decarboxylase in basophilic cells, Biochem Pharmacol, vol. 61, no. 9, pp. 1101–1106, 0006–2952 (Print) Journal Article.CrossRefGoogle Scholar
  6. 6.
    Fajardo, I., Urdiales, J.L., Paz, J.C., Chavarría, T., Sánchez-Jiménez, F. and Medina, M.A. (2001) Histamine prevents polyamine accumulation in mouse c57.1 mast cell cultures, Eur J Biochem, vol. 268, no. 3, pp. 768–773, 0014–2956 (Print) Journal Article.CrossRefGoogle Scholar
  7. 7.
    Rodríguez-Caso, C., Rodríguez-Agudo, D., Sánchez-Jiménez, F. and Medina, M.A. (2003) Green tea epigallocatechin-3-gallate is an inhibitor of mammalian histidine decarboxylase, Cell Mol Life Sci, vol. 60, no. 8, pp. 1760–1763, 1420–682X (Print) Journal Article.CrossRefGoogle Scholar
  8. 8.
    Rodríguez-Caso, C., Rodríguez-Agudo, D., Moya-García, A.A., Fajardo, I., Medina, M.A., Subramaniam, V. and Sánchez-Jiménez, F. (2993) Local changes in the catalytic site of mammalian histidine decarboxylase can affect its global conformation and stability, Eur J Biochem, vol. 270, no. 21, pp. 4376–4387, 0014–2956 (Print) Journal Article.CrossRefGoogle Scholar
  9. 9.
    Fleming, J.V., Fajardo, I., Langlois, M.R., Sánchez-Jiménez, F. and Wang, T.C. (2004) The c-terminus of rat l-histidine decarboxylase specifically inhibits enzymic activity and disrupts pyridoxal phosphate-dependent interactions with l-histidine substrate analogues, Biochem J, vol. 381, no. Pt 3, pp. 769–778, 1470–8728 (Electronic) Journal Article.Google Scholar
  10. 10.
    Fleming, J.V., Sánchez-Jiménez, F., Moya-García, A.A., Langlois, M.R. and Wang, T.C. (2004) Mapping of catalytically important residues in the rat l-histidine decarboxylase enzyme using bioinformatic and site-directed mutagenesis approaches, Biochem J, vol. 379, no. Pt 2, pp. 253–261, 1470–8728 (Electronic) Journal Article.CrossRefGoogle Scholar
  11. 11.
    Medina, M.A., Urdiales, J.L., Rodríguez-Caso, C., Ramírez, F.J. and Sánchez-Jiménez, F. (2003) Biogenic amines and polyamines: similar biochemistry for different physiological missions and biomedical applications, Crit Rev Biochem Mol Biol, vol. 38, no. 1, pp. 23–59, 1040–9238 (Print) Journal Article Review.CrossRefGoogle Scholar
  12. 12.
    Cohen, S.S. (1998) A Guide to the Polyamines. New York: Oxford University Press.Google Scholar
  13. 13.
    Medina, M.A., Correa-Fiz, F., Rodríguez-Caso, C. and Sánchez-Jiménez, F. (2005) A comprehensive view of polyamine and histamine metabolism to the light of new technologies, J Cell Mol Med, vol. 9, no. 4, pp. 854–864, 1582–1838 (Print) Journal Article Review.CrossRefGoogle Scholar
  14. 14.
    Berners-Lee, T., Hendler, J. and Lassila, O. (2001) The Semantic Web, Scientific American.Google Scholar
  15. 15.
    Baader, F., Calvanese, D., McGuinness, D.L., Nardi, D. and Patel-Schneider, P.F. (2003) The Description Logic Handbook: Theory, Implementation, and Applications. Cambridge University Press.Google Scholar
  16. 16.
    Hussain, F.K., Sidhu, A.S., Dillon, T.S. and Chang, E. (2006) Engineering trustworthy ontologies: Case study of protein ontology, CBMS’06: Proceedings of the 19th IEEE Symposium on Computer-Based Medical Systems. Washington, DC, USA: IEEE Computer Society, pp. 617–622.Google Scholar
  17. 17.
    Eilbeck, K., Lewis, S.E., Mungall, C.J., Yandell, M., Stein, L., Durbin, R. and Ashburner, M. (2006) The sequence ontology: a tool for the unification of genome annotations, Genome Biology, vol. 6, p. R44.CrossRefGoogle Scholar
  18. 18.
    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., Ring-wald, M., Rubin, G.M. and Sherlock, G. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet, vol. 25, no. 1, pp. 25–29.CrossRefGoogle Scholar
  19. 19.
    Navas-Delgado, I. and Aldana-Montes, J.F. (2004) A distributed semantic mediation architecture, Journal of Information and Organizational Sciences, vol. 28, no. 1–2, pp. 135–150.Google Scholar
  20. 20.
    Aldana-Montes, J.F., Navas-Delgado, I. and Roldan-Garcia, M.M. (2004) Solving Queries over Semantically Integrated Biological Data Sources, Int. Conf. on Web-Age Information Management (WAIM 2004). LNCS 3129.Google Scholar
  21. 21.
    Haarslev, V. and Möller, R. (2001) The Description Logic ALCNHR+ Extended with Concrete Domains: A Practically Motivated Approach, R. Goré, A. Leitsch, and T. Nipkow, editors, International Joint Conference on Automated Reasoning, IJCAR2001, June 18–23, Siena, Italy, pp. 29–44, Springer-Verlag.Google Scholar
  22. 22.
    Barabasi, A.L. (2002) Linked: The New Science of Networks. Cambridge: Perseus Books Group.Google Scholar
  23. 23.
    Lehner, B., Crombie, C., Tischler, J., Fortunato, A. and Fraser, A.G. (2006) Systematic mapping of genetic interactions in caenorhabditis elegans identifies common modifiers of diverse signaling pathways, Nat Genet, vol. 38, no. 8, pp. 896–903, 1061–4036 (Print) Journal Article.CrossRefGoogle Scholar
  24. 24.
    Basso, K., Margolin, A.A., Stolovitzky, G., Klein, U., Dalla-Favera, R. and Califano, A. (2005) Reverse engineering of regulatory networks in human b cells, Nat Genet, vol. 37, no. 4, pp. 382–90, 1061–4036 (Print) Journal Article.CrossRefGoogle Scholar
  25. 25.
    Vázquez, A., Dobrin, R., Sergi, D., Eckmann, J.P., Oltvai, Z.N. and Barabasi, A.L. (2004) The topological relationship between the large-scale attributes and local interaction patterns of complex networks, Proc Natl Acad Sci U S A, vol. 101, no. 52, pp. 17 940–945, 0027–8424 (Print) Journal Article.CrossRefGoogle Scholar
  26. 26.
    Fell, D. (1996) Understanding the Control of Metabolism, ser. Frontiers in Metabolism. Ashgate Publishing.Google Scholar
  27. 27.
    JM, L., EP, G. and JA, P. (1991) Flux balance analysis in the era of metabolomics, Brief Bioinform, vol. 7, no. 2, pp. 140–150.Google Scholar
  28. 28.
    Garcia-Viloca, M., Gao, J., Karplus, M. and Truhlar, D.G. (2004) How enzymes work: analysis by modern rate theory and computer simulations. Science, vol. 303, no. 5655, pp. 186–195.CrossRefGoogle Scholar
  29. 29.
    Rodríguez-Caso, C., Medina, M.A. and Solé, R.V. (2005) Topology, tinkering and evolution of the human transcription factor network, Febs J, vol. 272, no. 24, pp. 6423–6434, 1742–464X (Print) Journal Article.CrossRefGoogle Scholar
  30. 30.
    Rodríguez-Caso, C., Montañez, R., Cascante, M., Sánchez-Jiménez, F. and Medina, M.A. (2007) Mathematical modeling of polyamine metabolism in mammals, J Biol Chem, vol. 281, no. 31, pp. 21 799–812, 0021–9258 (Print) Journal Article.Google Scholar
  31. 31.
    Montañez, R., Rodríguez-Caso, C., Sánchez-Jiménez, F. and Medina, M.A. (2007) In silico analysis if arginine catabolism as a source of nitric oxide or polyamines in endothelian cells, Amino Acids, in press.Google Scholar
  32. 32.
    Moya-García, A.A., Pino-Ángeles, A. and Sánchez-Jiménez, F. (2006) New structural insights to help in the search for selective inhibitors of mammalian pyridoxal 5’-phosphate-dependent histidine decarboxylase, Inflammation Res., vol. 55, Supplement 1, pp. S55–S56.CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2008

Authors and Affiliations

  • Ismael Navas-Delgado
    • 1
  • Raúl Montañez
    • 2
    • 3
  • Miguel Ángel Medina
    • 2
    • 3
  • José Luis Urdiales
    • 2
    • 3
  • José F. Aldana
    • 1
  • Francisca Sánchez-Jiménez
    • 2
    • 3
  1. 1.Computer Languages and Computing Science DepartmentUniversity of MálagaSpain
  2. 2.Molecular Biology and Biochemistry DepartmentUniversity of MálagaSpain
  3. 3.Centre for Biomedical Research on Rare Diseases (CIBERER)MálagaSpain

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