Chemogenomics pp 159-172

Part of the Methods in Molecular Biology book series (MIMB, volume 575)

Database Systems for Knowledge-Based Discovery

  • Sarma A. R. P. Jagarlapudi
  • K. V. Radha Kishan

Summary

Several database systems have been developed to provide valuable information from the bench chemist to biologist, medical practitioner to pharmaceutical scientist in a structured format. The advent of information technology and computational power enhanced the ability to access large volumes of data in the form of a database where one could do compilation, searching, archiving, analysis, and finally knowledge derivation. Although, data are of variable types the tools used for database creation, searching and retrieval are similar. GVK BIO has been developing databases from publicly available scientific literature in specific areas like medicinal chemistry, clinical research, and mechanism-based toxicity so that the structured databases containing vast data could be used in several areas of research. These databases were classified as reference centric or compound centric depending on the way the database systems were designed. Integration of these databases with knowledge derivation tools would enhance the value of these systems toward better drug design and discovery.

Key words

GVK BIO databases Medchem database Toxicity database Clinical candidate database GPCR database Kinase database GOSTAR Biomarker database 

References

  1. 1.
    Wheeler, D.L., Barrett, T., Benson, D.A., Bryant, S.H., Canese, K., Chetvernin, V., Church, D.M., DiCuccio, M., Edgar, R., Federhen, S., Geer, L.Y., Helmberg, W., Kapustin, Y., Kenton, D.L., Khovayko, O., Lipman, D.J., Madden, T.L., Maglott, D.R., Ostell, J., Pruitt, K.D, Schuler, G.D., Schriml, L.M., Sequeira, E., Sherry, S.T., Sirotkin, K., Souvorov, A., Starchenko, G., Suzek, T.O., Tatusov, R., Tatusova, T.A., Wagner, L., and Yaschenko, E. (2006) National database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 34, D173–D180.PubMedCrossRefGoogle Scholar
  2. 2.
    Seiler, K.P., George, G.A., Happ, M.P., Bodycombe, N.E., Carrinski, H.A., Norton, S., Brudz, S., Sullivan, J.P., Muhlich, J., Serrano, M., Ferraiolo, P., Tolliday, N.J., Schreiber, S.L., and Clemons, P.A. (2008) ChemBank: A small-molecule screening and cheminformatics resource database. Nucleic Acids Res. 36, D351–D359.PubMedCrossRefGoogle Scholar
  3. 3.
    Aoki-Kinoshita, K.F., and Kanehisa, M. (2007) Gene annotation and pathway mapping in KEGG. Methods Mol. Biol. 396, 71–91.PubMedCrossRefGoogle Scholar
  4. 4.
    Ganter, B, Zidek, N., Hewitt, P.R., Müller, D., and Vladimirova, A. (2008) Pathway analysis tools and toxicogenomics reference database for risk assessment. Pharmacogenomics 9, 35–54.PubMedCrossRefGoogle Scholar
  5. 5.
    Leeson, P.D., and Springthorpe, B. (2007) The influence of drug-like concepts on decision-making in medicinal chemistry. Nat. Rev. Drug Discov. 6, 881–890.PubMedCrossRefGoogle Scholar
  6. 6.
    Southan, C., Várkonyi, P., and Muresan, S. (2007) Complementarity between public and commercial databases: New opportunities in medicinal chemistry informatics. Curr. Top. Med. Chem. 7, 1502–1508.PubMedCrossRefGoogle Scholar
  7. 7.
  8. 8.
  9. 9.
  10. 10.
  11. 11.
  12. 12.
  13. 13.
  14. 14.
  15. 15.
  16. 16.
  17. 17.
  18. 18.
  19. 19.
  20. 20.
  21. 21.
  22. 22.
  23. 23.
  24. 24.
    Curtis, D.K. (1998) Casarett and Doull’s Toxicology: The Basic Science of Poisons, 5th edn. McGraw-Hill, New York.Google Scholar
  25. 25.
    Hyman, J.Z. (1978) Hepatotoxicity: The Adverse Effects of Drugs and Other Chemicals on the Liver, 1st edn. Appleton-Century-Crofts, New York.Google Scholar
  26. 26.
    Hans, M., Siegfried, G.S., Roger, M., and Frank, W. (1999) Toxicology. Academic Press, San Diego.Google Scholar
  27. 27.
    Collin, D. (1999) Therapeutic Drugs, 2nd edn. Churchill Livingstone, London.Google Scholar
  28. 28.
  29. 29.
  30. 30.
  31. 31.

Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2009

Authors and Affiliations

  • Sarma A. R. P. Jagarlapudi
    • 1
  • K. V. Radha Kishan
    • 1
  1. 1.S-1, Phase-1, TIEGVK Biosciences Pvt. Ltd.HyderabadIndia

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