Current Trends in Biomedical Data and Applications

  • Amandeep S. Sidhu
  • Matthew Bellgard
  • Tharam S. Dillon
Part of the Studies in Computational Intelligence book series (SCI, volume 224)

Abstract

Bioinformatics tools and systems perform a diverse range of functions including: data collection, data mining, data analysis, data management, and data integration. Computer-aided technology directly supporting medical applications is excluded from this definition and is referred to as medical informatics. This book is not an attempt at authoritatively describing the gamut of information contained in this field. Instead, it focuses on the areas of biomedical data integration, access, and interoperability as these areas form the cornerstone of the field. However, most of the approaches presented are generic integration systems that can be used in many similar contexts.

Keywords

Macromolecule Hunt Stein Saccharomyces Ferro 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Achard, F., Barillot, E.: Ubiquitous distributed objects with CORBA. In: Pacific Symposium Biocomputing. World Scientific, London (1997)Google Scholar
  2. Achard, F., Dessen, P.: GenXref VI: automatic generation of links between two heterogeneous databases. Bioinformatics 14, 20–24 (1998)CrossRefGoogle Scholar
  3. Adams, M.D., Kelley, J.M., Gocayne, J.D., Dubnick, M., Polymeropou-Los, M.H., Xiao, H., Merril, C.R., Wu, A., Olde, B., Moreno, R.F., Kerlavage, A.R., Mccombie, W.R., Venter, J.C.: Complementary DNA sequencing: expressed sequence tags and human genome project. Science 252, 1651–1656 (1991)CrossRefGoogle Scholar
  4. Andrade, M.A., Valencia, A.: Automatic annotation for biological sequences by extraction of keywords from MEDLINE abstracts. In: Gaaster-Land, T., Karp, P., Karplus, K., Ouzonis, C., Sander, C., Valen-Cia, A. (eds.) 5th International Conference on Intelligent Systems for Molecular Biology. AAAI, Halkidiki (1997)Google Scholar
  5. Apweiler, R., Bairoch, A., 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.: UniProt: The Universal Protein knowledgebase. Nucleic Acids Research 32, 115–119 (2004)CrossRefGoogle Scholar
  6. Bairoch, A., Apweiler, R.: The SWISS-PROT protein sequence data bank and its supplement TrEMBL. Nucleic Acids Research 25, 31–36 (1997)CrossRefGoogle Scholar
  7. Bairoch, A., Bucher, P., Hofmann, K.: The PROSITE database, its status in 1997. Nucleic Acids Research 25, 217–221 (1997)CrossRefGoogle Scholar
  8. Barker, W.C., Garavelli, J.S., Haft, D.H., Hunt, L.T., Marzec, C.R., Orcutt, B.C.: The PIR-International Protein Sequence Database. Nucleic Acids Research 26, 27–32 (1998)CrossRefGoogle Scholar
  9. Bashford, D., Chothia, C., Lesk, A.M.: Determinants of a protein fold: Unique features of the globin amino acid sequences. Journal of Molecular Biology 196, 199–216 (1987)CrossRefGoogle Scholar
  10. Ben-Natan, R.: CORBA. McGraw-Hill, New York (1995)Google Scholar
  11. Benson, D., Karsch-Mizrachi, I., Lipman, D., Ostell, J., Rapp, B., Wheeler, D.: GenBank. Nucleic Acids Research 28, 8–15 (2000)CrossRefGoogle Scholar
  12. Bernstein, F.C., Koetzle, T.F., Williams, G.J., Meyer, E.F., Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi, T., Tasumi, M.: The Protein Data Bank: a computer-based archival file for macromolecular structures. Journal of Molecular Biology 112, 535–542 (1977)CrossRefGoogle Scholar
  13. Boeckmann, B., Bairoch, A., Apweiler, R., Blatter, M., Estreicher, A., Gasteiger, E., Martin, M.J., Michoud, K., Donovan, C., Phan, I., Pilbout, S., Schneider, M.: The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Research 31, 365–370 (2003)CrossRefGoogle Scholar
  14. Bork, P., Ouzounis, C., Sander, C., Scharf, M., Schneider, R., Sonn-Hammer, E.L.L.: Comprehensive sequence analysis of the 182 predicted open reading frames of yeast chromosome III. Protein Science 1, 1677–1690 (1992)CrossRefGoogle Scholar
  15. Bourne, P.E., Addess, K.J., Bluhm, W.F., Chen, L., Deshpande, N., Feng, Z., Fleri, W., Green, R., Merino-Ott, J.C., Townsend-Merino, W., Weissig, H., Westbrook, J., Berman, H.M.: The distribution and query systems of the RCSB Protein Data Bank. Nucleic Acids Research 32, D223–D225 (2004)CrossRefGoogle Scholar
  16. Casari, G., Ouzounis, C., Valencia, A., Sander, C.: GeneQuiz II: automatic function assignment for genome sequence analysis. In: Hunter, L., Klein, T.E. (eds.) 1st Annual Pacific Symposium on Biocomputing. World Scientific, Hawaii (1996)Google Scholar
  17. Cherry, J.M., Ball, C., Weng, S., Juvik, G., Schmidt, R., Adler, C., Dunn, B., Dwight, S., Riles, L., Mortimer, R.K., Botstein, D.: SGD: Saccharomyces Genome Database. Nucleic Acids Research 26, 73–79 (1998)CrossRefGoogle Scholar
  18. Dayhoff, M.O., Eck, R.V., Chang, M.A., Sochard, M.R.: Atlas of Protein Sequence and Structure. National Biomedical Research Foundation, USA (1965)Google Scholar
  19. Des Jardins, M., Karp, P., Krummenacker, M., Lee, T.J., Ouzounis, C.: Prediction of enzyme classification from protein sequence without the use of sequence similarity. In: Gaasterland, T., Karp, P., Karplus, K., Ouzonis, C., Sander, C., Valencia, A. (eds.) 5th International Conference on Intelligent Systems for Molecular Biology. AAAI, Halkidiki (1997)Google Scholar
  20. Dodge, C., Schneider, R., Sander, C.: The HSSP database of protein structure-sequence alignments and family profiles. Nucleic Acids Research 26, 313–315 (1998)CrossRefGoogle Scholar
  21. Eckman, B.A., Aaronson, J.S., Borkowski, J.A., Bailey, W.J., Elliston, K.O., Williamson, A.R., Blevins, R.A.: The Merck Gene Index browser: an extensible data integration system for gene finding, gene characterization and EST data mining. Bioinformatics 14, 2–13 (1997)CrossRefGoogle Scholar
  22. Etzold, T., Argos, P.: SRS: An Indexing and Retrieval Tool for Flat File Data Libraries. Computer Application of Biosciences 9, 49–57 (1993)Google Scholar
  23. Frishman, D., Mewes, H.W.: PEDANTic genome analysis. Trends in Genetics 13, 415–416 (1997)CrossRefGoogle Scholar
  24. Gaasterland, T., Sensen, C.W.: MAGPIE: automated genome interpretation. Trends in Genetics 12, 76–78 (1996)CrossRefGoogle Scholar
  25. Gelbart, W.M., Crosby, M., Matthews, B., Rindone, W.P., Chillemi, J., Twombly, S.R., Emmert, D., Bayraktaroglu, L.: FlyBase: a Drosophila database. Nucleic Acids Research 26, 85–88 (1998)CrossRefGoogle Scholar
  26. George, D.G., Mewes, H.-W., Kihara, H.: A standardized format for sequence data exchange. Protein Seq. Data Anal. 1, 27–29 (1987)Google Scholar
  27. Gouy, M., Gautier, C., Attimonelli, M., Lanave, C., Di Paola, G.: ACNUC–a portable retrieval system for nucleic acid sequence databases: logical and physical designs and usage. Computer applications in the biosciences 1, 167–172 (1985)Google Scholar
  28. Henikoff, S., Pietrokovski, S., Henikoff, J.G.: Superior performance in protein homology detection with the Blocks Database servers. Nucleic Acids Research 26, 309–312 (1998)CrossRefGoogle Scholar
  29. Hide, W., Burke, J., Christoffels, A., Miller, R.: Toward automated prediction of protein function from microbial genomic sequences. In: Miyano, S., Takagi, T. (eds.) Genome Informatics. Universal Academy Press, Tokyo (1997)Google Scholar
  30. Hooft, R.W., Sander, C., Vriend, G.: Objectively judging the quality of a protein structure from a Ramachandran plot. Computer Application of Biosciences 13, 425–430 (1997)Google Scholar
  31. Karp, P.D.: A strategy for database interoperation. Journal of Computational Biology 2, 573–583 (1996)CrossRefGoogle Scholar
  32. Koonin, E.V., Galperin, M.Y.: Prokaryotic genomes: the emerging paradigm of genome-based microbiology. Current Opinons in Genetic Development 7, 757–763 (1997)CrossRefGoogle Scholar
  33. Maidak, B.L., Olsen, G.J., Larsen, N., Overbeek, R., Mccaughey, M.J., Woese, C.R.: The ribosomal database project (RDP). Nucleic Acids Research 24, 82–85 (1996)CrossRefGoogle Scholar
  34. Maxam, A.M., Gilbert, W.: A new method for sequencing DNA. In: Proceedings of National Academic of Science, vol. 74, pp. 560–564 (1977)Google Scholar
  35. Mckusick, V.A.: Mendelian Inheritance in Man. In: A Catalog of Human Genes and Genetic Disorders. Johns Hopkins University Press, Baltimore (1998)Google Scholar
  36. Miyazaki, S., Sugawara, H., Gojobori, T., Tateno, Y.: DNA Databank of Japan (DDBJ) in XML. Nucleic Acids Research 31, 13–16 (2003)CrossRefGoogle Scholar
  37. Murzin, A.G., Brenner, S.E., Hubbard, T., Chothia, C.: SCOP: A Structural Classification of Proteins Database for the Investigation of Sequences and Structures. Journal of Molecular Biology 247, 536–540 (1995)Google Scholar
  38. Ritter, O.: The integrated genomic database. In: Suhai, S. (ed.) Computational Methods in Genome Research. Plenum, New York (1994)Google Scholar
  39. Robbins, R.J.: Genome Informatics I: community databases. Journal of Computational Biology 1, 173–190 (1994)CrossRefGoogle Scholar
  40. Roberts, R.J., Macelis, D.: REBASE - restriction enzymes and methylases. Nucleic Acids Research 26, 338–350 (1998)CrossRefGoogle Scholar
  41. Sanger, F., Nicklen, S., Coulson, A.R.: DNA sequencing with chain-terminating inhibitors. In: Proceedings of National Academic of Science, vol. 74, pp. 5463–5467 (1977)Google Scholar
  42. Scharf, M., Schneider, R., Casari, G., Bork, P., Valencia, A., Ouzounis, C., Sander, C.: GeneQuiz: a workbench for sequence analysis. In: Altman, R.B., Brutlag, D.L., Karp, P., Lathrop, R.H., Searls, D.B. (eds.) 2nd International Conference on Intelligent Systems for Molecular Biology. AAAI, Stanford (1994)Google Scholar
  43. Schuler, G.D., Boguski, M.S., Stewart, E.A., Stein, L.D., Gyapay, G., Rice, K., White, R.E., Rodriguez-Tome, P., Aggarwal, A., Ba-Jorek, E., Bentolila, S., Birren, B.B., Butler, A., Castle, A.B., Chiannilkulchai, N., Chu, A., Clee, C., Cowles, S., Day, P.J.R., Dibling, T., Drouot, N., Dunham, I., Duprat, S., East, C., Ed-Wards, C., Fan, J.-B., Fang, N., Fizames, C., Garrett, C., Green, L., Hadley, D., Harris, M., Harrison, A.P., Brady, S., Hicks, A., Holloway, E., Hui, L., Hussain, S., Louis-Dit-Sully, C., Ma, J., Macgilvery, A., Mader, C., Maratukulam, A., Matise, T.C., Mckusick, K.B., Morissette, J., Mungall, A., Muselet, D., Nusbaum, D.: A gene map of the human genome. Science 274, 540–546 (1996)CrossRefGoogle Scholar
  44. Sonnhammer, E.L.L., Eddy, S.R., Birney, E., Bateman, A., Durbin, R.: Pfam: multiple sequence alignments and HMM-profiles of protein domains. Nucleic Acids Research 26, 320–322 (1998)CrossRefGoogle Scholar
  45. Stein, L.D., Cartinhour, S., Thierry-Mieg, D., Thierry-Mieg, J.: JADE: An approach for interconnecting bioinformatics databases. Gene 209, 39–43 (1998)CrossRefGoogle Scholar
  46. Stoesser, G., Baker, W., Van Den Broek, A., Garcia-Pastor, M., Kanz, C., Kulikova, T.: The EMBL Nucleotide Sequence Database: Major new developments. Nucleic Acids Research 31, 17–22 (2003)CrossRefGoogle Scholar
  47. Walker, D.R., Koonin, E.V.: SEALS: a system for easy analysis of lots of sequences. In: Gaasterland, T., Karp, P., Karplus, K., Ouzonis, C., Sander, C., Valencia, A. (eds.) 5th International Conference on Intelligent Systems for Molecular Biology. AAAI, Halkidiki (1997)Google Scholar
  48. Weissig, H., Bourne, P.E.: Protein structure resources. Biological Crystallography D58, 908–915 (2002)CrossRefGoogle Scholar
  49. Wertheim, M.: Call to desegregate microbial databases. Science 269, 1516 (1995)CrossRefGoogle Scholar
  50. Wesbrook, J., Feng, Z., Jain, S., Bhat, T.N., Thanki, N., Ravichandran, V., Gilliland, G.L., Bluhm, W.F., Weissig, H., Greer, D.S., Bourne, P.E., Berman, H.M.: The Protein Data Bank: unifying the archive. Nucleic Acids Research 30, 245–248 (2002)CrossRefGoogle Scholar
  51. Westbrook, J., Fitzgerald, P.M.D.: The PDB format, mmCIF formats and other data formats. In: Bourne, P.E., Weissig, H. (eds.) Structural Bioinformatics. John Wiley & Sons, Inc, Hoboken (2003)Google Scholar
  52. White, O., Kerlavage, A.R.: TDB: new databases for biological discovery. Methods in Enzymology 266, 27–40 (1996)CrossRefGoogle Scholar
  53. Wingender, E., Dietze, P., Karas, H., Knuppel, R.: TRANSFAC: a database on transcription factors and their DNA binding sites. Nucleic Acids Research 24, 238–241 (1996)CrossRefGoogle Scholar
  54. Wu, C.H., Yeh, L.S., Huang, H., Arminski, L., Castro-Alvear, J., Chen, Y., Hu, Z., Kourtesis, P., Ledley, R.S., Suzek, B.E., Vinayaka, C.R., Zhang, J., Barker, W.C.: The Protein Information Resource. Nucleic Acids Research 31, 345–347 (2003)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2009

Authors and Affiliations

  • Amandeep S. Sidhu
    • 1
  • Matthew Bellgard
    • 1
  • Tharam S. Dillon
    • 2
  1. 1.WA Centre for Comparative GenomicsMurdoch UniversityPerthAustralia
  2. 2.Digital Ecosystems and Business Intelligence InstituteCurtin University of TechnologyPerthAustralia

Personalised recommendations