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Current Trends in Biomedical Data and Applications

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Biomedical Data and Applications

Part of the book series: Studies in Computational Intelligence ((SCI,volume 224))

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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.

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References

  • Achard, F., Barillot, E.: Ubiquitous distributed objects with CORBA. In: Pacific Symposium Biocomputing. World Scientific, London (1997)

    Google Scholar 

  • Achard, F., Dessen, P.: GenXref VI: automatic generation of links between two heterogeneous databases. Bioinformatics 14, 20–24 (1998)

    Article  Google Scholar 

  • 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)

    Article  Google Scholar 

  • 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 

  • 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)

    Article  Google Scholar 

  • Bairoch, A., Apweiler, R.: The SWISS-PROT protein sequence data bank and its supplement TrEMBL. Nucleic Acids Research 25, 31–36 (1997)

    Article  Google Scholar 

  • Bairoch, A., Bucher, P., Hofmann, K.: The PROSITE database, its status in 1997. Nucleic Acids Research 25, 217–221 (1997)

    Article  Google Scholar 

  • 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)

    Article  Google Scholar 

  • 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)

    Article  Google Scholar 

  • Ben-Natan, R.: CORBA. McGraw-Hill, New York (1995)

    Google Scholar 

  • Benson, D., Karsch-Mizrachi, I., Lipman, D., Ostell, J., Rapp, B., Wheeler, D.: GenBank. Nucleic Acids Research 28, 8–15 (2000)

    Article  Google Scholar 

  • 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)

    Article  Google Scholar 

  • 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)

    Article  Google Scholar 

  • 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)

    Article  Google Scholar 

  • 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)

    Article  Google Scholar 

  • 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 

  • 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)

    Article  Google Scholar 

  • 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 

  • 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 

  • Dodge, C., Schneider, R., Sander, C.: The HSSP database of protein structure-sequence alignments and family profiles. Nucleic Acids Research 26, 313–315 (1998)

    Article  Google Scholar 

  • 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)

    Article  Google Scholar 

  • 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 

  • Frishman, D., Mewes, H.W.: PEDANTic genome analysis. Trends in Genetics 13, 415–416 (1997)

    Article  Google Scholar 

  • Gaasterland, T., Sensen, C.W.: MAGPIE: automated genome interpretation. Trends in Genetics 12, 76–78 (1996)

    Article  Google Scholar 

  • 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)

    Article  Google Scholar 

  • 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 

  • 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 

  • 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)

    Article  Google Scholar 

  • 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 

  • 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 

  • Karp, P.D.: A strategy for database interoperation. Journal of Computational Biology 2, 573–583 (1996)

    Article  Google Scholar 

  • Koonin, E.V., Galperin, M.Y.: Prokaryotic genomes: the emerging paradigm of genome-based microbiology. Current Opinons in Genetic Development 7, 757–763 (1997)

    Article  Google Scholar 

  • 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)

    Article  Google Scholar 

  • 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 

  • Mckusick, V.A.: Mendelian Inheritance in Man. In: A Catalog of Human Genes and Genetic Disorders. Johns Hopkins University Press, Baltimore (1998)

    Google Scholar 

  • Miyazaki, S., Sugawara, H., Gojobori, T., Tateno, Y.: DNA Databank of Japan (DDBJ) in XML. Nucleic Acids Research 31, 13–16 (2003)

    Article  Google Scholar 

  • 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 

  • Ritter, O.: The integrated genomic database. In: Suhai, S. (ed.) Computational Methods in Genome Research. Plenum, New York (1994)

    Google Scholar 

  • Robbins, R.J.: Genome Informatics I: community databases. Journal of Computational Biology 1, 173–190 (1994)

    Article  Google Scholar 

  • Roberts, R.J., Macelis, D.: REBASE - restriction enzymes and methylases. Nucleic Acids Research 26, 338–350 (1998)

    Article  Google Scholar 

  • 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 

  • 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 

  • 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)

    Article  Google Scholar 

  • 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)

    Article  Google Scholar 

  • Stein, L.D., Cartinhour, S., Thierry-Mieg, D., Thierry-Mieg, J.: JADE: An approach for interconnecting bioinformatics databases. Gene 209, 39–43 (1998)

    Article  Google Scholar 

  • 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)

    Article  Google Scholar 

  • 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 

  • Weissig, H., Bourne, P.E.: Protein structure resources. Biological Crystallography D58, 908–915 (2002)

    Article  Google Scholar 

  • Wertheim, M.: Call to desegregate microbial databases. Science 269, 1516 (1995)

    Article  Google Scholar 

  • 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)

    Article  Google Scholar 

  • 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 

  • White, O., Kerlavage, A.R.: TDB: new databases for biological discovery. Methods in Enzymology 266, 27–40 (1996)

    Article  Google Scholar 

  • 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)

    Article  Google Scholar 

  • 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)

    Article  Google Scholar 

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Authors and Affiliations

  1. WA Centre for Comparative Genomics, Murdoch University, Perth, Australia

    Amandeep S. Sidhu & Matthew Bellgard

  2. Digital Ecosystems and Business Intelligence Institute, Curtin University of Technology, Perth, Australia

    Tharam S. Dillon

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  1. Amandeep S. Sidhu
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  2. Matthew Bellgard
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  3. Tharam S. Dillon
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Editors and Affiliations

  1. WA Centre for Comparative Genomics, Murdoch University, 6150, Murdoch, Western Australia, Australia

    Amandeep S. Sidhu

  2. Digital Ecosystems and Business Intelligence Institute, Curtin University of Technology, 6102, Park Bentley, WA, Australia

    Tharam S. Dillon

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Sidhu, A.S., Bellgard, M., Dillon, T.S. (2009). Current Trends in Biomedical Data and Applications. In: Sidhu, A.S., Dillon, T.S. (eds) Biomedical Data and Applications. Studies in Computational Intelligence, vol 224. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-02193-0_1

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  • DOI: https://doi.org/10.1007/978-3-642-02193-0_1

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  • Online ISBN: 978-3-642-02193-0

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