Skip to main content

Literature Review

  • Chapter
  • First Online:
Data Intensive Computing for Biodiversity

Part of the book series: Studies in Computational Intelligence ((DSCC,volume 485))

  • 510 Accesses

Abstract

Every research work goes through a very crucial stage, which is studying literatures related to the research. In this chapter, literatures concerning the area of research are reviewed thoroughly. Due to the multidisciplinary nature of this research, the literature review involved many different aspects which are discussed below.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • 3rd Millennium Inc (2002). Practical data integration in biopharmaceutical R&D: Strategies and technologies (online), 125 Cambridge Park Drive, Cambridge, MA 02140. Available from: www.3rdmill.com/resources/3rd_Millennium_Biopharma-data-integration.pdf. Accessed 4 November 2005.

  • Achour, M., Betz, F., Dovgal, A., Lopes, N., Olson, P., Richter, G., Seguy, S., & Vrana, J., et al. (2006). PHP manual (online). Available from: http://www.php.net/manual/en/. Accessed 1 August 2006.

  • Andrew, B., & Paula, T. (2005). An XML-based architecture for data integration in vulnerability assessments. Information Management and Computer Security, 13(4), 260–273. Emerald Group Publishing Limited 0968-5227.

    Article  Google Scholar 

  • Anthony and Leslie, (2002). The quest for data integration (online). Incyte Genomics, Inc. Available from: http://www.incyte.com/insidegenomics/. Accessed 5 September 2005.

  • Austin, D., Barbir, A., & Garg, S. (2002). Web services architecture requirements, W3C (online). Available from: http://www.w3.org/TR/2002/WD-wsa-reqs-20020429. Accessed 10 January 2006.

  • Berendsohn, W. (2006). ABCD schema (online). Taxonomic department of biodiversity informatics and laboratories of the botanic garden and botanical museum Berlin-Dahlem. Available from: http://bgbm3.bgbm.fu-berlin.de/TDWG/CODATA/Schema/default.htm. Accessed 18 January 2005.

  • Bertino, E., & Ferrari, E. (2001). XML and data integration. IEEE Internet Computing, 089-7801/01 November December 2001.

    Google Scholar 

  • Biodiversity Research Center (2005). Distributed generic information retrieval (online). Natural history museum. Available from: http://www.specifysoftware.org/Informatics/informaticsdigir/. Accessed 10 January 2005.

  • Box, D., Ehnebuske, D., Kakivaya, G., Layman, A., Mendelsohn, N., Nielsen, H. F., Thatte, S., & Winer, D. (2000). Simple object access protocol (SOAP) 1.1 (online). MIT computer science and artificial intelligence laboratory (CSAIL) U.S.A. Available from: http://www.w3.org/TR/2000/NOTE-SOAP-20000508/. Accessed 2 February 2006.

  • Brown, C. E. (2006). ASP versus PHP: Which one is right for you (online). Available from: http://www.pointafter.com/Archives/n10203.htm. Accessed 10 April 2005.

  • Buttler, D., Coleman, M., Critchlow, T., Fileto, R., Han, W., Liu, L., et al. (2002). Querying multiple bioinformatics data sources: Can semantic web research help? ACM SIGMOD Record, 31(4), 59–64.

    Article  Google Scholar 

  • Cali, A., Calvanese, D., de Giacomo, G., & Lenzerini, M. (2002). On the expressive power of data integration systems. Proceedings of the 21st International Conference on Conceptual Modeling (ER 2002).

    Google Scholar 

  • Canhos, V. P., Souza, S., de Giovanni, R., & Canhos, D. A. L. (2004). Global biodiversity informatics: Setting the scene for a “New World” of ecological modeling. Biodiversity Informatics, 1, 1–13.

    Google Scholar 

  • Davidson, S., Overton, C., & Buneman, P. (1995). Challenges in integrating biological data sources. Journal of Computational Biology, 2, 557–572.

    Article  Google Scholar 

  • Davidson, S., Crabtree, J., Brunk, B., Schug, J., Tannen, V., Overton, C., et al. (2001). K2/Kleisli and GUS: Experiments in integrated access to genomic data sources. IBM Systems Journal, 40(2), 512–531.

    Article  Google Scholar 

  • Eaglestone, B., & Ridley, M. (2001). Web database systems. London, UK: McGraw-Hill. ISBN 0077096002.

    Google Scholar 

  • Elbibas, A. A., & Ridely, M. J. (2003). Using metadata for developing automated web system interface. Copyright held by author.

    Google Scholar 

  • Elmasri, R., & Shamkant, B. (1994). Fundamentals of Database (2nd ed., p. 873). Reading, MA: Addison-Wesley. ISBN 0805317481.

    MATH  Google Scholar 

  • Federal Geographic Data Committee (2000). Biological data working group. U.S. Geological Survey, 590 National Center Reston, Virginia, 20192.

    Google Scholar 

  • Florescu, D., Levy, A. Y., & Mendelzon, A. O. (1998). Database techniques for the world-wide web: A survey. ACM SIGMOD Record, 27(3), 59–74.

    Article  Google Scholar 

  • Frederic A, Guy V, Emmanuel B (2001) XML, bioinformatics and data integration (Vol. 17(2), pp. 115–125). Oxford: Oxford University Press.

    Google Scholar 

  • GBIF (2004). Global biodiversity information facility (online), Copenhagen, Denmark. Available from: www.gbif.org. Accessed 20 November 2005.

  • Graham, S., Simeomov, S., Boubez, T., Daniels, G., Davis, D., Nakamura, Y., et al. (2001). Building web services with Java. Indiana: SAMS.

    Google Scholar 

  • Grosof, B.N., Labrou, Y., & Chan, H.Y. (1999). A declarative approach to business rules in contracts: Courteous logic programs in XML. Proceedings of the First ACM Conference on Electronic Commerce. ACM Press, New York.

    Google Scholar 

  • Haas, L. M., Schwarz, P. M., Kodali, P., Kotlar, E., Rice, J. E., & Swope, W. C. (2001). Discovery link: A system for integrated access to life sciences data sources. IBM Systems Journal, 40, 489–511.

    Article  Google Scholar 

  • Hall, M. (2002). Vendor profile: IBM in the Life Sciences. Bio-IT-Infrastructure. 27549.

    Google Scholar 

  • Hamilton, G., Cattell, R., & Fisher, M. (1997). JDBC database access with Java: A tutorial and annotated reference. Reading, MA: Addison Wesley. ISBN 0201309955.

    Google Scholar 

  • Hammer, J., & Schneider, M. (2003). Genomics algebra: A new, integrating data model, language and tool processing and querying genomic information. Proceedings of the 2003 CIDR Conference.

    Google Scholar 

  • Han, R., Perret, V., & Naghshineh, M. (2000). WebSplitter: A unified XML framework for multi-device collaborative web browsing. Proceedings of the 2000 ACM Conference on Computer Supported Cooperative Work. ACM Press, New York.

    Google Scholar 

  • Hatzigeorgiu, N., & Syropoulos, A. (1999). New technologies for rapid development of web orientated database applications. ACM SIGCUE Outlook, 27(1), 25–31.

    Article  Google Scholar 

  • Hernandez, T., & Kambhampati, S. (2004). Integration of biological sources: Current systems and challenges ahead. ACM SIGMOD Record, 33(3), 51–60.

    Article  Google Scholar 

  • HGMIS (2005). Human genome management information system (online). U.S. Department of Energy Human Genome Program. Available at: http://www.ornl.gov/sci/techresources/Human_Genome/project/about.shtml. Accessed 15 December 2005.

  • Hunter, J., & Crawford, W. (2001). Java Servlet Programming (2nd ed.). USA: O’Reilly and Associates. ISBN 1 -56592-391-x.

    Google Scholar 

  • Husain, W., Abdullah, R., Salam, R.A., & Zainol, Z. (2004). Development of a web-based system for integrated access to biological databases. Transactions of Engineering, Computing and Technology. ISSN 1305-5313.

    Google Scholar 

  • IABIN (2004a). Inter-American biodiversity information network (online). Available from: http://www.iabin.net/english/index.shtml. Accessed 8 November 2005.

  • IABIN (2004b). Biodiversity informatics: Information standards and metadata formats (online). Available from: http://www.iabin.net/english/bioinformatics/protocols/standards_&_formats.shtml. Accessed 15 January 2006.

  • InforMax (2001) GenoMax (online), United States. Available from: http://www2.informaxinc.com/solutions/genomax/index.html. Accessed 15 December 2005.

  • International Union of Biological Sciences (IUBS) (2005). Taxonomic databases working group: Time limited ballot (online), Natural History Museum, London, United Kingdom. Available from: http://www.tdwg.org/TDWGStandardsBallot2005.htm. Accessed 20 November 2005.

  • International Working Group on Taxonomic Databases. (2005). International union for biological sciences taxonomic database working group (online), TDWG standards. Available from: http://www.tdwg.org/TDWGStandardsBallot2005.htm. Accessed 12 October 2005.

  • Jacob, K. (2004). Integration of life sciences databases. DDT: BIOSILICO, 2(2), 61–69.

    Google Scholar 

  • Jennifer W (1999) Database management for XML. IEEE Data Engineering Bulletin, Special Issue on XML. 22(3), 44–52.

    Google Scholar 

  • Jones, A.C., Xu, X., Pittas, N., Gray, W.A., Fiddian, N.J., White, R.J., Robinson, J.S., Bisby, F.A., & Brandt, S.M. (2000). SPICE: A flexible architecture for integrating autonomous databases to comprise a distributed catalogue of life. To appear in Proceedings of 11th International Conference and Workshop on Database and Expert Systems Applications (DEXA 2000) (Lecture Notes in Computer Science). New York: Springer.

    Google Scholar 

  • Lawrence, S., & Giles, C. L. (1999). Accessibility of information on the web. Nature, 400, 107–109.

    Article  Google Scholar 

  • Lenzerini, M. (2002). Data integration: A theoretical perspective. ACM Symposium on Principles of Database Systems (PODS).

    Google Scholar 

  • MSDN Library (2002). XML web services (online). Available from: http://msdn.microsoft.com/library/default.asp?url=/nhp/default.asp?contentid=2800442. Accessed 10 July 2006.

  • Lim, B. B. L., & Wen, H. J. (2002). The impact of next generation XML. Information Management and Computer Security Journal, 10(1), 33–40.

    Article  Google Scholar 

  • Limi, A., Runyan, A., Anderson, V. (2005). Darwin core 2 (online), Taxonomic Databases Working Group (TDWG). Available from: http://darwincore.calacademy.org/Documentation/PurposeGoals. Accessed 12 January 2005.

  • Mork, P., Halevy, A., & Tarczy-Hornoch, P. (2001). A model for data integration systems of biomedical data applied to online genetic databases. Proceedings of the Symposium of the American Medical Informatics Association.

    Google Scholar 

  • Morrison, M., Morrison, J., & Keys, A. (2002). Integrating web sites and databases. Communications of the ACM, 45(9), 81–86.

    Article  Google Scholar 

  • Muse, D. (2006). Server Watch (online), Darien, Connecticut. Available from: http://www.serverwatch.com/stypes/index.php/d2Vi .Accessed 20 February 2006.

  • Nick, H., & Apostolos, S. (1999). New technologies for rapid development of Web oriented database applications. ACM SIGCUE Outlook., 27(1), 25–31.

    Article  Google Scholar 

  • Philippi, S. (2004). Light-weight integration of molecular biological databases. Bioinformatics, 20(1), 51–57. Oxford University Press.

    Google Scholar 

  • Povey, S., Lovering, R., Bruford, E., Wright, M., Lush, M., & Wain, H. (2001). The HUGO Gene Nomenclature Committee (HGNC). Hum Genet, 109, 678–680.

    Google Scholar 

  • Post, G. V. (2005). Database management systems; designing and building business applications. New York: McGraw Hill.

    Google Scholar 

  • Pullen, J. M., Brunton, R., Brutzman, D., Drake, D., Hieb, M., & Morse, K. L. (2005). Using web services to integrate heterogeneous simulations in a grid environment. Future Generation Computer Systems, 21(1), 97–106.

    Article  Google Scholar 

  • Rajagopalan, S., Rajamani, R., Krishnaswamy, R., & Vijendran, S. (2002). Java servlet programming Bible. USA: Hungry Minds Inc. ISBN 0-7645-4839-5.

    Google Scholar 

  • Schnase, J. (2000). Research directions in biodiversity informatics. Proceedings of the 26th VLDB Conference. Cairo, Egypt.

    Google Scholar 

  • Siegel, J. (1998). OMG overview: CORBA and the OMA in enterprise computing. Communications of the ACM, 41(10), 37–43.

    Article  Google Scholar 

  • Species2000 (2000). Indexing the world’s known species (online), University of Reading, UK. Available from: http://www.sp2000.org/about. Accessed 15 September 2005.

  • Stonebraker, M., Joseph, M., & Hellerstein, J.M. (2001). Content integration for e-business. Proceedings of the 2001 ACM SIGMOD International Conference on Management of Data. ACM Press, New York.

    Google Scholar 

  • Sujansky, W. (2001). Heterogeneous database integration in biomedicine. Methodological review. Journal of Biomedical Informatics, 34(4), 285–298.

    Article  Google Scholar 

  • Sun Microsystems, Inc. (1999). JavaServerTM web development Kit, Version 1.0.1 (online). Available from: http://java.sun.com/products/servlet/README.html. Accessed 20 November 2004.

  • Sun Microsystems, Inc. (2006). JavaServer pages technology documentation (online), U.S.A. Available from: http://java.sun.com/products/jsp/docs.html. Accessed 15 April 2006.

  • Taxonomic Databases Working Group (TDWG) (2006). Darwin core 2 (online), Bournemouth University. Available from: http://darwincore.calacademy.org/Documentation/PurposeGoals. Accessed 15 August 2006.

  • The Apache Software Foundation (2006). Apache (online), U.S.A. Available from: http://www.apache.org.my .Accessed 15 April 2006.

  • Thomas, H., & Subbarao, K. (2004). Integration of biological sources: Current systems and challenges ahead. ACM SIGMOD Record, 33(3), 51–60.

    Article  Google Scholar 

  • Turau, V. (2002). Web and e-business application: a framework for automatic generation of Web-based data entry applications based on XML. Proceedings of 2002 ACM Symposium on Applied Computing. ACM Press, New York.

    Google Scholar 

  • Vasudevan, A. (2001). PHP how-to (online). Available from: http://www.linuxdocs.org/HOWTOs/PHP-HOWTO-13.html. Accessed 19 December 2005.

  • Vieglais, D. (2003). The Darwin core (online) SpeciesAnalyst. Available from: http://speciesanalyst.net/docs/dwc/index.html. Accessed 12 January 2005.

  • Wikimedia Foundation Inc. (2006). ColdFusion (online), Florida. U.S.A. Available from: http://en.wikipedia.org/wiki/ColdFusion. Accessed 10 April 2006.

  • Wong, L. (2000a). Kleisli, a functional query system. Journal of Functional Programming, 10(1), 19–56.

    Article  Google Scholar 

  • Wong, L. (2000b). Kleisli, its exchange format, supporting tools, and an application in protein interaction extraction. Proceedings of IEEE International Symposium Bio-Informatics and Biomedical Engineering, pp. 21–28.

    Google Scholar 

  • Wong, L. (2002). Technologies for integrating biological data. Briefings in Bioinformatics, 3, 389–404.

    Article  Google Scholar 

  • Xia, Y., Stinner, R.E., Chu, P.C. (2002). Database integration with the web for biologist to share data and information. EJB Electronical Journal of Biotechnology ISSN: 0717-3458.

    Google Scholar 

  • Yang, J., Van den Heuvel, W.J., & Papazoglou, M.P. (2001). Service deployment for virtual enterprises. Australian computer science communications. Proceedings of the Workshop on Information Technology for Virtual Enterprises. ACM Press, New York.

    Google Scholar 

  • Yang, C., Chang, N., & Zhang, C. N. (2003). An XML-based administration method on role-based access control in the enterprise environment. Journal of Information Management and Computer Security, 11(5), 249–257.

    Article  Google Scholar 

  • Yu, S. C., & Chen, R. S. (2003). Web services: XML-based system integrated techniques. Emerald-The Electronic library, 21(4), 358–366. MCB UP Limited.

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Sarinder K. Dhillon .

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Dhillon, S.K., Sidhu, A.S. (2013). Literature Review. In: Data Intensive Computing for Biodiversity. Studies in Computational Intelligence(), vol 485. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-38047-1_3

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-38047-1_3

  • Published:

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-38046-4

  • Online ISBN: 978-3-642-38047-1

  • eBook Packages: EngineeringEngineering (R0)

Publish with us

Policies and ethics