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Bioinformatic Databases

  1. Katherine G. Herbert1,
  2. Junilda Spirollari2,
  3. Jason T. L. Wang2,
  4. Jason T. L. Wang2,
  5. William H. Piel3,
  6. John Westbrook4,
  7. Winona C. Barker5,
  8. Zhang-Zhi Hu5,
  9. Cathy H. Wu5

Published Online: 14 DEC 2007

DOI: 10.1002/9780470050118.ecse561

Wiley Encyclopedia of Computer Science and Engineering

Wiley Encyclopedia of Computer Science and Engineering

How to Cite

Herbert, K. G., Spirollari, J., Wang, J. T. L., Wang, J. T. L., Piel, W. H., Westbrook, J., Barker, W. C., Hu, Z.-Z. and Wu, C. H. 2007. Bioinformatic Databases. Wiley Encyclopedia of Computer Science and Engineering. .

Author Information

  1. 1

    Montclair State University, Montclair, New Jersey

  2. 2

    New Jersey Institute of Technology, Newark, New Jersey

  3. 3

    Peabody Museum of Natural History, Yale University, New Haven, Connecticut

  4. 4

    Protein Data Bank and Rutgers, The State University of New Jersey, Piscataway, New Jersey

  5. 5

    Protein Information Resource and Georgetown University Medical Center, Washington, D.C.

Publication History

  1. Published Online: 14 DEC 2007

Abstract

Biological database research encompasses many topics, such as biological data management, curation, quality, integration, and mining. Biological databases can be classified in many different ways, from the topic they cover, to how heavily annotated they are or which annotation method they employ, to how heavily annotated they are or which annotation method they employ,. to how heavily annotated they are or which annotation method they employ, to how highly integrated the database is with other databases. Popularly, the first two categories of classification are used most frequently. For example, there are archival nucleic acid data repositories (GenBank, the EMBL Data Library, and the DNA Databank of Japan) as well as protein sequence motif/domain databases, like PROSITE, that are derived from primary source data.

Modern biological databases comprise not only data, but also sophisticated query facities and bioinformatic data analysis tools; hence, the term “bioinformatic databases” is ofter used. This article presents information on some popular bioinformatic databased available online, including sequence, phylogenetic, structure and pathway, and microarray databases. It highlights features of these databases, discussing their unique charateristics, and focusing on types of data stored and query facilities available in the databaes. The concludes by summarizing important research and development challenges for these databases, namely knowledge discovery, large-scale knowledge integration, and data providence problems.

Keywords:

  • bioinformatics;
  • computational biology;
  • databases;
  • database applications;
  • data management