Searching NCBI Databases Using Entrez

Gretchen Gibney1, Andreas D. Baxevanis1

1 null, Bethesda, Maryland
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 1.3
DOI:  10.1002/0471250953.bi0103s34
Online Posting Date:  June, 2011
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One of the most widely used interfaces for the retrieval of information from biological databases is the NCBI Entrez system. Entrez capitalizes on the fact that there are pre‐existing, logical relationships between the individual entries found in numerous public databases. The existence of such natural connections, mostly biological in nature, argued for the development of a method through which all the information about a particular biological entity could be found without having to sequentially visit and query disparate databases. Two basic protocols describe simple, text‐based searches, illustrating the types of information that can be retrieved through the Entrez system. An alternate protocol builds upon the first basic protocol, using additional, built‐in features of the Entrez system, and providing alternative ways to issue the initial query. The support protocol reviews how to save frequently issued queries. Finally, Cn3D, a structure visualization tool, is also discussed. Curr. Protoc. Bioinform. 34:1.3.1‐1.3.25. © 2011 by John Wiley & Sons, Inc.

Keywords: Entrez; NCBI databases; biological databases; integrated information retrieval

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Table of Contents

  • Introduction
  • Basic Protocol 1: Querying Entrez
  • Support Protocol 1: Using My NCBI to Save Searches and Results
  • Alternate Protocol 1: Combining Entrez Queries
  • Basic Protocol 2: Examining Structures in Entrez
  • Commentary
  • Literature Cited
  • Figures
  • Tables
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Literature Cited

   Altschul, S., Gish, W., Miller, W., Myers, E., and Lipman, D. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403‐410.
   Barrett, T., Suzek, T.O., Troup, D.B., Wilhite, S.E., Ngau, W.C., Ledoux, P., Rudnev, D., Lash, A.E., Fujibuchi, W., and Edgar, R. 2005. NCBI GEO: Mining millions of expression profiles—database and tools. Nucleic Acids Res. 33:D562‐D566.
   Cho, K.R., Oliner, J.D., Simons, J.W., Hedrick, L., Fearon, E.R., Preisinger, A.C., Hedge, P., Silverman, G.A., and Vogelstein, B. 1994. The DCC gene: Structural analysis and mutations in colorectal carcinomas. Genomics 19:525‐531.
   Gibrat, J.‐F., Madej, T., and Bryant, S. 1996. Surprising similarities in structure comparison. Curr. Opin. Struct. Biol. 6:377‐385.
   Hamosh, A., Scott, A.F., Amberger, J., Bocchini, C., Valle, D., and McKusick, V.A. 2002. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res. 30:52‐55.
   Madej, T., Gibrat, J.‐F., and Bryant, S. 1995. Threading a database of protein cores. Proteins 23:356‐369.
   McKusick, V.A. 1998. Online Mendelian inheritance in man: A catalog of human genes and genetic disorders, 12th Edition. The Johns Hopkins University Press, Baltimore, Maryland.
   Mullikin, J.C. and Sherry, S.T. 2005. Sequence polymorphisms. In Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, 3rd Edition (A.D. Baxevanis and B.F.F. Ouellette, eds.) pp. 171‐193. John Wiley & Sons, Hoboken, New Jersey.
   Wilbur, W. and Coffee, L. 1994. The effectiveness of document neighboring in search enhancement. Inf. Process Manage. 30:253‐266.
   Wilbur, W. and Yang, Y. 1996. An analysis of statistical term strength and its use in the indexing and retrieval of molecular biology texts. Comput. Biol. Med. 26:209‐222.
Internet Resources
  NCBI Home page.
  NCBI Entrez Web page.
  NCBI Cn3D structure viewer.
  Ostell, J. 2003. The Entrez Search and Retrieval System. The NCBI Handbook, Chapter 15. National Center for Biotechnology Information, Bethesda, Maryland.
  NCBI GEO Overview.
  NCBI Reference Sequence (RefSeq) Project.
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