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UNIT 1.3 Searching NCBI Databases Using Entrez

  1. Gretchen Gibney,
  2. Andreas D. Baxevanis

Published Online: 1 JUN 2011

DOI: 10.1002/0471250953.bi0103s34

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Gibney, G. and Baxevanis, A. D. 2011. Searching NCBI Databases Using Entrez. Current Protocols in Bioinformatics. 34:1.3:1.3.1–1.3.25.

Author Information

  1. Bethesda, Maryland

Publication History

  1. Published Online: 1 JUN 2011
  2. Published Print: JUN 2011


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.


  • Entrez;
  • NCBI databases;
  • biological databases;
  • integrated information retrieval