UNIT 1.3 Searching the NCBI Databases Using Entrez

  1. Andreas D. Baxevanis

Published Online: 1 MAR 2006

DOI: 10.1002/0471250953.bi0103s13

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Baxevanis, A. D. 2006. Searching the NCBI Databases Using Entrez. Current Protocols in Bioinformatics. 13:1.3:1.3.1–1.3.24.

Author Information

  1. Bethesda, Maryland

Publication History

  1. Published Online: 1 MAR 2006
  2. Published Print: FEB 2006

This is not the most recent version of the article. View current version (1 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.


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