Searching NCBI Databases Using Entrez

Gretchen Gibney1, Andreas D. Baxevanis1

1 null, Bethesda, Maryland
Publication Name:  Current Protocols in Human Genetics
Unit Number:  Unit 6.10
DOI:  10.1002/0471142905.hg0610s71
Online Posting Date:  October, 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. Hum. Genet. 71:6.10.1‐6.10.24 © 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.
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   Baxevanis, A.D., Stein, L.D., Stormo, G.D., and Yates, J.R. III. 2011. Current Protocols in Bioinformatics. John Wiley & Sons, Hoboken, N.J.
   Bhagwat, M. 2010. Searching NCBI's dbSNP database. Curr. Protoc. Bioinform. 32:1.19.1‐1.19.18.
   Borate, B. and Baxevanis, A.D. 2009. Searching Online Mendelian Inheritance in Man (OMIM) for information on genetic loci involved in human disease. Curr. Protoc. Bioinform. 27:1.2.1‐1.2.13.
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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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