Entrez and Forward Database Searching

Abstract

Entrez is a text‐based search system that provides integrated access to multiple databases of interest to the molecular biology community. It was developed by and is available through a website (http://www.ncbi.nlm.nih.gov/sites/gquery) at the National Center for Biotechnology Information (NCBI). This tool provides the ability to query one or multiple databases. The interface also allows both simple and advanced searching. For example, one can enter one or a few terms in a search box to initiate a simple search, or, one can limit search terms to particular fields or use a controlled vocabulary. In addition, results include links to related entries and other relevant information that match the search criteria. The output can be saved to a local computer for further processing. There are also advanced tools – web‐based or programming tools – some discussed later.

Key concepts:

  • Entrez provides access to many different biologically oriented databases.

  • To restrict your search use features of Limits or Preview/Index.

  • Use ‘Batch Entrez’ to download lists of identifiers.

  • There are specific search options available for each database.

  • Help text specific to each database is available on its homepage.

  • Register for a My NCBI account so that you can define and store preferences and save search results.

  • There are several ways to download data retrieved from an Entrez search to a local computer.

  • The History feature is helpful to combine previous searches.

Keywords: text searching; literature searching; molecular databases

Figure 1.

Entrez main page shows all the databases and their descriptions.

Figure 2.

NCBI sequence viewer.

Figure 3.

Entrez – use of indexes and previews.

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References

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Further Reading

Baxevanis AD (2006) Searching the NCBI databases using Entrez. Current protocols in human genetics/editorial board, Jonathan L Haines et al. chap. 6: Unit 6.10.

Baxevanis AD (2006) Searching the NCBI databases using Entrez. Current protocols in bioinformatics/editoral board, Andreas D Baxevanis et al. chap. 1: Unit 1.3.

Baxevanis AD (2008) Searching NCBI databases using Entrez. Current protocols in bioinformatics/editoral board, Andreas D Baxevanis et al. chap. 1: Unit 1.3.

Geer RC and Sayers EW (2003) Entrez: making use of its power. Brief Bioinformatics 4(2) : 179–184.

McEntyre J (1998) Linking up with Entrez. Trends in Genetics 14(1) : 39–40.

Schuler GD, Epstein JA, Ohkawa H et al. (1996) Entrez: molecular biology database and retrieval system. Methods in Enzymology 266: 141–162.

Wheeler DL, Church DM, Federhen H et al. (2003) Database resources of the National Center for Biotechnology. Nucleic Acids Research 31(1) : 28–33.

Wheeler DL, Church DM, Edgar R et al. (2004) Database resources of the National Center for Biotechnology Information: update. Nucleic Acids Research 32(Database issue) : D35–D40.

Wheeler DL, Barrett T, Benson D et al. (2005) Database resources of the National Center for Biotechnology Information. Nucleic Acids Research 33(Database issue) : D39–D45.

Wheeler DL, Barrett T, Benson D et al. (2007) Database resources of the National Center for Biotechnology Information. Nucleic Acids Research 35(Database issue) : D5–D12.

Wheeler DL, Barrett T, Benson D et al. (2008) Database resources of the National Center for Biotechnology Information. Nucleic Acids Research 36(Database issue) : D13–D21.

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How to Cite close
Lewitter, Fran(Dec 2009) Entrez and Forward Database Searching. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0003035.pub2]