ENTREZ

BioCodeKb - Bioinformatics Knowledgebase

The Entrez is a Global Query Cross-Database Search System, a federated search engine, web portal or a text-based search and retrieval system that allows users to search many discrete health sciences databases at the National Center for Biotechnology Information (NCBI) website.


Entrez is at once an indexing and retrieval system, a collection of data from many sources, and an organizing principle for biomedical information.


It provides access to all databases simultaneously with a single query string and user interface. Entrez can efficiently retrieve related sequences, structures, and references. The Entrez system can provide views of gene and protein sequences and chromosome maps.


The Entrez front page provides, by default, access to the global query. All databases indexed by Entrez can be searched via a single query string, supporting boolean operators and search term tags to limit parts of the search statement to particular fields. This returns a unified results page, that shows the number of hits for the search in each of the databases, which are also links to actual search results for that particular database.


Entrez also provides a similar interface for searching each particular database and for refining search results. The Limits feature allows the user to narrow a search a web forms interface. The History feature gives a numbered list of recently performed queries. Results of previous queries can be referred to by number and combined via boolean operators. Search results can be saved temporarily in a Clipboard. Users with a MyNCBI account can save queries indefinitely and also choose to have updates with new search results e-mailed for saved queries of most databases. It is widely used in the field of biotechnology as a reference tool for students and professionals alike.


Entrez searches the following databases:

  • PubMed

  • PubMed Central

  • Books:

  • Online Mendelian Inheritance in Man (OMIM)

  • Nucleotide

  • Protein

  • Genome

  • Structure

  • Taxonomy

  • dbSNP

  • Gene

  • HomoloGene

  • PubChem Compound

  • PubChem Substance

  • Genome Project

  • UniGene

  • CDD

  • PopSet

  • GEO Profiles

  • GEO DataSets

  • Sequence read archive

  • Cancer Chromosomes

  • PubChem BioAssay

  • Probe

  • NLM Catalog


The Web-based Entrez retrieval program is a fast cgi application that uses the NCBI proprietary XML/XSLT-based Web application framework called Portal, for rapidly searching sequence and bibliographic data. The Entrez Web application provides a common set of features for any Entrez database, presenting users with a uniform look and feel across the nodes.


Entrez integrates data from a large number of sources, formats, and databases into a uniform information model and retrieval system. The actual databases from which records are retrieved and on which the Entrez indexes are based have different designs, based on the type of data, and reside on different machines. These will be referred to as the "source databases." A common theme in the implementation of Entrez is that some functions are unique to each source database, whereas others are common to all Entrez databases.

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