NCBI News: Fall2003/Winter2004 | Entrez Query Goes "Global"

Entrez Query Goes “Global”

The Entrez search and retrieval system now offers a cross-database search that allows a single query to span the traditional NCBI-sequence databases; Nucleotide and Protein; the literature databases, such as PubMed®, PMC, Books, OMIM™, Journals, and MeSH; the structurally-oriented databases, Structures, the Conserved Domain Database, 3D-Domains; the NCBI Taxonomy, Gene Expression Omnibus (GEO), Single Nucleotide Polymorphisms (SNPs), Population Sets, Genomes, Sequence Tagged Sites, UniGene, Gene-centered information (Gene), and, finally, the NCBI Web site itself. The cross database search option, labeled “Entrez” on the NCBI homepage search menu, replaces 'GenBank' as the default.

The New Entrez Home Page

The Entrez toolbar link on the NCBI Home Page leads to a new Entrez Home Page which provides a cross-database search box and a listing of the Entrez databases that can be searched in tandem. Question mark icons to the right of each database name lead to descriptions of database content. The database names and icons link to homepages where single-database queries can be constructed using lists of database-specific field restrictions, or tables that can be used to define search limits. In addition, the Entrez homepage toolbar provides links to popular NCBI tools and resources such as the Map Viewer and BLAST®.

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Figure 1. Entrez Home Page showing the new cross-database search engine with links to the 21 Entrez databases covered.

Cross-Database Search Results

When a cross-database search is completed, the number of matches for each database is displayed in boxes adjacent to the database name as shown in Figure 2. The Figure shows the results of a cross-database search using the Entrez query “rat[organism] AND kinase” indicating hits to a wide variety of databases, including those for literature, sequence, gene expression, and structure. The four representative Entrez displays indicated by the letters A, B, C, and D are reached by first clicking on the the database name, icon, or number of matches to reach the Entrez document summary of the hits, and then selecting a record and a format for viewing.

Beginning in the upper left hand corner, the figure shows one of the 54,988 hits to the PubMed database, using the “Abstract” display from the “display” pulldown menu. A link to the full text of the article in PubMed Central appears just to the right of the pulldown menu. Moving in a counter-clockwise direction, one of the 2,613 hits to the Nucleotide database is shown using the FASTA display format with other possible formats listed in the “display” pulldown menu. One of the 968 records from the Entrez Gene database that gives a detailed report on a gene. The report contains a gene description, a graphic of the gene's structure, along with links to bibliographical references, GenBank sequences, RefSeqs, computed and curated functional classifications, and sequence viewers such as the Map Viewer. The last example shows a single hit to the Conserved Domain Database (CDD) giving the sequence alignments used to define the domain indicated. A link to a KOG (see “KOGs and COGs are Now Included in CDD” in this issue) appears in the upper right-hand corner.

Advanced Entrez Features

A cross-database search produces an individual History page, giving a list of previously executed searches with links to the results, for each of the Entrez databases. Other familiar Entrez features such as the Clipboard, Details, Limits, and Preview/ Index are also retained separately for each database since the databases support specialized arrays of fields used to limit searches. For example, note that in Figure 2, some of the boxes containing the number of hits to the databases are shaded. The shading indicates that the cross-database query contained a field delimiter not supported by the database in question. The query of Figure 2, “rat[organism] AND kinase”, uses the “organism” field restriction; the “organism” field is supported within the Nucleotide, CDD and Gene databases, but not within the PubMed literature database. In this case, the search was performed using the term “rat” in “all fields”. This can be verified by clicking on PubMed in the cross-database results page, to reach the PubMed database display of the hits, and then clicking on the “Details” link in the PubMed display to see how the cross-database search was executed within the PubMed database.

The Entrez search and retrieval system is robust and flexible. To learn more about searching and navigating between Entrez databases or displaying and downloading results, see:

Geer RC, Sayers EW. Entrez: making use of its power. Briefings in Bioinformatics. 2003 Jun;4(2):179-84. PMID: 12846398