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<span class="links2"><br>
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</span> <span class="navon">Entrez Query Goes “Global”</span><br>
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<br>
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<a href="register.html" class="navoff">Register Your Genome Project
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Online at NCBI</a><br>
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<a href="kogs.html" class="navoff">KOGs and COGs Now in CDD</a><br>
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<a href="unigene.html" class="navoff">UniGene Adds Four</a><br>
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<span class="headlines">Entrez Query Goes “Global”</span></p>
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<p><span class="bodycopy" width="488"><br>
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The Entrez search and retrieval system now offers a cross-database search
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that allows a single query to span the traditional NCBI-sequence databases;
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Nucleotide and Protein; the literature databases, such as PubMed®,
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PMC, Books, OMIM™, Journals, and MeSH; the structurally-oriented
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databases, Structures, the Conserved Domain Database, 3D-Domains; the
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NCBI Taxonomy, Gene Expression Omnibus (GEO), Single Nucleotide Polymorphisms
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(SNPs), Population Sets, Genomes, Sequence Tagged Sites, UniGene, Gene-centered
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information (Gene), and, finally, the NCBI Web site itself. The cross
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database search option, labeled “Entrez” on the NCBI homepage
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search menu, replaces 'GenBank' as the default.</span></p>
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<p><span class="bodytext3">The New Entrez Home Page</span><span class="bodycopy">
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</span></p>
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<p><span class="bodycopy">The Entrez toolbar link on the NCBI Home Page
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leads to a new Entrez Home Page which provides a cross-database search
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box and a listing of the Entrez databases that can be searched in tandem.
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Question mark icons to the right of each database name lead to descriptions
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of database content. The database names and icons link to homepages
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where single-database queries can be constructed using lists of database-specific
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field restrictions, or tables that can be used to define search limits.
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In addition, the Entrez homepage toolbar provides links to popular NCBI
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tools and resources such as the Map Viewer and BLAST<53>. </span></p>
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<p align="center"><a href="javascript:;" onClick="MM_openBrWindow('images/EntrezFig1lrge.html','viewlarger','scrollbars=yes,resizable=yes,width=680,height=400')"><img src="images/EntrezFig1.png" width="460" height="244" border="1" alt="Figure 1. Entrez homepage showing the new cross-database search engine with links to the 21 Entrez databases covered."></a>
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<p><font color="#000000">Click on image to view larger</font></p>
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<p><span class="captions">Figure 1. </span><span class="captions2">Entrez
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Home Page showing the new cross-database search engine with links to
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the 21 Entrez databases covered.</span></p>
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<table width="488" border="0" cellspacing="1" cellpadding="0">
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<tr>
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<td width="486" height="1"></td>
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</table>
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<p><span class="bodytext3">Cross-Database Search Results</span><span class="bodycopy">
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</span></p>
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<p class="bodycopy">When a cross-database search is completed, the number
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of matches for each database is displayed in boxes adjacent to the database
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name as shown in Figure 2. The Figure shows the results of a cross-database
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search using the Entrez query <20>rat[organism] AND kinase<73> indicating
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hits to a wide variety of databases, including those for literature,
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sequence, gene expression, and structure. The four representative Entrez
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displays indicated by the letters A, B, C, and D are reached by first
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clicking on the the database name, icon, or number of matches to reach
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the Entrez document summary of the hits, and then selecting a record
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and a format for viewing.</p>
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<p class="bodycopy"><a href="javascript:;" onClick="MM_openBrWindow('mainlarge.htm','viewlarger','scrollbars=yes,resizable=yes,width=640,height=480')"><img src="images/EntrezF1Webver.gif" width="490" height="262" border="1"></a></p>
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<p class="bodycopy"><img src="images/Fig2PubMedsmall.png" width="240" height="259" border="1" onMouseDown="MM_openBrWindow('alarge.html','viewlarger','scrollbars=yes,resizable=yes,width=690,height=490')"><a href="javascript:;" onClick="MM_openBrWindow('blarge.html','viewlarger','scrollbars=yes,resizable=yes,width=600,height=539')"><img src="images/EntrezFig2NucleotideImagesmall.png" width="240" height="216" border="1"></a></p>
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<p class="bodycopy"><a href="javascript:;" onClick="MM_openBrWindow('EntrezFig2GeneImage.html','viewlarger','scrollbars=yes,resizable=yes,width=640,height=490')"><img src="images/EntrezFig2GeneImagesmall.png" width="240" height="164" border="1"></a><a href="javascript:;" onClick="MM_openBrWindow('EntrezFig2CDImage.html','viewlarger','scrollbars=yes,resizable=yes,width=640,height=480')"><img src="images/EntrezFig2CDImagesmall.png" width="240" height="96" border="1"></a></p>
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<p class="bodycopy">Beginning in the upper left hand corner, the figure
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shows one of the 54,988 hits to the PubMed database, using the <20>Abstract<63>
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display from the <20>display<61> pulldown menu. A link to the full text of
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the article in PubMed Central appears just to the right of the pulldown
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menu. Moving in a counter-clockwise direction, one of the 2,613 hits
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to the Nucleotide database is shown using the FASTA display format with
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other possible formats listed in the <20>display<61> pulldown menu. One of
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the 968 records from the Entrez Gene database that gives a detailed
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report on a gene. The report contains a gene description, a graphic
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of the gene's structure, along with links to bibliographical references,
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GenBank sequences, RefSeqs, computed and curated functional classifications,
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and sequence viewers such as the Map Viewer. The last example shows
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a single hit to the Conserved Domain Database (CDD) giving the sequence
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alignments used to define the domain indicated. A link to a KOG (<a href="kogs.html">see
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<20>KOGs and COGs are Now Included in CDD<44> in this issue</a>) appears in
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the upper right-hand corner. </p>
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<p><span class="bodytext3">Advanced Entrez Features</span><span class="bodycopy">
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</span></p>
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<p><span class="bodycopy">A cross-database search produces an individual
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History page, giving a list of previously executed searches with links
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to the results, for each of the Entrez databases. Other familiar Entrez
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features such as the Clipboard, Details, Limits, and Preview/ Index
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are also retained separately for each database since the databases support
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specialized arrays of fields used to limit searches. For example, note
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that in Figure 2, some of the boxes containing the number of hits to
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the databases are shaded. The shading indicates that the cross-database
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query contained a field delimiter not supported by the database in question.
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The query of Figure 2, <20>rat[organism] AND kinase<73>, uses the <20>organism<73>
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field restriction; the <20>organism<73> field is supported within the Nucleotide,
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CDD and Gene databases, but not within the PubMed literature database.
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In this case, the search was performed using the term <20>rat<61> in <20>all
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fields<64>. This can be verified by clicking on PubMed in the cross-database
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results page, to reach the PubMed database display of the hits, and
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then clicking on the <20>Details<6C> link in the PubMed display to see how
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the cross-database search was executed within the PubMed database. </span></p>
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<p><span class="bodycopy">The Entrez search and retrieval system is robust
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and flexible. To learn more about searching and navigating between Entrez
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databases or displaying and downloading results, see: </span></p>
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<p>
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<span class="bodycopy">Geer RC, Sayers EW. Entrez: making use of its power.
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<i>Briefings in Bioinformatics</i>. 2003 Jun;4(2):179-84. PMID: <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12846398&dopt=Abstract">12846398</a>
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<p>
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<table width="488" border="0" cellspacing="1" cellpadding="0">
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<tr>
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<td width="488" height="25" align="center" bgcolor="dfefff">
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<div align="center" class="links2"><a href="http://www.ncbi.nlm.nih.gov/Entrez">www.ncbi.nlm.nih.gov/Entrez</a></div>
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</td>
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</tr>
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</table>
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</span> </div>
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<br>
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<table width="488" height="25" border="0" cellpadding="0" bgcolor="#F2F2F2">
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<tr>
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<td width="8" height="213"></td>
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<td width="464" valign="top">
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<p class="tables2" align="center"><font size="2">Query Across All
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Entrez Databases by Script</font></p>
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<p class="tables">Entrez cross-database searches can be performed
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by script using a new E-Utility program called EGQuery. E-Utilities
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are programs residing on NCBI servers that can be accessed by posting
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a standard URL containing the script name and a set of parameters.
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For example, posting the following URL from within a script will
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return the number of hits to each Entrez database for the query
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"stem cells":<br>
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</p>
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<p class="links2" align="center"><a href="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/egquery.fcgi?term=stem%2Bcells">eutils.ncbi.nlm.nih.gov/entrez/eutils/egquery.fcgi?term=stem+cells</a></p>
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<p class="tables">Results are returned in XML format. For details
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on the use of EGQuery or other E-Utilities, see:</p>
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<p align="center" class="links2"><a href="http://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html">eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html</a></p>
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<p class="tables">To receive announcements of new E-Utility features,
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subscribe to the E-"utilities-announce" listserve at:</p>
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<p class="links2" align="center"><a href="http://www.ncbi.nlm.nih.gov/mailman/listinfo/utilities-announce">www.ncbi.nlm.nih.gov/mailman/listinfo/utilities-announce</a></p>
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<p class="authors">—MR, DW
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