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<div class="pre-content"><div><div class="bk_prnt"><p class="small">NCBI Bookshelf. A service of the National Library of Medicine, National Institutes of Health.</p><p>NCBI News [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 1991-2012. </p></div><div class="iconblock clearfix whole_rhythm no_top_margin bk_noprnt"><a class="img_link icnblk_img" title="Table of Contents Page" href="/books/n/newsncbi/"><img class="source-thumb" src="/corehtml/pmc/pmcgifs/bookshelf/thumbs/th-newsncbi-lrg.png" alt="Cover of NCBI News" height="100px" width="80px" /></a><div class="icnblk_cntnt eight_col"><h2>NCBI News [Internet].</h2><a data-jig="ncbitoggler" href="#__NBK430988_dtls__">Show details</a><div style="display:none" class="ui-widget" id="__NBK430988_dtls__"><div>Bethesda (MD): <a href="https://www.ncbi.nlm.nih.gov/news" ref="pagearea=page-banner&targetsite=external&targetcat=link&targettype=publisher">National Center for Biotechnology Information (US)</a>; 1991-2012.</div></div><div class="half_rhythm"><ul class="inline_list"><li style="margin-right:1em"><a class="bk_cntns" href="/books/n/newsncbi/">Index of Issues</a></li></ul></div><div class="bk_noprnt"><form method="get" action="/books/n/newsncbi/" id="bk_srch"><div class="bk_search"><label for="bk_term" class="offscreen_noflow">Search term</label><input type="text" title="Search this book" id="bk_term" name="term" value="" data-jig="ncbiclearbutton" /> <input type="submit" class="jig-ncbibutton" value="Search this book" submit="false" style="padding: 0.1em 0.4em;" /></div></form></div></div><div class="icnblk_cntnt two_col"><div class="pagination bk_noprnt"><a class="active page_link prev" href="/books/n/newsncbi/N2014-04/" title="Previous page in this title">< Prev</a><a class="active page_link next" href="/books/n/newsncbi/N2014-02/" title="Next page in this title">Next ></a></div></div></div></div></div>
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<div class="main-content lit-style" itemscope="itemscope" itemtype="http://schema.org/CreativeWork"><div class="meta-content fm-sec"><h1 id="_NBK430988_"><span class="title" itemprop="name">NCBI News, March 2014</span></h1><p><em>Estimated reading time: 5 minutes</em></p></div><div class="jig-ncbiinpagenav body-content whole_rhythm" data-jigconfig="allHeadingLevels: ['h2'],smoothScroll: false" itemprop="text"><div id="news_03-28-2014-BLAST-custom-databases-video"><h2 id="_news_03-28-2014-BLAST-custom-databases-video_">New NCBI YouTube video: Create custom databases for BLAST</h2><p>
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<i>Friday, March 28, 2014</i>
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</p><p>In the newest NCBI video on YouTube, we show you how to create custom databases in BLAST. This video gives you a step-by-step tutorial on limiting your web BLAST searches to a customized set of sequences. </p><p>
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<a href="https://www.youtube.com/watch?v=" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">YouTube</a>
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</p></div><div id="news_03-28-2014-come-to-2014-discovery-workshops"><h2 id="_news_03-28-2014-come-to-2014-discovery-workshops_">Come to the NCBI Discovery Workshops on May 6th & 7th!</h2><p>
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<i>Friday, March 28, 2014</i>
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</p><p>The NCBI Discovery Workshops will be held on the NIH Campus on May 6 and 7. To get more information and to register, visit the <a href="https://www.ncbi.nlm.nih.gov/education/workshops/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Discovery Workshops homepage</a>.</p><p>The NCBI Discovery Workshops, a 2-day event, comprise of four workshops that will teach you how to use the NCBI Web resources more effectively. The May 2014 Workshops consist of four 2.5-hour hands-on sessions, with each session focusing on a different related group of NCBI tools and databases:</p><ul><li class="half_rhythm"><div>
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<a href="https://www.ncbi.nlm.nih.gov/education/workshops/sequences-genomes-and-maps" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Sequences, Genomes, and Maps</a>
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</div></li><li class="half_rhythm"><div>
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<a href="https://www.ncbi.nlm.nih.gov/education/workshops/proteins-domains-and-structures" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Proteins, Domains, and Structures</a>
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</div></li><li class="half_rhythm"><div>
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<a href="https://www.ncbi.nlm.nih.gov/education/workshops/ncbi-blast-services" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">NCBI BLAST Services</a>
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</div></li><li class="half_rhythm"><div>
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<a href="https://www.ncbi.nlm.nih.gov/education/workshops/human-variation-and-disease-genes" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Human Variation and Disease Genes</a>
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</div></li></ul><p>Materials from all Discovery Workshops offerings are available from the <a href="ftp://ftp.ncbi.nih.gov/pub/education/discovery_workshops/Current/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Education FTP directory</a>.</p></div><div id="news_03-20-2014-ncbi-at-acmg"><h2 id="_news_03-20-2014-ncbi-at-acmg_">NCBI will attend the 2014 ACMG Annual Clinical Genetics Meeting</h2><p>
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<i>Thursday, March 20, 2014</i>
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</p><p>NCBI staff will attend the <a href="http://www.acmgmeeting.net/acmg2014/public/enter.aspx" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">2014 ACMG Annual Clinical Genetics Meeting</a> in Nashville, TN on March 25-29.</p><p>At Booth #1105, you’ll be able to do a variety of things including:</p><ul><li class="half_rhythm"><div>Generate a differential diagnosis based on clinical features,</div></li><li class="half_rhythm"><div>Search the ACMG incidental findings gene set against your variant result,</div></li><li class="half_rhythm"><div>Join NIH’s open access mission and submit data to GTR and ClinVar,</div></li><li class="half_rhythm"><div>And get hands-on help from staff.</div></li></ul><p>For more details, see the <a href="https://www.ncbi.nlm.nih.gov/gtr/docs/outreach/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">GTR page</a>.</p></div><div id="news_03-17-2014-blast-xml-feedback"><h2 id="_news_03-17-2014-blast-xml-feedback_">NCBI requests feedback on proposed BLAST XML specification update</h2><p>
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<i>Monday, March 17, 2014</i>
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</p><p>The BLAST development team is planning to update the BLAST XML specification in the Summer of 2014 and would like feedback from the user community on the proposed changes. This update is designed to improve consistency of the BLAST output with XML standards and implement new and useful elements. The <a href="ftp://ftp.ncbi.nlm.nih.gov/blast/documents/NEWXML/ProposedBLASTXMLChanges.pdf" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">BLAST proposal</a> outlines these intended changes.</p><p>If you are a BLAST XML user, please provide feedback on the proposed changes using this web form. We thank you in advance for your input.</p></div><div id="news_03-14-2014-refseq-release-64"><h2 id="_news_03-14-2014-refseq-release-64_">RefSeq full release 64 out</h2><p>
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<i>Friday, March 14, 2014</i>
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</p><p><a href="ftp://ftp.ncbi.nlm.nih.gov/refseq/release/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">The full RefSeq release 64</a> is now available with nearly 50 million records describing 37,818,139 proteins, 6,198,996 RNAs, and sequences from 33,693 different organisms.</p><p>Some important updates include the following:</p><p><b>SNP annotation update</b>: <a href="ftp://ftp.ncbi.nih.gov/snp/release-notes/RefSeq/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">A list of updated organisms and dbSNP annotation summary is available in the SNP RefSeq release notes folder on the FTP site ("refseq63.snp.rpt).</a></p><p><b>Domain annotation update</b>: RefSeq domain and site features that are provided by the <a href="https://www.ncbi.nlm.nih.gov/cdd" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Conserved Domain Database</a> were updated in conjunction with CDD release 3.11. For more information on release 3.11, <a href="/books/n/newsncbi/N2014-02/#news_02-19-2014-cdd-v311">see the NCBI News story from last month</a>.</p><p><b>New annotation for the updated human reference genome assembly, GRCh38</b>: <a href="/books/n/newsncbi/N2013-12/#news_12-23-2013-grch38-released">The Genome Reference Consortium released a major update to the human reference genome assembly (GRCh38) in late December 2013</a>. In January 2014, this updated assembly, plus two other human genome assemblies (HuRef and CHM1_1.1), was annotated using NCBI's eukaryotic genome annotation pipeline which integrated information from curated RefSeqs, cDNAs, ESTs, protein alignments, and RNA-Seq data from the Human BodyMap2 project. Results for all three genomes are available as <a href="https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Homo_sapiens/106/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">NCBI Annotation release 106</a>.</p><p>More details about the RefSeq release 64 is included in the <a href="ftp://ftp.ncbi.nlm.nih.gov/refseq/release/release-statistics/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">release statistics</a> and <a href="ftp://ftp.ncbi.nlm.nih.gov/refseq/release/release-notes/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">release notes</a>. In addition, reports indicating the accessions included <a href="ftp://ftp.ncbi.nlm.nih.gov/refseq/release/release-catalog/RefSeq-release64.catalog.gz" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">in the release</a> and <a href="ftp://ftp.ncbi.nlm.nih.gov/refseq/release/release-catalog/release64.files.installed" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">the files installed</a> are available.</p></div><div id="news_03-13-2014-gene-provides-orthologs-regions"><h2 id="_news_03-13-2014-gene-provides-orthologs-regions_">Orthologous genes and gene regions now accessible through Gene</h2><p>
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<i>Wednesday, March 12, 2014</i>
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</p><p>Each Gene record now provides access to orthologous genes and regions in the “General gene information” section of the Gene record (Figure 1). In addition, complex loci in a particular species, such as the human immunoglobulin heavy locus, now have links to the corresponding individual members.</p><div class="iconblock whole_rhythm clearfix ten_col fig" id="fignews03132014figure1generalgenein" co-legend-rid="figlgndnews03132014figure1generalgenein"><a href="/books/NBK430988/figure/news_03-13-2014.figure1generalgenein/?report=objectonly" target="object" title="Figure" class="img_link icnblk_img figpopup" rid-figpopup="fignews03132014figure1generalgenein" rid-ob="figobnews03132014figure1generalgenein"><img class="small-thumb" src="/books/NBK430988/bin/cms_News583_Fig1.gif" src-large="/books/NBK430988/bin/cms_News583_Fig1.jpg" alt="Figure 1" /></a><div class="icnblk_cntnt" id="figlgndnews03132014figure1generalgenein"><h4 id="news_03-13-2014.figure1generalgenein"><a href="/books/NBK430988/figure/news_03-13-2014.figure1generalgenein/?report=objectonly" target="object" rid-ob="figobnews03132014figure1generalgenein">Figure</a></h4><p class="float-caption no_bottom_margin"><i>Figure 1.</i> General gene information section of Gene records. <i>Top panel:</i> The Homology subsection of the zebrafish abl1 record (Gene ID: 100000720) showing the link to “Orthologs from Annotation Pipeline” (circled in red) as well <a href="/books/NBK430988/figure/news_03-13-2014.figure1generalgenein/?report=objectonly" target="object" rid-ob="figobnews03132014figure1generalgenein">(more...)</a></p></div></div><p>The “Orthologs from Annotation Pipeline” link under the Homology subsection of “General gene information” accesses the set of orthologs in selected vertebrae genomes using the method described in PMCID: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3882889/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">PMC3882889</a>. For example, this link from the zebrafish abl1 gene record (Gene ID: <a href="https://www.ncbi.nlm.nih.gov/gene/100000720" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">100000720</a>) or from any other member of this orthology group provides <a href="https://www.ncbi.nlm.nih.gov/gene/?Term=ortholog_gene_25[group]" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">80 orthologous gene records</a> from a wide range of vertebrate species (birds, mammals, turtles, fishes, and the coelacanth). These ortholog data are supplemental to those currently available from the HomoloGene resource also linked under the “Gene information: Homology” section of the Gene record. The Annotation Pipeline method is being improved to include more distantly related organisms in the future.</p><p>Region gene records are available for loci that are officially named and are composed of multiple parts or clusters of related genes. The “Related region members” section in a region gene record has a “Review record(s) in Gene” link that provides all genes that are components of the region. For example, the link from the human and mouse immunoglobulin H region records (Gene IDs: <a href="https://www.ncbi.nlm.nih.gov/gene/3492" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">3492</a> & <a href="https://www.ncbi.nlm.nih.gov/gene/111507" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">11507</a>) provide <a href="https://www.ncbi.nlm.nih.gov/gene/?Term=region_gene_3492[group]" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">182</a> and <a href="https://www.ncbi.nlm.nih.gov/gene/?Term=region_gene_111507[group]" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">215</a> records respectively.</p><p>The data for both gene orthology groups and gene regions are available in the <a href="ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_group.gz" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">gene_group.gz</a> file in the Gene area of the NCBI FTP site. In the file, the terms “Ortholog”, “Region members”, and “Region parent” are used to report these new relationships.</p></div><div id="news_03-12-2014-dbgap-features"><h2 id="_news_03-12-2014-dbgap-features_">New dbGaP online system for registering studies and applying for data access introduces time-saving features</h2><p>
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<i>Wednesday, March 12, 2014</i>
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</p><p>In an effort to reduce burden, NIH has developed an online system for researchers and their institutional officials to register studies, submit data, and access data in <a href="https://www.ncbi.nlm.nih.gov/gap" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">dbGaP</a>.  The online system introduces a number of time-saving features, such as automatically completing data fields from other sources, for example, using eRA Commons to provide the investigator’s name, institution, and Institutional Signing Official.</p><p>Tutorials on the online forms for study registration and data access are available on Youtube:</p><p>
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<b>
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<a href="https://www.youtube.com/watch?v=gIjN0Er39us&feature=youtu.be" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">dbGaP: Complete a Study Registration</a>
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</b>
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</p><p>
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<a href="https://www.youtube.com/watch?v=" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">YouTube</a>
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</p><p>
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<a href="http://www.youtube.com/watch?v=-3tUBeKbP5c" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">
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<b>dbGaP: </b>
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</a>
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<b>
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<a href="http://www.youtube.com/watch?v=-3tUBeKbP5c" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Controlled Access Data</a>
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</b>
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</p><p>
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<a href="https://www.youtube.com/watch?v=" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">YouTube</a>
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</p><p>
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<b>
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<a href="http://www.youtube.com/watch?v=PG9D5mUouXg" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">dbGaP: Renew Authorized Access</a>
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</b>
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</p><p>
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<a href="https://www.youtube.com/watch?v=" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">YouTube</a>
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</p><p>
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<b>
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<a href="http://www.youtube.com/watch?v=i85gl937ZPA" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">dbGaP: Close Out a Controlled Access Project</a>
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</b>
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</p><p>
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<a href="https://www.youtube.com/watch?v=" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">YouTube</a>
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</p><p>Additional information can be found in the <a href="http://grants.nih.gov/grants/guide/notice-files/NOT-OD-14-065.html" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">NIH Guide Notice</a>.</p></div><div id="news_03-10-2014-eutils-sorting"><h2 id="_news_03-10-2014-eutils-sorting_">New Sorting and Output Options for E-utilities</h2><p>
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<i>Monday, March 10, 2014</i>
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</p><p>E-utilities, the API to the NCBI Entrez system, now offers two new options for data retrieval.</p><p>First, ESearch now offers a fully supported <i>&sort</i> parameter that determines the sort order of the UIDs returned. While each Entrez database has a default sort order, each also provides a variety of other sorting options found in the “Display Settings” menu at the top of a search result page. Any of these options may now be given to ESearch using &sort. </p><div class="iconblock whole_rhythm clearfix ten_col fig" id="fignews03102014resultssortedbyrelev" co-legend-rid="figlgndnews03102014resultssortedbyrelev"><a href="/books/NBK430988/figure/news_03-10-2014.resultssortedbyrelev/?report=objectonly" target="object" title="Figure" class="img_link icnblk_img figpopup" rid-figpopup="fignews03102014resultssortedbyrelev" rid-ob="figobnews03102014resultssortedbyrelev"><img class="small-thumb" src="/books/NBK430988/bin/cms_pubmed_sort_by_relevance.gif" src-large="/books/NBK430988/bin/cms_pubmed_sort_by_relevance.jpg" alt="Results sorted by Relevance" /></a><div class="icnblk_cntnt" id="figlgndnews03102014resultssortedbyrelev"><h4 id="news_03-10-2014.resultssortedbyrelev"><a href="/books/NBK430988/figure/news_03-10-2014.resultssortedbyrelev/?report=objectonly" target="object" rid-ob="figobnews03102014resultssortedbyrelev">Figure</a></h4><p class="float-caption no_bottom_margin">Results sorted by Relevance. </p></div></div><p>For example, to sort a PubMed retrieval by First Author, simply add “<i>&sort=first+author</i>” to your ESearch URL. If you are also supplying “<i>&usehistory=y</i>”, then the UIDs will also be sorted on the Entrez History so that when retrieved by ESummary or EFetch, the sort order will be retained in that output. Of particular interest is the new <a href="http://www.nlm.nih.gov/pubs/techbull/so13/so13_pm_relevance.html" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">relevance sort option</a> now available in PubMed and several other databases. To enable this for ESearch, use “<i>&sort=relevance</i>”.</p><p>Second, the output for EInfo, ESearch and ESummary are now available in the popular <a href="http://json.org/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">JSON</a> format. To request data in JSON, simply append “<i>&retmode=json</i>” to the E-utility URL. Click on the following links for example outputs:</p><ul><li class="half_rhythm"><div>
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<a href="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?db=pubmed&retmode=json" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">EInfo</a>
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</div></li><li class="half_rhythm"><div>
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<a href="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=asthma&retmode=json" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">ESearch</a>
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</div></li><li class="half_rhythm"><div>
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<a href="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=protein&id=586979410,557636699,402766099&retmode=json" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">ESummary</a>
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</div></li></ul><p>
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Please see the <a href="https://www.ncbi.nlm.nih.gov/books/NBK25501/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">E-utilities documentation</a> for additional details.</p></div><div id="bk_toc_contnr"></div></div></div>
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<div class="post-content"><div><div class="half_rhythm"><a href="/books/about/copyright/">Copyright Notice</a></div><div class="small"><span class="label">Bookshelf ID: NBK430988</span></div><div style="margin-top:2em" class="bk_noprnt"><a class="bk_cntns" href="/books/n/newsncbi/">Index of Issues</a><div class="pagination bk_noprnt"><a class="active page_link prev" href="/books/n/newsncbi/N2014-04/" title="Previous page in this title">< Prev</a><a class="active page_link next" href="/books/n/newsncbi/N2014-02/" title="Next page in this title">Next ></a></div></div></div></div>
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