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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>SNP FAQ Archive [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2005-. </p></div><div class="messagearea bk_noprnt" style="margin-bottom:1.3846em "><ul class="messages"><li class="warn icon"><span class="icon">This publication is provided for historical reference only and the information may be out of date.</span></li></ul></div><div class="bk_prnt"><p style="color:red;"><strong>This publication is provided for historical reference only and the information may be out of date.</strong></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/helpsnpfaq/"><img class="source-thumb" src="/corehtml/pmc/pmcgifs/bookshelf/thumbs/th-helpsnpfaq-lrg.png" alt="Cover of SNP FAQ Archive" height="100px" width="80px" /></a><div class="icnblk_cntnt eight_col"><h2>SNP FAQ Archive [Internet].</h2><a data-jig="ncbitoggler" href="#__NBK573576_dtls__">Show details</a><div style="display:none" class="ui-widget" id="__NBK573576_dtls__"><div>Bethesda (MD): <a href="https://www.ncbi.nlm.nih.gov/" ref="pagearea=page-banner&amp;targetsite=external&amp;targetcat=link&amp;targettype=publisher">National Center for Biotechnology Information (US)</a>; 2005-.</div></div><div class="half_rhythm"><ul class="inline_list"><li style="margin-right:1em"><a class="bk_cntns" href="/books/n/helpsnpfaq/">Contents</a></li></ul></div></div><div class="icnblk_cntnt two_col"><div class="pagination bk_noprnt"><a class="active page_link prev" href="/books/n/helpsnpfaq/FTP_Updating_dbSNP/" title="Previous page in this title">&lt; Prev</a><a class="active page_link next" href="/books/n/helpsnpfaq/Schema/" title="Next page in this title">Next &gt;</a></div></div></div></div></div>
<div class="main-content lit-style" itemscope="itemscope" itemtype="http://schema.org/CreativeWork"><div class="meta-content fm-sec"><h1 id="_NBK573576_"><span class="title" itemprop="name">Eutils (E-utilities)</span></h1><p class="small">Created: <span itemprop="datePublished">July 7, 2005</span>; Last Update: <span itemprop="dateModified">February 18, 2014</span>.</p><p><em>Estimated reading time: 4 minutes</em></p></div><div class="jig-ncbiinpagenav body-content whole_rhythm" data-jigconfig="allHeadingLevels: ['h2'],smoothScroll: false" itemprop="text"><ul class="simple-list"><li><h4>Using eutils to Obtain Specific SNP Information</h4></li><li><p><a href="#FTP_Eutils.can_i_use_eutils_to_get_snp_l">Can I use eutils to get SNP location type, class, validation, function, molecular type, heterozygosity and weight for all the SNPs on a chromosome?</a></p></li><li><p><a href="#FTP_Eutils.how_do_i_use_eutils_to_extrac">How do I use eutils to extract from dbSNP some fields that are usually in the SNP annotation of the Illumina repositories? These fields include CytogeneticBand, GeneticMapPosition, LocationRelativeToGene, etc.</a></p></li><li><p><a href="#FTP_Eutils.how_do_i_extract_information">How do I extract information from dbSNP by using eutils and specifying the chromosome position interval?</a></p></li></ul><ul class="simple-list"><li><h4>Eutils Workshops and Tutorials</h4></li><li><p><a href="#FTP_Eutils.where_can_i_get_more_informat">Where can I get more information on NCBI workshops for data retrieval?</a></p></li><li><p><a href="#FTP_Eutils.is_there_an_online_tutorial_f">Is there an online tutorial for eutils?</a></p></li></ul><ul class="simple-list"><li><h4>Eutils Online Documentation</h4></li><li><p><a href="#FTP_Eutils.is_there_some_kind_of_help_do">Is there some kind of help documentation for eutils?</a></p></li></ul><ul class="simple-list"><li><h4>Using Eutils to Find Specific Data</h4></li><ul class="simple-list"><li><h4>Using Eutils to Find rs Merge Information</h4></li><li><p><a href="#FTP_Eutils.can_i_use_eutils_to_get_the_i">Can I use eutils to get the information about a particular rs number to include a notice that the rs number has merged into another rs number?</a></p></li></ul><ul class="simple-list"><li><h4>Using Eutils to Retrieve Population Diversity Files</h4></li><li><p><a href="#FTP_Eutils.is_it_possible_to_use_esearch">Is it possible to use eSearch and eFetch to get population diversity XML files?</a></p></li></ul></ul><ul class="simple-list"><li><h4>eFetch</h4></li><li><p><a href="#FTP_Eutils.how_do_i_use_efetch_with_entr">How do I use efetch with EntrezSNP?</a></p></li><li><p><a href="#FTP_Eutils.can_i_use_epost_and_esummary">Can I use ePost and eSummary or eFetch to get SNP records in various formats?</a></p></li><li><p><a href="#FTP_Eutils.how_do_i_fetch_data_for_a_giv">How do I fetch data for a given refSNP ID (rsID) in XML format using a simple URL-request?</a></p></li><li><p><a href="#FTP_Eutils.is_it_possible_to_use_esearch_1">Is it possible to use eSearch and eFetch to get population diversity XML files?</a></p></li></ul><ul class="simple-list"><li><h4>eSearch</h4></li><li><p><a href="#FTP_Eutils.will_the_hgvs_based_variation">Will the HGVS based variation search you are testing also be available through eutils?</a></p></li><li><p><a href="#FTP_Eutils.if_i_query_esearch_for_all_sn">If I query eSearch for all SNPs that hit on chromosome 1 in the 1 to 6000 bp range, I get 11 hits, but if I search our local MSSQL directly, I get 115 hits. Why the difference? How do I get the same results that I got from Entrez by using a direct SQL query, and vice versa?</a></p></li></ul><ul class="simple-list"><li><h4>XML Format for eutils</h4></li><li><p><a href="#FTP_Eutils.why_does_dbsnp_have_two_diffe">Why does dbSNP have two different XML formats (one for the file and one for data for Eutils) for SNP entries?</a></p></li><li><p><a href="#FTP_Eutils.i_m_using_the_command__http_e">I&#x02019;m using the command &#x0201c;http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=snp&#x00026;rettype=genxml&#x00026;id=$marker&#x0201d; to extract freq info from dbSNP, but can&#x02019;t get well formed XML.</a></p></li></ul><div id="FTP_Eutils.Using_eutils_to_Obtain_Specif"><h2 id="_FTP_Eutils_Using_eutils_to_Obtain_Specif_">Using eutils to Obtain Specific SNP Information</h2><div><h4 id="FTP_Eutils.can_i_use_eutils_to_get_snp_l">Can I use eutils to get SNP location type, class, validation, function, molecular type, heterozygosity and weight for all the SNPs on a chromosome?</h4><blockquote><p>As it would take entirely too long to get this information for 14 Million+ SNPs by eutils, you should get the information from the dbSNP FTP site. If you need to look at all the SNPs on a particular human chromosome, go to the <a href="ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/XML/" ref="pagearea=body&amp;targetsite=external&amp;targetcat=link&amp;targettype=ftp">organisms/human_9606/XML/</a> directory on the dbSNP FTP site, and select the chromsosome file you would like to see.(<b>10/06/08</b>)</p></blockquote></div><div><h4 id="FTP_Eutils.how_do_i_use_eutils_to_extrac">How do I use eutils to extract from dbSNP some fields that are usually in the SNP annotation of the Illumina repositories? These fields include CytogeneticBand, GeneticMapPosition, LocationRelativeToGene, etc.</h4><blockquote><p>Sorry, dbSNP doesn't have the Illumina fields you mention available in eUtils. The SNP data available in eUtils are documented in the <a href="/projects/SNP/docsum/docsum_doc.html" ref="pagearea=body&amp;targetsite=external&amp;targetcat=link&amp;targettype=uri">docsum schema</a>. (<b>10/25/07</b>)</p></blockquote></div><div><h4 id="FTP_Eutils.how_do_i_extract_information">How do I extract information from dbSNP by using eutils and specifying the chromosome position interval?</h4><blockquote><p>Use the following eSearch query: "100000:200000[Base Position] AND "1"[CHR] AND txid9606". See <a href="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=snp&#x00026;term=100000:200000%5bBase%20Position%5d%20AND%20%221%22%5bCHR%5d%20AND%20txid9606&#x00026;retmax=20&#x00026;usehistory=y" ref="pagearea=body&amp;targetsite=external&amp;targetcat=link&amp;targettype=uri">example</a>.</p><p>You can also get the result using <a href="http://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html" ref="pagearea=body&amp;targetsite=external&amp;targetcat=link&amp;targettype=uri">eFetch</a>.(<b>7/9/07</b>)</p></blockquote></div></div><div id="FTP_Eutils.Eutils_Workshops_and_Tutorial"><h2 id="_FTP_Eutils_Eutils_Workshops_and_Tutorial_">Eutils Workshops and Tutorials</h2><div><h4 id="FTP_Eutils.where_can_i_get_more_informat">Where can I get more information on NCBI workshops for data retrieval?</h4><blockquote><p>There is <a href="/Class/PowerTools/eutils/course.html" ref="pagearea=body&amp;targetsite=external&amp;targetcat=link&amp;targettype=uri">online information</a> for courses offered by NCBI.</p><p>You might also want to go to the <a href="http://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html" ref="pagearea=body&amp;targetsite=external&amp;targetcat=link&amp;targettype=uri">Eutils General Help page</a>, and look at the NCBI online short course book called &#x0201c;<a href="/books/n/coursework/eutils/">Building Customized Data Pipelines Using the Entrez Programming Utilities (eUtils)</a>&#x0201d; <b>(12/01/05)</b></p></blockquote></div><div><h4 id="FTP_Eutils.is_there_an_online_tutorial_f">Is there an online tutorial for eutils?</h4><blockquote><p>There is an <a href="/books/n/coursework/eutils/">online tutorial</a> for using eutils on the NCBI Bookshelf <b>(9/20/05)</b></p></blockquote></div></div><div id="FTP_Eutils.Eutils_Online_Documentation"><h2 id="_FTP_Eutils_Eutils_Online_Documentation_">Eutils Online Documentation</h2><div><h4 id="FTP_Eutils.is_there_some_kind_of_help_do">Is there some kind of help documentation for eutils?</h4><blockquote><p>There is an <a href="/books/n/coursework/eutils/">online book</a> that describes how to use eutils <b>(2005)</b></p></blockquote></div></div><div id="FTP_Eutils.Using_Eutils_to_Find_Specific"><h2 id="_FTP_Eutils_Using_Eutils_to_Find_Specific_">Using Eutils to Find Specific Data</h2><div id="FTP_Eutils.Using_Eutils_to_Find_rs_Merge"><h3>Using Eutils to Find rs Merge Information</h3><div><h4 id="FTP_Eutils.can_i_use_eutils_to_get_the_i">Can I use eutils to get the information about a particular rs number to include a notice that the rs number has merged into another rs number?</h4><blockquote><p>Currently, there are three different entry points in dbSNP that will lead you to the partner numbers of a merge:</p><dl class="temp-labeled-list"><dt>1.</dt><dd><p class="no_top_margin">You can retrieve a list of merged rs numbers from <a href="/sites/entrez?db=snp" ref="pagearea=body&amp;targetsite=external&amp;targetcat=link&amp;targettype=uri">Entrez SNP</a>. Just type &#x0201c;mergedrs&#x0201d; (without the quotation marks) in the text box at the top of the page and click the &#x0201c;go&#x0201d; button. Each entry in the returned list will include the old rs numbers that has merged, and the new rs number it has merged into (with a link to the refSNPpage for the new rs number). You can limit the output to merged rs numbers within a certain species by clicking on the &#x0201c;Limits&#x0201d; tab and then selecting the organism you wish from the organism selection box.</p></dd><dt>2.</dt><dd><p class="no_top_margin">If you enter an old rs number (in this case rs2857713) into the &#x0201c;Search for IDs&#x0201d; search on the dbSNP home page, the response page will state that the SNP has been merged, and will provide the new rs number (in this case <a href="/snp/?term=2229094" class="bk_tag" ref="pagearea=body&amp;targetsite=entrez&amp;targetcat=term&amp;targettype=snp">rs2229094</a>) and a link to the refSNP page for that new rs number.</p></dd><dt>3.</dt><dd><p class="no_top_margin">The <a href="ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/database/organism_data/RsMergeArch.bcp.gz" ref="pagearea=body&amp;targetsite=external&amp;targetcat=link&amp;targettype=ftp">RsMergeArch table</a> houses the merged SNPs, and is available on the dbSNP ftp site. A full description of the table can be found in the <a href="/SNP/snp_db_table_description.cgi?t=RsMergeArch" ref="pagearea=body&amp;targetsite=external&amp;targetcat=link&amp;targettype=uri">dbSNP Data Dictionary</a>, and the column definitions are located in the dbSNP_main_table.sql.gz, which can be found in the <a href="ftp://ftp.ncbi.nlm.nih.gov/snp/database/shared_schema" ref="pagearea=body&amp;targetsite=external&amp;targetcat=link&amp;targettype=ftp">shared<wbr style="display:inline-block"></wbr>_schema</a> directory of the dbSNP FTP site.</p></dd></dl><p>(<b>11/03/08</b>)</p></blockquote></div></div><div id="FTP_Eutils.Using_Eutils_to_Retrieve_Popu"><h3>Using Eutils to Retrieve Population Diversity Files</h3><div><h4 id="FTP_Eutils.is_it_possible_to_use_esearch">Is it possible to use eSearch and eFetch to get population diversity XML files?</h4><blockquote><p>You can use eSearch to search for SNPs that have genotype information (please see this <a href="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=snp&#x00026;term=true%5bgtype%5d" ref="pagearea=body&amp;targetsite=external&amp;targetcat=link&amp;targettype=uri">example</a>), and eFetch to retrieve the genotype report to get the population information. You can find additional report examples on the <a href="/projects/SNP/SNPeutils.htm" ref="pagearea=body&amp;targetsite=external&amp;targetcat=link&amp;targettype=uri">&#x0201c;Eutils for EntrezSNP&#x0201d; page</a>.</p><p>(<b>11/17/08</b>)</p></blockquote></div></div></div><div id="FTP_Eutils.eFetch"><h2 id="_FTP_Eutils_eFetch_">eFetch</h2><div><h4 id="FTP_Eutils.how_do_i_use_efetch_with_entr">How do I use efetch with EntrezSNP?</h4><blockquote><p>There is online <a href="/projects/SNP/SNPeutils.htm" ref="pagearea=body&amp;targetsite=external&amp;targetcat=link&amp;targettype=uri">documentation</a> for using efetch with EntrezSNP. <b>(5/13/05)</b></p></blockquote></div><div><h4 id="FTP_Eutils.can_i_use_epost_and_esummary">Can I use ePost and eSummary or eFetch to get SNP records in various formats?</h4><blockquote><p>You can retrieve SNP records using eFetch in various report formats if you already know the snp_id. (e.g. 3, 7775). Please take a look at our <a href="/projects/SNP/SNPeutils.htm" ref="pagearea=body&amp;targetsite=external&amp;targetcat=link&amp;targettype=uri">eutils page</a> for more information.</p><p>Here is an <a href="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=snp&#x00026;id=3,7775&#x00026;report=FASTA" ref="pagearea=body&amp;targetsite=external&amp;targetcat=link&amp;targettype=uri">example</a> of one of the report types delivered using efetch and the ID number mentioned above. (<b>4/30/07</b>)</p></blockquote></div><div><h4 id="FTP_Eutils.how_do_i_fetch_data_for_a_giv">How do I fetch data for a given refSNP ID (rsID) in XML format using a simple URL-request?</h4><blockquote><p>Please see the <a href="/books/n/coursework/eutils/">online short course</a> for using eutils (<b>9/15/06</b>)</p></blockquote></div><div><h4 id="FTP_Eutils.is_it_possible_to_use_esearch_1">Is it possible to use eSearch and eFetch to get population diversity XML files?</h4><blockquote><p>You can use eSearch to search for SNPs that have genotype information (please see this <a href="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=snp&#x00026;term=true%5bgtype%5d" ref="pagearea=body&amp;targetsite=external&amp;targetcat=link&amp;targettype=uri">example</a>), and eFetch to retrieve the genotype report to get the population information. You can find additional report examples on the <a href="/projects/SNP/SNPeutils.htm" ref="pagearea=body&amp;targetsite=external&amp;targetcat=link&amp;targettype=uri">&#x0201c;Eutils for EntrezSNP&#x0201d; page</a>.</p><p>(<b>11/17/08</b>)</p></blockquote></div></div><div id="FTP_Eutils.eSearch"><h2 id="_FTP_Eutils_eSearch_">eSearch</h2><div><h4 id="FTP_Eutils.will_the_hgvs_based_variation">Will the HGVS based variation search you are testing also be available through eutils?</h4><blockquote><p>Yes, it should also be available through eutils once we have finished developing the resource (<b>9/27/07</b>)</p></blockquote></div><div><h4 id="FTP_Eutils.if_i_query_esearch_for_all_sn">If I query eSearch for all SNPs that hit on chromosome 1 in the 1 to 6000 bp range, I get 11 hits, but if I search our local MSSQL directly, I get 115 hits. Why the difference? How do I get the same results that I got from Entrez by using a direct SQL query, and vice versa?</h4><blockquote><p>The answer to your first question is that Entrez only returns SNPs that clearly map once to the current genome build, while a direct SQL query will deliver SNPs that map more than once.</p><p>To get the same results that are returned by Entrez by using a direct SQL query, that is, to get an refSNP (rs) number with "clear", or as we call it, a "unique" map hit, please see the Database Dictionary description for <a href="/SNP/snp_db_table_description.cgi?t=SNPContigLoc" ref="pagearea=body&amp;targetsite=external&amp;targetcat=link&amp;targettype=uri">SNPContigLoc</a>, and for <a href="/SNP/snp_db_table_description.cgi?t=SNPMapInfo" ref="pagearea=body&amp;targetsite=external&amp;targetcat=link&amp;targettype=uri">SNPMAPInfo</a> (look for the weight information in SNPMAPInfo).</p><p>To get the same results that were delivered by SQL using an Entrez query is not really possible. When a SNP maps to multiple locations on multiple chromosomes, Entrez indexes the SNP as chrMulti. So if I use your example of finding SNPs with hits on chromosome1 in the 1:6000 bp range, you will find in SNPContigLoc all SNPs (including those with weight higher than 1) that hit in the 1:6000 range.</p><p>But if you use Entrez, however, you will find only weight 1 SNPs (weight 1 represents SNPs that align at exactly one locus) that hit chromosome 1 in the 1:6000 range. SNPs that are weight 2 (weight 2 represents SNPs that align at two loci on same chromosome) are not indexed in Entrez, so you will not find the same number of SNPs that hit chromosome 1 in the 1:6000 range using Entrez as you do using a direct SQL query. <b>(8/27/07)</b></p></blockquote></div></div><div id="FTP_Eutils.XML_Format_for_eutils"><h2 id="_FTP_Eutils_XML_Format_for_eutils_">XML Format for eutils</h2><div><h4 id="FTP_Eutils.why_does_dbsnp_have_two_diffe">Why does dbSNP have two different XML formats (one for the file and one for data for Eutils) for SNP entries?</h4><blockquote><p>We have plans to merge the two XML schemas in the near future. As for the schema merge it will be done some time this year. As we have a lot of ongoing projects currently, I&#x02019;m unable to be specific about when this will be accomplished. (<b>2/5/07</b>)</p></blockquote></div><div><h4 id="FTP_Eutils.i_m_using_the_command__http_e">I&#x02019;m using the command &#x0201c;http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=snp&#x00026;rettype=genxml&#x00026;id=$marker&#x0201d; to extract freq info from dbSNP, but can&#x02019;t get well formed XML.</h4><blockquote><p>Please add &#x0201c;retmode=text&#x0201d; (no quotes) to the command: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=snp&#x00026;rettype=genxml&#x00026;id=3000&#x00026;retmode=text (<b>09/05/08</b>)</p></blockquote></div></div><div id="bk_toc_contnr"></div></div></div>
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