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197 lines
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XML
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<html xmlns="http://www.w3.org/1999/xhtml">
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<head><meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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<title>Batch Entrez</title>
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<link rel="stylesheet" href="/corehtml/ncbi_test.css" />
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<script type="text/javascript" src="/core/jquery/jquery-3.6.0.min.js"> </script>
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<script type="text/javascript">
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jQuery.getScript("/core/alerts/alerts.js", function () {
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galert(['table'])
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});
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</script>
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<style type="text/css">
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body { color: black; background-color: white; }
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a:link { color: #03c; }
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a:visited { color: #c30; }
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table#header { width: 100%; border: none; border-collapse: collapse; border-spacing: 0; }
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li {margin-bottom: 0.75em; }
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</style>
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<link rel="shortcut icon" href="//www.ncbi.nlm.nih.gov/favicon.ico" /><meta name="ncbi_phid" content="CE8D73EC7C7F15410000000000E400BF.m_4" /><script type="text/javascript"><!--
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"children":[{"name":"BatchEntrez.GenPage","type":"Cluster","realname":"BatchEntrez.GenPage",
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"children":[{"name":"BatchEntrez.GenPage.DbList","type":"Portlet","realname":"BatchEntrez.GenPage.DbList","shortname":"DbList"}]}]};
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--></script>
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<meta name='referrer' content='origin-when-cross-origin'/><script type="text/javascript">
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var ObjectLinks=[{i:0, ename: "p$ExL", esid:"*", sname: "p$ExL", ssid:"*", dname:"p$el", dsid:"0",m:"CopyValue",p:[],f: function(src, dst) {fn_CopyValue(src, dst);}}]
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var ActiveNames = {"p$ExL":1};
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</script></head>
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<body>
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<form action="/portal/utils/batchentrez_p.cgi" method="POST" name="BATCH" enctype="multipart/form-data" id="BATCH">
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<!-- the header; start of first table -->
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<table id="header">
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<tr>
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<!-- logo -->
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<td>
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<table width="100%" border="0" cellpadding="0" cellspacing="0">
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<tr>
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<td align="left"><a href="/"><img src="/corehtml/left.GIF" width="130" height="45" border="0" alt="NCBI" /></a>
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</td>
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<td align="left"><!--@logo@-->
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<font size="+3" face="Arial, Helvetica, sans-serif">Batch
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Entrez</font>
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</td>
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</tr>
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</table>
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</td>
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</tr>
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<tr>
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<!--site map-->
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<td>
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<div><table class="TEXT" border="0" cellspacing="0" cellpadding="2" bgcolor="#000000" width="100%" id="toolbar">
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<tr class="TEXT" align="center">
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<td><a href="/sites/gquery?itool=toolbar" class="GUTTER3"><font color="#FFFFFF">All Databases</font></a></td>
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<td><a href="/pubmed?itool=toolbar" class="GUTTER3"><font color="#FFFFFF">PubMed</font></a></td>
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<td><a href="/nuccore?itool=toolbar" class="GUTTER3"><font color="#FFFFFF">Nucleotide</font></a></td>
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<td><a href="/protein?itool=toolbar" class="GUTTER3"><font color="#FFFFFF">Protein</font></a></td>
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<td><a href="/genome?itool=toolbar" class="GUTTER3"><font color="#FFFFFF">Genome</font></a></td>
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<td><a href="/structure?itool=toolbar" class="GUTTER3"><font color="#FFFFFF">Structure</font></a></td>
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<td><a href="/omim?itool=toolbar" class="GUTTER3"><font color="#FFFFFF">OMIM</font></a></td>
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<td><a href="/pmc/?itool=toolbar" class="GUTTER3"><font color="#FFFFFF">PMC</font></a></td>
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<td><a href="/books?itool=toolbar" class="GUTTER3"><font color="#FFFFFF">Books</font></a></td>
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</tr>
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</table>
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</div>
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</td>
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</tr>
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<tr>
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<!--query box-->
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<td>
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<table width="100%" border="0" bgcolor="#CCCCCC" cellspacing="0" cellpadding="1">
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<tr>
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<td class="SMALL1">Database <small><!--@DB_LIST@-->
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<select name="db"><option value="protein">Protein</option><option selected="selected" value="nuccore">Nucleotide</option><option value="ipg">Identical Protein Groups</option><option value="structure">Structure</option><option value="genome">Genome</option><option value="assembly">Assembly</option><option value="bioproject">BioProject</option><option value="biosample">BioSample</option><option value="books">Books</option><option value="cdd">Conserved Domains</option><option value="clinvar">ClinVar</option><option value="gap">dbGaP</option><option value="dbvar">dbVar</option><option value="gene">Gene</option><option value="gds">GEO DataSets</option><option value="geoprofiles">GEO Profiles</option><option value="medgen">MedGen</option><option value="mesh">MeSH</option><option value="nlmcatalog">NLM Catalog</option><option value="omim">OMIM</option><option value="pmc">PMC</option><option value="proteinclusters">Protein Clusters</option><option value="pcassay">PubChem BioAssay</option><option value="protfam">Protein Family Models</option><option value="pccompound">PubChem Compound</option><option value="pcsubstance">PubChem Substance</option><option value="snp">SNP</option><option value="sra">SRA</option><option value="taxonomy">Taxonomy</option><option value="biocollections">Biocollections</option><option value="toolkitall">ToolKitAll</option><option value="toolkitbookgh">ToolKitBookgh</option><option value="gtr">GTR</option></select>
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</small> File: <input type="file" name="file" value="" size="30" />
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<INPUT TYPE="submit" name="cmd" VALUE="Retrieve"></INPUT>
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</td>
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</tr>
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</table>
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</td>
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</tr>
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</table>
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<!--end of first table -->
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<!--start of 2nd table -->
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<table border="0" cellspacing="0" cellpadding="0" width="100%">
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<tr valign="TOP">
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<!-- right content column -->
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<td width="100%" bgcolor="#FFFFFF">
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<!-- -->
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<!-- -->
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<table BORDER="0" CELLSPACING="0" CELLPADDING="2" WIDTH="600">
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<tr>
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<td class="TEXT">
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<h2>Batch Entrez</h2>
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<p>Given a file of Entrez accession numbers or other
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identifiers, Batch Entrez downloads
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the corresponding records.
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</p>
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<h3>Instructions</h3>
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<ol>
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<li>Start with a local file containing a list of accession numbers or identifiers</li>
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<li>Select the database corresponding to the type of accession numbers
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or identifiers in your input file</li>
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<li> Use the <b>Browse</b> or <b>Choose File...</b> button to select the input file</li>
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<li>Press the <b>Retrieve</b> button to see a list
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of document summaries</li>
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<li>Select a format in which to display the data for
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viewing, and/or saving</li>
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<li> Select 'Send to file' to save the file.</li>
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</ol>
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<h3>Tips</h3>
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<ul>
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<li>To download entire genome records, check the NCBI FTP site, instead of using Batch Entrez.</li>
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<li>Some lists of record identifiers can be tens
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of thousands of lines long, so Batch Entrez may not retrieve
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all records from one list. Split the list of identifiers
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into smaller files using a file splitting software or a file
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split command at the command prompt in UNIX or LINUX
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systems. </li>
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<li>When loading large numbers of genome records, put several thousand record identifiers per file,
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one per line, left-adjusted.</li>
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<li>Please note that Batch Entrez will check for duplicate
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identifiers when reporting results from a list that you have
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imported.</li>
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<li>When retrieving a list of Nucleotide
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accessions, you must select the specific component database
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from which the accessions or GIs were saved. For Nucleotide,
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choose either the CoreNucleotide, the EST or the GSS
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selection from the database menu. If you have a mixed list
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of nucleotide accessions or UIDs, you will need to run the
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Batch Entrez search three times. Select the database from
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the pull-down menu, CoreNucleotide, EST, and GSS separately.
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</li>
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<li>In all cases, be certain to select the
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database that corresponds to the identifiers you
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are uploading. For example, if you have
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saved a list of protein accession numbers, be sure to select the Protein
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database.
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</li>
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</ul>
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</td>
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</tr>
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</table>
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</td>
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<!-- end of right content column -->
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</tr>
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</table>
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<!-- end of content -->
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<input type="hidden" name="p$a" id="p$a" /><input type="hidden" name="p$l" id="p$l" value="BatchEntrez" /><input type="hidden" name="p$st" id="p$st" value="batchentrez" /><input name="SessionId" id="SessionId" value="CE8B5AF87C7FFCB1_0191SID" disabled="disabled" type="hidden" /><input name="Snapshot" id="Snapshot" value="/projects/entrez/BatchEntrez/BatchEntrez@1.15" disabled="disabled" type="hidden" /></form>
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<!-- @footer@ -->
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<div class="medium1">
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<center>
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<a href="mailto:info@ncbi.nlm.nih.gov">Write to the Help Desk</a><br />
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<a href="/">NCBI</a> | <a href="http://www.nlm.nih.gov">NLM</a> | <a href="http://www.nih.gov">NIH</a><br />
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<a href="http://www.dhhs.gov/">Department of Health & Human Services</a><br />
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<a href="http://www.nlm.nih.gov/privacy.html">Privacy Statement</a> | <a href="http://www.nih.gov/icd/od/foia/index.htm">Freedom of Information Act</a> |
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<a href="/About/disclaimer.html">Disclaimer</a>
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</center>
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</div>
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<script type="text/javascript">
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<!-- host:<@HOST@> -->
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<!-- CE8B5AF87C7FFCB1_0191SID /projects/entrez/BatchEntrez/BatchEntrez@1.15 portal106 v4.1.r689238 Tue, Oct 22 2024 16:10:51 -->
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<script type='text/javascript' src='/portal/js/portal.js'></script></body>
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</html> |