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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"><html xmlns="http://www.w3.org/1999/xhtml"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8" /><title>refdb-pubmed</title><link rel="stylesheet" type="text/css" href="manual.css" /><meta name="generator" content="DocBook XSL Stylesheets V1.78.1" /><link rel="home" href="index.html" title="RefDB handbook" /><link rel="up" href="ch14.html#idp69978912" title="Tools" /><link rel="prev" href="re16.html" title="med2ris" /><link rel="next" href="re18.html" title="refdb_dos2unix" /></head><body><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">refdb-pubmed</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="re16.html">Prev</a> </td><th width="60%" align="center">Tools</th><td width="20%" align="right"> <a accesskey="n" href="re18.html">Next</a></td></tr></table><hr /></div><div class="refentry"><a id="refentry-refdb-pubmed"></a><div class="titlepage"></div><div class="refnamediv"><a id="refdb-pubmed-name"></a><h2>Name</h2><p>refdb-pubmed — retrieves an XML representation of Pubmed (http://pubmed.org) entries by their Pubmed IDs</p></div><div class="refsynopsisdiv"><a id="refdb-pubmed-synopsis"></a><h2>Synopsis</h2><div class="cmdsynopsis"><p><code class="command">refdb-pubmed</code> [-d <em class="replaceable"><code>database</code></em>] [-h ] [-m <em class="replaceable"><code>mode</code></em>] [-t <em class="replaceable"><code>type</code></em>] [PMID...]</p></div></div><div class="refsect1"><a id="refdb-pubmed-description"></a><h2>Description</h2><p>refdb-pubmed retrieves datasets from the Pubmed database using the <a class="ulink" href="http://eutils.ncbi.nlm.nih.gov/corehtml/query/static/efetchlit_help.html" target="_top">efetch utility</a>. refdb-pubmed reads Pubmed IDs (PMIDs) either as parameters from the command line, or on stdin. Input data should contain PMIDs separated by non-digits (spaces, tabs, newlines, commas,...). All results are written to stdout.</p></div><div class="refsect1"><a id="refdb-pubmed-options"></a><h2>Options</h2><div class="variablelist"><dl class="variablelist"><dt><span class="term"><code class="option">-d</code> <em class="replaceable"><code>database</code></em></span></dt><dd><p>Specify the Pubmed database to query. Allowed values are <span class="emphasis"><em>pubmed</em></span>, <span class="emphasis"><em>pmc</em></span>, <span class="emphasis"><em>journals</em></span>, or <span class="emphasis"><em>omim</em></span>. Default is pubmed.</p></dd><dt><span class="term"><code class="option">-h</code></span></dt><dd><p>Displays help and usage screen, then exits.</p></dd><dt><span class="term"><code class="option">-m</code> <em class="replaceable"><code>mode</code></em></span></dt><dd><p>Specify the retrieval mode. Allowed values are <span class="emphasis"><em>xml</em></span>, <span class="emphasis"><em>html</em></span>, <span class="emphasis"><em>text</em></span>, and <span class="emphasis"><em>asn.1</em></span>. Default is xml.</p></dd><dt><span class="term"><code class="option">-t</code> <em class="replaceable"><code>type</code></em></span></dt><dd><p>Select the retrieval type. Allowed values are <span class="emphasis"><em>uilist</em></span>, <span class="emphasis"><em>abstract</em></span>, <span class="emphasis"><em>citation</em></span>, <span class="emphasis"><em>medline</em></span>, or <span class="emphasis"><em>full</em></span>. Default is full.</p></dd></dl></div></div><div class="refsect1"><a id="refdb-pubmed-see_also"></a><h2>See also</h2><p><span class="emphasis"><em>RefDB</em></span> (7),
<span class="emphasis"><em><a class="link" href="re16.html" title="med2ris">med2ris</a></em></span> (1).</p><p><span class="emphasis"><em>RefDB manual (local copy) </em></span> PREFIX/share/doc/refdb-<version>/refdb-manual/index.html</p><p><span class="emphasis"><em>RefDB manual (web) </em></span> <<a class="ulink" href="http://refdb.sourceforge.net/manual/index.html" target="_top">http://refdb.sourceforge.net/manual/index.html</a>></p><p><span class="emphasis"><em>RefDB on the web </em></span> <<a class="ulink" href="http://refdb.sourceforge.net/" target="_top">http://refdb.sourceforge.net/</a>></p></div><div class="refsect1"><a id="refdb-pubmed-author"></a><h2>Author</h2><p>refdb-pubmed was written by Markus Hoenicka <markus@mhoenicka.de>.</p></div></div><div class="navfooter"><hr /><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="re16.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="ch14.html#idp69978912">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="re18.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">med2ris </td><td width="20%" align="center"><a accesskey="h" href="index.html">Home</a></td><td width="40%" align="right" valign="top"> refdb_dos2unix</td></tr></table></div></body></html>
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