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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>med2ris</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="re15.html" title="marc2ris" /><link rel="next" href="re17.html" title="refdb-pubmed" /></head><body><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">med2ris</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="re15.html">Prev</a> </td><th width="60%" align="center">Tools</th><td width="20%" align="right"> <a accesskey="n" href="re17.html">Next</a></td></tr></table><hr /></div><div class="refentry"><a id="refentry-med2ris"></a><div class="titlepage"></div><div class="refnamediv"><a id="name"></a><h2>Name</h2><p>med2ris — converts Medline/Pubmed bibliographic data to the RIS format</p></div><div class="refsynopsisdiv"><a id="synopsis"></a><h2>Synopsis</h2><div class="cmdsynopsis"><p><code class="command">med2ris</code> [-e <em class="replaceable"><code>logdest</code></em>] [-f <em class="replaceable"><code>from-encoding</code></em>] [-h ] [-i ] [-l <em class="replaceable"><code>loglevel</code></em>] [-L <em class="replaceable"><code>logfile</code></em>] [-o <em class="replaceable"><code>file</code></em>] [-O <em class="replaceable"><code>file</code></em>] [-q ] [-t <em class="replaceable"><code>to-encoding</code></em>] [-T <em class="replaceable"><code>type</code></em>] [-y <em class="replaceable"><code>path</code></em>]</p></div></div><div class="refsect1"><a id="med2ris-description"></a><h2>Description</h2><p>med2ris converts Pubmed reference data into RIS data. The converter understands both the tagged Pubmed format (which superficially resembles RIS) and the XML format according to the <a class="ulink" href="http://www.ncbi.nlm.nih.gov/entrez/query/DTD/pubmed_020114.dtd" target="_top">PubMedArticle DTD</a>. In most cases med2ris is able to automatically detect the input data type.</p></div><div class="refsect1"><a id="med2ris-options"></a><h2>Options</h2><div class="variablelist"><dl class="variablelist"><dt><span class="term"><code class="option">-e</code> <em class="replaceable"><code>log-destination</code></em></span></dt><dd><p>log-destination can have the values 0, 1, or 2, or the equivalent strings <span class="emphasis"><em>stderr</em></span>, <span class="emphasis"><em>syslog</em></span>, or <span class="emphasis"><em>file</em></span>, respectively. This value specifies where the log information goes to. <code class="literal">0</code> (zero) means the messages are sent to stderr. They are immediately available on the screen but they may interfere with command output. <code class="literal">1</code> will send the output to the syslog facility. Keep in mind that syslog must be configured to accept log messages from user programs, see the syslog(8) man page for further information. Unix-like systems usually save these messages in <code class="filename">/var/log/user.log</code>. <code class="literal">2</code> will send the messages to a custom log file which can be specified with the <code class="option">-L</code> option.</p></dd><dt><span class="term"><code class="option">-f</code> <em class="replaceable"><code>from-encoding</code></em></span></dt><dd><p>Select the input character encoding. Supported encodings are platform-dependent and can usually be found in iconv_open(3). If no encodings are specified, <span class="emphasis"><em>ISO-8859-1</em></span> aka Latin-1 is assumed.</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">-i</code></span></dt><dd><p>Output additional information about unknown or unused tags. Mainly useful to debug the conversion if the input format has changed.</p></dd><dt><span class="term"><code class="option">-l</code> <em class="replaceable"><code>log-level</code></em></span></dt><dd><p>Specify the priority up to which events are logged. This is either a number between <code class="literal">0</code> and <code class="literal">7</code> or one of the strings <span class="emphasis"><em>emerg</em></span>, <span class="emphasis"><em>alert</em></span>, <span class="emphasis"><em>crit</em></span>, <span class="emphasis"><em>err</em></span>, <span class="emphasis"><em>warning</em></span>, <span class="emphasis"><em>notice</em></span>, <span class="emphasis"><em>info</em></span>, <span class="emphasis"><em>debug</em></span>, respectively (see also Log level definitions). <code class="option">-1</code> disables logging completely. A low log level like <code class="literal">0</code> means that only the most critical messages are logged. A higher log level means that less critical events are logged as well. <code class="literal">7</code> will include debug messages. The latter can be verbose and abundant, so you want to avoid this log level unless you need to track down problems.</p></dd><dt><span class="term"><code class="option">-L</code> <em class="replaceable"><code>log-file</code></em></span></dt><dd><p>Specify the full path to a log file that will receive the log messages. Typically this would be <code class="filename">/var/log/refdba</code>.</p></dd><dt><span class="term"><code class="option">-o</code> <em class="replaceable"><code>file</code></em></span></dt><dd><p>Send output to <span class="emphasis"><em>file</em></span>. If <span class="emphasis"><em>file</em></span> exists, its contents will be overwritten.</p></dd><dt><span class="term"><code class="option">-O</code> <em class="replaceable"><code>file</code></em></span></dt><dd><p>Send output to <span class="emphasis"><em>file</em></span>. If <span class="emphasis"><em>file</em></span> exists, the output will be appended.</p></dd><dt><span class="term"><code class="option">-q</code></span></dt><dd><p>Start without reading the configuration files. The client will use the compile-time defaults for all values that you do not set with command-line switches.</p></dd><dt><span class="term"><code class="option">-t</code> <em class="replaceable"><code>to-encoding</code></em></span></dt><dd><p>Select the output character encoding. Supported encodings are platform-dependent and can usually be found in iconv_open(3). If no encodings are specified, <span class="emphasis"><em>ISO-8859-1</em></span> aka Latin-1 is assumed.</p></dd><dt><span class="term"><code class="option">-T</code> <em class="replaceable"><code>type</code></em></span></dt><dd><p>Overrides the automatic type detection. Allowed values for <em class="replaceable"><code>type</code></em> are "tag" and "xml" for the tagged Pubmed format and the XML Pubmed format, respectively.</p></dd><dt><span class="term"><code class="option">-y</code> <em class="replaceable"><code>confdir</code></em></span></dt><dd><p>Specify the directory where the global configuration files are
Note: By default, all RefDB applications look for their configuration files in a directory that is specified during the configure step when building the package. That is, you don't need the <code class="option">-y</code> option unless you use precompiled binaries in unusual locations, e.g. by relocating a rpm package.</p></dd></dl></div></div><div class="refsect1"><a id="med2ris-configuration"></a><h2>Configuration</h2><p><span class="command"><strong>med2ris</strong></span> evaluates the file <code class="filename">med2risrc</code> to initialize itself.</p><div class="table"><a id="idp74374592"></a><p class="title"><strong>Table 14.6. med2risrc</strong></p><div class="table-contents"><table summary="med2risrc" border="1"><colgroup><col /><col /><col /></colgroup><thead><tr><th>Variable</th><th>Default</th><th>Comment</th></tr></thead><tbody><tr><td>outfile</td><td>(none)</td><td>The default output file name.</td></tr><tr><td>outappend</td><td>t</td><td>Determines whether output is appended (<em class="replaceable"><code>t</code></em>) to an existing file or overwrites (<em class="replaceable"><code>f</code></em>) an existing file.</td></tr><tr><td>unmapped</td><td>t</td><td>If set to <em class="replaceable"><code>t</code></em>, unknown tags in the input data will be output following a <unmapped> tag; the resulting data can be inspected and then be sent through <span class="command"><strong>sed</strong></span> to strip off these additional lines. If set to <em class="replaceable"><code>f</code></em>, unknown tags will be gracefully ignored.</td></tr><tr><td>from_enc</td><td>ISO-8859-1</td><td>The character encoding of the input data</td></tr><tr><td>to_enc</td><td>ISO-8859-1</td><td>The character encoding of the output data</td></tr><tr><td>logfile</td><td>/var/log/med2ris.log</td><td>The full path of a custom log file. This is used only if logdest is set appropriately.</td></tr><tr><td>logdest</td><td>1</td><td>The destination of the log information. 0 = print to stderr; 1 = use the syslog facility; 2 = use a custom logfile. The latter needs a proper setting of logfile.</td></tr><tr><td>loglevel</td><td>6</td><td>The log level up to which messages will be sent. A low setting (0) allows only the most important messages, a high setting (7) allows all messages including debug messages. -1 means nothing will be logged.</td></tr></tbody></table></div></div><br class="table-break" /></div><div class="refsect1"><a id="med2ris-data-processing"></a><h2>Data Processing</h2><p>Keywords with multiple MeSH subheadings are split into multiple keywords with one MeSH subheading each. This simplifies searching for MeSH subheadings greatly.</p><p><span class="command"><strong>med2ris</strong></span> does not validate the input files. That is, the input files must stick to the rules of the data sources, otherwise the conversion results are not predictable.</p></div><div class="refsect1"><a id="med2ris-files"></a><h2>Files</h2><div class="variablelist"><dl class="variablelist"><dt><span class="term"><code class="filename">PREFIX/etc/refdb/med2risrc</code></span></dt><dd><p>The global configuration file of med2ris.</p></dd><dt><span class="term"><code class="filename">$HOME/.med2risrc</code></span></dt><dd><p>The user configuration file of med2ris.</p></dd></dl></div></div><div class="refsect1"><a id="med2ris-see_also"></a><h2>See also</h2><p><span class="emphasis"><em>RefDB</em></span> (7),
<span class="emphasis"><em><a class="link" href="re12.html" title="bib2ris">bib2ris</a></em></span> (1),
<span class="emphasis"><em><a class="link" href="re13.html" title="db2ris">db2ris</a></em></span> (1),
<span class="emphasis"><em><a class="link" href="re14.html" title="en2ris">en2ris</a></em></span> (1),
<span class="emphasis"><em><a class="link" href="re15.html" title="marc2ris">marc2ris</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="med2ris-author"></a><h2>Author</h2><p>med2ris 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="re15.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="re17.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">marc2ris </td><td width="20%" align="center"><a accesskey="h" href="index.html">Home</a></td><td width="40%" align="right" valign="top"> refdb-pubmed</td></tr></table></div></body></html>
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