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<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Data set with 67,108 microorganisms — microorganisms • AMR (for R)</title>
<title>Data set with 67,150 microorganisms — microorganisms • AMR (for R)</title>
<!-- favicons -->
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
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<link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script>
<meta property="og:title" content="Data set with 67,108 microorganisms — microorganisms" />
<meta property="og:title" content="Data set with 67,150 microorganisms — microorganisms" />
<meta property="og:description" content="A data set containing the microbial taxonomy of six kingdoms from the Catalogue of Life. MO codes can be looked up using as.mo()." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
</span>
</div>
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</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
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<a href="https://github.com/msberends/AMR">
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<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Data set with 67,108 microorganisms</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
<h1>Data set with 67,150 microorganisms</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
<div class="hidden name"><code>microorganisms.Rd</code></div>
</div>
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<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
<p>A <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with 67,108 observations and 16 variables:</p><ul>
<p>A <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with 67,150 observations and 16 variables:</p><ul>
<li><p><code>mo</code><br /> ID of microorganism as used by this package</p></li>
<li><p><code>fullname</code><br /> Full name, like <code>"Escherichia coli"</code></p></li>
<li><p><code>kingdom</code>, <code>phylum</code>, <code>class</code>, <code>order</code>, <code>family</code>, <code>genus</code>, <code>species</code>, <code>subspecies</code><br /> Taxonomic rank of the microorganism</p></li>
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<li><p>1 entry of <em>Blastocystis</em> (<em>Blastocystis hominis</em>), although it officially does not exist (Noel <em>et al.</em> 2005, PMID 15634993)</p></li>
<li><p>5 other 'undefined' entries (unknown, unknown Gram negatives, unknown Gram positives, unknown yeast and unknown fungus)</p></li>
<li><p>6 families under the Enterobacterales order, according to Adeolu <em>et al.</em> (2016, PMID 27620848), that are not (yet) in the Catalogue of Life</p></li>
<li><p>7,369 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) since the DSMZ contain the latest taxonomic information based on recent publications</p></li>
<li><p>7,411 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) since the DSMZ contain the latest taxonomic information based on recent publications</p></li>
</ul>
<h3>Direct download</h3>
<p>This data set is available as 'flat file' for use even without R - you can find the file here:</p><ul>
<li><p><a href='https://gitlab.com/msberends/AMR/raw/master/data-raw/microorganisms.txt'>https://gitlab.com/msberends/AMR/raw/master/data-raw/microorganisms.txt</a></p></li>
<li><p><a href='https://github.com/msberends/AMR/raw/master/data-raw/microorganisms.txt'>https://github.com/msberends/AMR/raw/master/data-raw/microorganisms.txt</a></p></li>
</ul>
<p>The file in R format (with preserved data structure) can be found here:</p><ul>
<li><p><a href='https://gitlab.com/msberends/AMR/raw/master/data/microorganisms.rda'>https://gitlab.com/msberends/AMR/raw/master/data/microorganisms.rda</a></p></li>
<li><p><a href='https://github.com/msberends/AMR/raw/master/data/microorganisms.rda'>https://github.com/msberends/AMR/raw/master/data/microorganisms.rda</a></p></li>
</ul>
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<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code><a href='as.mo.html'>as.mo()</a></code>, <code><a href='mo_property.html'>mo_property()</a></code>, <a href='microorganisms.codes.html'>microorganisms.codes</a></p></div>