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<h1>Property of a microorganism</h1>
<div class="hidden name"><code>mo_property.Rd</code></div>
</div>
<div class="ref-description">
<p>Use these functions to return a specific property of a microorganism from the <code><a href='microorganisms.html'>microorganisms</a></code> data set. All input values will be evaluated internally with <code><a href='as.mo.html'>as.mo</a></code>.</p>
</div>
<pre class="usage"><span class='fu'>mo_name</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
<span class='fu'>mo_fullname</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
<span class='fu'>mo_shortname</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
<span class='fu'>mo_subspecies</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
<span class='fu'>mo_species</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
<span class='fu'>mo_genus</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
<span class='fu'>mo_family</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
<span class='fu'>mo_order</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
<span class='fu'>mo_class</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
<span class='fu'>mo_phylum</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
<span class='fu'>mo_kingdom</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
<span class='fu'>mo_type</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
<span class='fu'>mo_gramstain</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
<span class='fu'>mo_ref</span>(<span class='no'>x</span>, <span class='no'>...</span>)
<span class='fu'>mo_authors</span>(<span class='no'>x</span>, <span class='no'>...</span>)
<span class='fu'>mo_year</span>(<span class='no'>x</span>, <span class='no'>...</span>)
<span class='fu'>mo_rank</span>(<span class='no'>x</span>, <span class='no'>...</span>)
<span class='fu'>mo_taxonomy</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
<span class='fu'>mo_url</span>(<span class='no'>x</span>, <span class='kw'>open</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)
<span class='fu'>mo_property</span>(<span class='no'>x</span>, <span class='kw'>property</span> <span class='kw'>=</span> <span class='st'>"fullname"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>x</th>
<td><p>any (vector of) text that can be coerced to a valid microorganism code with <code><a href='as.mo.html'>as.mo</a></code></p></td>
</tr>
<tr>
<th>language</th>
<td><p>language of the returned text, defaults to system language (see <code><a href='translate.html'>get_locale</a></code>) and can also be set with <code><a href='https://www.rdocumentation.org/packages/base/topics/options'>getOption</a>("AMR_locale")</code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></td>
</tr>
<tr>
<th>...</th>
<td><p>other parameters passed on to <code><a href='as.mo.html'>as.mo</a></code></p></td>
</tr>
<tr>
<th>open</th>
<td><p>browse the URL using <code><a href='https://www.rdocumentation.org/packages/utils/topics/browseURL'>browseURL</a>()</code></p></td>
</tr>
<tr>
<th>property</th>
<td><p>one of the column names of the <code><a href='microorganisms.html'>microorganisms</a></code> data set or <code>"shortname"</code></p></td>
</tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<ul>
<li><p>An <code>integer</code> in case of <code>mo_year</code></p></li>
<li><p>A <code>list</code> in case of <code>mo_taxonomy</code></p></li>
<li><p>A named <code>character</code> in case of <code>mo_url</code></p></li>
<li><p>A <code>character</code> in all other cases</p></li>
</ul>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>All functions will return the most recently known taxonomic property according to the Catalogue of Life, except for <code>mo_ref</code>, <code>mo_authors</code> and <code>mo_year</code>. This leads to the following results:</p><ul>
<li><p><code>mo_name("Chlamydia psittaci")</code> will return <code>"Chlamydophila psittaci"</code> (with a warning about the renaming)</p></li>
<li><p><code>mo_ref("Chlamydia psittaci")</code> will return <code>"Page, 1968"</code> (with a warning about the renaming)</p></li>
<li><p><code>mo_ref("Chlamydophila psittaci")</code> will return <code>"Everett et al., 1999"</code> (without a warning)</p></li>
</ul>
<p>The Gram stain - <code>mo_gramstain()</code> - will be determined on the taxonomic kingdom and phylum. According to Cavalier-Smith (2002) who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes. These bacteria are considered Gram positive - all other bacteria are considered Gram negative. Species outside the kingdom of Bacteria will return a value <code>NA</code>.</p>
<p>All output will be <a href='translate.html'>translate</a>d where possible.</p>
<p>The function <code>mo_url()</code> will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species.</p>
<h2 class="hasAnchor" id="catalogue-of-life"><a class="anchor" href="#catalogue-of-life"></a>Catalogue of Life</h2>
<p><img src='figures/logo_col.png' height=40px style=margin-bottom:5px /> <br />
This package contains the complete taxonomic tree of almost all microorganisms (~65,000 species) from the authoritative and comprehensive Catalogue of Life (<a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.</p>
<p><a href='catalogue_of_life.html'>Click here</a> for more information about the included taxa. The Catalogue of Life releases updates annually; check which version was included in this package with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version</a>()</code>.</p>
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
<p>[1] Becker K <em>et al.</em> <strong>Coagulase-Negative Staphylococci</strong>. 2014. Clin Microbiol Rev. 27(4): 870–926. <a href='https://dx.doi.org/10.1128/CMR.00109-13'>https://dx.doi.org/10.1128/CMR.00109-13</a></p>
<p>[2] Becker K <em>et al.</em> <strong>Implications of identifying the recently defined members of the <em>S. aureus</em> complex, <em>S. argenteus</em> and <em>S. schweitzeri</em>: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).</strong> 2019. Clin Microbiol Infect. <a href='https://doi.org/10.1016/j.cmi.2019.02.028'>https://doi.org/10.1016/j.cmi.2019.02.028</a></p>
<p>[3] Lancefield RC <strong>A serological differentiation of human and other groups of hemolytic streptococci</strong>. 1933. J Exp Med. 57(4): 571–95. <a href='https://dx.doi.org/10.1084/jem.57.4.571'>https://dx.doi.org/10.1084/jem.57.4.571</a></p>
<p>[4] Catalogue of Life: Annual Checklist (public online taxonomic database), <a href='www.catalogueoflife.org'>www.catalogueoflife.org</a> (check included annual version with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version</a>()</code>).</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
<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 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>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code><a href='microorganisms.html'>microorganisms</a></code></p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># NOT RUN {</span>
<span class='co'>## taxonomic tree</span>
<span class='fu'>mo_kingdom</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Bacteria"</span>
<span class='fu'>mo_phylum</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Proteobacteria"</span>
<span class='fu'>mo_class</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Gammaproteobacteria"</span>
<span class='fu'>mo_order</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Enterobacteriales"</span>
<span class='fu'>mo_family</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Enterobacteriaceae"</span>
<span class='fu'>mo_genus</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Escherichia"</span>
<span class='fu'>mo_species</span>(<span class='st'>"E. coli"</span>) <span class='co'># "coli"</span>
<span class='fu'>mo_subspecies</span>(<span class='st'>"E. coli"</span>) <span class='co'># ""</span>
<span class='co'>## colloquial properties</span>
<span class='fu'>mo_name</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Escherichia coli"</span>
<span class='fu'>mo_fullname</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Escherichia coli", same as mo_name()</span>
<span class='fu'>mo_shortname</span>(<span class='st'>"E. coli"</span>) <span class='co'># "E. coli"</span>
<span class='co'>## other properties</span>
<span class='fu'>mo_gramstain</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Gram negative"</span>
<span class='fu'>mo_type</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Bacteria" (equal to kingdom)</span>
<span class='fu'>mo_rank</span>(<span class='st'>"E. coli"</span>) <span class='co'># "species"</span>
<span class='fu'>mo_url</span>(<span class='st'>"E. coli"</span>) <span class='co'># get the direct url to the online database entry</span>
<span class='co'>## scientific reference</span>
<span class='fu'>mo_ref</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Castellani et al., 1919"</span>
<span class='fu'>mo_authors</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Castellani et al."</span>
<span class='fu'>mo_year</span>(<span class='st'>"E. coli"</span>) <span class='co'># 1919</span>
<span class='co'># Abbreviations known in the field</span>
<span class='fu'>mo_genus</span>(<span class='st'>"MRSA"</span>) <span class='co'># "Staphylococcus"</span>
<span class='fu'>mo_species</span>(<span class='st'>"MRSA"</span>) <span class='co'># "aureus"</span>
<span class='fu'>mo_shortname</span>(<span class='st'>"MRSA"</span>) <span class='co'># "S. aureus"</span>
<span class='fu'>mo_gramstain</span>(<span class='st'>"MRSA"</span>) <span class='co'># "Gram positive"</span>
<span class='fu'>mo_genus</span>(<span class='st'>"VISA"</span>) <span class='co'># "Staphylococcus"</span>
<span class='fu'>mo_species</span>(<span class='st'>"VISA"</span>) <span class='co'># "aureus"</span>
<span class='co'># Known subspecies</span>
<span class='fu'>mo_name</span>(<span class='st'>"doylei"</span>) <span class='co'># "Campylobacter jejuni doylei"</span>
<span class='fu'>mo_genus</span>(<span class='st'>"doylei"</span>) <span class='co'># "Campylobacter"</span>
<span class='fu'>mo_species</span>(<span class='st'>"doylei"</span>) <span class='co'># "jejuni"</span>
<span class='fu'>mo_subspecies</span>(<span class='st'>"doylei"</span>) <span class='co'># "doylei"</span>
<span class='fu'>mo_fullname</span>(<span class='st'>"K. pneu rh"</span>) <span class='co'># "Klebsiella pneumoniae rhinoscleromatis"</span>
<span class='fu'>mo_shortname</span>(<span class='st'>"K. pneu rh"</span>) <span class='co'># "K. pneumoniae"</span>
<span class='co'># Becker classification, see ?as.mo</span>
<span class='fu'>mo_fullname</span>(<span class='st'>"S. epi"</span>) <span class='co'># "Staphylococcus epidermidis"</span>
<span class='fu'>mo_fullname</span>(<span class='st'>"S. epi"</span>, <span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># "Coagulase-negative Staphylococcus (CoNS)"</span>
<span class='fu'>mo_shortname</span>(<span class='st'>"S. epi"</span>) <span class='co'># "S. epidermidis"</span>
<span class='fu'>mo_shortname</span>(<span class='st'>"S. epi"</span>, <span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># "CoNS"</span>
<span class='co'># Lancefield classification, see ?as.mo</span>
<span class='fu'>mo_fullname</span>(<span class='st'>"S. pyo"</span>) <span class='co'># "Streptococcus pyogenes"</span>
<span class='fu'>mo_fullname</span>(<span class='st'>"S. pyo"</span>, <span class='kw'>Lancefield</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># "Streptococcus group A"</span>
<span class='fu'>mo_shortname</span>(<span class='st'>"S. pyo"</span>) <span class='co'># "S. pyogenes"</span>
<span class='fu'>mo_shortname</span>(<span class='st'>"S. pyo"</span>, <span class='kw'>Lancefield</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># "GAS" ('Group A streptococci')</span>
<span class='co'># language support for German, Dutch, Spanish, Portuguese, Italian and French</span>
<span class='fu'>mo_gramstain</span>(<span class='st'>"E. coli"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='st'>"de"</span>) <span class='co'># "Gramnegativ"</span>
<span class='fu'>mo_gramstain</span>(<span class='st'>"E. coli"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='st'>"nl"</span>) <span class='co'># "Gram-negatief"</span>
<span class='fu'>mo_gramstain</span>(<span class='st'>"E. coli"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='st'>"es"</span>) <span class='co'># "Gram negativo"</span>
<span class='co'># mo_type is equal to mo_kingdom, but mo_kingdom will remain official</span>
<span class='fu'>mo_kingdom</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Bacteria" on a German system</span>
<span class='fu'>mo_type</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Bakterien" on a German system</span>
<span class='fu'>mo_type</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Bacteria" on an English system</span>
<span class='fu'>mo_fullname</span>(<span class='st'>"S. pyogenes"</span>,
<span class='kw'>Lancefield</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>language</span> <span class='kw'>=</span> <span class='st'>"de"</span>) <span class='co'># "Streptococcus Gruppe A"</span>
<span class='fu'>mo_fullname</span>(<span class='st'>"S. pyogenes"</span>,
<span class='kw'>Lancefield</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>language</span> <span class='kw'>=</span> <span class='st'>"nl"</span>) <span class='co'># "Streptococcus groep A"</span>
<span class='co'># get a list with the complete taxonomy (from kingdom to subspecies)</span>
<span class='fu'>mo_taxonomy</span>(<span class='st'>"E. coli"</span>)
<span class='co'># }</span></pre>
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