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Catalogue of life

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dr. M.S. (Matthijs) Berends
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@ -318,7 +318,7 @@ When using <code>allow_uncertain = TRUE</code> (which is the default setting), i
<li><p>It strips off values between brackets and the brackets itself, and re-evaluates the input with all previous rules</p></li>
<li><p>It strips off words from the end one by one and re-evaluates the input with all previous rules</p></li>
<li><p>It strips off words from the start one by one and re-evaluates the input with all previous rules</p></li>
<li><p>It tries to look for some manual changes which are not yet published to the ITIS database (like <em>Propionibacterium</em> not yet being <em>Cutibacterium</em>)</p></li>
<li><p>It tries to look for some manual changes which are not yet published to the Catalogue of Life (like <em>Propionibacterium</em> not yet being <em>Cutibacterium</em>)</p></li>
</ul>
<p>Examples:</p><ul>
<li><p><code>"Streptococcus group B (known as S. agalactiae)"</code>. The text between brackets will be removed and a warning will be thrown that the result <em>Streptococcus group B</em> (<code>B_STRPT_GRB</code>) needs review.</p></li>
@ -335,15 +335,22 @@ When using <code>allow_uncertain = TRUE</code> (which is the default setting), i
<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] 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>[3] Integrated Taxonomic Information System (ITIS). Retrieved September 2018. <a href='http://www.itis.gov'>http://www.itis.gov</a></p>
<p>[3] Catalogue of Life: Annual Checklist (public online database), <a href='www.catalogueoflife.org'>www.catalogueoflife.org</a>.</p>
<h2 class="hasAnchor" id="itis"><a class="anchor" href="#itis"></a>ITIS</h2>
<h2 class="hasAnchor" id="catalogue-of-life"><a class="anchor" href="#catalogue-of-life"></a>Catalogue of Life</h2>
<p><img src='figures/logo_itis.jpg' height=60px style=margin-bottom:5px /> <br />
This package contains the <strong>complete microbial taxonomic data</strong> (with all nine taxonomic ranks - from kingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, <a href='https://www.itis.gov'>https://www.itis.gov</a>).</p>
<p>All ~20,000 (sub)species from <strong>the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package</strong>, as well as all their ~2,500 previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since ITIS honours the taxonomic branching order of bacterial phyla according to Cavalier-Smith (2002), which defines that all bacteria are classified into either subkingdom Negibacteria or subkingdom Posibacteria.</p>
<p>ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3].</p>
<p><img src='figures/logo_col.png' height=60px style=margin-bottom:5px /> <br />
This package contains the complete taxonomic tree of almost all microorganisms from the authoritative and comprehensive Catalogue of Life (<a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). This data is updated annually - check the included version with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version</a></code>.</p>
<p>Included are:</p><ul>
<li><p>All ~55,000 (sub)species from the kingdoms of Archaea, Bacteria, Protozoa and Viruses</p></li>
<li><p>All ~3,000 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales and Schizosaccharomycetales. The kingdom of Fungi is a very large taxon with almost 300,000 different species, of which most are not microbial. Including everything tremendously slows down our algortihms, and not all fungi fit the scope of this package. By only including the aforementioned taxonomic orders, the most relevant species are covered (like genera <em>Aspergillus</em>, <em>Candida</em>, <em>Pneumocystis</em>, <em>Saccharomyces</em> and <em>Trichophyton</em>).</p></li>
<li><p>All ~15,000 previously accepted names of (sub)species that have been taxonomically renamed</p></li>
<li><p>The complete taxonomic tree of all included (sub)species: from kingdom to subspecies</p></li>
<li><p>The responsible author(s) and year of scientific publication</p></li>
</ul>
<p>The Catalogue of Life (<a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>) is the most comprehensive and authoritative global index of species currently available. It holds essential information on the names, relationships and distributions of over 1.6 million species. The Catalogue of Life is used to support the major biodiversity and conservation information services such as the Global Biodiversity Information Facility (GBIF), Encyclopedia of Life (EoL) and the International Union for Conservation of Nature Red List. It is recognised by the Convention on Biological Diversity as a significant component of the Global Taxonomy Initiative and a contribution to Target 1 of the Global Strategy for Plant Conservation.</p>
<p>The syntax used to transform the original data to a cleansed R format, can be found here: <a href='https://gitlab.com/msberends/AMR/blob/master/reproduction_of_microorganisms.R'>https://gitlab.com/msberends/AMR/blob/master/reproduction_of_microorganisms.R</a>.</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>
@ -353,7 +360,7 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
<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> for the <code>data.frame</code> with ITIS content that is being used to determine ID's. <br />
<div class='dont-index'><p><code><a href='microorganisms.html'>microorganisms</a></code> for the <code>data.frame</code> that is being used to determine ID's. <br />
The <code><a href='mo_property.html'>mo_property</a></code> functions (like <code><a href='mo_property.html'>mo_genus</a></code>, <code><a href='mo_property.html'>mo_gramstain</a></code>) to get properties based on the returned code.</p></div>
@ -418,7 +425,7 @@ The <code><a href='mo_property.html'>mo_property</a></code> functions (like <cod
<li><a href="#source">Source</a></li>
<li><a href="#itis">ITIS</a></li>
<li><a href="#catalogue-of-life">Catalogue of Life</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>

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<h1>The Catalogue of Life</h1>
<div class="hidden name"><code>catalogue_of_life.Rd</code></div>
</div>
<div class="ref-description">
<p>This package contains the complete taxonomic tree of almost all microorganisms from the authoritative and comprehensive Catalogue of Life.</p>
</div>
<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=60px style=margin-bottom:5px /> <br />
This package contains the complete taxonomic tree of almost all microorganisms from the authoritative and comprehensive Catalogue of Life (<a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). This data is updated annually - check the included version with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version</a></code>.</p>
<p>Included are:</p><ul>
<li><p>All ~55,000 (sub)species from the kingdoms of Archaea, Bacteria, Protozoa and Viruses</p></li>
<li><p>All ~3,000 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales and Schizosaccharomycetales. The kingdom of Fungi is a very large taxon with almost 300,000 different species, of which most are not microbial. Including everything tremendously slows down our algortihms, and not all fungi fit the scope of this package. By only including the aforementioned taxonomic orders, the most relevant species are covered (like genera <em>Aspergillus</em>, <em>Candida</em>, <em>Pneumocystis</em>, <em>Saccharomyces</em> and <em>Trichophyton</em>).</p></li>
<li><p>All ~15,000 previously accepted names of (sub)species that have been taxonomically renamed</p></li>
<li><p>The complete taxonomic tree of all included (sub)species: from kingdom to subspecies</p></li>
<li><p>The responsible author(s) and year of scientific publication</p></li>
</ul>
<p>The Catalogue of Life (<a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>) is the most comprehensive and authoritative global index of species currently available. It holds essential information on the names, relationships and distributions of over 1.6 million species. The Catalogue of Life is used to support the major biodiversity and conservation information services such as the Global Biodiversity Information Facility (GBIF), Encyclopedia of Life (EoL) and the International Union for Conservation of Nature Red List. It is recognised by the Convention on Biological Diversity as a significant component of the Global Taxonomy Initiative and a contribution to Target 1 of the Global Strategy for Plant Conservation.</p>
<p>The syntax used to transform the original data to a cleansed R format, can be found here: <a href='https://gitlab.com/msberends/AMR/blob/master/reproduction_of_microorganisms.R'>https://gitlab.com/msberends/AMR/blob/master/reproduction_of_microorganisms.R</a>.</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><img src='figures/logo.png' height=40px style=margin-bottom:5px /> <br />
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>
<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'># Get version info of included data set</span>
<span class='fu'><a href='catalogue_of_life_version.html'>catalogue_of_life_version</a></span>()
<span class='co'># Get a note when a species was renamed</span>
<span class='fu'><a href='mo_property.html'>mo_shortname</a></span>(<span class='st'>"Chlamydia psittaci"</span>)
<span class='co'># Note: 'Chlamydia psittaci' (Page, 1968) was renamed</span>
<span class='co'># 'Chlamydophila psittaci' (Everett et al., 1999)</span>
<span class='co'># [1] "C. psittaci"</span>
<span class='co'># Get any property from the entire taxonomic tree for all included species</span>
<span class='fu'><a href='mo_property.html'>mo_class</a></span>(<span class='st'>"E. coli"</span>)
<span class='co'># [1] "Gammaproteobacteria"</span>
<span class='fu'><a href='mo_property.html'>mo_family</a></span>(<span class='st'>"E. coli"</span>)
<span class='co'># [1] "Enterobacteriaceae"</span>
<span class='fu'><a href='mo_property.html'>mo_gramstain</a></span>(<span class='st'>"E. coli"</span>) <span class='co'># based on kingdom and phylum, see ?mo_gramstain</span>
<span class='co'># [1] "Gram negative"</span>
<span class='fu'><a href='mo_property.html'>mo_ref</a></span>(<span class='st'>"E. coli"</span>)
<span class='co'># [1] "Castellani et al., 1919"</span>
<span class='co'># Do not get mistaken - the package only includes microorganisms</span>
<span class='fu'><a href='mo_property.html'>mo_phylum</a></span>(<span class='st'>"C. elegans"</span>)
<span class='co'># [1] "Cyanobacteria" # Bacteria?!</span>
<span class='fu'><a href='mo_property.html'>mo_fullname</a></span>(<span class='st'>"C. elegans"</span>)
<span class='co'># [1] "Chroococcus limneticus elegans" # Because a microorganism was found</span>
<span class='co'># }</span></pre>
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<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#catalogue-of-life">Catalogue of Life</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#examples">Examples</a></li>
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<h1>Version info of included Catalogue of Life</h1>
<div class="hidden name"><code>catalogue_of_life_version.Rd</code></div>
</div>
<div class="ref-description">
<p>Version info of included Catalogue of Life</p>
</div>
<pre class="usage"><span class='fu'>catalogue_of_life_version</span>()</pre>
<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=60px style=margin-bottom:5px /> <br />
This package contains the complete taxonomic tree of almost all microorganisms from the authoritative and comprehensive Catalogue of Life (<a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). This data is updated annually - check the included version with <code>catalogue_of_life_version</code>.</p>
<p>Included are:</p><ul>
<li><p>All ~55,000 (sub)species from the kingdoms of Archaea, Bacteria, Protozoa and Viruses</p></li>
<li><p>All ~3,000 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales and Schizosaccharomycetales. The kingdom of Fungi is a very large taxon with almost 300,000 different species, of which most are not microbial. Including everything tremendously slows down our algortihms, and not all fungi fit the scope of this package. By only including the aforementioned taxonomic orders, the most relevant species are covered (like genera <em>Aspergillus</em>, <em>Candida</em>, <em>Pneumocystis</em>, <em>Saccharomyces</em> and <em>Trichophyton</em>).</p></li>
<li><p>All ~15,000 previously accepted names of (sub)species that have been taxonomically renamed</p></li>
<li><p>The complete taxonomic tree of all included (sub)species: from kingdom to subspecies</p></li>
<li><p>The responsible author(s) and year of scientific publication</p></li>
</ul>
<p>The Catalogue of Life (<a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>) is the most comprehensive and authoritative global index of species currently available. It holds essential information on the names, relationships and distributions of over 1.6 million species. The Catalogue of Life is used to support the major biodiversity and conservation information services such as the Global Biodiversity Information Facility (GBIF), Encyclopedia of Life (EoL) and the International Union for Conservation of Nature Red List. It is recognised by the Convention on Biological Diversity as a significant component of the Global Taxonomy Initiative and a contribution to Target 1 of the Global Strategy for Plant Conservation.</p>
<p>The syntax used to transform the original data to a cleansed R format, can be found here: <a href='https://gitlab.com/msberends/AMR/blob/master/reproduction_of_microorganisms.R'>https://gitlab.com/msberends/AMR/blob/master/reproduction_of_microorganisms.R</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>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#catalogue-of-life">Catalogue of Life</a></li>
<li><a href="#see-also">See also</a></li>
</ul>
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</tr><tr>
<td>
<p><code><a href="ITIS.html">ITIS</a></code> </p>
<p><code><a href="catalogue_of_life.html">catalogue_of_life</a></code> </p>
</td>
<td><p>ITIS: Integrated Taxonomic Information System</p></td>
<td><p>The Catalogue of Life</p></td>
</tr><tr>
<td>
<p><code><a href="catalogue_of_life_version.html">catalogue_of_life_version()</a></code> </p>
</td>
<td><p>Version info of included Catalogue of Life</p></td>
</tr><tr>
<td>
@ -349,7 +355,7 @@
</tr><tr>
<td>
<p><code><a href="mo_property.html">mo_fullname()</a></code> <code><a href="mo_property.html">mo_shortname()</a></code> <code><a href="mo_property.html">mo_subspecies()</a></code> <code><a href="mo_property.html">mo_species()</a></code> <code><a href="mo_property.html">mo_genus()</a></code> <code><a href="mo_property.html">mo_family()</a></code> <code><a href="mo_property.html">mo_order()</a></code> <code><a href="mo_property.html">mo_class()</a></code> <code><a href="mo_property.html">mo_phylum()</a></code> <code><a href="mo_property.html">mo_subkingdom()</a></code> <code><a href="mo_property.html">mo_kingdom()</a></code> <code><a href="mo_property.html">mo_type()</a></code> <code><a href="mo_property.html">mo_gramstain()</a></code> <code><a href="mo_property.html">mo_ref()</a></code> <code><a href="mo_property.html">mo_authors()</a></code> <code><a href="mo_property.html">mo_year()</a></code> <code><a href="mo_property.html">mo_taxonomy()</a></code> <code><a href="mo_property.html">mo_property()</a></code> </p>
<p><code><a href="mo_property.html">mo_fullname()</a></code> <code><a href="mo_property.html">mo_shortname()</a></code> <code><a href="mo_property.html">mo_subspecies()</a></code> <code><a href="mo_property.html">mo_species()</a></code> <code><a href="mo_property.html">mo_genus()</a></code> <code><a href="mo_property.html">mo_family()</a></code> <code><a href="mo_property.html">mo_order()</a></code> <code><a href="mo_property.html">mo_class()</a></code> <code><a href="mo_property.html">mo_phylum()</a></code> <code><a href="mo_property.html">mo_kingdom()</a></code> <code><a href="mo_property.html">mo_type()</a></code> <code><a href="mo_property.html">mo_gramstain()</a></code> <code><a href="mo_property.html">mo_ref()</a></code> <code><a href="mo_property.html">mo_authors()</a></code> <code><a href="mo_property.html">mo_year()</a></code> <code><a href="mo_property.html">mo_taxonomy()</a></code> <code><a href="mo_property.html">mo_url()</a></code> <code><a href="mo_property.html">mo_property()</a></code> </p>
</td>
<td><p>Property of a microorganism</p></td>
</tr><tr>

19
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@ -250,13 +250,20 @@
<dt><code>mo</code></dt><dd><p>ID of the microorganism in the <code><a href='microorganisms.html'>microorganisms</a></code> data set</p></dd>
</dl>
<h2 class="hasAnchor" id="itis"><a class="anchor" href="#itis"></a>ITIS</h2>
<h2 class="hasAnchor" id="catalogue-of-life"><a class="anchor" href="#catalogue-of-life"></a>Catalogue of Life</h2>
<p><img src='figures/logo_itis.jpg' height=60px style=margin-bottom:5px /> <br />
This package contains the <strong>complete microbial taxonomic data</strong> (with all nine taxonomic ranks - from kingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, <a href='https://www.itis.gov'>https://www.itis.gov</a>).</p>
<p>All ~20,000 (sub)species from <strong>the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package</strong>, as well as all their ~2,500 previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since ITIS honours the taxonomic branching order of bacterial phyla according to Cavalier-Smith (2002), which defines that all bacteria are classified into either subkingdom Negibacteria or subkingdom Posibacteria.</p>
<p>ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3].</p>
<p><img src='figures/logo_col.png' height=60px style=margin-bottom:5px /> <br />
This package contains the complete taxonomic tree of almost all microorganisms from the authoritative and comprehensive Catalogue of Life (<a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). This data is updated annually - check the included version with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version</a></code>.</p>
<p>Included are:</p><ul>
<li><p>All ~55,000 (sub)species from the kingdoms of Archaea, Bacteria, Protozoa and Viruses</p></li>
<li><p>All ~3,000 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales and Schizosaccharomycetales. The kingdom of Fungi is a very large taxon with almost 300,000 different species, of which most are not microbial. Including everything tremendously slows down our algortihms, and not all fungi fit the scope of this package. By only including the aforementioned taxonomic orders, the most relevant species are covered (like genera <em>Aspergillus</em>, <em>Candida</em>, <em>Pneumocystis</em>, <em>Saccharomyces</em> and <em>Trichophyton</em>).</p></li>
<li><p>All ~15,000 previously accepted names of (sub)species that have been taxonomically renamed</p></li>
<li><p>The complete taxonomic tree of all included (sub)species: from kingdom to subspecies</p></li>
<li><p>The responsible author(s) and year of scientific publication</p></li>
</ul>
<p>The Catalogue of Life (<a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>) is the most comprehensive and authoritative global index of species currently available. It holds essential information on the names, relationships and distributions of over 1.6 million species. The Catalogue of Life is used to support the major biodiversity and conservation information services such as the Global Biodiversity Information Facility (GBIF), Encyclopedia of Life (EoL) and the International Union for Conservation of Nature Red List. It is recognised by the Convention on Biological Diversity as a significant component of the Global Taxonomy Initiative and a contribution to Target 1 of the Global Strategy for Plant Conservation.</p>
<p>The syntax used to transform the original data to a cleansed R format, can be found here: <a href='https://gitlab.com/msberends/AMR/blob/master/reproduction_of_microorganisms.R'>https://gitlab.com/msberends/AMR/blob/master/reproduction_of_microorganisms.R</a>.</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>
@ -276,7 +283,7 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
<li><a href="#format">Format</a></li>
<li><a href="#itis">ITIS</a></li>
<li><a href="#catalogue-of-life">Catalogue of Life</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>

50
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@ -245,27 +245,26 @@
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
<p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 56,659 observations and 15 variables:</p><dl class='dl-horizontal'>
<dt><code>mo</code></dt><dd><p>ID of microorganism</p></dd>
<p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 56,672 observations and 14 variables:</p><dl class='dl-horizontal'>
<dt><code>mo</code></dt><dd><p>ID of microorganism as used by this package</p></dd>
<dt><code>col_id</code></dt><dd><p>Catalogue of Life ID</p></dd>
<dt><code>genus</code></dt><dd><p>Taxonomic genus of the microorganism as found in ITIS, see Source</p></dd>
<dt><code>species</code></dt><dd><p>Taxonomic species of the microorganism as found in ITIS, see Source</p></dd>
<dt><code>subspecies</code></dt><dd><p>Taxonomic subspecies of the microorganism as found in ITIS, see Source</p></dd>
<dt><code>fullname</code></dt><dd><p>Full name, like <code>"Echerichia coli"</code></p></dd>
<dt><code>family</code></dt><dd><p>Taxonomic family of the microorganism as found in ITIS, see Source</p></dd>
<dt><code>order</code></dt><dd><p>Taxonomic order of the microorganism as found in ITIS, see Source</p></dd>
<dt><code>class</code></dt><dd><p>Taxonomic class of the microorganism as found in ITIS, see Source</p></dd>
<dt><code>phylum</code></dt><dd><p>Taxonomic phylum of the microorganism as found in ITIS, see Source</p></dd>
<dt><code>subkingdom</code></dt><dd><p>Taxonomic subkingdom of the microorganism as found in ITIS, see Source</p></dd>
<dt><code>kingdom</code></dt><dd><p>Taxonomic kingdom of the microorganism as found in ITIS, see Source</p></dd>
<dt><code>gramstain</code></dt><dd><p>Gram of microorganism, like <code>"Gram negative"</code></p></dd>
<dt><code>prevalence</code></dt><dd><p>An integer based on estimated prevalence of the microorganism in humans. Used internally by <code><a href='as.mo.html'>as.mo</a></code>, otherwise quite meaningless. It has a value of 25 for manually added items and a value of 1000 for all unprevalent microorganisms whose genus was somewhere in the top 250 (with another species).</p></dd>
<dt><code>ref</code></dt><dd><p>Author(s) and year of concerning publication as found in ITIS, see Source</p></dd>
<dt><code>kingdom</code></dt><dd><p>Taxonomic kingdom of the microorganism</p></dd>
<dt><code>phylum</code></dt><dd><p>Taxonomic phylum of the microorganism</p></dd>
<dt><code>class</code></dt><dd><p>Taxonomic class of the microorganism</p></dd>
<dt><code>order</code></dt><dd><p>Taxonomic order of the microorganism</p></dd>
<dt><code>family</code></dt><dd><p>Taxonomic family of the microorganism</p></dd>
<dt><code>genus</code></dt><dd><p>Taxonomic genus of the microorganism</p></dd>
<dt><code>species</code></dt><dd><p>Taxonomic species of the microorganism</p></dd>
<dt><code>subspecies</code></dt><dd><p>Taxonomic subspecies of the microorganism</p></dd>
<dt><code>rank</code></dt><dd><p>Taxonomic rank of the microorganism, like <code>"species"</code> or <code>"genus"</code></p></dd>
<dt><code>ref</code></dt><dd><p>Author(s) and year of concerning scientific publication</p></dd>
<dt><code>species_id</code></dt><dd><p>ID of the species as used by the Catalogue of Life</p></dd>
</dl>
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
<p>Integrated Taxonomic Information System (ITIS) public online database, <a href='https://www.itis.gov'>https://www.itis.gov</a>.</p>
<p>Catalogue of Life: Annual Checklist (public online database), <a href='www.catalogueoflife.org'>www.catalogueoflife.org</a>.</p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
@ -275,13 +274,20 @@
<li><p>2 other undefined (unknown Gram negatives and unknown Gram positives)</p></li>
</ul>
<h2 class="hasAnchor" id="itis"><a class="anchor" href="#itis"></a>ITIS</h2>
<h2 class="hasAnchor" id="catalogue-of-life"><a class="anchor" href="#catalogue-of-life"></a>Catalogue of Life</h2>
<p><img src='figures/logo_itis.jpg' height=60px style=margin-bottom:5px /> <br />
This package contains the <strong>complete microbial taxonomic data</strong> (with all nine taxonomic ranks - from kingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, <a href='https://www.itis.gov'>https://www.itis.gov</a>).</p>
<p>All ~20,000 (sub)species from <strong>the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package</strong>, as well as all their ~2,500 previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since ITIS honours the taxonomic branching order of bacterial phyla according to Cavalier-Smith (2002), which defines that all bacteria are classified into either subkingdom Negibacteria or subkingdom Posibacteria.</p>
<p>ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3].</p>
<p><img src='figures/logo_col.png' height=60px style=margin-bottom:5px /> <br />
This package contains the complete taxonomic tree of almost all microorganisms from the authoritative and comprehensive Catalogue of Life (<a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). This data is updated annually - check the included version with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version</a></code>.</p>
<p>Included are:</p><ul>
<li><p>All ~55,000 (sub)species from the kingdoms of Archaea, Bacteria, Protozoa and Viruses</p></li>
<li><p>All ~3,000 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales and Schizosaccharomycetales. The kingdom of Fungi is a very large taxon with almost 300,000 different species, of which most are not microbial. Including everything tremendously slows down our algortihms, and not all fungi fit the scope of this package. By only including the aforementioned taxonomic orders, the most relevant species are covered (like genera <em>Aspergillus</em>, <em>Candida</em>, <em>Pneumocystis</em>, <em>Saccharomyces</em> and <em>Trichophyton</em>).</p></li>
<li><p>All ~15,000 previously accepted names of (sub)species that have been taxonomically renamed</p></li>
<li><p>The complete taxonomic tree of all included (sub)species: from kingdom to subspecies</p></li>
<li><p>The responsible author(s) and year of scientific publication</p></li>
</ul>
<p>The Catalogue of Life (<a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>) is the most comprehensive and authoritative global index of species currently available. It holds essential information on the names, relationships and distributions of over 1.6 million species. The Catalogue of Life is used to support the major biodiversity and conservation information services such as the Global Biodiversity Information Facility (GBIF), Encyclopedia of Life (EoL) and the International Union for Conservation of Nature Red List. It is recognised by the Convention on Biological Diversity as a significant component of the Global Taxonomy Initiative and a contribution to Target 1 of the Global Strategy for Plant Conservation.</p>
<p>The syntax used to transform the original data to a cleansed R format, can be found here: <a href='https://gitlab.com/msberends/AMR/blob/master/reproduction_of_microorganisms.R'>https://gitlab.com/msberends/AMR/blob/master/reproduction_of_microorganisms.R</a>.</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>
@ -291,7 +297,7 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
<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> <code><a href='microorganisms.codes.html'>microorganisms.codes</a></code></p></div>
<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>, <code><a href='microorganisms.codes.html'>microorganisms.codes</a></code></p></div>
</div>
@ -305,7 +311,7 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
<li><a href="#details">Details</a></li>
<li><a href="#itis">ITIS</a></li>
<li><a href="#catalogue-of-life">Catalogue of Life</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>

29
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@ -47,7 +47,7 @@
<script src="../extra.js"></script>
<meta property="og:title" content="Data set with previously accepted taxonomic names — microorganisms.old" />
<meta property="og:description" content="A data set containing old (previously valid or accepted) taxonomic names according to ITIS. This data set is used internally by as.mo." />
<meta property="og:description" content="A data set containing old (previously valid or accepted) taxonomic names according to the Catalogue of Life. This data set is used internally by as.mo." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
<meta name="twitter:card" content="summary" />
@ -237,7 +237,7 @@
<div class="ref-description">
<p>A data set containing old (previously valid or accepted) taxonomic names according to ITIS. This data set is used internally by <code><a href='as.mo.html'>as.mo</a></code>.</p>
<p>A data set containing old (previously valid or accepted) taxonomic names according to the Catalogue of Life. This data set is used internally by <code><a href='as.mo.html'>as.mo</a></code>.</p>
</div>
@ -248,21 +248,28 @@
<p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 14,506 observations and 4 variables:</p><dl class='dl-horizontal'>
<dt><code>col_id</code></dt><dd><p>Catalogue of Life ID</p></dd>
<dt><code>tsn_new</code></dt><dd><p>New Catalogue of Life ID</p></dd>
<dt><code>fullname</code></dt><dd><p>Old taxonomic name of the microorganism as found in the CoL, see Source</p></dd>
<dt><code>ref</code></dt><dd><p>Author(s) and year of concerning publication as found in the CoL, see Source</p></dd>
<dt><code>fullname</code></dt><dd><p>Old taxonomic name of the microorganism</p></dd>
<dt><code>ref</code></dt><dd><p>Author(s) and year of concerning scientific publication</p></dd>
</dl>
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
<p>[3] Integrated Taxonomic Information System (ITIS) on-line database, <a href='https://www.itis.gov'>https://www.itis.gov</a>.</p>
<p>[3] Catalogue of Life: Annual Checklist (public online database), <a href='www.catalogueoflife.org'>www.catalogueoflife.org</a>.</p>
<h2 class="hasAnchor" id="itis"><a class="anchor" href="#itis"></a>ITIS</h2>
<h2 class="hasAnchor" id="catalogue-of-life"><a class="anchor" href="#catalogue-of-life"></a>Catalogue of Life</h2>
<p><img src='figures/logo_itis.jpg' height=60px style=margin-bottom:5px /> <br />
This package contains the <strong>complete microbial taxonomic data</strong> (with all nine taxonomic ranks - from kingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, <a href='https://www.itis.gov'>https://www.itis.gov</a>).</p>
<p>All ~20,000 (sub)species from <strong>the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package</strong>, as well as all their ~2,500 previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since ITIS honours the taxonomic branching order of bacterial phyla according to Cavalier-Smith (2002), which defines that all bacteria are classified into either subkingdom Negibacteria or subkingdom Posibacteria.</p>
<p>ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3].</p>
<p><img src='figures/logo_col.png' height=60px style=margin-bottom:5px /> <br />
This package contains the complete taxonomic tree of almost all microorganisms from the authoritative and comprehensive Catalogue of Life (<a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). This data is updated annually - check the included version with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version</a></code>.</p>
<p>Included are:</p><ul>
<li><p>All ~55,000 (sub)species from the kingdoms of Archaea, Bacteria, Protozoa and Viruses</p></li>
<li><p>All ~3,000 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales and Schizosaccharomycetales. The kingdom of Fungi is a very large taxon with almost 300,000 different species, of which most are not microbial. Including everything tremendously slows down our algortihms, and not all fungi fit the scope of this package. By only including the aforementioned taxonomic orders, the most relevant species are covered (like genera <em>Aspergillus</em>, <em>Candida</em>, <em>Pneumocystis</em>, <em>Saccharomyces</em> and <em>Trichophyton</em>).</p></li>
<li><p>All ~15,000 previously accepted names of (sub)species that have been taxonomically renamed</p></li>
<li><p>The complete taxonomic tree of all included (sub)species: from kingdom to subspecies</p></li>
<li><p>The responsible author(s) and year of scientific publication</p></li>
</ul>
<p>The Catalogue of Life (<a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>) is the most comprehensive and authoritative global index of species currently available. It holds essential information on the names, relationships and distributions of over 1.6 million species. The Catalogue of Life is used to support the major biodiversity and conservation information services such as the Global Biodiversity Information Facility (GBIF), Encyclopedia of Life (EoL) and the International Union for Conservation of Nature Red List. It is recognised by the Convention on Biological Diversity as a significant component of the Global Taxonomy Initiative and a contribution to Target 1 of the Global Strategy for Plant Conservation.</p>
<p>The syntax used to transform the original data to a cleansed R format, can be found here: <a href='https://gitlab.com/msberends/AMR/blob/master/reproduction_of_microorganisms.R'>https://gitlab.com/msberends/AMR/blob/master/reproduction_of_microorganisms.R</a>.</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>
@ -284,7 +291,7 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
<li><a href="#source">Source</a></li>
<li><a href="#itis">ITIS</a></li>
<li><a href="#catalogue-of-life">Catalogue of Life</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>

32
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View File

@ -259,8 +259,6 @@
<span class='fu'>mo_phylum</span>(<span class='no'>x</span>, <span class='no'>...</span>)
<span class='fu'>mo_subkingdom</span>(<span class='no'>x</span>, <span class='no'>...</span>)
<span class='fu'>mo_kingdom</span>(<span class='no'>x</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='get_locale.html'>get_locale</a></span>(), <span class='no'>...</span>)
@ -275,6 +273,8 @@
<span class='fu'>mo_taxonomy</span>(<span class='no'>x</span>, <span class='no'>...</span>)
<span class='fu'>mo_url</span>(<span class='no'>x</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='get_locale.html'>get_locale</a></span>(), <span class='no'>...</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
@ -310,31 +310,40 @@
<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 ITIS, except for <code>mo_ref</code>, <code>mo_authors</code> and <code>mo_year</code>. This leads to the following results:</p><ul>
<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_fullname("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 (ref: <a href='https://itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&amp;search_value=956097'>https://itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&amp;search_value=956097</a>). 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>The function <code>mo_url()</code> will return the direct URL to the species in the Catalogue of Life.</p>
<h2 class="hasAnchor" id="supported-languages"><a class="anchor" href="#supported-languages"></a>Supported languages</h2>
<p>Supported languages are <code>"en"</code> (English), <code>"de"</code> (German), <code>"nl"</code> (Dutch), <code>"es"</code> (Spanish), <code>"it"</code> (Italian), <code>"fr"</code> (French), and <code>"pt"</code> (Portuguese).</p>
<h2 class="hasAnchor" id="itis"><a class="anchor" href="#itis"></a>ITIS</h2>
<h2 class="hasAnchor" id="catalogue-of-life"><a class="anchor" href="#catalogue-of-life"></a>Catalogue of Life</h2>
<p><img src='figures/logo_itis.jpg' height=60px style=margin-bottom:5px /> <br />
This package contains the <strong>complete microbial taxonomic data</strong> (with all nine taxonomic ranks - from kingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, <a href='https://www.itis.gov'>https://www.itis.gov</a>).</p>
<p>All ~20,000 (sub)species from <strong>the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package</strong>, as well as all their ~2,500 previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since ITIS honours the taxonomic branching order of bacterial phyla according to Cavalier-Smith (2002), which defines that all bacteria are classified into either subkingdom Negibacteria or subkingdom Posibacteria.</p>
<p>ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3].</p>
<p><img src='figures/logo_col.png' height=60px style=margin-bottom:5px /> <br />
This package contains the complete taxonomic tree of almost all microorganisms from the authoritative and comprehensive Catalogue of Life (<a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). This data is updated annually - check the included version with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version</a></code>.</p>
<p>Included are:</p><ul>
<li><p>All ~55,000 (sub)species from the kingdoms of Archaea, Bacteria, Protozoa and Viruses</p></li>
<li><p>All ~3,000 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales and Schizosaccharomycetales. The kingdom of Fungi is a very large taxon with almost 300,000 different species, of which most are not microbial. Including everything tremendously slows down our algortihms, and not all fungi fit the scope of this package. By only including the aforementioned taxonomic orders, the most relevant species are covered (like genera <em>Aspergillus</em>, <em>Candida</em>, <em>Pneumocystis</em>, <em>Saccharomyces</em> and <em>Trichophyton</em>).</p></li>
<li><p>All ~15,000 previously accepted names of (sub)species that have been taxonomically renamed</p></li>
<li><p>The complete taxonomic tree of all included (sub)species: from kingdom to subspecies</p></li>
<li><p>The responsible author(s) and year of scientific publication</p></li>
</ul>
<p>The Catalogue of Life (<a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>) is the most comprehensive and authoritative global index of species currently available. It holds essential information on the names, relationships and distributions of over 1.6 million species. The Catalogue of Life is used to support the major biodiversity and conservation information services such as the Global Biodiversity Information Facility (GBIF), Encyclopedia of Life (EoL) and the International Union for Conservation of Nature Red List. It is recognised by the Convention on Biological Diversity as a significant component of the Global Taxonomy Initiative and a contribution to Target 1 of the Global Strategy for Plant Conservation.</p>
<p>The syntax used to transform the original data to a cleansed R format, can be found here: <a href='https://gitlab.com/msberends/AMR/blob/master/reproduction_of_microorganisms.R'>https://gitlab.com/msberends/AMR/blob/master/reproduction_of_microorganisms.R</a>.</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] 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>[3] Integrated Taxonomic Information System (ITIS). Retrieved September 2018. <a href='http://www.itis.gov'>http://www.itis.gov</a></p>
<p>[3] Catalogue of Life: Annual Checklist (public online database), <a href='www.catalogueoflife.org'>www.catalogueoflife.org</a>.</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>
@ -352,14 +361,13 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
<span class='co'># All properties of Escherichia coli</span>
<span class='co'>## taxonomic properties</span>
<span class='fu'>mo_kingdom</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Bacteria"</span>
<span class='fu'>mo_subkingdom</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Negibacteria"</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'># NA</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_fullname</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Escherichia coli"</span>
@ -440,7 +448,7 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
<li><a href="#supported-languages">Supported languages</a></li>
<li><a href="#itis">ITIS</a></li>
<li><a href="#catalogue-of-life">Catalogue of Life</a></li>
<li><a href="#source">Source</a></li>