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<img src="../logo.svg" class="logo" alt=""><h1>The Catalogue of Life</h1>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/catalogue_of_life.R" class="external-link"><code>R/catalogue_of_life.R</code></a></small>
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<div class="d-none name"><code>catalogue_of_life.Rd</code></div>
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<div class="ref-description section level2">
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<p>This package contains the complete taxonomic tree (last updated: 5 October 2021) of almost all microorganisms from the authoritative and comprehensive Catalogue of Life (CoL), supplemented with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN).</p>
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<div class="section level2">
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<h2 id="catalogue-of-life">Catalogue of Life<a class="anchor" aria-label="anchor" href="#catalogue-of-life"></a></h2>
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<p><img src="figures/logo_col.png" height="40" style='margin-bottom:"5"'><br>
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This package contains the complete taxonomic tree of almost all microorganisms (~71,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, <a href="http://www.catalogueoflife.org" class="external-link">http://www.catalogueoflife.org</a>). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, <a href="https://lpsn.dsmz.de" class="external-link">lpsn.dsmz.de</a>). This supplementation is needed until the <a href="https://github.com/CatalogueOfLife/general" class="external-link">CoL+ project</a> is finished, which we await.</p>
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<p>Click here for more information about the included taxa. Check which versions of the CoL and LPSN were included in this package with <code><a href="catalogue_of_life_version.html">catalogue_of_life_version()</a></code>.</p>
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</div>
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<div class="section level2">
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<h2 id="included-taxa">Included Taxa<a class="anchor" aria-label="anchor" href="#included-taxa"></a></h2>
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<p>Included are:</p><ul><li><p>All ~58,000 (sub)species from the kingdoms of Archaea, Bacteria, Chromista and Protozoa</p></li>
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<li><p>All ~5,000 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Microascales, Mucorales, Onygenales, Pneumocystales, Saccharomycetales, Schizosaccharomycetales and Tremellales, as well as ~4,600 other fungal (sub)species. The kingdom of Fungi is a very large taxon with almost 300,000 different (sub)species, of which most are not microbial (but rather macroscopic, like mushrooms). Because of this, not all fungi fit the scope of this package and including everything would tremendously slow down our algorithms too. By only including the aforementioned taxonomic orders, the most relevant fungi are covered (such as all species of <em>Aspergillus</em>, <em>Candida</em>, <em>Cryptococcus</em>, <em>Histplasma</em>, <em>Pneumocystis</em>, <em>Saccharomyces</em> and <em>Trichophyton</em>).</p></li>
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<li><p>All ~2,200 (sub)species from ~50 other relevant genera from the kingdom of Animalia (such as <em>Strongyloides</em> and <em>Taenia</em>)</p></li>
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<li><p>All ~14,000 previously accepted names of all included (sub)species (these were taxonomically renamed)</p></li>
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<li><p>The complete taxonomic tree of all included (sub)species: from kingdom to subspecies</p></li>
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<li><p>The responsible author(s) and year of scientific publication</p></li>
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</ul><p>The Catalogue of Life (<a href="http://www.catalogueoflife.org" class="external-link">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 1.9 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>
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<p>The syntax used to transform the original data to a cleansed <span style="R">R</span> format, can be found here: <a href="https://github.com/msberends/AMR/blob/main/data-raw/reproduction_of_microorganisms.R" class="external-link">https://github.com/msberends/AMR/blob/main/data-raw/reproduction_of_microorganisms.R</a>.</p>
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</div>
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<div class="section level2">
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<h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
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<div class="dont-index"><p>Data set <a href="microorganisms.html">microorganisms</a> for the actual data. <br>
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Function <code><a href="as.mo.html">as.mo()</a></code> to use the data for intelligent determination of microorganisms.</p></div>
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</div>
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<div class="section level2">
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<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># Get version info of included data set</span></span></span>
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<span class="r-in"><span><span class="fu"><a href="catalogue_of_life_version.html">catalogue_of_life_version</a></span><span class="op">(</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> Included in this AMR package (v1.8.1.9030) are:</span>
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<span class="r-out co"><span class="r-pr">#></span> </span>
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<span class="r-out co"><span class="r-pr">#></span> Catalogue of Life: 2019 Annual Checklist</span>
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<span class="r-out co"><span class="r-pr">#></span> Available at: http://www.catalogueoflife.org</span>
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<span class="r-out co"><span class="r-pr">#></span> Number of included microbial species: 49,029</span>
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<span class="r-out co"><span class="r-pr">#></span> List of Prokaryotic names with Standing in Nomenclature (5 October 2021)</span>
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<span class="r-out co"><span class="r-pr">#></span> Available at: https://lpsn.dsmz.de</span>
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<span class="r-out co"><span class="r-pr">#></span> Number of included bacterial species: 21,701</span>
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<span class="r-out co"><span class="r-pr">#></span> </span>
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<span class="r-out co"><span class="r-pr">#></span> => Total number of species included: 70,764</span>
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<span class="r-out co"><span class="r-pr">#></span> => Total number of synonyms included: 14,338</span>
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<span class="r-out co"><span class="r-pr">#></span> </span>
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<span class="r-out co"><span class="r-pr">#></span> See for more info `?microorganisms` and `?catalogue_of_life`.</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># Get a note when a species was renamed</span></span></span>
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<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_shortname</a></span><span class="op">(</span><span class="st">"Chlamydophila psittaci"</span><span class="op">)</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Chlamydophila psittaci (Everett et al. , 1999) was renamed back to</span>
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<span class="r-msg co"><span class="r-pr">#></span> Chlamydia psittaci (Page, 1968) [B_CHLMY_PSTT]</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "C. psittaci"</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># Get any property from the entire taxonomic tree for all included species</span></span></span>
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<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_class</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
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<span class="r-msg co"><span class="r-pr">#></span> coli). Run `mo_uncertainties()` to review this.</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Gammaproteobacteria"</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_family</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
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<span class="r-msg co"><span class="r-pr">#></span> coli). Run `mo_uncertainties()` to review this.</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Enterobacteriaceae"</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># based on kingdom and phylum, see ?mo_gramstain</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
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<span class="r-msg co"><span class="r-pr">#></span> coli). Run `mo_uncertainties()` to review this.</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Gram-negative"</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_ref</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
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<span class="r-msg co"><span class="r-pr">#></span> coli). Run `mo_uncertainties()` to review this.</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Castellani et al., 1919"</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># Do not get mistaken - this package is about microorganisms</span></span></span>
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<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_kingdom</a></span><span class="op">(</span><span class="st">"C. elegans"</span><span class="op">)</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Function `as.mo()` is uncertain about "C. elegans" (assuming Cladosporium</span>
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<span class="r-msg co"><span class="r-pr">#></span> elegans). Run `mo_uncertainties()` to review this.</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Fungi"</span>
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<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"C. elegans"</span><span class="op">)</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Function `as.mo()` is uncertain about "C. elegans" (assuming Cladosporium</span>
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<span class="r-msg co"><span class="r-pr">#></span> elegans). Run `mo_uncertainties()` to review this.</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Cladosporium elegans"</span>
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</code></pre></div>
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<p></p><p><code>AMR</code> (for R). Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> in collaboration with non-profit organisations<br><a target="_blank" href="https://www.certe.nl" class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p>
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<p></p><p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_rug.png" style="max-width: 200px;"></a></p>
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