<metaproperty="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()."/>
<p>A data set containing the microbial taxonomy of six kingdoms from the Catalogue of Life. MO codes can be looked up using <code><ahref='as.mo.html'>as.mo()</a></code>.</p>
<li><p><code>snomed</code><br/> SNOMED code of the microorganism. Use <code><ahref='mo_property.html'>mo_snomed()</a></code> to retrieve it quickly, see <code><ahref='mo_property.html'>mo_property()</a></code>.</p></li>
<p>Catalogue of Life: Annual Checklist (public online taxonomic database), <ahref='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a> (check included annual version with <code><ahref='catalogue_of_life_version.html'>catalogue_of_life_version()</a></code>).</p>
<p>Parte, A.C. (2018). LPSN — List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; doi: <ahref='https://doi.org/10.1099/ijsem.0.002786'>10.1099/ijsem.0.002786</a></p>
<p>Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Germany, Prokaryotic Nomenclature Up-to-Date, <ahref='https://www.dsmz.de/services/online-tools/prokaryotic-nomenclature-up-to-date'>https://www.dsmz.de/services/online-tools/prokaryotic-nomenclature-up-to-date</a> and <ahref='https://lpsn.dsmz.de'>https://lpsn.dsmz.de</a> (check included version with <code><ahref='catalogue_of_life_version.html'>catalogue_of_life_version()</a></code>).</p>
<p>Please note that entries are only based on the Catalogue of Life and the LPSN (see below). Since these sources incorporate entries based on (recent) publications in the International Journal of Systematic and Evolutionary Microbiology (IJSEM), it can happen that the year of publication is sometimes later than one might expect.</p>
<p>For example, <em>Staphylococcus pettenkoferi</em> was newly named in Diagnostic Microbiology and Infectious Disease in 2002 (PMID 12106949), but it was not before 2007 that a publication in IJSEM followed (PMID 17625191). Consequently, the AMR package returns 2007 for <code><ahref='mo_property.html'>mo_year("S. pettenkoferi")</a></code>.</p><h3class='hasAnchor'id='arguments'><aclass='anchor'href='#arguments'></a>Manually additions</h3>
<p>For convenience, some entries were added manually:</p><ul>
<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>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>7,411 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) since the DSMZ contain the latest taxonomic information based on recent publications</p></li>
<h2class="hasAnchor"id="about-the-records-from-dsmz-see-source-"><aclass="anchor"href="#about-the-records-from-dsmz-see-source-"></a>About the Records from DSMZ (see <em>Source</em>)</h2>
<p>Names of prokaryotes are defined as being validly published by the International Code of Nomenclature of Bacteria. Validly published are all names which are included in the Approved Lists of Bacterial Names and the names subsequently published in the International Journal of Systematic Bacteriology (IJSB) and, from January 2000, in the International Journal of Systematic and Evolutionary Microbiology (IJSEM) as original articles or in the validation lists.
This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, <ahref='http://www.catalogueoflife.org'>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, <ahref='https://lpsn.dsmz.de'>lpsn.dsmz.de</a>). This supplementation is needed until the <ahref='https://github.com/CatalogueOfLife/general'>CoL+ project</a> is finished, which we await.</p>
<p><ahref='catalogue_of_life.html'>Click here</a> for more information about the included taxa. Check which versions of the CoL and LSPN were included in this package with <code><ahref='catalogue_of_life_version.html'>catalogue_of_life_version()</a></code>.</p>
<h2class="hasAnchor"id="reference-data-publicly-available"><aclass="anchor"href="#reference-data-publicly-available"></a>Reference Data Publicly Available</h2>
<p>All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find <ahref='https://msberends.github.io/AMR/articles/datasets.html'>all download links on our website</a>, which is automatically updated with every code change.</p>
<p>On our website <ahref='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <ahref='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <ahref='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <ahref='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <ahref='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<p>Developed by <ahref='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <ahref='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <ahref='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <ahref='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <ahref='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <ahref='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
