<metaproperty="og:description"content="Use this function to determine a valid microorganism ID (mo). Determination is done using Artificial Intelligence (AI) and the complete taxonomic kingdoms Archaea, Bacteria, Protozoa, Viruses and most microbial species from the kingdom Fungi (see Source), so the input can be almost anything: a full name (like "Staphylococcus aureus"), an abbreviated name (like "S. aureus"), an abbreviation known in the field (like "MRSA"), or just a genus. You could also select a genus and species column, zie Examples."/>
<p>Use this function to determine a valid microorganism ID (<code>mo</code>). Determination is done using Artificial Intelligence (AI) and the complete taxonomic kingdoms Archaea, Bacteria, Protozoa, Viruses and most microbial species from the kingdom Fungi (see Source), so the input can be almost anything: a full name (like <code>"Staphylococcus aureus"</code>), an abbreviated name (like <code>"S. aureus"</code>), an abbreviation known in the field (like <code>"MRSA"</code>), or just a genus. You could also <code>select</code> a genus and species column, zie Examples.</p>
<td><p>a character vector or a <code>data.frame</code> with one or two columns</p></td>
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<th>Becker</th>
<td><p>a logical to indicate whether <em>Staphylococci</em> should be categorised into Coagulase Negative <em>Staphylococci</em> ("CoNS") and Coagulase Positive <em>Staphylococci</em> ("CoPS") instead of their own species, according to Karsten Becker <em>et al.</em> [1].</p>
<p>This excludes <em>Staphylococcus aureus</em> at default, use <code>Becker = "all"</code> to also categorise <em>S. aureus</em> as "CoPS".</p></td>
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<th>Lancefield</th>
<td><p>a logical to indicate whether beta-haemolytic <em>Streptococci</em> should be categorised into Lancefield groups instead of their own species, according to Rebecca C. Lancefield [2]. These <em>Streptococci</em> will be categorised in their first group, e.g. <em>Streptococcus dysgalactiae</em> will be group C, although officially it was also categorised into groups G and L.</p>
<p>This excludes <em>Enterococci</em> at default (who are in group D), use <code>Lancefield = "all"</code> to also categorise all <em>Enterococci</em> as group D.</p></td>
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<th>allow_uncertain</th>
<td><p>a logical to indicate whether the input should be checked for less possible results, see Details</p></td>
<td><p>a <code>data.frame</code> to use for extra reference when translating <code>x</code> to a valid <code>mo</code>. See <code><ahref='mo_source.html'>set_mo_source</a></code> and <code><ahref='mo_source.html'>get_mo_source</a></code> to automate the usage of your own codes (e.g. used in your analysis or organisation).</p></td>
<li><p>Human pathogenic prevalence: it first searches in more prevalent microorganisms, then less prevalent ones (see section <em>Microbial prevalence of pathogens in humans</em>)</p></li>
<li><p>Valid MO codes and full names: it first searches in already valid MO code and known genus/species combinations</p></li>
<li><p>Breakdown of input values: from here it starts to breakdown input values to find possible matches</p></li>
</ul>
<p>A couple of effects because of these rules:</p><ul>
<li><p><code>"E. coli"</code> will return the ID of <em>Escherichia coli</em> and not <em>Entamoeba coli</em>, although the latter would alphabetically come first</p></li>
<li><p><code>"H. influenzae"</code> will return the ID of <em>Haemophilus influenzae</em> and not <em>Haematobacter influenzae</em> for the same reason</p></li>
<li><p>Something like <code>"stau"</code> or <code>"S aur"</code> will return the ID of <em>Staphylococcus aureus</em> and not <em>Staphylococcus auricularis</em></p></li>
</ul><p>This means that looking up human pathogenic microorganisms takes less time than looking up human <strong>non</strong>-pathogenic microorganisms.</p>
When using <code>allow_uncertain = TRUE</code> (which is the default setting), it will use additional rules if all previous AI rules failed to get valid results. These are:</p><ul>
<li><p>It tries to look for previously accepted (but now invalid) taxonomic names</p></li>
<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 Catalogue of Life (like <em>Propionibacterium</em> being <em>Cutibacterium</em>)</p></li>
<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>
<li><p><code>"S. aureus - please mind: MRSA"</code>. The last word will be stripped, after which the function will try to find a match. If it does not, the second last word will be stripped, etc. Again, a warning will be thrown that the result <em>Staphylococcus aureus</em> (<code>B_STPHY_AUR</code>) needs review.</p></li>
<li><p><code>"Fluoroquinolone-resistant Neisseria gonorrhoeae"</code>. The first word will be stripped, after which the function will try to find a match. A warning will be thrown that the result <em>Neisseria gonorrhoeae</em> (<code>B_NESSR_GON</code>) needs review.</p></li>
<h2class="hasAnchor"id="microbial-prevalence-of-pathogens-in-humans"><aclass="anchor"href="#microbial-prevalence-of-pathogens-in-humans"></a>Microbial prevalence of pathogens in humans</h2>
<p>The artificial intelligence takes into account microbial prevalence of pathogens in humans. It uses three groups and every (sub)species is in the group it matches first. These groups are:</p><ul>
<li><p>1 (most prevalent): class is Gammaproteobacteria <strong>or</strong> genus is one of: <em>Enterococcus</em>, <em>Staphylococcus</em>, <em>Streptococcus</em>.</p></li>
<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. <ahref='https://dx.doi.org/10.1084/jem.57.4.571'>https://dx.doi.org/10.1084/jem.57.4.571</a></p>
<p>[3] Catalogue of Life: Annual Checklist (public online taxonomic database), <ahref='www.catalogueoflife.org'>www.catalogueoflife.org</a> (check included annual version with <code><ahref='catalogue_of_life_version.html'>catalogue_of_life_version</a>()</code>).</p>
This package contains the complete taxonomic tree of almost all microorganisms from the authoritative and comprehensive Catalogue of Life (<ahref='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). This data is updated annually - check the included version with <code><ahref='catalogue_of_life_version.html'>catalogue_of_life_version</a>()</code>.</p>
<li><p>All ~3,500 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales, Schizosaccharomycetales and Tremellales. This covers the most relevant microbial fungi (like 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>
<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 (<ahref='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: <ahref='https://gitlab.com/msberends/AMR/blob/master/reproduction_of_microorganisms.R'>https://gitlab.com/msberends/AMR/blob/master/reproduction_of_microorganisms.R</a>.</p>
<p>On our website <ahref='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <ahref='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <ahref='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <ahref='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<divclass='dont-index'><p><code><ahref='microorganisms.html'>microorganisms</a></code> for the <code>data.frame</code> that is being used to determine ID's. <br/>
The <code><ahref='mo_property.html'>mo_property</a></code> functions (like <code><ahref='mo_property.html'>mo_genus</a></code>, <code><ahref='mo_property.html'>mo_gramstain</a></code>) to get properties based on the returned code.</p></div>
<spanclass='fu'>as.mo</span>(<spanclass='st'>"S. epidermidis"</span>) <spanclass='co'># will remain species: B_STPHY_EPI</span>
<spanclass='fu'>as.mo</span>(<spanclass='st'>"S. epidermidis"</span>, <spanclass='kw'>Becker</span><spanclass='kw'>=</span><spanclass='fl'>TRUE</span>) <spanclass='co'># will not remain species: B_STPHY_CNS</span>
<spanclass='fu'>as.mo</span>(<spanclass='st'>"S. pyogenes"</span>) <spanclass='co'># will remain species: B_STRPT_PYO</span>
<spanclass='fu'>as.mo</span>(<spanclass='st'>"S. pyogenes"</span>, <spanclass='kw'>Lancefield</span><spanclass='kw'>=</span><spanclass='fl'>TRUE</span>) <spanclass='co'># will not remain species: B_STRPT_GRA</span>
<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/c.glasner/'>Corinna Glasner</a>, <ahref='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <ahref='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>.</p>
