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<img src="../logo.svg" class="logo" alt=""><h1>Data Set with 52 171 Microorganisms</h1>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/data.R" class="external-link"><code>R/data.R</code></a></small>
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<div class="d-none name"><code>microorganisms.Rd</code></div>
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<div class="ref-description section level2">
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<p>A data set containing the full microbial taxonomy (<strong>last updated: January 8th, 2024</strong>) of five kingdoms from the List of Prokaryotic names with Standing in Nomenclature (LPSN) and the Global Biodiversity Information Facility (GBIF). This data set is the backbone of this <code>AMR</code> package. MO codes can be looked up using <code><a href="as.mo.html">as.mo()</a></code>.</p>
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</div>
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<div class="section level2">
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<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">microorganisms</span></span></code></pre></div>
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</div>
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<div class="section level2">
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<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
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<p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 52 171 observations and 23 variables:</p><ul><li><p><code>mo</code><br> ID of microorganism as used by this package. <em>This is a unique identifier.</em></p></li>
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<li><p><code>fullname</code><br> Full name, like <code>"Escherichia coli"</code>. For the taxonomic ranks genus, species and subspecies, this is the 'pasted' text of genus, species, and subspecies. For all taxonomic ranks higher than genus, this is the name of the taxon. <em>This is a unique identifier.</em></p></li>
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<li><p><code>status</code> <br> Status of the taxon, either "accepted" or "synonym"</p></li>
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<li><p><code>kingdom</code>, <code>phylum</code>, <code>class</code>, <code>order</code>, <code>family</code>, <code>genus</code>, <code>species</code>, <code>subspecies</code><br> Taxonomic rank of the microorganism</p></li>
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<li><p><code>rank</code><br> Text of the taxonomic rank of the microorganism, such as <code>"species"</code> or <code>"genus"</code></p></li>
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<li><p><code>ref</code><br> Author(s) and year of related scientific publication. This contains only the <em>first surname</em> and year of the <em>latest</em> authors, e.g. "Wallis <em>et al.</em> 2006 <em>emend.</em> Smith and Jones 2018" becomes "Smith <em>et al.</em>, 2018". This field is directly retrieved from the source specified in the column <code>source</code>. Moreover, accents were removed to comply with CRAN that only allows ASCII characters.</p></li>
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<li><p><code>lpsn</code><br> Identifier ('Record number') of the List of Prokaryotic names with Standing in Nomenclature (LPSN). This will be the first/highest LPSN identifier to keep one identifier per row. For example, <em>Acetobacter ascendens</em> has LPSN Record number 7864 and 11011. Only the first is available in the <code>microorganisms</code> data set.</p></li>
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<li><p><code>oxygen_tolerance</code> <br> Oxygen tolerance, either "aerobe", "anaerobe", "anaerobe/microaerophile", "facultative anaerobe", "likely facultative anaerobe", or "microaerophile". These data were retrieved from BacDive (see <em>Source</em>). Items that contain "likely" are missing from BacDive and were extrapolated from other species within the same genus to guess the oxygen tolerance. Currently 73.4% of all ~37 000 bacteria in the data set contain an oxygen tolerance.</p></li>
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<li><p><code>lpsn_parent</code><br> LPSN identifier of the parent taxon</p></li>
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<li><p><code>lpsn_renamed_to</code><br> LPSN identifier of the currently valid taxon</p></li>
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<li><p><code>gbif</code><br> Identifier ('taxonID') of the Global Biodiversity Information Facility (GBIF)</p></li>
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<li><p><code>gbif_parent</code><br> GBIF identifier of the parent taxon</p></li>
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<li><p><code>gbif_renamed_to</code><br> GBIF identifier of the currently valid taxon</p></li>
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<li><p><code>source</code><br> Either "GBIF", "LPSN", or "manually added" (see <em>Source</em>)</p></li>
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<li><p><code>prevalence</code><br> Prevalence of the microorganism based on Bartlett <em>et al.</em> (2022, <a href="https://doi.org/10.1099/mic.0.001269" class="external-link">doi:10.1099/mic.0.001269</a>
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), see <code><a href="mo_matching_score.html">mo_matching_score()</a></code> for the full explanation</p></li>
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<li><p><code>snomed</code><br> Systematized Nomenclature of Medicine (SNOMED) code of the microorganism, version of July 1st, 2021 (see <em>Source</em>). Use <code><a href="mo_property.html">mo_snomed()</a></code> to retrieve it quickly, see <code><a href="mo_property.html">mo_property()</a></code>.</p></li>
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</ul></div>
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<div class="section level2">
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<h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
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<ul><li><p>Parte, AC <em>et al.</em> (2020). <strong>List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ.</strong> International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; <a href="https://doi.org/10.1099/ijsem.0.004332" class="external-link">doi:10.1099/ijsem.0.004332</a>
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. Accessed from <a href="https://lpsn.dsmz.de" class="external-link">https://lpsn.dsmz.de</a> on December 11th, 2022.</p></li>
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<li><p>GBIF Secretariat (2023). GBIF Backbone Taxonomy. Checklist dataset <a href="https://doi.org/10.15468/39omei" class="external-link">doi:10.15468/39omei</a>
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. Accessed from <a href="https://www.gbif.org" class="external-link">https://www.gbif.org</a> on January 8th, 2024.</p></li>
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<li><p>Reimer, LC <em>et al.</em> (2022). <strong><em>BacDive</em> in 2022: the knowledge base for standardized bacterial and archaeal data.</strong> Nucleic Acids Res., 50(D1):D741-D74; <a href="https://doi.org/10.1093/nar/gkab961" class="external-link">doi:10.1093/nar/gkab961</a>
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. Accessed from <a href="https://bacdive.dsmz.de" class="external-link">https://bacdive.dsmz.de</a> on May 12th, 2023.</p></li>
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<li><p>Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020. Value Set Name 'Microorganism', OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href="https://phinvads.cdc.gov" class="external-link">https://phinvads.cdc.gov</a></p></li>
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<li><p>Grimont <em>et al.</em> (2007). Antigenic Formulae of the Salmonella Serovars, 9th Edition. WHO Collaborating Centre for Reference and Research on <em>Salmonella</em> (WHOCC-SALM).</p></li>
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<li><p>Bartlett <em>et al.</em> (2022). <strong>A comprehensive list of bacterial pathogens infecting humans</strong> <em>Microbiology</em> 168:001269; <a href="https://doi.org/10.1099/mic.0.001269" class="external-link">doi:10.1099/mic.0.001269</a></p></li>
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</ul></div>
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<div class="section level2">
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<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
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<p>Please note that entries are only based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) and the Global Biodiversity Information Facility (GBIF) (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>
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<p>For example, <em>Staphylococcus pettenkoferi</em> was described for the first time in Diagnostic Microbiology and Infectious Disease in 2002 (<a href="https://doi.org/10.1016/s0732-8893%2802%2900399-1" class="external-link">doi:10.1016/s0732-8893(02)00399-1</a>
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), but it was not before 2007 that a publication in IJSEM followed (<a href="https://doi.org/10.1099/ijs.0.64381-0" class="external-link">doi:10.1099/ijs.0.64381-0</a>
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). Consequently, the <code>AMR</code> package returns 2007 for <code>mo_year("S. pettenkoferi")</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 taxonomic data are:</p><ul><li><p>All ~37 000 (sub)species from the kingdoms of Archaea and Bacteria</p></li>
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<li><p>~7 900 (sub)species from the kingdom of Fungi. 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. Only relevant fungi are covered (such as all species of <em>Aspergillus</em>, <em>Candida</em>, <em>Cryptococcus</em>, <em>Histoplasma</em>, <em>Pneumocystis</em>, <em>Saccharomyces</em> and <em>Trichophyton</em>).</p></li>
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<li><p>~5 100 (sub)species from the kingdom of Protozoa</p></li>
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<li><p>~1 400 (sub)species from 43 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 ~9 800 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 identifier of the parent taxons</p></li>
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<li><p>The year and first author of the related scientific publication</p></li>
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</ul><div class="section">
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<h3 id="manual-additions">Manual additions<a class="anchor" aria-label="anchor" href="#manual-additions"></a></h3>
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<p>For convenience, some entries were added manually:</p><ul><li><p>~1 500 entries of <em>Salmonella</em>, such as the city-like serovars and groups A to H</p></li>
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<li><p>36 species groups (such as the beta-haemolytic <em>Streptococcus</em> groups A to K, coagulase-negative <em>Staphylococcus</em> (CoNS), <em>Mycobacterium tuberculosis</em> complex, etc.), of which the group compositions are stored in the <a href="microorganisms.groups.html">microorganisms.groups</a> data set</p></li>
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||
<li><p>1 entry of <em>Blastocystis</em> (<em>B. hominis</em>), although it officially does not exist (Noel <em>et al.</em> 2005, PMID 15634993)</p></li>
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||
<li><p>1 entry of <em>Moraxella</em> (<em>M. catarrhalis</em>), which was formally named <em>Branhamella catarrhalis</em> (Catlin, 1970) though this change was never accepted within the field of clinical microbiology</p></li>
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||
<li><p>8 other 'undefined' entries (unknown, unknown Gram-negatives, unknown Gram-positives, unknown yeast, unknown fungus, and unknown anaerobic Gram-pos/Gram-neg bacteria)</p></li>
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||
</ul><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">
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||
<h3 id="direct-download">Direct download<a class="anchor" aria-label="anchor" href="#direct-download"></a></h3>
|
||
|
||
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||
<p>Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. Please visit <a href="https://msberends.github.io/AMR/articles/datasets.html">our website for the download links</a>. The actual files are of course available on <a href="https://github.com/msberends/AMR/tree/main/data-raw" class="external-link">our GitHub repository</a>.</p>
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||
</div>
|
||
|
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</div>
|
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<div class="section level2">
|
||
<h2 id="about-the-records-from-lpsn-see-source-">About the Records from LPSN (see <em>Source</em>)<a class="anchor" aria-label="anchor" href="#about-the-records-from-lpsn-see-source-"></a></h2>
|
||
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<p>LPSN is the main source for bacteriological taxonomy of this <code>AMR</code> package.</p>
|
||
<p>The List of Prokaryotic names with Standing in Nomenclature (LPSN) provides comprehensive information on the nomenclature of prokaryotes. LPSN is a free to use service founded by Jean P. Euzeby in 1997 and later on maintained by Aidan C. Parte.</p>
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||
</div>
|
||
<div class="section level2">
|
||
<h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></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>, <a href="microorganisms.groups.html">microorganisms.groups</a>, <a href="microorganisms.codes.html">microorganisms.codes</a>, <a href="intrinsic_resistant.html">intrinsic_resistant</a></p></div>
|
||
</div>
|
||
|
||
<div class="section level2">
|
||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">microorganisms</span></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 52,171 × 23</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> mo fullname status kingdom phylum class order family genus</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> B_GRAMN (unknown Gra… accep… Bacter… (unkn… (unk… (unk… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un…</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> B_GRAMP (unknown Gra… accep… Bacter… (unkn… (unk… (unk… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un…</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> B_ANAER-NEG (unknown ana… accep… Bacter… (unkn… (unk… (unk… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un…</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> B_ANAER-POS (unknown ana… accep… Bacter… (unkn… (unk… (unk… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un…</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> B_ANAER (unknown ana… accep… Bacter… (unkn… (unk… (unk… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un…</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> F_FUNGUS (unknown fun… accep… Fungi (unkn… (unk… (unk… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un…</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> UNKNOWN (unknown nam… accep… (unkno… (unkn… (unk… (unk… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un…</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> F_YEAST (unknown yea… accep… Fungi (unkn… (unk… (unk… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un…</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> B_[FAM]_ABDTBCTR Abditibacter… accep… Bacter… Abdit… Abdi… Abdi… <span style="color: #949494;">"</span>Abdi… <span style="color: #949494;">""</span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> B_[ORD]_ABDTBCTR Abditibacter… accep… Bacter… Abdit… Abdi… Abdi… <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 52,161 more rows</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 14 more variables: species <chr>, subspecies <chr>, rank <chr>, ref <chr>,</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># oxygen_tolerance <chr>, source <chr>, lpsn <chr>, lpsn_parent <chr>,</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># lpsn_renamed_to <chr>, gbif <chr>, gbif_parent <chr>,</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># gbif_renamed_to <chr>, prevalence <dbl>, snomed <list></span></span>
|
||
</code></pre></div>
|
||
</div>
|
||
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|
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|
||
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|
||
<p></p><p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p>
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