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<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Data Set with 96 982 Taxonomic Records of Microorganisms — microorganisms • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="96x96" href="../favicon-96x96.png"><link rel="icon" type="”image/svg+xml”" href="../favicon.svg"><link rel="apple-touch-icon" sizes="180x180" href="../apple-touch-icon.png"><link rel="icon" sizes="any" href="../favicon.ico"><link rel="manifest" href="../site.webmanifest"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.8/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.8/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.10/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.10/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Data Set with 96 982 Taxonomic Records of Microorganisms — microorganisms"><meta name="description" content="A data set containing the full microbial taxonomy (last updated: 7th of May, 2026) of 15 kingdoms. This data set is the backbone of this AMR package. MO codes can be looked up using as.mo() and microorganism properties can be looked up using any of the mo_* functions.
This data set is carefully crafted, yet made 100% reproducible from public and authoritative taxonomic sources (using this script), namely: List of Prokaryotic names with Standing in Nomenclature (LPSN) for bacteria, MycoBank for fungi, and Global Biodiversity Information Facility (GBIF), via Catalogue of Life (COL) for all others taxons."><meta property="og:description" content="A data set containing the full microbial taxonomy (last updated: 7th of May, 2026) of 15 kingdoms. This data set is the backbone of this AMR package. MO codes can be looked up using as.mo() and microorganism properties can be looked up using any of the mo_* functions.
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Data Set with 96 982 Taxonomic Records of Microorganisms — microorganisms • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="96x96" href="../favicon-96x96.png"><link rel="icon" type="”image/svg+xml”" href="../favicon.svg"><link rel="apple-touch-icon" sizes="180x180" href="../apple-touch-icon.png"><link rel="icon" sizes="any" href="../favicon.ico"><link rel="manifest" href="../site.webmanifest"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.8/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.8/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.10/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.10/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Data Set with 96 982 Taxonomic Records of Microorganisms — microorganisms"><meta name="description" content="A data set containing the full microbial taxonomy (last updated: 7th of May, 2026) of seven domains. This data set is the backbone of this AMR package. MO codes can be looked up using as.mo() and microorganism properties can be looked up using any of the mo_* functions.
This data set is carefully crafted, yet made 100% reproducible from public and authoritative taxonomic sources (using this script), namely: List of Prokaryotic names with Standing in Nomenclature (LPSN) for bacteria, MycoBank for fungi, and Global Biodiversity Information Facility (GBIF), via Catalogue of Life (COL) for all others taxons."><meta property="og:description" content="A data set containing the full microbial taxonomy (last updated: 7th of May, 2026) of seven domains. This data set is the backbone of this AMR package. MO codes can be looked up using as.mo() and microorganism properties can be looked up using any of the mo_* functions.
This data set is carefully crafted, yet made 100% reproducible from public and authoritative taxonomic sources (using this script), namely: List of Prokaryotic names with Standing in Nomenclature (LPSN) for bacteria, MycoBank for fungi, and Global Biodiversity Information Facility (GBIF), via Catalogue of Life (COL) for all others taxons."><meta property="og:image" content="https://amr-for-r.org/logo.svg"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous"><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script></head><body>
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@@ -9,7 +9,7 @@ This data set is carefully crafted, yet made 100% reproducible from public and a
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9063</small>
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@@ -52,7 +52,7 @@ This data set is carefully crafted, yet made 100% reproducible from public and a
</div>
<div class="ref-description section level2">
<p>A data set containing the full microbial taxonomy (<strong>last updated: 7th of May, 2026</strong>) of 15 kingdoms. 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> and microorganism properties can be looked up using any of the <code><a href="mo_property.html">mo_*</a></code> functions.</p>
<p>A data set containing the full microbial taxonomy (<strong>last updated: 7th of May, 2026</strong>) of seven domains. 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> and microorganism properties can be looked up using any of the <code><a href="mo_property.html">mo_*</a></code> functions.</p>
<p>This data set is carefully crafted, yet made 100% reproducible from public and authoritative taxonomic sources (using <a href="https://github.com/msberends/AMR/blob/main/data-raw/_reproduction_scripts/reproduction_of_microorganisms.R" class="external-link">this script</a>), namely: <em>List of Prokaryotic names with Standing in Nomenclature (LPSN)</em> for bacteria, <em>MycoBank</em> for fungi, and <em>Global Biodiversity Information Facility (GBIF), via Catalogue of Life (COL)</em> for all others taxons.</p>
</div>
@@ -69,8 +69,8 @@ This data set is carefully crafted, yet made 100% reproducible from public and a
<li><p><code>domain</code>, <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. Note that for fungi, <em>phylum</em> is used for their taxonomic <em>division</em>. Also, for fungi, <em>subkingdom</em> and <em>subdivision</em> were left out since they do not occur in the bacterial taxonomy. For all species outside the domains of Bacteria and Archaea, the <code>domain</code> and <code>kingdom</code> are identical.</p></li>
<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>
<li><p><code>ref</code><br> Abbreviated authority citation for the nomenclatural act that established the current name combination, following ICNP conventions. For species described in their current genus (<em>sp. nov.</em>), this is the original description author(s) and year. For species transferred to a different genus (<em>comb. nov.</em>), this is the reclassification author(s) and year. Emendations are excluded. For synonyms, this is the authority under which the synonym was originally published. This field is directly retrieved from the source specified in the column <code>source</code>. Diacritics were removed to comply with CRAN, that only allows ASCII characters.</p></li>
<li><p><code>oxygen_tolerance</code> <br> Oxygen tolerance, either <code>"aerobe"</code>, <code>"anaerobe"</code>, <code>"anaerobe/microaerophile"</code>, <code>"facultative anaerobe"</code>, <code>"likely facultative anaerobe"</code>, <code>"microaerophile"</code>, or NA. 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 1.3784 × 10<sup>6</sup>% of all 2 bacteria in the data set contain an oxygen tolerance.</p></li>
<li><p><code>morphology</code> <br> Morphology (cell shape), either <code>"cocci"</code>, <code>"coccobacilli"</code>, <code>"filamentous"</code>, <code>"likely cocci"</code>, <code>"likely coccobacilli"</code>, <code>"likely filamentous"</code>, <code>"likely rods"</code>, <code>"likely spirilla"</code>, <code>"rods"</code>, <code>"spirilla"</code>, or NA. These data were retrieved from BacDive (see <em>Source</em>). Genera that are clinically established as coccobacilli (the HACEK group and beyond, such as <em>Haemophilus</em> and <em>Acinetobacter</em>) are classified as such regardless of BacDive majority vote. Items that contain "likely" are missing from BacDive and were extrapolated from other species within the same genus. Currently 1.3232 × 10<sup>6</sup>% of all 2 bacteria in the data set contain a morphology.</p></li>
<li><p><code>oxygen_tolerance</code> <br> Oxygen tolerance, either <code>"aerobe"</code>, <code>"anaerobe"</code>, <code>"anaerobe/microaerophile"</code>, <code>"facultative anaerobe"</code>, <code>"likely facultative anaerobe"</code>, <code>"microaerophile"</code>, or NA. 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 59.5% of all ~46 000 bacteria in the data set contain an oxygen tolerance.</p></li>
<li><p><code>morphology</code> <br> Morphology (cell shape), either <code>"cocci"</code>, <code>"coccobacilli"</code>, <code>"filamentous"</code>, <code>"likely cocci"</code>, <code>"likely coccobacilli"</code>, <code>"likely filamentous"</code>, <code>"likely rods"</code>, <code>"likely spirilla"</code>, <code>"rods"</code>, <code>"spirilla"</code>, or NA. These data were retrieved from BacDive (see <em>Source</em>). Genera that are clinically established as coccobacilli (the HACEK group and beyond, such as <em>Haemophilus</em> and <em>Acinetobacter</em>) are classified as such regardless of BacDive majority vote. Items that contain "likely" are missing from BacDive and were extrapolated from other species within the same genus. Currently 57.1% of all ~46 000 bacteria in the data set contain a morphology.</p></li>
<li><p><code>source</code><br> Either <code>"GBIF"</code>, <code>"LPSN"</code>, <code>"MycoBank"</code>, or <code>"manually added"</code> (see <em>Source</em>)</p></li>
<li><p><code>lpsn</code><br> Identifier ('Record number') of 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. <em><strong>This is a unique identifier</strong></em>, though available for only ~36 000 records.</p></li>
<li><p><code>lpsn_parent</code><br> LPSN identifier of the parent taxon</p></li>
@@ -96,12 +96,12 @@ This data set is carefully crafted, yet made 100% reproducible from public and a
<h2 id="included-taxa">Included Taxa<a class="anchor" aria-label="anchor" href="#included-taxa"></a></h2>
<p>Included taxonomic data from <a href="https://lpsn.dsmz.de" class="external-link">LPSN</a>, <a href="https://www.mycobank.org" class="external-link">MycoBank</a>, and <a href="https://www.gbif.org" class="external-link">GBIF</a> are:</p><ul><li><p>All 2 (sub)species from the kingdoms of Archaea and Bacteria</p></li>
<p>Included taxonomic data from <a href="https://lpsn.dsmz.de" class="external-link">LPSN</a>, <a href="https://www.mycobank.org" class="external-link">MycoBank</a>, and <a href="https://www.gbif.org" class="external-link">GBIF</a> are:</p><ul><li><p>All ~46 000 (sub)species from the domains of Archaea and Bacteria</p></li>
<li><p>~36 000 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>
<li><p>~11 000 (sub)species from the kingdom of Protozoa</p></li>
<li><p>~2 000 (sub)species from ~60 other relevant genera from the kingdom of Animalia (such as <em>Strongyloides</em> and <em>Taenia</em>)</p></li>
<li><p>All ~31 000 previously accepted names of all included (sub)species (these were taxonomically renamed)</p></li>
<li><p>The complete taxonomic tree of all included (sub)species: from kingdom to subspecies</p></li>
<li><p>The complete taxonomic tree of all included (sub)species: from domain to subspecies</p></li>
<li><p>The identifier of the parent taxons</p></li>
<li><p>The year and first author of the related scientific publication</p></li>
</ul><div class="section">
@@ -179,7 +179,7 @@ Public Health Information Network Vocabulary Access and Distribution System (PHI
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<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>
<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 GPL 2.0</a>. 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, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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