Built site for AMR@3.0.1.9061: 0c1709c

2026-06-24 10:16:23 +02:00 · 2026-06-23 18:00:14 +00:00
parent 9447e0f2c2
commit 2a7bfb9ffb
328 changed files with 5357 additions and 3687 deletions
--- a/reference/mo_property.html
+++ b/reference/mo_property.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- 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>Get Properties of a Microorganism — mo_property • 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-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/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="Get Properties of a Microorganism — mo_property"><meta name="description" content="Use these functions to return a specific property of a microorganism based on the latest accepted taxonomy. All input values will be evaluated internally with as.mo(), which makes it possible to use microbial abbreviations, codes and names as input. See Examples."><meta property="og:description" content="Use these functions to return a specific property of a microorganism based on the latest accepted taxonomy. All input values will be evaluated internally with as.mo(), which makes it possible to use microbial abbreviations, codes and names as input. See Examples."><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>
+<!-- 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>Get Properties of a Microorganism — mo_property • 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="Get Properties of a Microorganism — mo_property"><meta name="description" content="Use these functions to return a specific property of a microorganism based on the latest accepted taxonomy. All input values will be evaluated internally with as.mo(), which makes it possible to use microbial abbreviations, codes and names as input. See Examples."><meta property="og:description" content="Use these functions to return a specific property of a microorganism based on the latest accepted taxonomy. All input values will be evaluated internally with as.mo(), which makes it possible to use microbial abbreviations, codes and names as input. See Examples."><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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@@ -7,7 +7,7 @@

    <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="">3.0.1.9057</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9061</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -55,115 +55,270 @@

    <div class="section level2">
    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mo_name</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
-<span>  keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mo_name</span><span class="op">(</span></span>
+<span>  <span class="va">x</span>,</span>
+<span>  language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
+<span>  keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
+<span>  <span class="va">...</span></span>
+<span><span class="op">)</span></span>
 <span></span>
-<span><span class="fu">mo_fullname</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
-<span>  keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
+<span><span class="fu">mo_fullname</span><span class="op">(</span></span>
+<span>  <span class="va">x</span>,</span>
+<span>  language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
+<span>  keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
+<span>  <span class="va">...</span></span>
+<span><span class="op">)</span></span>
 <span></span>
-<span><span class="fu">mo_shortname</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
-<span>  keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
+<span><span class="fu">mo_shortname</span><span class="op">(</span></span>
+<span>  <span class="va">x</span>,</span>
+<span>  language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
+<span>  keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
+<span>  <span class="va">...</span></span>
+<span><span class="op">)</span></span>
 <span></span>
-<span><span class="fu">mo_subspecies</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
-<span>  keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
+<span><span class="fu">mo_subspecies</span><span class="op">(</span></span>
+<span>  <span class="va">x</span>,</span>
+<span>  language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
+<span>  keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
+<span>  <span class="va">...</span></span>
+<span><span class="op">)</span></span>
 <span></span>
-<span><span class="fu">mo_species</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
-<span>  keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
+<span><span class="fu">mo_species</span><span class="op">(</span></span>
+<span>  <span class="va">x</span>,</span>
+<span>  language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
+<span>  keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
+<span>  <span class="va">...</span></span>
+<span><span class="op">)</span></span>
 <span></span>
-<span><span class="fu">mo_genus</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
-<span>  keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
+<span><span class="fu">mo_genus</span><span class="op">(</span></span>
+<span>  <span class="va">x</span>,</span>
+<span>  language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
+<span>  keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
+<span>  <span class="va">...</span></span>
+<span><span class="op">)</span></span>
 <span></span>
-<span><span class="fu">mo_family</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
-<span>  keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
+<span><span class="fu">mo_family</span><span class="op">(</span></span>
+<span>  <span class="va">x</span>,</span>
+<span>  language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
+<span>  keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
+<span>  <span class="va">...</span></span>
+<span><span class="op">)</span></span>
 <span></span>
-<span><span class="fu">mo_order</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
-<span>  keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
+<span><span class="fu">mo_order</span><span class="op">(</span></span>
+<span>  <span class="va">x</span>,</span>
+<span>  language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
+<span>  keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
+<span>  <span class="va">...</span></span>
+<span><span class="op">)</span></span>
 <span></span>
-<span><span class="fu">mo_class</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
-<span>  keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
+<span><span class="fu">mo_class</span><span class="op">(</span></span>
+<span>  <span class="va">x</span>,</span>
+<span>  language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
+<span>  keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
+<span>  <span class="va">...</span></span>
+<span><span class="op">)</span></span>
 <span></span>
-<span><span class="fu">mo_phylum</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
-<span>  keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
+<span><span class="fu">mo_phylum</span><span class="op">(</span></span>
+<span>  <span class="va">x</span>,</span>
+<span>  language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
+<span>  keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
+<span>  <span class="va">...</span></span>
+<span><span class="op">)</span></span>
 <span></span>
-<span><span class="fu">mo_kingdom</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
-<span>  keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
+<span><span class="fu">mo_kingdom</span><span class="op">(</span></span>
+<span>  <span class="va">x</span>,</span>
+<span>  language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
+<span>  keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
+<span>  <span class="va">...</span></span>
+<span><span class="op">)</span></span>
 <span></span>
-<span><span class="fu">mo_domain</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
-<span>  keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
+<span><span class="fu">mo_domain</span><span class="op">(</span></span>
+<span>  <span class="va">x</span>,</span>
+<span>  language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
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+<span>  <span class="va">x</span>,</span>
+<span>  language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
+<span>  keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
+<span>  <span class="va">...</span></span>
+<span><span class="op">)</span></span>
 <span></span>
-<span><span class="fu">mo_rank</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
-<span>  keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
+<span><span class="fu">mo_gbif</span><span class="op">(</span></span>
+<span>  <span class="va">x</span>,</span>
+<span>  language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
+<span>  keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
+<span>  <span class="va">...</span></span>
+<span><span class="op">)</span></span>
 <span></span>
-<span><span class="fu">mo_taxonomy</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
-<span>  keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
+<span><span class="fu">mo_rank</span><span class="op">(</span></span>
+<span>  <span class="va">x</span>,</span>
+<span>  language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
+<span>  keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
+<span>  <span class="va">...</span></span>
+<span><span class="op">)</span></span>
 <span></span>
-<span><span class="fu">mo_synonyms</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
-<span>  keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
+<span><span class="fu">mo_taxonomy</span><span class="op">(</span></span>
+<span>  <span class="va">x</span>,</span>
+<span>  language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
+<span>  keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
+<span>  <span class="va">...</span></span>
+<span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">mo_synonyms</span><span class="op">(</span></span>
+<span>  <span class="va">x</span>,</span>
+<span>  language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
+<span>  keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
+<span>  <span class="va">...</span></span>
+<span><span class="op">)</span></span>
 <span></span>
 <span><span class="fu">mo_current</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
-<span><span class="fu">mo_group_members</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
-<span>  keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
+<span><span class="fu">mo_group_members</span><span class="op">(</span></span>
+<span>  <span class="va">x</span>,</span>
+<span>  language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
+<span>  keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
+<span>  <span class="va">...</span></span>
+<span><span class="op">)</span></span>
 <span></span>
-<span><span class="fu">mo_info</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
-<span>  keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
+<span><span class="fu">mo_info</span><span class="op">(</span></span>
+<span>  <span class="va">x</span>,</span>
+<span>  language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
+<span>  keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
+<span>  <span class="va">...</span></span>
+<span><span class="op">)</span></span>
 <span></span>
-<span><span class="fu">mo_url</span><span class="op">(</span><span class="va">x</span>, open <span class="op">=</span> <span class="cn">FALSE</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
-<span>  keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
+<span><span class="fu">mo_url</span><span class="op">(</span></span>
+<span>  <span class="va">x</span>,</span>
+<span>  open <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>  language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
+<span>  keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
+<span>  <span class="va">...</span></span>
+<span><span class="op">)</span></span>
 <span></span>
-<span><span class="fu">mo_property</span><span class="op">(</span><span class="va">x</span>, property <span class="op">=</span> <span class="st">"fullname"</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
-<span>  keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
+<span><span class="fu">mo_property</span><span class="op">(</span></span>
+<span>  <span class="va">x</span>,</span>
+<span>  property <span class="op">=</span> <span class="st">"fullname"</span>,</span>
+<span>  language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
+<span>  keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
+<span>  <span class="va">...</span></span>
+<span><span class="op">)</span></span></code></pre></div>
    </div>

    <div class="section level2">
@@ -187,6 +342,10 @@
 <dd><p>Other arguments passed on to <code><a href="as.mo.html">as.mo()</a></code>, such as 'minimum_matching_score', 'ignore_pattern', and 'remove_from_input'.</p></dd>


+<dt id="arg-add-morphology">add_morphology<a class="anchor" aria-label="anchor" href="#arg-add-morphology"></a></dt>
+<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether the morphology (from <code>mo_morphology()</code>) should be added to the Gram stain result, e.g. <code>"Gram-negative rods"</code> instead of <code>"Gram-negative"</code>. The default is <code>FALSE</code>.</p></dd>
+
+
 <dt id="arg-ab">ab<a class="anchor" aria-label="anchor" href="#arg-ab"></a></dt>
 <dd><p>Any (vector of) text that can be coerced to a valid antibiotic drug code with <code><a href="as.ab.html">as.ab()</a></code>.</p></dd>

@@ -196,37 +355,39 @@


 <dt id="arg-property">property<a class="anchor" aria-label="anchor" href="#arg-property"></a></dt>
-<dd><p>One of the column names of the <a href="microorganisms.html">microorganisms</a> data set: <code>"mo"</code>, <code>"fullname"</code>, <code>"status"</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>, <code>"rank"</code>, <code>"ref"</code>, <code>"oxygen_tolerance"</code>, <code>"source"</code>, <code>"lpsn"</code>, <code>"lpsn_parent"</code>, <code>"lpsn_renamed_to"</code>, <code>"mycobank"</code>, <code>"mycobank_parent"</code>, <code>"mycobank_renamed_to"</code>, <code>"gbif"</code>, <code>"gbif_parent"</code>, <code>"gbif_renamed_to"</code>, <code>"prevalence"</code>, or <code>"snomed"</code>, or must be <code>"shortname"</code>.</p></dd>
+<dd><p>One of the column names of the <a href="microorganisms.html">microorganisms</a> data set: <code>"mo"</code>, <code>"fullname"</code>, <code>"status"</code>, <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>, <code>"rank"</code>, <code>"ref"</code>, <code>"oxygen_tolerance"</code>, <code>"morphology"</code>, <code>"source"</code>, <code>"lpsn"</code>, <code>"lpsn_parent"</code>, <code>"lpsn_renamed_to"</code>, <code>"mycobank"</code>, <code>"mycobank_parent"</code>, <code>"mycobank_renamed_to"</code>, <code>"gbif"</code>, <code>"gbif_parent"</code>, <code>"gbif_renamed_to"</code>, <code>"prevalence"</code>, or <code>"snomed"</code>, or must be <code>"shortname"</code>.</p></dd>

 </dl></div>
    <div class="section level2">
    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    <p>- An [integer] in case of [mo_year()]
- An [ordered factor][factor] in case of [mo_pathogenicity()]
- A [list] in case of [mo_taxonomy()], [mo_synonyms()], [mo_snomed()], and [mo_info()]
- A [logical] in case of [mo_is_anaerobic()], [mo_is_gram_negative()], [mo_is_gram_positive()], [mo_is_intrinsic_resistant()], and [mo_is_yeast()]
- A named [character] in case of [mo_synonyms()] and [mo_url()]
- A [character] in all other cases</p>
-    </div>
+
+<ul><li><p>An <a href="https://rdrr.io/r/base/integer.html" class="external-link">integer</a> in case of <code>mo_year()</code></p></li>
+<li><p>An <a href="https://rdrr.io/pkg/data.table/man/fctr.html" class="external-link">ordered factor</a> in case of <code>mo_pathogenicity()</code></p></li>
+<li><p>A <a href="https://rdrr.io/r/base/list.html" class="external-link">list</a> in case of <code>mo_taxonomy()</code>, <code>mo_synonyms()</code>, <code>mo_snomed()</code>, and <code>mo_info()</code></p></li>
+<li><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> in case of <code>mo_is_anaerobic()</code>, <code>mo_is_gram_negative()</code>, <code>mo_is_gram_positive()</code>, <code>mo_is_intrinsic_resistant()</code>, and <code>mo_is_yeast()</code></p></li>
+<li><p>A named <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> in case of <code>mo_synonyms()</code> and <code>mo_url()</code></p></li>
+<li><p>A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> in all other cases</p></li>
+</ul></div>
    <div class="section level2">
    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
-    <p>All functions will, at default, **not** keep old taxonomic properties, as synonyms are automatically replaced with the current taxonomy. Take for example *Enterobacter aerogenes*, which was initially named in 1960 but renamed to *Klebsiella aerogenes* in 2017:
- `mo_genus("Enterobacter aerogenes")` will return `"Klebsiella"` (with a note about the renaming)
- `mo_genus("Enterobacter aerogenes", keep_synonyms = TRUE)` will return `"Enterobacter"` (with a once-per-session warning that the name is outdated)
- `mo_ref("Enterobacter aerogenes")` will return `"Tindall et al., 2017"` (with a note about the renaming)
- `mo_ref("Enterobacter aerogenes", keep_synonyms = TRUE)` will return `"Hormaeche et al., 1960"` (with a once-per-session warning that the name is outdated)</p>
-<p>The short name ([mo_shortname()]) returns the first character of the genus and the full species, such as `"E. coli"`, for species and subspecies. Exceptions are abbreviations of staphylococci (such as *"CoNS"*, Coagulase-Negative Staphylococci) and beta-haemolytic streptococci (such as *"GBS"*, Group B Streptococci). Please bear in mind that e.g. *E. coli* could mean *Escherichia coli* (kingdom of Bacteria) as well as *Entamoeba coli* (kingdom of Protozoa). Returning to the full name will be done using [as.mo()] internally, giving priority to bacteria and human pathogens, i.e. `"E. coli"` will be considered *Escherichia coli*. As a result, `mo_fullname(mo_shortname("Entamoeba coli"))` returns `"Escherichia coli"`.</p>
-<p>Since the top-level of the taxonomy is sometimes referred to as 'kingdom' and sometimes as 'domain', the functions [mo_kingdom()] and [mo_domain()] return the exact same results.</p>
-<p>Determination of human pathogenicity ([mo_pathogenicity()]) is strongly based on Bartlett *et al.* (2022, <a href="https://doi.org/10.1099/mic.0.001269" class="external-link">doi:10.1099/mic.0.001269</a>
-). This function returns a [factor] with the levels *Pathogenic*, *Potentially pathogenic*, *Non-pathogenic*, and *Unknown*.</p>
-<p>Determination of the Gram stain ([mo_gramstain()]) will be based on the taxonomic kingdom and phylum. Originally, Cavalier-Smith defined the so-called subkingdoms Negibacteria and Posibacteria (2002, [PMID 11837318](https://pubmed.ncbi.nlm.nih.gov/11837318/)), and only considered these phyla as Posibacteria: Actinobacteria, Chloroflexi, Firmicutes, and Tenericutes. These phyla were later renamed to Actinomycetota, Chloroflexota, Bacillota, and Mycoplasmatota (2021, [PMID 34694987](https://pubmed.ncbi.nlm.nih.gov/34694987/)). Bacteria in these phyla are considered Gram-positive in this `AMR` package, except for members of the class Negativicutes (within phylum Bacillota) which are Gram-negative. All other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value `NA`. Functions [mo_is_gram_negative()] and [mo_is_gram_positive()] always return `TRUE` or `FALSE` (or `NA` when the input is `NA` or the MO code is `UNKNOWN`), thus always return `FALSE` for species outside the taxonomic kingdom of Bacteria.</p>
-<p>Determination of yeasts ([mo_is_yeast()]) will be based on the taxonomic kingdom and class. *Budding yeasts* are yeasts that reproduce asexually through a process called budding, where a new cell develops from a small protrusion on the parent cell. Taxonomically, these are members of the phylum Ascomycota, class Saccharomycetes (also called Hemiascomycetes) or Pichiomycetes. *True yeasts* quite specifically refers to yeasts in the underlying order Saccharomycetales (such as *Saccharomyces cerevisiae*). Thus, for all microorganisms that are member of the taxonomic class Saccharomycetes or Pichiomycetes, the function will return `TRUE`. It returns `FALSE` otherwise (or `NA` when the input is `NA` or the MO code is `UNKNOWN`).</p>
-<p>Determination of intrinsic resistance ([mo_is_intrinsic_resistant()]) will be based on the [intrinsic_resistant] data set, which is based on `r format_eucast_version_nr(names(EUCAST_VERSION_EXPECTED_PHENOTYPES[1]))`. The [mo_is_intrinsic_resistant()] function can be vectorised over both argument `x` (input for microorganisms) and `ab` (input for antimicrobials).</p>
-<p>Determination of bacterial oxygen tolerance ([mo_oxygen_tolerance()]) will be based on BacDive, see *Source*. The function [mo_is_anaerobic()] only returns `TRUE` if the oxygen tolerance is `"anaerobe"`, indicting an obligate anaerobic species or genus. It always returns `FALSE` for species outside the taxonomic kingdom of Bacteria.</p>
-<p>The function [mo_url()] will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species. [This MycoBank URL](`r TAXONOMY_VERSION$MycoBank$url`) will be used for fungi wherever available , [this LPSN URL](`r TAXONOMY_VERSION$MycoBank$url`) for bacteria wherever available, and [this GBIF link](`r TAXONOMY_VERSION$GBIF$url`) otherwise.</p>
-<p>SNOMED codes ([mo_snomed()]) was last updated on `r documentation_date(TAXONOMY_VERSION$SNOMED$accessed_date)`. See *Source* and the [microorganisms] data set for more info.</p>
-<p>Old taxonomic names (so-called 'synonyms') can be retrieved with [mo_synonyms()] (which will have the scientific reference as [name][base::names()]), the current taxonomic name can be retrieved with [mo_current()]. Both functions return full names.</p>
-<p>All output [will be translated][translate] where possible.</p>
+    <p>All functions will, at default, <strong>not</strong> keep old taxonomic properties, as synonyms are automatically replaced with the current taxonomy. Take for example <em>Enterobacter aerogenes</em>, which was initially named in 1960 but renamed to <em>Klebsiella aerogenes</em> in 2017:</p><ul><li><p><code>mo_genus("Enterobacter aerogenes")</code> will return <code>"Klebsiella"</code> (with a note about the renaming)</p></li>
+<li><p><code>mo_genus("Enterobacter aerogenes", keep_synonyms = TRUE)</code> will return <code>"Enterobacter"</code> (with a once-per-session warning that the name is outdated)</p></li>
+<li><p><code>mo_ref("Enterobacter aerogenes")</code> will return <code>"Tindall et al., 2017"</code> (with a note about the renaming)</p></li>
+<li><p><code>mo_ref("Enterobacter aerogenes", keep_synonyms = TRUE)</code> will return <code>"Hormaeche et al., 1960"</code> (with a once-per-session warning that the name is outdated)</p></li>
+</ul><p><code>mo_ref()</code> returns the abbreviated authority of the nomenclatural act that created the queried name combination. When <code>keep_synonyms = FALSE</code> (default), this is the authority of the currently accepted name. When <code>keep_synonyms = TRUE</code>, this is the authority under which the queried (possibly outdated) name was published. Emendations (changes to the species description without a name change) are not reflected; only the combination or original description authority is returned.</p>
+<p>The short name (<code>mo_shortname()</code>) returns the first character of the genus and the full species, such as <code>"E. coli"</code>, for species and subspecies. Exceptions are abbreviations of staphylococci (such as <em>"CoNS"</em>, Coagulase-Negative Staphylococci) and beta-haemolytic streptococci (such as <em>"GBS"</em>, Group B Streptococci). Please bear in mind that e.g. <em>E. coli</em> could mean <em>Escherichia coli</em> (kingdom of Bacteria) as well as <em>Entamoeba coli</em> (kingdom of Protozoa). Returning to the full name will be done using <code><a href="as.mo.html">as.mo()</a></code> internally, giving priority to bacteria and human pathogens, i.e. <code>"E. coli"</code> will always be considered <em>Escherichia coli</em>. As a result, <code>mo_fullname(mo_shortname("Entamoeba coli"))</code> returns <code>"Escherichia coli"</code>.</p>
+<p>Following the formal introduction of the new kingdom rank into prokaryotic nomenclature in 2024 (<a href="https://doi.org/10.1099/ijsem.0.006242" class="external-link">doi:10.1099/ijsem.0.006242</a>
+), <code>mo_kingdom()</code> and <code>mo_domain()</code> return different results for bacteria and archaea: <code>mo_kingdom()</code> returns the new formal kingdom (e.g. "Pseudomonadati", "Bacillati"), while <code>mo_domain()</code> returns the new domain (e.g. "Bacteria", "Archaea"). For non-prokaryotic organisms, both functions return identical results.</p>
+<p>Determination of human pathogenicity (<code>mo_pathogenicity()</code>) is strongly 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>
+). This function returns a <a href="https://rdrr.io/pkg/data.table/man/fctr.html" class="external-link">factor</a> with the levels <em>Pathogenic</em>, <em>Potentially pathogenic</em>, <em>Non-pathogenic</em>, and <em>Unknown</em>.</p>
+<p>Determination of the Gram stain (<code>mo_gramstain()</code> is based on the taxonomic kingdom and phylum. Originally, Cavalier-Smith defined the so-called subkingdoms Negibacteria and Posibacteria (2002, <a href="https://pubmed.ncbi.nlm.nih.gov/11837318/" class="external-link">PMID 11837318</a>), and only considered these phyla as Posibacteria: Actinobacteria, Chloroflexi, Firmicutes, and Tenericutes. These phyla were later renamed to Actinomycetota, Chloroflexota, Bacillota, and Mycoplasmatota (2021, <a href="https://pubmed.ncbi.nlm.nih.gov/34694987/" class="external-link">PMID 34694987</a>). Bacteria in these phyla are considered Gram-positive in this <code>AMR</code> package, except for members of the class Negativicutes (within phylum Bacillota) which are Gram-negative. All other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value <code>NA</code>. Functions <code>mo_is_gram_negative()</code> and <code>mo_is_gram_positive()</code> always return <code>TRUE</code> or <code>FALSE</code> (or <code>NA</code> when the input is <code>NA</code> or the MO code is <code>UNKNOWN</code>), thus always return <code>FALSE</code> for species outside the taxonomic kingdom of Bacteria.</p>
+<p>Determination of yeasts (<code>mo_is_yeast()</code>) is based on the taxonomic kingdom and class. <em>Budding yeasts</em> are yeasts that reproduce asexually through a process called budding, where a new cell develops from a small protrusion on the parent cell. Taxonomically, these are members of the phylum Ascomycota, class Saccharomycetes (also called Hemiascomycetes) or Pichiomycetes. <em>True yeasts</em> quite specifically refers to yeasts in the underlying order Saccharomycetales (such as <em>Saccharomyces cerevisiae</em>). Thus, for all microorganisms that are member of the taxonomic class Saccharomycetes or Pichiomycetes, the function will return <code>TRUE</code>. It returns <code>FALSE</code> otherwise (or <code>NA</code> when the input is <code>NA</code> or the MO code is <code>UNKNOWN</code>).</p>
+<p>Determination of intrinsic resistance (<code>mo_is_intrinsic_resistant()</code>) is based on the <a href="intrinsic_resistant.html">intrinsic_resistant</a> data set, which is based on <a href="https://www.eucast.org/bacteria/important-additional-information/expert-rules/" class="external-link">'EUCAST Expected Resistant Phenotypes' v1.2</a> (2023). The <code>mo_is_intrinsic_resistant()</code> function can be vectorised over both argument <code>x</code> (input for microorganisms) and <code>ab</code> (input for antimicrobials).</p>
+<p>Determination of both bacterial oxygen tolerance (<code>mo_oxygen_tolerance()</code>) and morphology (<code>mo_morphology()</code>) are  based on BacDive, see <em>Source</em>. The function <code>mo_is_anaerobic()</code> only returns <code>TRUE</code> if the oxygen tolerance is <code>"anaerobe"</code>, indicating an obligate anaerobic species or genus. It always returns <code>FALSE</code> for species outside the taxonomic kingdom of Bacteria.</p>
+<p>The function <code>mo_url()</code> will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species. <a href="https://www.mycobank.org" class="external-link">This MycoBank URL</a> is used for fungi wherever available , <a href="https://www.mycobank.org" class="external-link">this LPSN URL</a> for bacteria wherever available, and <a href="https://www.gbif.org" class="external-link">this GBIF link</a> otherwise.</p>
+<p>SNOMED codes (<code>mo_snomed()</code>) was last updated on 16th of July, 2024. See <em>Source</em> and the <a href="microorganisms.html">microorganisms</a> data set for more info.</p>
+<p>Old taxonomic names (so-called 'synonyms') can be retrieved with <code>mo_synonyms()</code> (which will have the scientific reference as <a href="https://rdrr.io/r/base/names.html" class="external-link">name</a>), the current taxonomic name can be retrieved with <code>mo_current()</code>. Both functions return full names.</p>
+<p>All output <a href="translate.html">will be translated</a> where possible.</p>
    </div>
    <div class="section level2">
    <h2 id="matching-score-for-microorganisms">Matching Score for Microorganisms<a class="anchor" aria-label="anchor" href="#matching-score-for-microorganisms"></a></h2>
@@ -239,14 +400,14 @@


 <ul><li><p>Berends MS <em>et al.</em> (2022). <strong>AMR: An R Package for Working with Antimicrobial Resistance Data</strong>. <em>Journal of Statistical Software</em>, 104(3), 1-31; <a href="https://doi.org/10.18637/jss.v104.i03" class="external-link">doi:10.18637/jss.v104.i03</a></p></li>
-<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>
-. Accessed from <a href="https://lpsn.dsmz.de" class="external-link">https://lpsn.dsmz.de</a> on June 24th, 2024.</p></li>
+<li><p>Freese, HM <em>et al.</em> (2026). <strong>TYGS and LPSN in 2025: a Global Core Biodata Resource for genome-based classification and nomenclature of prokaryotes within DSMZ Digital Diversity.</strong> Nucleic Acids Research, 54, D884–D891; <a href="https://doi.org/10.1093/nar/gkaf1110" class="external-link">doi:10.1093/nar/gkaf1110</a>
+. Accessed from <a href="https://lpsn.dsmz.de" class="external-link">https://lpsn.dsmz.de</a> on 7th of May, 2026.</p></li>
 <li><p>Vincent, R <em>et al</em> (2013). <strong>MycoBank gearing up for new horizons.</strong> IMA Fungus, 4(2), 371-9; <a href="https://doi.org/10.5598/imafungus.2013.04.02.16" class="external-link">doi:10.5598/imafungus.2013.04.02.16</a>
-. Accessed from <a href="https://www.mycobank.org" class="external-link">https://www.mycobank.org</a> on June 24th, 2024.</p></li>
-<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>
-. Accessed from <a href="https://www.gbif.org" class="external-link">https://www.gbif.org</a> on June 24th, 2024.</p></li>
+. Accessed from <a href="https://www.mycobank.org" class="external-link">https://www.mycobank.org</a> on 7th of May, 2026.</p></li>
+<li><p>Banki, O. <em>et al.</em> (2026). Catalogue of Life (2026-04-18 XR). Catalogue of Life Foundation, Amsterdam, Netherlands. <a href="https://doi.org/10.48580/dgxjw" class="external-link">doi:10.48580/dgxjw</a>
+. Accessed from <a href="https://www.gbif.org" class="external-link">https://www.gbif.org</a> on 7th of May, 2026.</p></li>
 <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>
-. Accessed from <a href="https://bacdive.dsmz.de" class="external-link">https://bacdive.dsmz.de</a> on July 16th, 2024.</p></li>
+. Accessed from <a href="https://bacdive.dsmz.de" class="external-link">https://bacdive.dsmz.de</a> on 7th of May, 2026.</p></li>
 <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://www.cdc.gov/phin/php/phinvads/" class="external-link">https://www.cdc.gov/phin/php/phinvads/</a></p></li>
 <li><p>Bartlett A <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>
 </ul></div>
@@ -268,7 +429,7 @@
    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># taxonomic tree -----------------------------------------------------------</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu">mo_kingdom</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Bacteria"</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Pseudomonadati"</span>
 <span class="r-in"><span><span class="fu">mo_phylum</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Pseudomonadota"</span>
 <span class="r-in"><span><span class="fu">mo_class</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
@@ -297,11 +458,15 @@
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># other properties ---------------------------------------------------------</span></span></span>
 <span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="fu">mo_morphology</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Rods"</span>
+<span class="r-in"><span><span class="fu">mo_gramstain</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Gram-negative"</span>
+<span class="r-in"><span><span class="fu">mo_gramstain</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span>, add_morphology <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Gram-negative rods"</span>
 <span class="r-in"><span><span class="fu">mo_pathogenicity</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] Pathogenic</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Levels: Pathogenic &lt; Potentially pathogenic &lt; Non-pathogenic &lt; Unknown</span>
-<span class="r-in"><span><span class="fu">mo_gramstain</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Gram-negative"</span>
 <span class="r-in"><span><span class="fu">mo_snomed</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [[1]]</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "1098101000112102" "446870005"        "1098201000112108" "409801009"       </span>
@@ -362,7 +527,7 @@
 <span class="r-in"><span><span class="fu">mo_lpsn</span><span class="op">(</span><span class="st">"Klebsiella aerogenes"</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "777146"</span>
 <span class="r-in"><span><span class="fu">mo_gbif</span><span class="op">(</span><span class="st">"Klebsiella aerogenes"</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "9281703"</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "CSHB4"</span>
 <span class="r-in"><span><span class="fu">mo_mycobank</span><span class="op">(</span><span class="st">"Candida albicans"</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "256187"</span>
 <span class="r-in"><span><span class="fu">mo_mycobank</span><span class="op">(</span><span class="st">"Candida krusei"</span><span class="op">)</span></span></span>
@@ -440,11 +605,11 @@
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># mo_type is equal to mo_kingdom, but mo_kingdom will remain untranslated</span></span></span>
 <span class="r-in"><span><span class="fu">mo_kingdom</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Bacteria"</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Pseudomonadati"</span>
 <span class="r-in"><span><span class="fu">mo_type</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Bacteria"</span>
 <span class="r-in"><span><span class="fu">mo_kingdom</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span>, language <span class="op">=</span> <span class="st">"zh"</span><span class="op">)</span> <span class="co"># Chinese, no effect</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Bacteria"</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Pseudomonadati"</span>
 <span class="r-in"><span><span class="fu">mo_type</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span>, language <span class="op">=</span> <span class="st">"zh"</span><span class="op">)</span> <span class="co"># Chinese, translated</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "细菌"</span>
 <span class="r-in"><span></span></span>
@@ -517,9 +682,12 @@
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># get a list with the complete taxonomy (from kingdom to subspecies)</span></span></span>
 <span class="r-in"><span><span class="fu">mo_taxonomy</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> $kingdom</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> $domain</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Bacteria"</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> $kingdom</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Pseudomonadati"</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> $phylum</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Pseudomonadota"</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
@@ -551,9 +719,12 @@
 <span class="r-out co"><span class="r-pr">#&gt;</span> $rank</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "species"</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> $kingdom</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> $domain</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Bacteria"</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> $kingdom</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Pseudomonadati"</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> $phylum</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Pseudomonadota"</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
@@ -584,6 +755,9 @@
 <span class="r-out co"><span class="r-pr">#&gt;</span> $gramstain</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Gram-negative"</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> $morphology</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Rods"</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> $oxygen_tolerance</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "facultative anaerobe"</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
@@ -604,7 +778,7 @@
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] NA</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> $gbif</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "3221874"</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "CSHCH"</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> $group_members</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> character(0)</span>