mirror of
https://github.com/msberends/AMR.git
synced 2024-12-25 18:06:12 +01:00
347 lines
16 KiB
HTML
347 lines
16 KiB
HTML
<!-- Generated by pkgdown: do not edit by hand -->
|
|
<!DOCTYPE html>
|
|
<html lang="en">
|
|
<head>
|
|
<meta charset="utf-8">
|
|
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
|
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
|
|
|
<title>The Catalogue of Life — catalogue_of_life • AMR (for R)</title>
|
|
|
|
<!-- favicons -->
|
|
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
|
|
<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
|
|
<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png" />
|
|
<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png" />
|
|
<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png" />
|
|
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
|
|
|
|
<!-- jquery -->
|
|
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
|
<!-- Bootstrap -->
|
|
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
|
|
|
|
|
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
|
|
|
<!-- bootstrap-toc -->
|
|
<link rel="stylesheet" href="../bootstrap-toc.css">
|
|
<script src="../bootstrap-toc.js"></script>
|
|
|
|
<!-- Font Awesome icons -->
|
|
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
|
|
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
|
|
|
|
<!-- clipboard.js -->
|
|
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
|
|
|
|
<!-- headroom.js -->
|
|
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
|
|
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
|
|
|
|
<!-- pkgdown -->
|
|
<link href="../pkgdown.css" rel="stylesheet">
|
|
<script src="../pkgdown.js"></script>
|
|
|
|
|
|
|
|
<link href="../extra.css" rel="stylesheet">
|
|
<script src="../extra.js"></script>
|
|
|
|
<meta property="og:title" content="The Catalogue of Life — catalogue_of_life" />
|
|
<meta property="og:description" content="This package contains the complete taxonomic tree of almost all microorganisms from the authoritative and comprehensive Catalogue of Life." />
|
|
<meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<!-- mathjax -->
|
|
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
|
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
|
|
|
<!--[if lt IE 9]>
|
|
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
|
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
|
<![endif]-->
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
</head>
|
|
|
|
<body data-spy="scroll" data-target="#toc">
|
|
|
|
|
|
<div class="container template-reference-topic">
|
|
<header>
|
|
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
|
|
<div class="container">
|
|
<div class="navbar-header">
|
|
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
|
|
<span class="sr-only">Toggle navigation</span>
|
|
<span class="icon-bar"></span>
|
|
<span class="icon-bar"></span>
|
|
<span class="icon-bar"></span>
|
|
</button>
|
|
<span class="navbar-brand">
|
|
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
|
|
</span>
|
|
</div>
|
|
|
|
<div id="navbar" class="navbar-collapse collapse">
|
|
<ul class="nav navbar-nav">
|
|
<li>
|
|
<a href="../index.html">
|
|
<span class="fa fa-home"></span>
|
|
|
|
Home
|
|
</a>
|
|
</li>
|
|
<li class="dropdown">
|
|
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
|
<span class="fa fa-question-circle"></span>
|
|
|
|
How to
|
|
|
|
<span class="caret"></span>
|
|
</a>
|
|
<ul class="dropdown-menu" role="menu">
|
|
<li>
|
|
<a href="../articles/AMR.html">
|
|
<span class="fa fa-directions"></span>
|
|
|
|
Conduct AMR analysis
|
|
</a>
|
|
</li>
|
|
<li>
|
|
<a href="../articles/resistance_predict.html">
|
|
<span class="fa fa-dice"></span>
|
|
|
|
Predict antimicrobial resistance
|
|
</a>
|
|
</li>
|
|
<li>
|
|
<a href="../articles/datasets.html">
|
|
<span class="fa fa-database"></span>
|
|
|
|
Data sets for download / own use
|
|
</a>
|
|
</li>
|
|
<li>
|
|
<a href="../articles/PCA.html">
|
|
<span class="fa fa-compress"></span>
|
|
|
|
Conduct principal component analysis for AMR
|
|
</a>
|
|
</li>
|
|
<li>
|
|
<a href="../articles/MDR.html">
|
|
<span class="fa fa-skull-crossbones"></span>
|
|
|
|
Determine multi-drug resistance (MDR)
|
|
</a>
|
|
</li>
|
|
<li>
|
|
<a href="../articles/WHONET.html">
|
|
<span class="fa fa-globe-americas"></span>
|
|
|
|
Work with WHONET data
|
|
</a>
|
|
</li>
|
|
<li>
|
|
<a href="../articles/SPSS.html">
|
|
<span class="fa fa-file-upload"></span>
|
|
|
|
Import data from SPSS/SAS/Stata
|
|
</a>
|
|
</li>
|
|
<li>
|
|
<a href="../articles/EUCAST.html">
|
|
<span class="fa fa-exchange-alt"></span>
|
|
|
|
Apply EUCAST rules
|
|
</a>
|
|
</li>
|
|
<li>
|
|
<a href="../reference/mo_property.html">
|
|
<span class="fa fa-bug"></span>
|
|
|
|
Get properties of a microorganism
|
|
</a>
|
|
</li>
|
|
<li>
|
|
<a href="../reference/ab_property.html">
|
|
<span class="fa fa-capsules"></span>
|
|
|
|
Get properties of an antibiotic
|
|
</a>
|
|
</li>
|
|
<li>
|
|
<a href="../articles/benchmarks.html">
|
|
<span class="fa fa-shipping-fast"></span>
|
|
|
|
Other: benchmarks
|
|
</a>
|
|
</li>
|
|
</ul>
|
|
</li>
|
|
<li>
|
|
<a href="../reference/index.html">
|
|
<span class="fa fa-book-open"></span>
|
|
|
|
Manual
|
|
</a>
|
|
</li>
|
|
<li>
|
|
<a href="../authors.html">
|
|
<span class="fa fa-users"></span>
|
|
|
|
Authors
|
|
</a>
|
|
</li>
|
|
<li>
|
|
<a href="../news/index.html">
|
|
<span class="far fa-newspaper"></span>
|
|
|
|
Changelog
|
|
</a>
|
|
</li>
|
|
</ul>
|
|
<ul class="nav navbar-nav navbar-right">
|
|
<li>
|
|
<a href="https://github.com/msberends/AMR">
|
|
<span class="fab fa-github"></span>
|
|
|
|
Source Code
|
|
</a>
|
|
</li>
|
|
<li>
|
|
<a href="../survey.html">
|
|
<span class="fa fa-clipboard-list"></span>
|
|
|
|
Survey
|
|
</a>
|
|
</li>
|
|
</ul>
|
|
|
|
</div><!--/.nav-collapse -->
|
|
</div><!--/.container -->
|
|
</div><!--/.navbar -->
|
|
|
|
|
|
|
|
</header>
|
|
|
|
<div class="row">
|
|
<div class="col-md-9 contents">
|
|
<div class="page-header">
|
|
<h1>The Catalogue of Life</h1>
|
|
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/catalogue_of_life.R'><code>R/catalogue_of_life.R</code></a></small>
|
|
<div class="hidden name"><code>catalogue_of_life.Rd</code></div>
|
|
</div>
|
|
|
|
<div class="ref-description">
|
|
<p>This package contains the complete taxonomic tree of almost all microorganisms from the authoritative and comprehensive Catalogue of Life.</p>
|
|
</div>
|
|
|
|
|
|
|
|
<h2 class="hasAnchor" id="catalogue-of-life"><a class="anchor" href="#catalogue-of-life"></a>Catalogue of Life</h2>
|
|
|
|
|
|
|
|
<p><img src='figures/logo_col.png' height=40px style=margin-bottom:5px /> <br />
|
|
This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, <a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, <a href='https://lpsn.dsmz.de'>lpsn.dsmz.de</a>). This supplementation is needed until the <a href='https://github.com/CatalogueOfLife/general'>CoL+ project</a> is finished, which we await.</p>
|
|
<p>Click here for more information about the included taxa. Check which versions of the CoL and LPSN were included in this package with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version()</a></code>.</p>
|
|
<h2 class="hasAnchor" id="included-taxa"><a class="anchor" href="#included-taxa"></a>Included Taxa</h2>
|
|
|
|
|
|
|
|
<p>Included are:</p><ul>
|
|
<li><p>All ~58,000 (sub)species from the kingdoms of Archaea, Bacteria, Chromista and Protozoa</p></li>
|
|
<li><p>All ~5,000 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Microascales, Mucorales, Onygenales, Pneumocystales, Saccharomycetales, Schizosaccharomycetales and Tremellales, as well as ~4,600 other fungal (sub)species. 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 and including everything would tremendously slow down our algorithms too. By only including the aforementioned taxonomic orders, the most relevant fungi are covered (such as all species of <em>Aspergillus</em>, <em>Candida</em>, <em>Cryptococcus</em>, <em>Histplasma</em>, <em>Pneumocystis</em>, <em>Saccharomyces</em> and <em>Trichophyton</em>).</p></li>
|
|
<li><p>All ~2,200 (sub)species from ~50 other relevant genera from the kingdom of Animalia (such as <em>Strongyloides</em> and <em>Taenia</em>)</p></li>
|
|
<li><p>All ~14,000 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 responsible author(s) and year of scientific publication</p></li>
|
|
</ul>
|
|
|
|
<p>The Catalogue of Life (<a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>) is the most comprehensive and authoritative global index of species currently available. It holds essential information on the names, relationships and distributions of over 1.9 million species. The Catalogue of Life is used to support the major biodiversity and conservation information services such as the Global Biodiversity Information Facility (GBIF), Encyclopedia of Life (EoL) and the International Union for Conservation of Nature Red List. It is recognised by the Convention on Biological Diversity as a significant component of the Global Taxonomy Initiative and a contribution to Target 1 of the Global Strategy for Plant Conservation.</p>
|
|
<p>The syntax used to transform the original data to a cleansed <span style="R">R</span> format, can be found here: <a href='https://github.com/msberends/AMR/blob/master/data-raw/reproduction_of_microorganisms.R'>https://github.com/msberends/AMR/blob/master/data-raw/reproduction_of_microorganisms.R</a>.</p>
|
|
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on Our Website!</h2>
|
|
|
|
|
|
|
|
<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
|
|
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
|
|
|
|
<div class='dont-index'><p>Data set <a href='microorganisms.html'>microorganisms</a> for the actual data. <br />
|
|
Function <code><a href='as.mo.html'>as.mo()</a></code> to use the data for intelligent determination of microorganisms.</p></div>
|
|
|
|
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
|
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='co'># Get version info of included data set</span>
|
|
<span class='fu'><a href='catalogue_of_life_version.html'>catalogue_of_life_version</a></span><span class='op'>(</span><span class='op'>)</span>
|
|
|
|
|
|
<span class='co'># Get a note when a species was renamed</span>
|
|
<span class='fu'><a href='mo_property.html'>mo_shortname</a></span><span class='op'>(</span><span class='st'>"Chlamydophila psittaci"</span><span class='op'>)</span>
|
|
<span class='co'># Note: 'Chlamydophila psittaci' (Everett et al., 1999) was renamed back to</span>
|
|
<span class='co'># 'Chlamydia psittaci' (Page, 1968)</span>
|
|
<span class='co'>#> [1] "C. psittaci"</span>
|
|
|
|
<span class='co'># Get any property from the entire taxonomic tree for all included species</span>
|
|
<span class='fu'><a href='mo_property.html'>mo_class</a></span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span>
|
|
<span class='co'>#> [1] "Gammaproteobacteria"</span>
|
|
|
|
<span class='fu'><a href='mo_property.html'>mo_family</a></span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span>
|
|
<span class='co'>#> [1] "Enterobacteriaceae"</span>
|
|
|
|
<span class='fu'><a href='mo_property.html'>mo_gramstain</a></span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># based on kingdom and phylum, see ?mo_gramstain</span>
|
|
<span class='co'>#> [1] "Gram-negative"</span>
|
|
|
|
<span class='fu'><a href='mo_property.html'>mo_ref</a></span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span>
|
|
<span class='co'>#> [1] "Castellani et al., 1919"</span>
|
|
|
|
<span class='co'># Do not get mistaken - this package is about microorganisms</span>
|
|
<span class='fu'><a href='mo_property.html'>mo_kingdom</a></span><span class='op'>(</span><span class='st'>"C. elegans"</span><span class='op'>)</span>
|
|
<span class='co'>#> [1] "Fungi" # Fungi?!</span>
|
|
<span class='fu'><a href='mo_property.html'>mo_name</a></span><span class='op'>(</span><span class='st'>"C. elegans"</span><span class='op'>)</span>
|
|
<span class='co'>#> [1] "Cladosporium elegans" # Because a microorganism was found</span>
|
|
</code></pre></div>
|
|
</div>
|
|
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
|
<nav id="toc" data-toggle="toc" class="sticky-top">
|
|
<h2 data-toc-skip>Contents</h2>
|
|
</nav>
|
|
</div>
|
|
</div>
|
|
|
|
|
|
<footer>
|
|
<div class="copyright">
|
|
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
|
|
</div>
|
|
|
|
<div class="pkgdown">
|
|
<p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 1.6.1.9001.</p></p>
|
|
</div>
|
|
|
|
</footer>
|
|
</div>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
</body>
|
|
</html>
|
|
|
|
|