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<div class="col-md-9 contents">
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<h1 data-toc-skip>Data sets for download / own use</h1>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/datasets.Rmd"><code>vignettes/datasets.Rmd</code></a></small>
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<div class="hidden name"><code>datasets.Rmd</code></div>
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<p>This package contains a lot of reference data sets that are all reliable, up-to-date and free to download. You can even use them outside of R, for example to teach your laboratory information system (LIS) about intrinsic resistance!</p>
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<p>We included them in our <code>AMR</code> package, but also automatically ‘mirror’ them to our public repository in different software formats. On this page, we explain how to download them and how the structure of the data sets look like. The tab separated files <strong>allow for machine reading taxonomic data and EUCAST and CLSI interpretation guidelines</strong>, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. We also offer all data sets in formats for R, SPSS, SAS, Stata and Excel.</p>
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<p><em>Note: Years and dates of updates mentioned on this page, are from on <code>AMR</code> package version 1.3.0.9005, online released on 17 August 2020. <strong>If you are reading this page from within R, please <a href="https://msberends.github.io/AMR/articles/datasets.html">visit our website</a> for the latest update.</strong></em></p>
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<div id="microorganisms-currently-accepted-names" class="section level2">
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<h2 class="hasAnchor">
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<a href="#microorganisms-currently-accepted-names" class="anchor"></a>Microorganisms (currently accepted names)</h2>
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<p>This data set is in R available as <code>microorganisms</code>, after you load the <code>AMR</code> package.</p>
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<p>It was last updated on 28 July 2020 20:52:40 CEST.</p>
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<p>Direct download links:<br><a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.rds">R file (.rds)</a>, 2.7 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.xlsx">Excel workbook (.xlsx)</a>, 6.1 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.sav">SPSS file (.sav)</a>, 28.2 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.sav">Stata file (.dta)</a>, 28.2 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.dta">SAS file (.sas)</a>, 25.2 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.txt">Tab separated file (.txt)</a>, 13.3 MB.</p>
|
||
<div id="source" class="section level3">
|
||
<h3 class="hasAnchor">
|
||
<a href="#source" class="anchor"></a>Source</h3>
|
||
<p>Our full taxonomy of microorganisms is based on the authoritative and comprehensive:</p>
|
||
<ul>
|
||
<li>
|
||
<a href="http://www.catalogueoflife.org">Catalogue of Life</a> (included version: 2019)</li>
|
||
<li>
|
||
<a href="https://lpsn.dsmz.de">List of Prokaryotic names with Standing in Nomenclature</a> (LPSN, included version: May 2020)</li>
|
||
</ul>
|
||
</div>
|
||
<div id="structure" class="section level3">
|
||
<h3 class="hasAnchor">
|
||
<a href="#structure" class="anchor"></a>Structure</h3>
|
||
<p>A data set with 67,151 rows and 16 columns, containing the following column names:<br><em>mo, fullname, kingdom, phylum, class, order, family, genus, species, subspecies, rank, ref, species_id, source, prevalence, snomed</em>.</p>
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<p>Included (sub)species per taxonomic kingdom:</p>
|
||
<table class="table">
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||
<thead><tr class="header">
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||
<th align="center">Kingdom</th>
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||
<th align="center">Number of (sub)species</th>
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</tr></thead>
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<tbody>
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<tr class="odd">
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<td align="center">(unknown kingdom)</td>
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<td align="center">1</td>
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</tr>
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<tr class="even">
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<td align="center">Animalia</td>
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||
<td align="center">2,153</td>
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||
</tr>
|
||
<tr class="odd">
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||
<td align="center">Archaea</td>
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||
<td align="center">697</td>
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||
</tr>
|
||
<tr class="even">
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||
<td align="center">Bacteria</td>
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||
<td align="center">19,244</td>
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||
</tr>
|
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<tr class="odd">
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||
<td align="center">Chromista</td>
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||
<td align="center">32,164</td>
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||
</tr>
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||
<tr class="even">
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||
<td align="center">Fungi</td>
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||
<td align="center">9,582</td>
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</tr>
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</tbody>
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</table>
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<p>Example rows when filtering on genus <em>Escherichia</em>:</p>
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||
<table class="table">
|
||
<colgroup>
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||
<col width="5%">
|
||
<col width="9%">
|
||
<col width="3%">
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||
<col width="6%">
|
||
<col width="8%">
|
||
<col width="6%">
|
||
<col width="7%">
|
||
<col width="5%">
|
||
<col width="4%">
|
||
<col width="4%">
|
||
<col width="3%">
|
||
<col width="9%">
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||
<col width="13%">
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<col width="3%">
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<col width="4%">
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<col width="4%">
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</colgroup>
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<thead><tr class="header">
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||
<th align="center">mo</th>
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<th align="center">fullname</th>
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<th align="center">kingdom</th>
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||
<th align="center">phylum</th>
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||
<th align="center">class</th>
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||
<th align="center">order</th>
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||
<th align="center">family</th>
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||
<th align="center">genus</th>
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||
<th align="center">species</th>
|
||
<th align="center">subspecies</th>
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||
<th align="center">rank</th>
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||
<th align="center">ref</th>
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||
<th align="center">species_id</th>
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||
<th align="center">source</th>
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||
<th align="center">prevalence</th>
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||
<th align="center">snomed</th>
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||
</tr></thead>
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||
<tbody>
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||
<tr class="odd">
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||
<td align="center">B_ESCHR</td>
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<td align="center">Escherichia</td>
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||
<td align="center">Bacteria</td>
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||
<td align="center">Proteobacteria</td>
|
||
<td align="center">Gammaproteobacteria</td>
|
||
<td align="center">Enterobacterales</td>
|
||
<td align="center">Enterobacteriaceae</td>
|
||
<td align="center">Escherichia</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center">genus</td>
|
||
<td align="center"></td>
|
||
<td align="center">bc4fdde6867d5ecfc728000b0bfb49a3</td>
|
||
<td align="center">CoL</td>
|
||
<td align="center">1</td>
|
||
<td align="center">64735005</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">B_ESCHR_ALBR</td>
|
||
<td align="center">Escherichia albertii</td>
|
||
<td align="center">Bacteria</td>
|
||
<td align="center">Proteobacteria</td>
|
||
<td align="center">Gammaproteobacteria</td>
|
||
<td align="center">Enterobacterales</td>
|
||
<td align="center">Enterobacteriaceae</td>
|
||
<td align="center">Escherichia</td>
|
||
<td align="center">albertii</td>
|
||
<td align="center"></td>
|
||
<td align="center">species</td>
|
||
<td align="center">Huys et al., 2003</td>
|
||
<td align="center">36618b1ed3b8b7e5a61f40eb9386e63c</td>
|
||
<td align="center">CoL</td>
|
||
<td align="center">1</td>
|
||
<td align="center">419388003</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">B_ESCHR_COLI</td>
|
||
<td align="center">Escherichia coli</td>
|
||
<td align="center">Bacteria</td>
|
||
<td align="center">Proteobacteria</td>
|
||
<td align="center">Gammaproteobacteria</td>
|
||
<td align="center">Enterobacterales</td>
|
||
<td align="center">Enterobacteriaceae</td>
|
||
<td align="center">Escherichia</td>
|
||
<td align="center">coli</td>
|
||
<td align="center"></td>
|
||
<td align="center">species</td>
|
||
<td align="center">Castellani et al., 1919</td>
|
||
<td align="center">3254b3db31bf16fdde669ac57bf8c4fe</td>
|
||
<td align="center">CoL</td>
|
||
<td align="center">1</td>
|
||
<td align="center">112283007</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">B_ESCHR_FRGS</td>
|
||
<td align="center">Escherichia fergusonii</td>
|
||
<td align="center">Bacteria</td>
|
||
<td align="center">Proteobacteria</td>
|
||
<td align="center">Gammaproteobacteria</td>
|
||
<td align="center">Enterobacterales</td>
|
||
<td align="center">Enterobacteriaceae</td>
|
||
<td align="center">Escherichia</td>
|
||
<td align="center">fergusonii</td>
|
||
<td align="center"></td>
|
||
<td align="center">species</td>
|
||
<td align="center">Farmer et al., 1985</td>
|
||
<td align="center">82d98b10c456ce5f4c8c515f4e1567e2</td>
|
||
<td align="center">CoL</td>
|
||
<td align="center">1</td>
|
||
<td align="center">72461005</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">B_ESCHR_HRMN</td>
|
||
<td align="center">Escherichia hermannii</td>
|
||
<td align="center">Bacteria</td>
|
||
<td align="center">Proteobacteria</td>
|
||
<td align="center">Gammaproteobacteria</td>
|
||
<td align="center">Enterobacterales</td>
|
||
<td align="center">Enterobacteriaceae</td>
|
||
<td align="center">Escherichia</td>
|
||
<td align="center">hermannii</td>
|
||
<td align="center"></td>
|
||
<td align="center">species</td>
|
||
<td align="center">Brenner et al., 1983</td>
|
||
<td align="center">b16086aee36e3b46b565510083ab4b65</td>
|
||
<td align="center">CoL</td>
|
||
<td align="center">1</td>
|
||
<td align="center">85786000</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">B_ESCHR_MRMT</td>
|
||
<td align="center">Escherichia marmotae</td>
|
||
<td align="center">Bacteria</td>
|
||
<td align="center">Proteobacteria</td>
|
||
<td align="center">Gammaproteobacteria</td>
|
||
<td align="center">Enterobacterales</td>
|
||
<td align="center">Enterobacteriaceae</td>
|
||
<td align="center">Escherichia</td>
|
||
<td align="center">marmotae</td>
|
||
<td align="center"></td>
|
||
<td align="center">species</td>
|
||
<td align="center">Liu et al., 2015</td>
|
||
<td align="center">792928</td>
|
||
<td align="center">DSMZ</td>
|
||
<td align="center">1</td>
|
||
<td align="center"></td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
</div>
|
||
</div>
|
||
<div id="microorganisms-previously-accepted-names" class="section level2">
|
||
<h2 class="hasAnchor">
|
||
<a href="#microorganisms-previously-accepted-names" class="anchor"></a>Microorganisms (previously accepted names)</h2>
|
||
<p>This data set is in R available as <code>microorganisms.old</code>, after you load the <code>AMR</code> package.</p>
|
||
<p>It was last updated on 28 May 2020 11:17:56 CEST.</p>
|
||
<p>Direct download links:<br><a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.rds">R file (.rds)</a>, 0.3 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.xlsx">Excel workbook (.xlsx)</a>, 0.4 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.sav">SPSS file (.sav)</a>, 1.9 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.sav">Stata file (.dta)</a>, 1.9 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.dta">SAS file (.sas)</a>, 1.8 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.txt">Tab separated file (.txt)</a>, 0.8 MB.</p>
|
||
<div id="source-1" class="section level3">
|
||
<h3 class="hasAnchor">
|
||
<a href="#source-1" class="anchor"></a>Source</h3>
|
||
<p>This data set contains old, previously accepted taxonomic names. The data sources are the same as the <code>microorganisms</code> data set:</p>
|
||
<ul>
|
||
<li>
|
||
<a href="http://www.catalogueoflife.org">Catalogue of Life</a> (included version: 2019)</li>
|
||
<li>
|
||
<a href="https://lpsn.dsmz.de">List of Prokaryotic names with Standing in Nomenclature</a> (LPSN, included version: May 2020)</li>
|
||
</ul>
|
||
</div>
|
||
<div id="structure-1" class="section level3">
|
||
<h3 class="hasAnchor">
|
||
<a href="#structure-1" class="anchor"></a>Structure</h3>
|
||
<p>A data set with 12,708 rows and 4 columns, containing the following column names:<br><em>fullname, fullname_new, ref, prevalence</em>.</p>
|
||
<p><strong>Note:</strong> remember that the ‘ref’ columns contains the scientific reference to the old taxonomic entries, i.e. of column <em>fullname</em>. For the scientific reference of the new names, i.e. of column <em>fullname_new</em>, see the <code>microorganisms</code> data set.</p>
|
||
<p>Example rows when filtering on <em>Escherichia</em>:</p>
|
||
<table class="table">
|
||
<thead><tr class="header">
|
||
<th align="center">fullname</th>
|
||
<th align="center">fullname_new</th>
|
||
<th align="center">ref</th>
|
||
<th align="center">prevalence</th>
|
||
</tr></thead>
|
||
<tbody>
|
||
<tr class="odd">
|
||
<td align="center">Escherichia adecarboxylata</td>
|
||
<td align="center">Leclercia adecarboxylata</td>
|
||
<td align="center">Leclerc, 1962</td>
|
||
<td align="center">1</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">Escherichia blattae</td>
|
||
<td align="center">Shimwellia blattae</td>
|
||
<td align="center">Burgess et al., 1973</td>
|
||
<td align="center">1</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">Escherichia vulneris</td>
|
||
<td align="center">Pseudescherichia vulneris</td>
|
||
<td align="center">Brenner et al., 1983</td>
|
||
<td align="center">1</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
</div>
|
||
</div>
|
||
<div id="antibiotic-agents" class="section level2">
|
||
<h2 class="hasAnchor">
|
||
<a href="#antibiotic-agents" class="anchor"></a>Antibiotic agents</h2>
|
||
<p>This data set is in R available as <code>antibiotics</code>, after you load the <code>AMR</code> package.</p>
|
||
<p>It was last updated on 31 July 2020 12:12:13 CEST.</p>
|
||
<p>Direct download links:<br><a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.rds">R file (.rds)</a>, 37 kB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.xlsx">Excel workbook (.xlsx)</a>, 65 kB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.sav">SPSS file (.sav)</a>, 1.3 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.sav">Stata file (.dta)</a>, 1.3 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.dta">SAS file (.sas)</a>, 0.3 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.txt">Tab separated file (.txt)</a>, 0.1 MB.</p>
|
||
<div id="source-2" class="section level3">
|
||
<h3 class="hasAnchor">
|
||
<a href="#source-2" class="anchor"></a>Source</h3>
|
||
<p>This data set contains all EARS-Net and ATC codes gathered from WHO and WHONET, and all compound IDs from PubChem. It also contains all brand names (synonyms) as found on PubChem and Defined Daily Doses (DDDs) for oral and parenteral administration.</p>
|
||
<ul>
|
||
<li>
|
||
<a href="https://www.whocc.no/atc_ddd_index/">ATC/DDD index from WHO Collaborating Centre for Drug Statistics Methodology</a> (note: this may not be used for commercial purposes, but is frelly available from the WHO CC website for personal use)</li>
|
||
<li><a href="https://pubchem.ncbi.nlm.nih.gov">PubChem by the US National Library of Medicine</a></li>
|
||
<li><a href="https://whonet.org">WHONET software 2019</a></li>
|
||
</ul>
|
||
</div>
|
||
<div id="structure-2" class="section level3">
|
||
<h3 class="hasAnchor">
|
||
<a href="#structure-2" class="anchor"></a>Structure</h3>
|
||
<p>A data set with 456 rows and 14 columns, containing the following column names:<br><em>ab, atc, cid, name, group, atc_group1, atc_group2, abbreviations, synonyms, oral_ddd, oral_units, iv_ddd, iv_units, loinc</em>.</p>
|
||
<p>Example rows:</p>
|
||
<table class="table">
|
||
<colgroup>
|
||
<col width="1%">
|
||
<col width="2%">
|
||
<col width="3%">
|
||
<col width="9%">
|
||
<col width="8%">
|
||
<col width="14%">
|
||
<col width="19%">
|
||
<col width="6%">
|
||
<col width="11%">
|
||
<col width="3%">
|
||
<col width="3%">
|
||
<col width="2%">
|
||
<col width="3%">
|
||
<col width="10%">
|
||
</colgroup>
|
||
<thead><tr class="header">
|
||
<th align="center">ab</th>
|
||
<th align="center">atc</th>
|
||
<th align="center">cid</th>
|
||
<th align="center">name</th>
|
||
<th align="center">group</th>
|
||
<th align="center">atc_group1</th>
|
||
<th align="center">atc_group2</th>
|
||
<th align="center">abbreviations</th>
|
||
<th align="center">synonyms</th>
|
||
<th align="center">oral_ddd</th>
|
||
<th align="center">oral_units</th>
|
||
<th align="center">iv_ddd</th>
|
||
<th align="center">iv_units</th>
|
||
<th align="center">loinc</th>
|
||
</tr></thead>
|
||
<tbody>
|
||
<tr class="odd">
|
||
<td align="center">AMK</td>
|
||
<td align="center">J01GB06</td>
|
||
<td align="center">37768</td>
|
||
<td align="center">Amikacin</td>
|
||
<td align="center">Aminoglycosides</td>
|
||
<td align="center">Aminoglycoside antibacterials</td>
|
||
<td align="center">Other aminoglycosides</td>
|
||
<td align="center">ak, ami, amik, …</td>
|
||
<td align="center">amicacin, amikacillin, amikacin, …</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center">1.0</td>
|
||
<td align="center">g</td>
|
||
<td align="center">13546-7, 15098-7, 17798-0, …</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">AMX</td>
|
||
<td align="center">J01CA04</td>
|
||
<td align="center">33613</td>
|
||
<td align="center">Amoxicillin</td>
|
||
<td align="center">Beta-lactams/penicillins</td>
|
||
<td align="center">Beta-lactam antibacterials, penicillins</td>
|
||
<td align="center">Penicillins with extended spectrum</td>
|
||
<td align="center">ac, amox, amx</td>
|
||
<td align="center">actimoxi, amoclen, amolin, …</td>
|
||
<td align="center">1.0</td>
|
||
<td align="center">g</td>
|
||
<td align="center">1.0</td>
|
||
<td align="center">g</td>
|
||
<td align="center">16365-9, 25274-2, 3344-9, …</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">AMC</td>
|
||
<td align="center">J01CR02</td>
|
||
<td align="center">23665637</td>
|
||
<td align="center">Amoxicillin/clavulanic acid</td>
|
||
<td align="center">Beta-lactams/penicillins</td>
|
||
<td align="center">Beta-lactam antibacterials, penicillins</td>
|
||
<td align="center">Combinations of penicillins, incl. beta-lactamase inhibitors</td>
|
||
<td align="center">a/c, amcl, aml, …</td>
|
||
<td align="center">amocla, amoclan, amoclav, …</td>
|
||
<td align="center">1.0</td>
|
||
<td align="center">g</td>
|
||
<td align="center">3.0</td>
|
||
<td align="center">g</td>
|
||
<td align="center"></td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">AMP</td>
|
||
<td align="center">J01CA01</td>
|
||
<td align="center">6249</td>
|
||
<td align="center">Ampicillin</td>
|
||
<td align="center">Beta-lactams/penicillins</td>
|
||
<td align="center">Beta-lactam antibacterials, penicillins</td>
|
||
<td align="center">Penicillins with extended spectrum</td>
|
||
<td align="center">am, amp, ampi</td>
|
||
<td align="center">acillin, adobacillin, amblosin, …</td>
|
||
<td align="center">2.0</td>
|
||
<td align="center">g</td>
|
||
<td align="center">2.0</td>
|
||
<td align="center">g</td>
|
||
<td align="center">21066-6, 3355-5, 33562-0, …</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">AZM</td>
|
||
<td align="center">J01FA10</td>
|
||
<td align="center">447043</td>
|
||
<td align="center">Azithromycin</td>
|
||
<td align="center">Macrolides/lincosamides</td>
|
||
<td align="center">Macrolides, lincosamides and streptogramins</td>
|
||
<td align="center">Macrolides</td>
|
||
<td align="center">az, azi, azit, …</td>
|
||
<td align="center">aritromicina, azasite, azenil, …</td>
|
||
<td align="center">0.3</td>
|
||
<td align="center">g</td>
|
||
<td align="center">0.5</td>
|
||
<td align="center">g</td>
|
||
<td align="center">16420-2, 25233-8</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">CZO</td>
|
||
<td align="center">J01DB04</td>
|
||
<td align="center">33255</td>
|
||
<td align="center">Cefazolin</td>
|
||
<td align="center">Cephalosporins (1st gen.)</td>
|
||
<td align="center">Other beta-lactam antibacterials</td>
|
||
<td align="center">First-generation cephalosporins</td>
|
||
<td align="center">cfz, cfzl, cz, …</td>
|
||
<td align="center">atirin, cefamezin, cefamezine, …</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center">3.0</td>
|
||
<td align="center">g</td>
|
||
<td align="center">16566-2, 25235-3, 3442-1, …</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
</div>
|
||
</div>
|
||
<div id="antiviral-agents" class="section level2">
|
||
<h2 class="hasAnchor">
|
||
<a href="#antiviral-agents" class="anchor"></a>Antiviral agents</h2>
|
||
<p>This data set is in R available as <code>antivirals</code>, after you load the <code>AMR</code> package.</p>
|
||
<p>It was last updated on 23 November 2019 19:03:43 CET.</p>
|
||
<p>Direct download links:<br><a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.rds">R file (.rds)</a>, 5 kB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.xlsx">Excel workbook (.xlsx)</a>, 14 kB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.sav">SPSS file (.sav)</a>, 68 kB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.sav">Stata file (.dta)</a>, 68 kB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.dta">SAS file (.sas)</a>, 67 kB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.txt">Tab separated file (.txt)</a>, 16 kB.</p>
|
||
<div id="source-3" class="section level3">
|
||
<h3 class="hasAnchor">
|
||
<a href="#source-3" class="anchor"></a>Source</h3>
|
||
<p>This data set contains all ATC codes gathered from WHO and all compound IDs from PubChem. It also contains all brand names (synonyms) as found on PubChem and Defined Daily Doses (DDDs) for oral and parenteral administration.</p>
|
||
<ul>
|
||
<li>
|
||
<a href="https://www.whocc.no/atc_ddd_index/">ATC/DDD index from WHO Collaborating Centre for Drug Statistics Methodology</a> (note: this may not be used for commercial purposes, but is frelly available from the WHO CC website for personal use)</li>
|
||
<li><a href="https://pubchem.ncbi.nlm.nih.gov">PubChem by the US National Library of Medicine</a></li>
|
||
</ul>
|
||
</div>
|
||
<div id="structure-3" class="section level3">
|
||
<h3 class="hasAnchor">
|
||
<a href="#structure-3" class="anchor"></a>Structure</h3>
|
||
<p>A data set with 102 rows and 9 columns, containing the following column names:<br><em>atc, cid, name, atc_group, synonyms, oral_ddd, oral_units, iv_ddd, iv_units</em>.</p>
|
||
<p>Example rows:</p>
|
||
<table class="table">
|
||
<colgroup>
|
||
<col width="4%">
|
||
<col width="5%">
|
||
<col width="9%">
|
||
<col width="32%">
|
||
<col width="30%">
|
||
<col width="4%">
|
||
<col width="5%">
|
||
<col width="3%">
|
||
<col width="4%">
|
||
</colgroup>
|
||
<thead><tr class="header">
|
||
<th align="center">atc</th>
|
||
<th align="center">cid</th>
|
||
<th align="center">name</th>
|
||
<th align="center">atc_group</th>
|
||
<th align="center">synonyms</th>
|
||
<th align="center">oral_ddd</th>
|
||
<th align="center">oral_units</th>
|
||
<th align="center">iv_ddd</th>
|
||
<th align="center">iv_units</th>
|
||
</tr></thead>
|
||
<tbody>
|
||
<tr class="odd">
|
||
<td align="center">J05AF06</td>
|
||
<td align="center">441300</td>
|
||
<td align="center">abacavir</td>
|
||
<td align="center">Nucleoside and nucleotide reverse transcriptase inhibitors</td>
|
||
<td align="center">Abacavir, Abacavir sulfate, Ziagen</td>
|
||
<td align="center">0.6</td>
|
||
<td align="center">g</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">J05AB01</td>
|
||
<td align="center">135398513</td>
|
||
<td align="center">aciclovir</td>
|
||
<td align="center">Nucleosides and nucleotides excl. reverse transcriptase inhibitors</td>
|
||
<td align="center">Acicloftal, Aciclovier, Aciclovir, …</td>
|
||
<td align="center">4.0</td>
|
||
<td align="center">g</td>
|
||
<td align="center">4</td>
|
||
<td align="center">g</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">J05AF08</td>
|
||
<td align="center">60871</td>
|
||
<td align="center">adefovir dipivoxil</td>
|
||
<td align="center">Nucleoside and nucleotide reverse transcriptase inhibitors</td>
|
||
<td align="center">Adefovir di ester, Adefovir dipivoxil, Adefovir Dipivoxil, …</td>
|
||
<td align="center">10.0</td>
|
||
<td align="center">mg</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">J05AE05</td>
|
||
<td align="center">65016</td>
|
||
<td align="center">amprenavir</td>
|
||
<td align="center">Protease inhibitors</td>
|
||
<td align="center">Agenerase, Amprenavir, Amprenavirum, …</td>
|
||
<td align="center">1.2</td>
|
||
<td align="center">g</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">J05AP06</td>
|
||
<td align="center">16076883</td>
|
||
<td align="center">asunaprevir</td>
|
||
<td align="center">Antivirals for treatment of HCV infections</td>
|
||
<td align="center">Asunaprevir, Sunvepra</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">J05AE08</td>
|
||
<td align="center">148192</td>
|
||
<td align="center">atazanavir</td>
|
||
<td align="center">Protease inhibitors</td>
|
||
<td align="center">Atazanavir, Atazanavir Base, Latazanavir, …</td>
|
||
<td align="center">0.3</td>
|
||
<td align="center">g</td>
|
||
<td align="center"></td>
|
||
<td align="center"></td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
</div>
|
||
</div>
|
||
<div id="intrinsic-bacterial-resistance" class="section level2">
|
||
<h2 class="hasAnchor">
|
||
<a href="#intrinsic-bacterial-resistance" class="anchor"></a>Intrinsic bacterial resistance</h2>
|
||
<p>This data set is in R available as <code>intrinsic_resistant</code>, after you load the <code>AMR</code> package.</p>
|
||
<p>It was last updated on 14 August 2020 14:18:20 CEST.</p>
|
||
<p>Direct download links:<br><a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.rds">R file (.rds)</a>, 97 kB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.xlsx">Excel workbook (.xlsx)</a>, 0.5 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.sav">SPSS file (.sav)</a>, 4.2 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.sav">Stata file (.dta)</a>, 4.2 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.dta">SAS file (.sas)</a>, 3.7 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.txt">Tab separated file (.txt)</a>, 1.8 MB.</p>
|
||
<div id="source-4" class="section level3">
|
||
<h3 class="hasAnchor">
|
||
<a href="#source-4" class="anchor"></a>Source</h3>
|
||
<p>This data set contains all defined intrinsic resistance by EUCAST of all bug-drug combinations.</p>
|
||
<p>The data set is based on ‘EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes’, version 3.1, 2016.</p>
|
||
</div>
|
||
<div id="structure-4" class="section level3">
|
||
<h3 class="hasAnchor">
|
||
<a href="#structure-4" class="anchor"></a>Structure</h3>
|
||
<p>A data set with 49,462 rows and 2 columns, containing the following column names:<br><em>microorganism, antibiotic</em>.</p>
|
||
<p>Example rows when filtering on <em>Klebsiella</em>:</p>
|
||
<table class="table">
|
||
<thead><tr class="header">
|
||
<th align="center">microorganism</th>
|
||
<th align="center">antibiotic</th>
|
||
</tr></thead>
|
||
<tbody>
|
||
<tr class="odd">
|
||
<td align="center">Klebsiella</td>
|
||
<td align="center">Amoxicillin</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">Klebsiella</td>
|
||
<td align="center">Ampicillin</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">Klebsiella</td>
|
||
<td align="center">Azithromycin</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">Klebsiella</td>
|
||
<td align="center">Clarithromycin</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">Klebsiella</td>
|
||
<td align="center">Daptomycin</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">Klebsiella</td>
|
||
<td align="center">Erythromycin</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
</div>
|
||
</div>
|
||
<div id="interpretation-from-mic-values-disk-diameters-to-rsi" class="section level2">
|
||
<h2 class="hasAnchor">
|
||
<a href="#interpretation-from-mic-values-disk-diameters-to-rsi" class="anchor"></a>Interpretation from MIC values / disk diameters to R/SI</h2>
|
||
<p>This data set is in R available as <code>rsi_translation</code>, after you load the <code>AMR</code> package.</p>
|
||
<p>It was last updated on 29 July 2020 13:12:34 CEST.</p>
|
||
<p>Direct download links:<br><a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.rds">R file (.rds)</a>, 55 kB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.xlsx">Excel workbook (.xlsx)</a>, 0.6 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.sav">SPSS file (.sav)</a>, 3.4 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.sav">Stata file (.dta)</a>, 3.4 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.dta">SAS file (.sas)</a>, 3 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.txt">Tab separated file (.txt)</a>, 1.5 MB.</p>
|
||
<div id="source-5" class="section level3">
|
||
<h3 class="hasAnchor">
|
||
<a href="#source-5" class="anchor"></a>Source</h3>
|
||
<p>This data set contains interpretation rules for MIC values and disk diffusion diameters. Included guidelines are CLSI (2010-2019) and EUCAST (2011-2020).</p>
|
||
</div>
|
||
<div id="structure-5" class="section level3">
|
||
<h3 class="hasAnchor">
|
||
<a href="#structure-5" class="anchor"></a>Structure</h3>
|
||
<p>A data set with 18,650 rows and 10 columns, containing the following column names:<br><em>guideline, method, site, mo, ab, ref_tbl, disk_dose, breakpoint_S, breakpoint_R, uti</em>.</p>
|
||
<p>Example rows:</p>
|
||
<table class="table">
|
||
<colgroup>
|
||
<col width="8%">
|
||
<col width="5%">
|
||
<col width="4%">
|
||
<col width="12%">
|
||
<col width="20%">
|
||
<col width="17%">
|
||
<col width="7%">
|
||
<col width="9%">
|
||
<col width="9%">
|
||
<col width="4%">
|
||
</colgroup>
|
||
<thead><tr class="header">
|
||
<th align="center">guideline</th>
|
||
<th align="center">method</th>
|
||
<th align="center">site</th>
|
||
<th align="center">mo</th>
|
||
<th align="center">ab</th>
|
||
<th align="center">ref_tbl</th>
|
||
<th align="center">disk_dose</th>
|
||
<th align="center">breakpoint_S</th>
|
||
<th align="center">breakpoint_R</th>
|
||
<th align="center">uti</th>
|
||
</tr></thead>
|
||
<tbody>
|
||
<tr class="odd">
|
||
<td align="center">EUCAST 2020</td>
|
||
<td align="center">DISK</td>
|
||
<td align="center"></td>
|
||
<td align="center">Enterobacterales</td>
|
||
<td align="center">Amoxicillin/clavulanic acid</td>
|
||
<td align="center">Enterobacterales</td>
|
||
<td align="center">20-10ug</td>
|
||
<td align="center">19</td>
|
||
<td align="center">19</td>
|
||
<td align="center">FALSE</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">EUCAST 2020</td>
|
||
<td align="center">DISK</td>
|
||
<td align="center">UTI</td>
|
||
<td align="center">Enterobacterales</td>
|
||
<td align="center">Amoxicillin/clavulanic acid</td>
|
||
<td align="center">Enterobacterales</td>
|
||
<td align="center">20-10ug</td>
|
||
<td align="center">16</td>
|
||
<td align="center">16</td>
|
||
<td align="center">TRUE</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">EUCAST 2020</td>
|
||
<td align="center">MIC</td>
|
||
<td align="center"></td>
|
||
<td align="center">Enterobacterales</td>
|
||
<td align="center">Amoxicillin/clavulanic acid</td>
|
||
<td align="center">Enterobacterales</td>
|
||
<td align="center"></td>
|
||
<td align="center">8</td>
|
||
<td align="center">8</td>
|
||
<td align="center">FALSE</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">EUCAST 2020</td>
|
||
<td align="center">MIC</td>
|
||
<td align="center">UTI</td>
|
||
<td align="center">Enterobacterales</td>
|
||
<td align="center">Amoxicillin/clavulanic acid</td>
|
||
<td align="center">Enterobacterales</td>
|
||
<td align="center"></td>
|
||
<td align="center">32</td>
|
||
<td align="center">32</td>
|
||
<td align="center">TRUE</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="center">EUCAST 2020</td>
|
||
<td align="center">MIC</td>
|
||
<td align="center"></td>
|
||
<td align="center">Actinomyces</td>
|
||
<td align="center">Amoxicillin/clavulanic acid</td>
|
||
<td align="center">Anaerobes, Grampositive</td>
|
||
<td align="center"></td>
|
||
<td align="center">4</td>
|
||
<td align="center">8</td>
|
||
<td align="center">FALSE</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="center">EUCAST 2020</td>
|
||
<td align="center">MIC</td>
|
||
<td align="center"></td>
|
||
<td align="center">Bacteroides</td>
|
||
<td align="center">Amoxicillin/clavulanic acid</td>
|
||
<td align="center">Anaerobes, Gramnegative</td>
|
||
<td align="center"></td>
|
||
<td align="center">4</td>
|
||
<td align="center">8</td>
|
||
<td align="center">FALSE</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
|
||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||
|
||
<nav id="toc" data-toggle="toc"><h2 data-toc-skip>Contents</h2>
|
||
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|
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|
||
|
||
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|
||
|
||
|
||
|
||
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|
||
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>.</p>
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