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@@ -171,13 +171,15 @@
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<li><p><i>p<sub>n</sub></i> is the human pathogenic prevalence group of <i>n</i>, as described below;</p></li>
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<li><p><i>k<sub>n</sub></i> is the taxonomic kingdom of <i>n</i>, set as Bacteria = 1, Fungi = 2, Protozoa = 3, Archaea = 4, others = 5.</p></li>
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</ul><p>The grouping into human pathogenic prevalence (\(p\)) is based on recent work from Bartlett <em>et al.</em> (2022, <a href="https://doi.org/10.1099/mic.0.001269" class="external-link">doi:10.1099/mic.0.001269</a>
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) who extensively studied medical-scientific literature to categorise all bacterial species into these groups:</p><ul><li><p><strong>Established</strong>, if a taxonomic species has infected at least three persons in three or more references. These records have <code>prevalence = 1.0</code> in the <a href="microorganisms.html">microorganisms</a> data set.</p></li>
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<li><p><strong>Putative</strong>, if a taxonomic species has fewer than three known cases. These records have <code>prevalence = 2.0</code> in the <a href="microorganisms.html">microorganisms</a> data set.</p></li>
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</ul><p>Furthermore,</p><ul><li><p>Any <em>other</em> bacterial genus, species or subspecies of which the genus is present in the two aforementioned groups, has <code>prevalence = 2.5</code> in the <a href="microorganisms.html">microorganisms</a> data set.</p></li>
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<li><p>Any <em>non-bacterial</em> genus, species or subspecies of which the genus is present in the following list, also has <code>prevalence = 2.5</code> in the <a href="microorganisms.html">microorganisms</a> data set: <em>Absidia</em>, <em>Acanthamoeba</em>, <em>Acremonium</em>, <em>Aedes</em>, <em>Alternaria</em>, <em>Amoeba</em>, <em>Ancylostoma</em>, <em>Angiostrongylus</em>, <em>Anisakis</em>, <em>Anopheles</em>, <em>Apophysomyces</em>, <em>Aspergillus</em>, <em>Aureobasidium</em>, <em>Basidiobolus</em>, <em>Beauveria</em>, <em>Blastocystis</em>, <em>Blastomyces</em>, <em>Candida</em>, <em>Capillaria</em>, <em>Chaetomium</em>, <em>Chrysonilia</em>, <em>Cladophialophora</em>, <em>Cladosporium</em>, <em>Conidiobolus</em>, <em>Contracaecum</em>, <em>Cordylobia</em>, <em>Cryptococcus</em>, <em>Curvularia</em>, <em>Demodex</em>, <em>Dermatobia</em>, <em>Dientamoeba</em>, <em>Diphyllobothrium</em>, <em>Dirofilaria</em>, <em>Echinostoma</em>, <em>Entamoeba</em>, <em>Enterobius</em>, <em>Exophiala</em>, <em>Exserohilum</em>, <em>Fasciola</em>, <em>Fonsecaea</em>, <em>Fusarium</em>, <em>Giardia</em>, <em>Haloarcula</em>, <em>Halobacterium</em>, <em>Halococcus</em>, <em>Hendersonula</em>, <em>Heterophyes</em>, <em>Histomonas</em>, <em>Histoplasma</em>, <em>Hymenolepis</em>, <em>Hypomyces</em>, <em>Hysterothylacium</em>, <em>Leishmania</em>, <em>Malassezia</em>, <em>Malbranchea</em>, <em>Metagonimus</em>, <em>Meyerozyma</em>, <em>Microsporidium</em>, <em>Microsporum</em>, <em>Mortierella</em>, <em>Mucor</em>, <em>Mycocentrospora</em>, <em>Necator</em>, <em>Nectria</em>, <em>Ochroconis</em>, <em>Oesophagostomum</em>, <em>Oidiodendron</em>, <em>Opisthorchis</em>, <em>Pediculus</em>, <em>Phlebotomus</em>, <em>Phoma</em>, <em>Pichia</em>, <em>Piedraia</em>, <em>Pithomyces</em>, <em>Pityrosporum</em>, <em>Pneumocystis</em>, <em>Pseudallescheria</em>, <em>Pseudoterranova</em>, <em>Pulex</em>, <em>Rhizomucor</em>, <em>Rhizopus</em>, <em>Rhodotorula</em>, <em>Saccharomyces</em>, <em>Sarcoptes</em>, <em>Scolecobasidium</em>, <em>Scopulariopsis</em>, <em>Scytalidium</em>, <em>Spirometra</em>, <em>Sporobolomyces</em>, <em>Stachybotrys</em>, <em>Strongyloides</em>, <em>Syngamus</em>, <em>Taenia</em>, <em>Toxocara</em>, <em>Trichinella</em>, <em>Trichobilharzia</em>, <em>Trichoderma</em>, <em>Trichomonas</em>, <em>Trichophyton</em>, <em>Trichosporon</em>, <em>Trichostrongylus</em>, <em>Trichuris</em>, <em>Tritirachium</em>, <em>Trombicula</em>, <em>Trypanosoma</em>, <em>Tunga</em> or <em>Wuchereria</em>.</p></li>
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<li><p>All other records have <code>prevalence = 3.0</code> in the <a href="microorganisms.html">microorganisms</a> data set.</p></li>
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) who extensively studied medical-scientific literature to categorise all bacterial species into these groups:</p><ul><li><p><strong>Established</strong>, if a taxonomic species has infected at least three persons in three or more references. These records have <code>prevalence = 1.0</code> in the <a href="microorganisms.html">microorganisms</a> data set;</p></li>
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<li><p><strong>Putative</strong>, if a taxonomic species has fewer than three known cases. These records have <code>prevalence = 1.25</code> in the <a href="microorganisms.html">microorganisms</a> data set.</p></li>
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</ul><p>Furthermore,</p><ul><li><p>Any genus present in the <strong>established</strong> list also has <code>prevalence = 1.0</code> in the <a href="microorganisms.html">microorganisms</a> data set;</p></li>
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<li><p>Any other genus present in the <strong>putative</strong> list has <code>prevalence = 1.25</code> in the <a href="microorganisms.html">microorganisms</a> data set;</p></li>
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<li><p>Any other species or subspecies of which the genus is present in the two aforementioned groups, has <code>prevalence = 1.5</code> in the <a href="microorganisms.html">microorganisms</a> data set;</p></li>
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<li><p>Any <em>non-bacterial</em> genus, species or subspecies of which the genus is present in the following list, has <code>prevalence = 1.5</code> in the <a href="microorganisms.html">microorganisms</a> data set: <em>Absidia</em>, <em>Acanthamoeba</em>, <em>Acremonium</em>, <em>Aedes</em>, <em>Alternaria</em>, <em>Amoeba</em>, <em>Ancylostoma</em>, <em>Angiostrongylus</em>, <em>Anisakis</em>, <em>Anopheles</em>, <em>Apophysomyces</em>, <em>Aspergillus</em>, <em>Aureobasidium</em>, <em>Basidiobolus</em>, <em>Beauveria</em>, <em>Blastocystis</em>, <em>Blastomyces</em>, <em>Candida</em>, <em>Capillaria</em>, <em>Chaetomium</em>, <em>Chrysonilia</em>, <em>Cladophialophora</em>, <em>Cladosporium</em>, <em>Conidiobolus</em>, <em>Contracaecum</em>, <em>Cordylobia</em>, <em>Cryptococcus</em>, <em>Curvularia</em>, <em>Demodex</em>, <em>Dermatobia</em>, <em>Dientamoeba</em>, <em>Diphyllobothrium</em>, <em>Dirofilaria</em>, <em>Echinostoma</em>, <em>Entamoeba</em>, <em>Enterobius</em>, <em>Exophiala</em>, <em>Exserohilum</em>, <em>Fasciola</em>, <em>Fonsecaea</em>, <em>Fusarium</em>, <em>Giardia</em>, <em>Haloarcula</em>, <em>Halobacterium</em>, <em>Halococcus</em>, <em>Hendersonula</em>, <em>Heterophyes</em>, <em>Histomonas</em>, <em>Histoplasma</em>, <em>Hymenolepis</em>, <em>Hypomyces</em>, <em>Hysterothylacium</em>, <em>Leishmania</em>, <em>Malassezia</em>, <em>Malbranchea</em>, <em>Metagonimus</em>, <em>Meyerozyma</em>, <em>Microsporidium</em>, <em>Microsporum</em>, <em>Mortierella</em>, <em>Mucor</em>, <em>Mycocentrospora</em>, <em>Necator</em>, <em>Nectria</em>, <em>Ochroconis</em>, <em>Oesophagostomum</em>, <em>Oidiodendron</em>, <em>Opisthorchis</em>, <em>Pediculus</em>, <em>Phlebotomus</em>, <em>Phoma</em>, <em>Pichia</em>, <em>Piedraia</em>, <em>Pithomyces</em>, <em>Pityrosporum</em>, <em>Pneumocystis</em>, <em>Pseudallescheria</em>, <em>Pseudoterranova</em>, <em>Pulex</em>, <em>Rhizomucor</em>, <em>Rhizopus</em>, <em>Rhodotorula</em>, <em>Saccharomyces</em>, <em>Sarcoptes</em>, <em>Scolecobasidium</em>, <em>Scopulariopsis</em>, <em>Scytalidium</em>, <em>Spirometra</em>, <em>Sporobolomyces</em>, <em>Stachybotrys</em>, <em>Strongyloides</em>, <em>Syngamus</em>, <em>Taenia</em>, <em>Toxocara</em>, <em>Trichinella</em>, <em>Trichobilharzia</em>, <em>Trichoderma</em>, <em>Trichomonas</em>, <em>Trichophyton</em>, <em>Trichosporon</em>, <em>Trichostrongylus</em>, <em>Trichuris</em>, <em>Tritirachium</em>, <em>Trombicula</em>, <em>Trypanosoma</em>, <em>Tunga</em> or <em>Wuchereria</em>;</p></li>
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<li><p>All other records have <code>prevalence = 2.0</code> in the <a href="microorganisms.html">microorganisms</a> data set.</p></li>
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</ul><p>When calculating the matching score, all characters in \(x\) and \(n\) are ignored that are other than A-Z, a-z, 0-9, spaces and parentheses.</p>
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<p>All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., <code>"E. coli"</code> will return the microbial ID of <em>Escherichia coli</em> (\(m = 0.688\), a highly prevalent microorganism found in humans) and not <em>Entamoeba coli</em> (\(m = 0.095\), a less prevalent microorganism in humans), although the latter would alphabetically come first.</p>
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<p>All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., <code>"E. coli"</code> will return the microbial ID of <em>Escherichia coli</em> (\(m = 0.688\), a highly prevalent microorganism found in humans) and not <em>Entamoeba coli</em> (\(m = 0.159\), a less prevalent microorganism in humans), although the latter would alphabetically come first.</p>
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</div>
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<div class="section level2">
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<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2>
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@@ -206,22 +208,22 @@
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<span class="r-out co"><span class="r-pr">#></span> Also matched: Klebsiella pneumoniae ozaenae (0.707), Klebsiella</span>
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<span class="r-out co"><span class="r-pr">#></span> pneumoniae pneumoniae (0.688), Klebsiella pneumoniae rhinoscleromatis</span>
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<span class="r-out co"><span class="r-pr">#></span> (0.658), Klebsiella pasteurii (0.500), Klebsiella planticola (0.500),</span>
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<span class="r-out co"><span class="r-pr">#></span> Kingella potus (0.250), Kosakonia pseudosacchari (0.217),</span>
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<span class="r-out co"><span class="r-pr">#></span> Kroppenstedtia pulmonis (0.203), Kaistella palustris (0.200), Kocuria</span>
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<span class="r-out co"><span class="r-pr">#></span> palustris (0.200), Kocuria pelophila (0.200), Kocuria polaris (0.200),</span>
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<span class="r-out co"><span class="r-pr">#></span> Kibdelosporangium phytohabitans (0.188), Kitasatospora putterlickiae</span>
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<span class="r-out co"><span class="r-pr">#></span> (0.179), Kibdelosporangium philippinense (0.177), Kalamiella piersonii</span>
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<span class="r-out co"><span class="r-pr">#></span> (0.175), Kitasatospora psammotica (0.174), Kallotenue papyrolyticum</span>
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<span class="r-out co"><span class="r-pr">#></span> (0.167), Kangiella profundi (0.167), Kangsaoukella pontilimi (0.167),</span>
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<span class="r-out co"><span class="r-pr">#></span> Katagnymene pelagic (0.167), Keratinibaculum paraultunense (0.167),</span>
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<span class="r-out co"><span class="r-pr">#></span> Kibdelosporangium persicum (0.167), Kitasatoa purpurea (0.167) and</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Kitasatospora paracochleata (0.167) [showing first 25]</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Kingella potus (0.400), Kosakonia pseudosacchari (0.361), Kaistella</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> palustris (0.333), Kocuria palustris (0.333), Kocuria pelophila</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> (0.333), Kocuria polaris (0.333), Kroppenstedtia pulmonis (0.304),</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Kibdelosporangium phytohabitans (0.282), Kitasatospora putterlickiae</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> (0.269), Kibdelosporangium philippinense (0.266), Kalamiella piersonii</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> (0.262), Kitasatospora psammotica (0.260), Kallotenue papyrolyticum</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> (0.250), Kangiella profundi (0.250), Kangsaoukella pontilimi (0.250),</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Katagnymene pelagic (0.250), Keratinibaculum paraultunense (0.250),</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Kibdelosporangium persicum (0.250), Kitasatoa purpurea (0.250) and</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Kitasatospora paracochleata (0.250) [showing first 25]</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="fu">mo_matching_score</span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> x <span class="op">=</span> <span class="st">"E. coli"</span>,</span></span>
|
||||
<span class="r-in"><span> n <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Escherichia coli"</span>, <span class="st">"Entamoeba coli"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.6875000 0.0952381</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.6875000 0.1587302</span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
||||
|
||||
Reference in New Issue
Block a user