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<!DOCTYPE html>
<html>
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<div class = "section_header">
<center><p class="title">MDPD - Microbiome Database of Pulmonary Diseases</p></center>
</div>
<div class = "section_menu">
<center>
<table cellpadding="3px">
<tr class="nav">
<td class="nav"><a href="index.php" class="side_nav">Home</a></td>
<td class="nav"><a href="browse.php" class="side_nav">Browse</a></td>
<td class="nav"><a href="analysis.php" class="side_nav">Analysis</a></td>
<td class="nav"><a href="statistics.php" class="side_nav">Statistics</a></td>
<td class="nav"><a href="about.php" class="side_nav">About</a></td>
<td class="nav"><a href="#" class="active">Help</a></td>
<td class="nav"><a href="submission.php" class="side_nav">Submit data</a></td>
<td class="nav"><a href="team.html" class="side_nav">Team</a></td>
</tr>
</table>
</center>
</div>
<div class = "section_left" id="section_left">
<!-- TOC START -->
<div id="dw__toc" class="dw__toc">
<h4 class="toggle open" style="margin:5px;">Table of Contents</h4>
<div style="" aria-expanded="true">
<ul class="toc">
<li class="level1"><div class="li"><a href="#mdpd_website_navigation_map">MDPD website navigation map</a></div>
<li class="level1"><div class="li"><a href="#home_page">Home page</a></div>
<ul class="toc">
<li class="level2"><div class="li"><a href="#search_mdpd">Search MDPD</a></div></li>
<li class="level2"><div class="li"><a href="#result_of_search_queries">Result of search queries</a></div></li>
</ul>
</li>
<li class="level1"><div class="li"><a href="#browse_page">Browse page</a></div>
<ul class="toc">
<li class="level2"><div class="li"><a href="#group-wise_bioprojects">Group-wise BioProjects</a></div></li>
<li class="level2"><div class="li"><a href="#body-site-wise_bioprojects">Body-site-wise BioProjects</a></div></li>
<li class="level2"><div class="li"><a href="#domain-wise_taxa">Domain-wise taxa</a></div></li>
</ul>
</li>
<li class="level1"><div class="li"><a href="#run_page">Run page</a></div>
<ul class="toc">
<li class="level2"><div class="li"><a href="#basic_information_of_a_run">Basic information of a run</a></div></li>
<li class="level2"><div class="li"><a href="#microbial_composition_of_the_run">Microbial composition of the run</a></div></li>
<li class="level2"><div class="li"><a href="#top_10_abundant_taxa_in_the_run">Top 10 abundant taxa in the run</a></div></li>
</ul>
</li>
<li class="level1"><div class="li"><a href="#bioproject_page">BioProject page</a></div>
<ul class="toc">
<li class="level2"><div class="li"><a href="#basic_information_of_a_bioproject">Basic information of a BioProject</a></div></li>
<li class="level2"><div class="li"><a href="#metadata_of_runs_in_the_bioproject">Metadata of runs in the BioProject</a></div></li>
<li class="level2"><div class="li"><a href="#analyses_of_runs_in_the_bioproject">Analyses of runs in the BioProject</a></div></li>
<li class="level2"><div class="li"><a href="#download_biom_file_of_the_bioproject">Download .biom file of the BioProject</a></div></li>
</ul>
</li>
<li class="level1"><div class="li"><a href="#microbial_taxonomic_profile_of_runs_in_a_bioproject">Microbial taxonomic profile of runs in a BioProject</a></div>
<ul class="toc">
<li class="level2"><div class="li"><a href="#taxonomic_composition">Taxonomic composition</a></div></li>
<li class="level2"><div class="li"><a href="#top_10_abundant_taxa_in_each_subgroup_of_the_bioproject">Top 10 abundant taxa in each subgroup of the BioProject</a></div></li>
</ul>
</li>
<li class="level1"><div class="li"><a href="#discriminant_analysis_of_runs_in_a_bioproject">Discriminant analysis of runs in a BioProject</a></div></li>
<li class="level1"><div class="li"><a href="#multivariate_association_analysis_of_runs_in_a_bioproject">Multivariate association analysis of runs in a BioProject</a></div></li>
<li class="level1"><div class="li"><a href="#microbial_co-occurrence_analysis_of_runs_in_a_bioproject">Microbial co-occurrence analysis of runs in a BioProject</a></div></li>
<li class="level1"><div class="li"><a href="#taxa_page">Taxa page</a></div>
<ul class="toc">
<li class="level2"><div class="li"><a href="#basic_information_of_the_taxon">Basic information of the taxon</a></div></li>
<li class="level2"><div class="li"><a href="#relative_abundances_of_the_taxon_across_body_sites">Relative abundances of the taxon across body sites</a></div></li>
<li class="level2"><div class="li"><a href="#relative_abundances_of_the_taxon_across_subgroups">Relative abundances of the taxon across subgroups</a></div></li>
</ul>
</li>
<li class="level1"><div class="li"><a href="#analysis_page">Analysis page</a></div>
<ul class="toc">
<li class="level2"><div class="li"><a href="#user-defined_taxonomic_analysis">User-defined taxonomic analysis</a></div>
<ul class="toc">
<li class="level3"><div class="li"><a href="#input">Input</a></div></li>
<li class="level3"><div class="li"><a href="#output">Output</a></div></li>
</ul>
</li>
<li class="level2"><div class="li"><a href="#user-defined_discriminant_analysis">User-defined discriminant analysis</a></div>
<ul class="toc">
<li class="level3"><div class="li"><a href="#input1">Input</a></div></li>
<li class="level3"><div class="li"><a href="#output1">Output</a></div></li>
</ul>
</li>
<li class="level2"><div class="li"><a href="#microbe_search">Microbe Search</a></div></li>
</ul>
</li>
<li class="level1"><div class="li"><a href="#figure_buttons">Figure buttons</a></div></li>
</ul>
</div>
</div>
<!-- TOC END -->
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<div class="dokuwiki export" style="width:70%; margin: 10px 20% 0 10%;">
<h1 class="sectionedit1" id="mdpd_website_navigation_map">MDPD website navigation map</h1>
<div class="level1">
<p>
<img src="resource/help_figures/flow_chart.PNG" class="media" loading="lazy" alt="" style="max-width:100%; max-height:500px">
</p>
</div>
<h1 class="sectionedit1" id="home_page">Home page</h1>
<div class="level1">
<p>
The home page provides a brief introduction of MDPD and a
<a href="#search_mdpd" class="wikilink1" title="start" data-wiki-id="start">Search option</a>.
</p>
<p>
<img src="resource/help_figures/home_page.PNG" class="media" loading="lazy" alt="" style="max-width:100%; max-height:500px">
</p>
</div>
<!-- EDIT{"target":"section","name":"Home Page","hid":"home_page","codeblockOffset":0,"secid":1,"range":"1-56"} -->
<h2 class="sectionedit2" id="search_mdpd">Search MDPD</h2>
<div class="level2">
<p>
MDPD is equipped with a <strong>"Search Section"</strong>
that allows users to generate extensive and customizable queries with
just a few clicks. Users can search runs/samples using relevant
technical metadata, including <strong>Group</strong> (diseases, healthy),
<strong>Assay type</strong> (Amplicon-16S, Amplicon-ITS, WMS),
<strong>Body site</strong> (Lung, Gut),
<strong>Library layout</strong> (Single, Paired),
<strong>Country</strong>, and <strong>Year</strong>.
</p>
<p>
For example, the screenshot below shows a user query to search for runs/samples that were
from <em>COPD</em> individuals, sequenced by <em>Amplicon-16S</em>, and obtained from the
<em>Lower Respiratory Tract</em>.
</p>
<p>
<img src="resource/help_figures/search_MDPD.PNG" class="media" loading="lazy" alt="" style="max-width:100%; max-height:400px">
</p>
<p>
Users can also make some complex inquiries.
</p>
<ul>
<li class="level1"><div class="li"> Choose <code>=/≠/</>/<=/>=</code> for predicates, and choose <code>AND/OR</code> to combine predicates.</div>
</li>
<li class="level1"><div class="li"> <em>Add</em> or <em>delete</em> search predicates.</div>
</li>
<li class="level1"><div class="li"> <em>Reset</em> all the search predicates.</div>
</li>
</ul>
</div>
<!-- EDIT{"target":"section","name":"Search MDPD","hid":"search_mdpd","codeblockOffset":0,"secid":2,"range":"57-952"} -->
<h2 class="sectionedit3" id="result_of_search_queries">Result of search queries</h2>
<div class="level2">
<p>
Search result page provides information of the runs matching the input
query in a <strong>tabular format</strong>. It contains different attributes -
Run ID, BioProject ID, SRA Study ID, Disease, Disease Subgroup, Body site,
Instrument, Assay Type, Library Layout, Processed reads (%), Country,
and Year. The table displayed in the search result <strong>can be downloaded in
CSV format</strong> by clicking on the <strong>"Download table"</strong> button
located at the top of the page. An example search result is shown below.
</p>
<ul>
<li class="level1"><div class="li"> Click on each <strong>Run ID</strong> to view the details of the run in the
<a href="#run_page" class="wikilink1" title="start" data-wiki-id="start">Run page</a>.</div>
</li>
<li class="level1"><div class="li"> Click on <strong>BioProject ID</strong> to view the details of the BioProject in the
<a href="#bioproject_page" class="wikilink1" title="start" data-wiki-id="start">BioProject page</a>.</div>
</li>
</ul>
<p>
<img src="resource/help_figures/result_of_search_queries.PNG" class="media" loading="lazy" alt="" style="max-width:100%; max-height:500px">
</p>
<hr>
</div>
<!-- EDIT{"target":"section","name":"Result of search queries","hid":"result_of_search_queries","codeblockOffset":0,"secid":3,"range":"953-1723"} -->
<h1 class="sectionedit4" id="browse_page">Browse page</h1>
<div class="level1">
<p>
The browse page can be accessed from the menubar present at the top of
every page. It has three sections to find the BioProjects and the microbes.
</p>
<p>
<img src="resource/help_figures/browse_page.PNG" class="media" loading="lazy" alt="" style="max-width:100%; max-height:50px">
</p>
</div>
<!-- EDIT{"target":"section","name":"Browse Page","hid":"browse_page","codeblockOffset":0,"secid":4,"range":"1724-1928"} -->
<h2 class="sectionedit5" id="group-wise_bioprojects">Group-wise BioProjects</h2>
<div class="level2">
<p>
This allows users to browse BioProjects on the basis of the 19 pulmonary diseases (categorized into five classes) and the healthy group.
</p>
<ol>
<li class="level1"><div class="li"> <strong>Obstructive -</strong> Asthma, Asthma-COPD Overlap (ACO), Bronchiectasis, Bronchitis, COPD and COPD- Bronchiectasis Association (CBA).</div>
</li>
<li class="level1"><div class="li"> <strong>Restrictive –</strong> Acute Respiratory
Distress Syndrome (ARDS), Cystic Fibrosis, Interstitial Lung Disease
(ILD), Idiopathic Pulmonary Fibrosis (IPF), Sarcoidosis and Pneumonitis.</div>
</li>
<li class="level1"><div class="li"> <strong>Infectious –</strong> Bronchiolitis, COVID-19, Pneumonia, Tuberculosis, Other Pulmonary Infections (OPI).</div>
</li>
<li class="level1"><div class="li"> <strong>Vascular –</strong> Pulmonary Hypertension.</div>
</li>
<li class="level1"><div class="li"> <strong>Malignancy –</strong> Lung Cancer.</div>
</li>
<li class="level1"><div class="li"> <strong>Healthy –</strong> Healthy.</div>
</li>
</ol>
<p>
<img src="resource/help_figures/group_wise_bioprojects.PNG" class="media" loading="lazy" alt="" style="max-width:100%; max-height:600px">
</p>
<p>
The <em>'n'</em> represents the number of runs/samples in the respective group.
Click on the <strong>group names</strong> to get the details as shown in the following
figure.
</p>
<ul>
<li class="level1"><div class="li"> Shows the basic information about the BioProjects in tabular format.</div>
</li>
<li class="level1"><div class="li"> Click on the BioProject ID to view details in the
<a href="#bioproject_page" class="wikilink1" title="start" data-wiki-id="start">BioProject page</a>.</div>
</li>
<li class="level1"><div class="li"> Customize the list using the filter buttons.</div>
</li>
</ul>
<p>
<img src="resource/help_figures/group_COPD.PNG" class="media" loading="lazy" alt="" style="max-width:100%; max-height:600px">
</p>
</div>
<!-- EDIT{"target":"section","name":"Group-wise BioProjects","hid":"group-wise_bioprojects","codeblockOffset":0,"secid":5,"range":"1929-3085"} -->
<h2 class="sectionedit6" id="body-site-wise_bioprojects">Body-site-wise BioProjects</h2>
<div class="level2">
<p>
This allows the users to browse BioProjects across the 10 body sites - (i) Nasal,
(ii) Oral, (iii) Upper Respiratory Tract, (iv) Lower Respiratory Tract,
(v) Lung, (vi) Stomach, (vii) Large Intestine, (viii) Gut, (ix) Rectum
and (x) Anus. <!--To view the mapping between the isolation sources and body sites,
please check the supplementary files.-->
</p>
<p>
<img src="resource/help_figures/body_site_wise_bioprojects.PNG" class="media" loading="lazy" alt="" style="max-width:100%; max-height:600px">
</p>
<p>
The <em>'n'</em> represents the number of runs/samples in the respective body
site. Click on the <strong>body sites</strong> to get the details as shown in the
following figure.
</p>
<ul>
<li class="level1"><div class="li"> Shows the basic information about the BioProjects in tabular format.</div>
</li>
<li class="level1"><div class="li"> Click on the BioProject ID to view details in the
<a href="#bioproject_page" class="wikilink1" title="start" data-wiki-id="start">BioProject page</a>.</div>
</li>
<li class="level1"><div class="li"> Customize the list using the filter buttons.</div>
</li>
</ul>
<p>
<img src="resource/help_figures/lower_respiratory_tract.PNG" class="media" loading="lazy" alt="" style="max-width:100%; max-height:500px">
</p>
</div>
<!-- EDIT{"target":"section","name":"Body-site-wise BioProjects","hid":"body-site-wise_bioprojects","codeblockOffset":0,"secid":6,"range":"3086-4085"} -->
<h2 class="sectionedit7" id="domain-wise_taxa">Domain-wise taxa</h2>
<div class="level2">
<p>
This allows the users to browse microbes and their abundances across
subgroups and body sites across the four domains - (i) Bacteria,
(ii) Viruses, (iii) Eukaryota, and (iv) Archaea.
</p>
<p>
<img src="resource/help_figures/domain_wise_taxa.PNG" class="media" loading="lazy" alt="" style="max-width:100%; max-height:200px">
</p>
<p>
Click on any domain to get a list of microbes as shown in the following figure.
Click on the microbe names to view taxa information and their abundances across
subgroups and body sites in the
<a href="#taxa_page" class="wikilink1" title="start" data-wiki-id="start">Taxa page</a>.
</p>
<p>
<img src="resource/help_figures/microbe_list.PNG" class="media" loading="lazy" alt="" style="max-width:100%; max-height:600px">
</p>
<p>
The taxon information were retrieved from "bugphyzz: A harmonized data
resource and software for enrichment analysis of microbial physiologies"
accessed on 19th January, 2025.
</p>
<hr>
</div>
<!-- EDIT{"target":"section","name":"Domain-wise taxa","hid":"domain-wise_taxa","codeblockOffset":0,"secid":7,"range":"4086-4604"} -->
<h1 class="sectionedit8" id="run_page">Run page</h1>
<div class="level1">
<p>
The Run page provides:
</p>
<ul>
<li class="level1"><div class="li">
<a href="#basic_information_of_a_run" class="wikilink1" title="start" data-wiki-id="start">Basic information of the run/sample</a>,</div>
</li>
<li class="level1"><div class="li">
<a href="#microbial_composition_of_the_run" class="wikilink1" title="start" data-wiki-id="start">Microbial composition of the run/sample</a>, and</div>
</li>
<li class="level1"><div class="li">
<a href="#top_10_abundant_taxa_in_the_run" class="wikilink1" title="start" data-wiki-id="start">Top 10 most abundant taxa in tha run/sample</a>.</div>
</li>
</ul>
</div>
<!-- EDIT{"target":"section","name":"Run page","hid":"run_page","codeblockOffset":0,"secid":8,"range":"4605-4628"} -->
<h2 class="sectionedit9" id="basic_information_of_a_run">Basic information of a run</h2>
<div class="level2">
<p>
It includes different attributes associated with the run/sample -
Run ID, Experiment ID, BioSample ID, Number of Bases, Number of Bytes,
Country, Assay Type, Body site, Isolation Source, Library Layout,
Variable Region, Instrument, Year, Disease, Disease Subgroup, Gender,
Age, Smoking Status, Therapeutics, Comorbidity, and Processed Reads (%).
A link is available that leads to the NCBI SRA page. Click on the
BioProject ID to view the BioProject details in the
<a href="#bioproject_page" class="wikilink1" title="start" data-wiki-id="start">BioProject page</a>.
</p>
<p>
<img src="resource/help_figures/run_page.PNG" class="media" loading="lazy" alt="" style="max-width:100%; max-height:500px">
</p>
</div>
<!-- EDIT{"target":"section","name":"Basic information of a run","hid":"basic_information_of_a_run","codeblockOffset":0,"secid":9,"range":"4629-5305"} -->
<h2 class="sectionedit10" id="microbial_composition_of_the_run">Microbial composition of the run</h2>
<div class="level2">
<p>
The microbial composition of the run is visualized as an interactive
Krona plot. The colors denote the abundance of the microbes, where
red color represents the abundant ones. Interact with the Krona plot
using the buttons available in the upper left corner to change the
depth, font, and chart size. Click on the "Snapshot" button to
download the plot in SVG format.
</p>
</div>
<!-- EDIT{"target":"section","name":"Microbial composition of the run","hid":"microbial_composition_of_the_run","codeblockOffset":0,"secid":10,"range":"5306-5685"} -->
<h2 class="sectionedit11" id="top_10_abundant_taxa_in_the_run">Top 10 abundant taxa in the run</h2>
<div class="level2">
<p>
The top 10 taxa of the run are visualized as a bar plot. Hover on
the bar to view the relative abundance value of a particular taxon.
Click on "↓" button at the top right corner of the plot to download
the Krona plot in SVG format. Click on the microbe buttons below
the plot to view detailed information in the
<a href="#taxa_page" class="wikilink1" title="start" data-wiki-id="start">Taxa page</a>.
</p>
<p>
<img src="resource/help_figures/taxonomic_composition_run.PNG" class="media" loading="lazy" alt="" style="max-width:100%; max-height:500px">
</p>
<hr>
</div>
<!-- EDIT{"target":"section","name":"Top 10 abundant taxa in the run","hid":"top_10_abundant_taxa_in_the_run","codeblockOffset":0,"secid":11,"range":"5686-6100"} -->
<h1 class="sectionedit12" id="bioproject_page">BioProject page</h1>
<div class="level1">
<p>
The BioProject page provides:
</p>
<ul>
<li class="level1"><div class="li">
<a href="#basic_information_of_a_bioproject" class="wikilink1" title="start" data-wiki-id="start">Basic information of the BioProject</a>,</div>
</li>
<li class="level1"><div class="li">
<a href="#metadata_of_runs_in_the_bioproject" class="wikilink1" title="start" data-wiki-id="start">Metadata of runs in the BioProject</a>,</div>
</li>
<li class="level1"><div class="li">
<a href="#analyses_of_runs_in_the_bioproject" class="wikilink1" title="start" data-wiki-id="start">Analyses of runs in the BioProject</a>, and</div>
</li>
<li class="level1"><div class="li">
<a href="#download_biom_file_of_the_bioproject" class="wikilink1" title="start" data-wiki-id="start">Downloading of .biom files of the BioProject</a>.</div>
</li>
</ul>
</div>
<!-- EDIT{"target":"section","name":"BioProject page","hid":"bioproject_page","codeblockOffset":0,"secid":12,"range":"6101-6131"} -->
<h2 class="sectionedit13" id="basic_information_of_a_bioproject">Basic information of a BioProject</h2>
<div class="level2">
<p>
It includes different attributes associated with the BioProject -
BioProject ID, SRA ID, Disease subgroup(s), Isolation Source,
Body Site, Assay Type, Instrument, Library Layout, Year,
Processed Runs, Variable Region, PMID and Country.
A link is available that leads to the NCBI BioProject page.
</p>
<p>
<img src="resource/help_figures/bioproject_page.PNG" class="media" loading="lazy" alt="" style="max-width:100%; max-height:500px">
</p>
</div>
<!-- EDIT{"target":"section","name":"Basic information of a BioProject","hid":"basic_information_of_a_bioproject","codeblockOffset":0,"secid":13,"range":"6132-6452"} -->
<h2 class="sectionedit14" id="metadata_of_runs_in_the_bioproject">Metadata of runs in the BioProject</h2>
<div class="level2">
<p>
BioProject page shows the metadata of available runs in the BioProject. Click
on the Run ID to view the details of the run in the
<a href="#run_page" class="wikilink1" title="start" data-wiki-id="start">Run page</a>.
</p>
<p>
<img src="resource/help_figures/runs_bioproject.PNG" class="media" loading="lazy" alt="" style="max-width:100%; max-height:500px">
</p>
</div>
<!-- EDIT{"target":"section","name":"Metadata of runs in the BioProject","hid":"metadata_of_runs_in_the_bioproject","codeblockOffset":0,"secid":14,"range":"6453-6611"} -->
<h2 class="sectionedit15" id="analyses_of_runs_in_the_bioproject">Analyses of runs in the BioProject</h2>
<div class="level2">
<p>
Users can perform different types of analyses of runs in the BioProject.
</p>
<ol>
<li class="level1"><div class="li"> <a href="#microbial_taxonomic_profile_of_runs_in_a_bioproject" class="wikilink1" title="start" data-wiki-id="start">Microbial taxonomic profile analysis</a></div>
</li>
<li class="level1"><div class="li"> <a href="#discriminant_analysis_of_runs_in_a_bioproject" class="wikilink1" title="start" data-wiki-id="start">Discriminant analysis</a></div>
</li>
<li class="level1"><div class="li"> <a href="#multivariate_association_analysis_of_runs_in_a_bioproject" class="wikilink1" title="start" data-wiki-id="start">Multivariate association analysis</a></div>
</li>
<li class="level1"><div class="li"> <a href="#microbial_co-occurrence_analysis_of_runs_in_a_bioproject" class="wikilink1" title="start" data-wiki-id="start">Microbial co-occurrence network analysis</a></div>
</li>
</ol>
<p>
<img src="resource/help_figures/analyses_in_bioproject.PNG" class="media" loading="lazy" alt="" style="max-width:100%; max-height:200px">
</p>
</div>
<!-- EDIT{"target":"section","name":"Analyses of runs in the BioProject","hid":"analyses_of_runs_in_the_bioproject","codeblockOffset":0,"secid":15,"range":"6612-6990"} -->
<h2 class="sectionedit16" id="download_biom_file_of_the_bioproject">Download .biom file of the BioProject</h2>
<div class="level2">
<p>
Users can download the .biom file of the respective BioProject.
</p>
<p>
<img src="resource/help_figures/biom_file_download.PNG" class="media" loading="lazy" alt="" style="max-width:100%; max-height:90px">
</p>
<hr>
</div>
<!-- EDIT{"target":"section","name":"Download .biom file of the BioProject","hid":"download_biom_file_of_the_bioproject","codeblockOffset":0,"secid":16,"range":"6991-7153"} -->
<h1 class="sectionedit17" id="microbial_taxonomic_profile_of_runs_in_a_bioproject">Microbial taxonomic profile of runs in a BioProject</h1>
<div class="level1">
</div>
<!-- EDIT{"target":"section","name":"Microbial taxonomic profile of runs in a BioProject","hid":"microbial_taxonomic_profile_of_runs_in_a_bioproject","codeblockOffset":0,"secid":17,"range":"7154-7220"} -->
<h2 class="sectionedit18" id="taxonomic_composition">Taxonomic composition</h2>
<div class="level2">
<p>
The taxonomic composition of the all runs of each subgroup and isolation
sources in the BioProject is visualized as an interactive Krona plot.
The hierarchical taxonomic classification can be seen with this plot with
genus/species at the outer ring and the inner ring denoting the domains.
The color gradient shows the abundance of microbes where red color
indicating more abundant taxa. Select the subgroups and modify the krona
plot by changing the depth, font, and chart size using the buttons available
in the upper left corner. Click on the "Snapshot" button to download the
plot in SVG format. Click on the "Download krona data" to download the plot
in <abbr title="HyperText Markup Language">HTML</abbr> format.
</p>
<p>
<img src="resource/help_figures/krona_bioproject.PNG" class="media" loading="lazy" alt="" style="max-width:100%; max-height:600px">
</p>
</div>
<!-- EDIT{"target":"section","name":"Taxonomic composition","hid":"taxonomic_composition","codeblockOffset":0,"secid":18,"range":"7221-7936"} -->
<h2 class="sectionedit19" id="top_10_abundant_taxa_in_each_subgroup_of_the_bioproject">Top 10 abundant taxa in each subgroup of the BioProject</h2>
<div class="level2">
<p>
The top 10 abundant taxa in each subgroup of the BioProject are visualized
as a box plot. Each box shows the distribution of relative abundance of a
microbe across the runs in the BioProject. Hover on a particular box to
view the min, median, max values of that taxon. Click on "↓" button at the
top right corner of the plot to download the plot in SVG format. Click on
"Download figure data" button to download the data used to plot the figure.
Click on the microbe buttons below the plot to view detailed information in the
<a href="#taxa_page" class="wikilink1" title="start" data-wiki-id="start">Taxa page</a>.
</p>
<p>
<img src="resource/help_figures/box_bioproject.PNG" class="media" loading="lazy" alt="" style="max-width:100%; max-height:600px">
</p>
<hr>
</div>
<!-- EDIT{"target":"section","name":"Top 10 abundant taxa in each subgroup of the BioProject","hid":"top_10_abundant_taxa_in_each_subgroup_of_the_bioproject","codeblockOffset":0,"secid":19,"range":"7937-8501"} -->
<h1 class="sectionedit20" id="discriminant_analysis_of_runs_in_a_bioproject">Discriminant analysis of runs in a BioProject</h1>
<div class="level1">
<p>
It allows users to find the differential microbial signatures between
the subgroups of the BioProject. The differential taxa are visualized
as a bar plot. The length of the bar denotes the LDA score
(log<sub>10</sub>) or log<sub>2</sub> fold change depending on the
chosen method. LDA score signifies the effect size of each
differentially abundant microbe. Click on "↓" button at the top right
corner of the plot to download the plot in SVG format. Click on
"Download figure data" button to download the data used to plot the
figure. Click on the microbe buttons below the plot to view detailed
information in the
<a href="#taxa_page" class="wikilink1" title="start" data-wiki-id="start">Taxa page</a>.
</p>
<p>
<img src="resource/help_figures/lda_bioproject.PNG" class="media" loading="lazy" alt="" style="max-width:100%; max-height:600px">
</p>
<p>
<img src="resource/help_figures/buttons_lda_bioproject.PNG" class="media" loading="lazy" alt="" style="max-width:100%; max-height:135px">
</p>
<p>
Users can modify different parameters of the analysis:
</p>
<ol>
<li class="level1"><div class="li"> Statistical "Method"</div>
</li>
<li class="level1"><div class="li"> P-Value (Only for LEfSe)</div>
</li>
<li class="level1"><div class="li"> Filter threshold</div>
</li>
<li class="level1 node"><div class="li"> Taxa level (Order through Genus in Amplicon-16S/Amplicon-ITS and Order through species in WMS) </div>
</li>
<li class="level1"><div class="li">Cut-off value</div>
</li>
</ol>
<p>
Click on the "Submit" button to perform the analysis with the updated
parameters. Users can also see the selected parameters for the current
analysis.
</p>
<hr>
</div>
<!-- EDIT{"target":"section","name":"Discriminant analysis of runs in a BioProject","hid":"discriminant_analysis_of_runs_in_a_bioproject","codeblockOffset":0,"secid":20,"range":"8502-9715"} -->
<h1 class="sectionedit21" id="multivariate_association_analysis_of_runs_in_a_bioproject">Multivariate association analysis of runs in a BioProject</h1>
<div class="level1">
<p>
It allows users to find associations of the microbes with the
covariates such as age groups, gender, and smoking status.
MaAsLin2 is used to find the associations. Each cell of the
heatmap is annotated with asterisks denoting the significance
based on FDR-adjusted <em>p</em>-values (<code>***</code> denotes
<code>p-value < 0.001</code>, <code>**</code> denotes
<code>p-value < 0.01</code>, <code>*</code> denotes
<code>p-value < 0.05</code>, no asterisks denote
<code>p-value > 0.05</code>). Positive MaAsLin2 coefficient
indicates a positive correlation between microbe and the covariates
while negative coefficient denotes inverse associations. Hover
mouse on each cell to highlight the taxa name, covariate and
the MaAsLin2 coefficient. Click on "↓" button at the top right
corner of the plot to download the plot in SVG format. Click on
"Download figure data" button to download the data used to plot
the figure. Click on the microbe buttons below the plot to view
detailed information in the
<a href="#taxa_page" class="wikilink1" title="start" data-wiki-id="start">Taxa page</a>.
</p>
<p>
<img src="resource/help_figures/multivariate_association_bioproject.PNG" class="media" loading="lazy" alt="" style="max-width:100%; max-height:600px">
</p>
<hr>
</div>
<!-- EDIT{"target":"section","name":"Multivariate association analysis of runs in a BioProject","hid":"multivariate_association_analysis_of_runs_in_a_bioproject","codeblockOffset":0,"secid":21,"range":"9716-10722"} -->
<h1 class="sectionedit22" id="microbial_co-occurrence_analysis_of_runs_in_a_bioproject">Microbial co-occurrence analysis of runs in a BioProject</h1>
<div class="level1">
<p>
It allows the users to visualize the dynamics of microbial community with
co-occurrence networks. Gradient Boosted Linear Model (GBLM) method was
applied to build the networks. The nodes represent the microbes (bacteria,
virus, eukaryota, and/or archaea). The edges indicate relationships between
microbes. The colours denote <font color="green">positive</font> (in
<font color="green">green</font>) or <font color="red">negative</font>
(in <font color="red">red</font>) interactions while the color intensity
is proportional to edge weights. Change the layout of network using the
drop-down menu. Click on "JPEG", "PNG", "SVG", and "JSON" buttons to download
the network in the respective formats. Double click on a node to view detailed
information of the taxa in the
<a href="#taxa_page" class="wikilink1" title="start" data-wiki-id="start">Taxa page</a>.
</p>
<p>
<img src="resource/help_figures/network_bioproject.PNG" class="media" loading="lazy" alt="" style="max-width:100%; max-height:700px">
</p>
<hr>
</div>
<!-- EDIT{"target":"section","name":"Microbial co-occurrence analysis of runs in a BioProject","hid":"microbial_co-occurrence_analysis_of_runs_in_a_bioproject","codeblockOffset":0,"secid":22,"range":"10723-11519"} -->
<h1 class="sectionedit23" id="taxa_page">Taxa page</h1>
<div class="level1">
</div>
<!-- EDIT{"target":"section","name":"Taxa page","hid":"taxa_page","codeblockOffset":0,"secid":23,"range":"11520-11544"} -->
<h2 class="sectionedit24" id="basic_information_of_the_taxon">Basic information of the taxon</h2>
<div class="level2">
<p>
<img src="resource/help_figures/taxa_page.PNG" class="media" loading="lazy" alt="" style="max-width:100%; max-height:500px">
</p>
<p>
Users get information about (i) Biofilm formation, (ii) Gram staining,
(iii) Spore formation, (iv) Aerophilicity, (v) Genome size, (vi) Coding
genes, (vii) Antimicrobial resistance, (viii) Antimicrobial sensitivity,
(ix) shape, and (x) Pathogenicity.
</p>
<p>
The abbreviations of the evidences supporting an annotation are as follows:
</p>
<ul>
<li class="level1"><div class="li"> EXP: Experiment</div>
</li>
<li class="level1"><div class="li"> IGC: Inferred from genomic context</div>
</li>
<li class="level1"><div class="li"> TAS: Traceable author statement</div>
</li>
<li class="level1"><div class="li"> NAS: Non-traceable author statement</div>
</li>
<li class="level1"><div class="li"> IBD: Inferred from biological aspect of descendant</div>
</li>
<li class="level1"><div class="li"> ASR: Ancestral state reconstruction</div>
</li>
</ul>
</div>
<!-- EDIT{"target":"section","name":"Basic information of the taxon","hid":"basic_information_of_the_taxon","codeblockOffset":0,"secid":24,"range":"11545-12179"} -->
<h2 class="sectionedit25" id="relative_abundances_of_the_taxon_across_body_sites">Relative abundances of the taxon across body sites</h2>
<div class="level2">
<p>
<img src="resource/help_figures/taxa_body_site_wise.PNG" class="media" loading="lazy" alt="" style="max-width:100%; max-height:600px">
</p>
<p>
The plot can be downloaded as a SVG image by clicking on the "↓" button
in the menu bar located at the top right corner of the plot.
</p>
</div>
<!-- EDIT{"target":"section","name":"Relative abundances of the taxon across body sites","hid":"relative_abundances_of_the_taxon_across_body_sites","codeblockOffset":0,"secid":25,"range":"12180-12421"} -->
<h2 class="sectionedit26" id="relative_abundances_of_the_taxon_across_subgroups">Relative abundances of the taxon across subgroups</h2>
<div class="level2">
<p>
<img src="resource/help_figures/taxa_subgroup_wise.PNG" class="media" loading="lazy" alt="" style="max-width:100%; max-height:600px">
</p>
<p>
The plot can be downloaded as a SVG image by clicking on the "↓" button
in the menu bar located at the top right corner of the plot.
</p>
<hr>
</div>
<!-- EDIT{"target":"section","name":"Relative abundances of the taxon across subgroups","hid":"relative_abundances_of_the_taxon_across_subgroups","codeblockOffset":0,"secid":26,"range":"12422-12667"} -->
<h1 class="sectionedit27" id="analysis_page">Analysis page</h1>
<div class="level1">
<p>
The Analysis page can be accessed from the menubar present at the top of
every page. It provides three analyses for user-defined queries. It
allows to find the microbial signatures of different subgroups, BioProjects,
and isolation sources within a group. It allows to identify microbial
markers across different subgroups, BioProjects, and isolation sources
of one or more groups. It also allows users to search taxon details.
</p>
<p>
<img src="resource/help_figures/analysis_page.PNG" class="media" loading="lazy" alt="" style="max-width:100%; max-height:50px">
</p>
</div>
<!-- EDIT{"target":"section","name":"Analysis page","hid":"analysis_page","codeblockOffset":0,"secid":27,"range":"12668-13076"} -->
<h2 class="sectionedit28" id="user-defined_taxonomic_analysis">User-defined taxonomic analysis</h2>
<div class="level2">
<p>
It helps researchers to understand if a microbe has the similar trend
across subgroups or in BioProjects or different or no trend. For
simplicity, the subgroups with highest number of runs/samples were
taken for the analysis. However, users can use other subgroups as they
can download the <em>.biom files</em> of respective BioProject(s).
</p>
</div>
<!-- EDIT{"target":"section","name":"User-defined taxonomic analysis","hid":"user-defined_taxonomic_analysis","codeblockOffset":0,"secid":28,"range":"13077-13457"} -->
<h3 class="sectionedit29" id="input">Input</h3>
<div class="level3">
<p>
Users can select the Groups, which will open a dialog box where they can
select/deselect options such as Subgroups, Isolation Source, Assay Type
and Library Layouts. For example, Group – Healthy is shown here and the
selected parameters are:
</p>
<ul>
<li class="level1"><div class="li"> Subgroup – Healthy Smoker and Healthy Non Smoker</div>
</li>
<li class="level1"><div class="li"> Isolation Source – BALF, Sputum, and Stool</div>
</li>
<li class="level1"><div class="li"> Assay Type – Amplicon-16S</div>
</li>
<li class="level1"><div class="li"> Library Layout – PAIRED and SINGLE</div>
</li>
</ul>
<p>
<img src="resource/help_figures/query_taxonomic_analysis.PNG" class="media" loading="lazy" alt="" style="max-width:100%; max-height:600px">
</p>
<p>
Users can also customize the BioProjects selection. Among the selected
BioProjects, only the runs that satisfy the selection criteria above
are used for the analysis.
</p>
<p>
<img src="resource/help_figures/bps_taxonomic_analysis.PNG" class="media" loading="lazy" alt="" style="max-width:100%; max-height:600px">
</p>
</div>
<!-- EDIT{"target":"section","name":"Input","hid":"input","codeblockOffset":0,"secid":29,"range":"13458-14032"} -->
<h3 class="sectionedit30" id="output">Output</h3>
<div class="level3">
<p>
This heatmap shows the relative abundances (%) of the microbes across the
queried Subgroups, Isolation Sources, and BioProjects. It shows the top 25
abundant taxa. The blank cells indicate the absence of the taxa. Hover mouse
on each cell to highlight the taxa name, subgroup, isolation source, BioProject
and the relative abundance. Click on "↓" button at the top right corner of
the plot to download the plot in SVG format. Click on "Download figure data"
button to download the data used to plot the figure. Click on the microbe
buttons below the plot to view detailed information in the
<a href="#taxa_page" class="wikilink1" title="start" data-wiki-id="start">Taxa page</a>.
</p>
<p>
<img src="resource/help_figures/result_taxonomic_analysis.PNG" class="media" loading="lazy" alt="" style="max-width:100%; max-height:600px">
</p>
</div>
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<h2 class="sectionedit31" id="user-defined_discriminant_analysis">User-defined discriminant analysis</h2>
<div class="level2">
<p>
It helps researchers to understand if a microbial marker is unique
to a subgroup, or shared by different subgroups. For simplicity, the
subgroups with highest number of runs/samples were taken for the
comparison. However, users can use other subgroups as they can download
the <em>.biom files</em> of respective BioProject(s).
</p>
</div>
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<h3 class="sectionedit32" id="input1">Input</h3>
<div class="level3">
<p>
Users can select the Groups (1 and/or 2) to compare. For each selection a
dialog box gets opened where they can select the subgroups and isolation
sources, and it also allows the selection of assay type and library layouts.
For example, comparison between "Bronchiectasis and Cystic Fibrosis" is
shown here and the selected parameters are:
</p>
<ul>
<li class="level1"><div class="li"> Subgroups – Bronchiectasis and Cystic Fibrosis Exacerbation</div>
</li>
<li class="level1"><div class="li"> Isolation Source – Sputum</div>
</li>
<li class="level1"><div class="li"> Assay Type – WMS</div>
</li>
<li class="level1"><div class="li"> Library Layout – PAIRED</div>
</li>
</ul>
<p>
<img src="resource/help_figures/discriminant_analysis.PNG" class="media" loading="lazy" alt="" style="max-width:100%; max-height:600px">
<img src="resource/help_figures/query_discriminant_analysis.PNG" class="media" loading="lazy" alt="" style="max-width:100%; max-height:600px">
</p>
<p>
Users have several options to modify the analysis.
</p>
<ol>
<li class="level1"><div class="li"> Users can change the statistical "Method"</div>
</li>
<li class="level1"><div class="li"> Users can set different "P-Value" (Only for LEfSe)</div>
</li>
<li class="level1"><div class="li"> Users can set different "Filter threshold"</div>
</li>
<li class="level1"><div class="li"> Users can change the "Taxa level"</div>
</li>
<li class="level1"><div class="li"> Users can modify the "Cut-off value"</div>
</li>
<li class="level1"><div class="li"> Click to "Submit"</div>
</li>
</ol>
<p>
<img src="resource/help_figures/buttons_discriminant_analysis.PNG" class="media" loading="lazy" alt="" style="max-width:100%; max-height:120px">
</p>
<p>
Users can also customize the BioProjects selection. Among the selected
BioProjects, only the runs that satisfy the selection criteria above
are used for the analysis.
</p>
<p>
<img src="resource/help_figures/bps_discriminant_analysis.PNG" class="media" loading="lazy" alt="" style="max-width:100%; max-height:500px">
</p>
</div>
<!-- EDIT{"target":"section","name":"Input","hid":"input1","codeblockOffset":0,"secid":32,"range":"14907-15977"} -->
<h3 class="sectionedit33" id="output1">Output</h3>
<div class="level3">
</div>
<h4 id="individual_bioproject_wise">Individual BioProject wise</h4>
<div class="level4">
<p>
This heatmap shows the microbial markers in individual BioProjects
of the respective subgroups. Here, LEfSe method was chosen to find
the differential markers. The blank cells indicate absence of the
taxa. The colour intensity denotes the LDA score (log<sub>10</sub>).
LDA score signifies the effect size of each differentially abundant
microbe. Hover mouse on each cell to highlight the taxa name, subgroup,
isolation source, BioProject and the LDA score. Click on "↓" button
at the top right corner of the plot to download the plot in SVG format.
Click on "Download figure data" button to download the data used to
plot the figure. Click on the microbe buttons below the plot to view
detailed information in the
<a href="#taxa_page" class="wikilink1" title="start" data-wiki-id="start">Taxa page</a>.
</p>
<p>
<img src="resource/help_figures/result_individual_bioproject.PNG" class="media" loading="lazy" alt="" style="max-width:100%; max-height:600px">
</p>
</div>
<h4 id="merged_bioproject_wise">Merged BioProject wise</h4>
<div class="level4">
<p>
This heatmap shows microbial markers in the respective subgroups by
merging the Bioprojects. Here, LEfSe method was chosen to find the
differential markers. The blank cells indicate absence of the
taxa. The colour intensity denotes the LDA score (log<sub>10</sub>).
LDA score signifies the effect size of each differentially abundant
microbe. Hover mouse on each cell to highlight the taxa name, subgroup,
isolation source, BioProject and the LDA score. Click on "↓" button
at the top right corner of the plot to download the plot in SVG format.
Click on "Download figure data" button to download the data used to
plot the figure. Click on the microbe buttons below the plot to view
detailed information in the
<a href="#taxa_page" class="wikilink1" title="start" data-wiki-id="start">Taxa page</a>.
</p>
<p>
<img src="resource/help_figures/result_merged_bioproject.PNG" class="media" loading="lazy" alt="" style="max-width:100%; max-height:500px">
</p>
</div>
<!-- EDIT{"target":"section","name":"Output","hid":"output1","codeblockOffset":0,"secid":33,"range":"15978-17497"} -->
<h2 class="sectionedit34" id="microbe_search">Microbe Search</h2>
<div class="level2">
<p>
Users can search for specific microbial taxa (Genus or Species) of
Domain Bacteria, Eukaryota (e.g. Fungi and Protozoa), Virus and Archaea
with their scientific name as valid search term. For example, genus
Aspergillus is shown here. Submitting the query will open a table of
taxa with the name Aspergillus including the species as shown below.
The result of the taxa search shows a list of microbes matching the
query. Click on a specific taxon to view detailed information of the
microbe in the
<a href="#taxa_page" class="wikilink1" title="start" data-wiki-id="start">Taxa page</a>.