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<body>
<a name="top" />
<!-- header -->
<!--end of header-->
<!--middle part-->
<header id="jgi-header">
<div id="jgi-logo">
<a target="_parent" href="" title="DOE Joint Genome Institute - BBTools Taxonomy Server">
<img width="480" height="70" src="https://genome.jgi.doe.gov/portal/images/logo-JGI-BBTools.png" alt="BBTools Taxonomy Server Logo" />
</a>
</div>
<nav class="jgi-nav">
<ul>
<li id="skipto"><a href="#skipnav" accesskey="S">Skip To Main Content</a></li>
<li><a href="http://jgi.doe.gov" target="_blank">JGI Home</a></li>
</ul>
</nav>
</header>
<div class="wrapper">
<div class="menu_holder">
<div class="menu_group">
<ul>
<li id="skipto"><a href="#skipnav" accesskey="S">Skip To Main Content</a></li>
<li><a href="http://jgi.doe.gov" target="_parent" class="selected">Home</a></li>
<li><a href="#" onClick="$('#tax_server').show();$('#stats').hide();return false;">Find Taxonomy Info</a></li>
<li><a href="http://bbtools.jgi.doe.gov" target="_blank">Other BBTools</a></li>
<li><a href="https://jgi.doe.gov/contact-us/" target="_blank">Contact Us</a></li>
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</div>
<div class="clear"></div>
<div class="no_frame">
<div id='tax_server'>
<div class="container_block">
<a name="skipnav"></a>
<h1 class="header">Welcome to the BBTools Taxonomy Server!</h1>
This service provides taxonomy information from NCBI taxID numbers, gi numbers, organism names, and accessions. <br/>Vertical bars (|) may cause problems on the command line and can be replaced by tilde (~).
</p>
<ul>
<li>/name/homo_sapiens will give taxonomy information for an organism name. (Names are case-insensitive and underscores are equivalent to spaces.)
</li>
<li>/id/9606 will give taxonomy information for an NCBI taxID.</li>
<li>/gi/1234 will give taxonomy information from an NCBI gi number.</li>
<li>/accession/NZ_AAAA01000057.1 will give taxonomy information from an accession.</li>
<li>/header/ will accept an NCBI sequence header such as gi|7|emb|X51700.1| Bos taurus</li>
<li>/silvaheader/ will accept a Silva sequence header such as KC415233.1.1497 Bacteria;Spirochaetae;Spirochaetes</li>
<li>/img/ will accept an IMG id such as 2724679250</li>
</ul>
<h2 class="header">Benefits of using the BBTools Taxonomy Server</h2>
<ul class="other_names">
<li>Identifies all intermediate stages of taxonomy tree such as order, phylum, tribe, etc.</li>
<li>Provides the information in json format</li>
<li>Fast processing</li>
<li>Allows queries in bulk with lists instead of single query</li>
</ul>
</div>
<!--2 sections content -->
<div style="" id="content-flex">
<div class="flex_left">
<div class="border_block">
<div class="header">Examples of Basic Usage</div>
<div class="content">
<div class="container_block">
<p>
All addresses below are assumed to be prefixed by https://taxonomy.jgi.doe.gov, e.g. /name/homo_sapiens implies a full URL of:
<ul>
<li>https://taxonomy.jgi.doe.gov/name/homo_sapiens</li>
</ul>
</p>
<p>
For a simplified taxonomic tree, add "simple".
This will ignore unranked or uncommon levels like tribe and parvorder, and only display the following levels: SUBSPECIES, SPECIES, GENUS, FAMILY, ORDER, CLASS, PHYLUM, KINGDOM, SUPERKINGDOM, DOMAIN
For example:
<ul class="other_names">
<li>/simple/id/1234</li>
</ul>
</p>
<p>To print taxonomy from the command line in Linux, use curl:
<ul>
<li>curl https://taxonomy.jgi.doe.gov/id/9606</li>
</ul></p>
<p>
Queries longer than around 8kB can be sent via POST: curl https://taxonomy.jgi.doe.gov/POST...where the data sent is, for example:
<ul><li>name/e.coli,h.sapiens,c.lupus</li></ul>
</p>
</div>
</div>
</div>
</div>
<div class="flex_right">
<div class="border_block">
<div class="header">Examples of Advanced Usage</div>
<div class="content">
<div class="container_block">
<p>Comma-delimited lists are accepted for bulk queries, such as tax/gi/1234,7000,42
For plaintext (non-Json) results, add the term /pt/ or /sc/.
pt will give just the taxID, while sc will give the whole lineage, semicolon-delimited. For example:
<ul class="other_names">
<li>/pt/name/homo_sapiens</li>
<li>/sc/gi/1234</li>
</ul>
</p>
<p>Additional supported display options are children, numchildren, range, simple, path, size, and ancestor.
The order is not important but they need to come before the query term. For example:
<ul class="other_names">
<li>/children/numchildren/range/gi/1234</li>
</ul>
</p>
<p>To find the common ancestor of multiple organisms, add /ancestor/. For example:
<ul class="other_names">
<li>/id/ancestor/1234,5678,42</li>
<li>/name/ancestor/homo_sapiens,canis_lupus,bos_taurus</li>
</ul>
</p>
</div>
</div>
</div>
</div>
<!--end of three sections content -->
<div class="clear"></div>
</div><!-- end of div that is shown only when search is not executed -->
<div class="clear"></div>
</div>
</div> <!-- end of info -->
<div id='stats' style='margin:5px;display:none'>
<pre>
STATISTICSSTRING
</pre>
</div>
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