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REST API for the OMA Browser
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data-target="#menu-content"></i> <div class="menu-list"> <ul id="menu-content" class="menu-content collapse out"> <li data-toggle="collapse" data-target="#enrichment-dropdown" class="collapsed"> <a><i class="fa fa-dot-circle-o fa-lg"></i> enrichment <span class="arrow"></span></a> <ul class="sub-menu collapse" id="enrichment-dropdown"> <li><a href="#enrichment-create">create</a></li> <li><a href="#enrichment-status-read">status > read</a></li> </ul> </li> <li data-toggle="collapse" data-target="#function-dropdown" class="collapsed"> <a><i class="fa fa-dot-circle-o fa-lg"></i> function <span class="arrow"></span></a> <ul class="sub-menu collapse" id="function-dropdown"> <li><a href="#function-list">list</a></li> </ul> </li> <li data-toggle="collapse" data-target="#genome-dropdown" class="collapsed"> <a><i class="fa fa-dot-circle-o fa-lg"></i> genome <span class="arrow"></span></a> <ul class="sub-menu collapse" id="genome-dropdown"> <li><a href="#genome-list">list</a></li> <li><a href="#genome-read">read</a></li> <li><a href="#genome-genes">genes</a></li> <li><a href="#genome-proteins">proteins</a></li> </ul> </li> <li data-toggle="collapse" data-target="#group-dropdown" class="collapsed"> <a><i class="fa fa-dot-circle-o fa-lg"></i> group <span class="arrow"></span></a> <ul class="sub-menu collapse" id="group-dropdown"> <li><a href="#group-list">list</a></li> <li><a href="#group-read">read</a></li> <li><a href="#group-close_groups">close_groups</a></li> </ul> </li> <li data-toggle="collapse" data-target="#hog-dropdown" class="collapsed"> <a><i class="fa fa-dot-circle-o fa-lg"></i> hog <span class="arrow"></span></a> <ul class="sub-menu collapse" id="hog-dropdown"> <li><a href="#hog-list">list</a></li> <li><a href="#hog-read">read</a></li> <li><a href="#hog-gene_ontology">gene_ontology</a></li> <li><a href="#hog-members">members</a></li> <li><a href="#hog-similar_profile_hogs">similar_profile_hogs</a></li> </ul> </li> <li data-toggle="collapse" data-target="#pairs-dropdown" class="collapsed"> <a><i class="fa fa-dot-circle-o fa-lg"></i> pairs <span class="arrow"></span></a> <ul class="sub-menu collapse" id="pairs-dropdown"> <li><a href="#pairs-read">read</a></li> </ul> </li> <li data-toggle="collapse" data-target="#protein-dropdown" class="collapsed"> <a><i class="fa fa-dot-circle-o fa-lg"></i> protein <span class="arrow"></span></a> <ul class="sub-menu collapse" id="protein-dropdown"> <li><a href="#protein-bulk_retrieve">bulk_retrieve</a></li> <li><a href="#protein-read">read</a></li> <li><a href="#protein-domains">domains</a></li> <li><a href="#protein-gene_ontology">gene_ontology</a></li> <li><a href="#protein-hog_derived_orthologs">hog_derived_orthologs</a></li> <li><a href="#protein-homoeologs">homoeologs</a></li> <li><a href="#protein-isoforms">isoforms</a></li> <li><a href="#protein-ontology">ontology</a></li> <li><a href="#protein-orthologs">orthologs</a></li> <li><a href="#protein-xref">xref</a></li> </ul> </li> <li data-toggle="collapse" data-target="#sequence-dropdown" class="collapsed"> <a><i class="fa fa-dot-circle-o fa-lg"></i> sequence <span class="arrow"></span></a> <ul class="sub-menu collapse" id="sequence-dropdown"> <li><a href="#sequence-list">list</a></li> </ul> </li> <li data-toggle="collapse" data-target="#summary-dropdown" class="collapsed"> <a><i class="fa fa-dot-circle-o fa-lg"></i> summary <span class="arrow"></span></a> <ul class="sub-menu collapse" id="summary-dropdown"> <li><a href="#summary-shared_ancestry-read">shared_ancestry > read</a></li> </ul> </li> <li data-toggle="collapse" data-target="#synteny-dropdown" class="collapsed"> <a><i class="fa fa-dot-circle-o fa-lg"></i> synteny <span class="arrow"></span></a> <ul class="sub-menu collapse" id="synteny-dropdown"> <li><a href="#synteny-list">list</a></li> <li><a href="#synteny-read">read</a></li> </ul> </li> <li data-toggle="collapse" data-target="#taxonomy-dropdown" class="collapsed"> <a><i class="fa fa-dot-circle-o fa-lg"></i> taxonomy <span class="arrow"></span></a> <ul class="sub-menu collapse" id="taxonomy-dropdown"> <li><a href="#taxonomy-list">list</a></li> <li><a href="#taxonomy-read">read</a></li> </ul> </li> <li data-toggle="collapse" data-target="#version-dropdown" class="collapsed"> <a><i class="fa fa-dot-circle-o fa-lg"></i> version <span class="arrow"></span></a> <ul class="sub-menu collapse" id="version-dropdown"> <li><a href="#version-list">list</a></li> </ul> </li> <li data-toggle="collapse" data-target="#xref-dropdown" class="collapsed"> <a><i class="fa fa-dot-circle-o fa-lg"></i> xref <span class="arrow"></span></a> <ul class="sub-menu collapse" id="xref-dropdown"> <li><a href="#xref-list">list</a></li> </ul> </li> </ul> <ul class="menu-list menu-list-bottom"> <li data-toggle="collapse" data-target="#auth-control" class="collapsed"> <a><i class="fa fa-user fa-lg"></i> Authentication</a> <span id="selected-authentication">none</span> </li> <ul class="sub-menu collapse out" id="auth-control"> <li class="active"><a data-auth="none" href="#">none</a></li> <li><a data-auth="token" data-toggle="modal" data-target="#auth_token_modal" href="#">token</a></li> <li><a data-auth="basic" data-toggle="modal" data-target="#auth_basic_modal" href="#">basic</a></li> <li ><a data-auth="session" data-toggle="modal" data-target="#auth_session_modal" href="#">session</a></li> </ul> <li data-toggle="collapse" data-target="#language-control" class="collapsed"> <a><i class="fa fa-code fa-lg"></i> Source Code</a> <span id="selected-language">shell</span> </li> <ul class="sub-menu collapse out" id="language-control"> <li><a href="#" data-language="shell">shell</a></li> <li><a href="#" data-language="javascript">javascript</a></li> <li><a href="#" data-language="python">python</a></li> </ul> </ul> </div> </div> <div class="container" id="main"> <div class="row"> <div class="col-md-12 main-container"> <div class="row intro"> <div class="col-md-6 intro-title"> <h1>REST API for the OMA Browser</h1> <p><p style="text-align:justify">The OMA Brower now supports its own REST API, which serves as a window into its database. It enables the abstraction of OMA browser’s data which also allows it to be more accessible via other programming languages. Furthermore, due to its RESTful architecture, it allows the users to access the data they need easily through HTTP requests sent to the server which can be found at:</p> <p><a href="/api">http://omabrowser.org/api</a></p> <p style="text-align:justify">The OMA REST API supports many data formats and its predominant use of the JSON data format makes it very browser-compatible.To further facilitate the ease of access, we have also developed a Python library and R package to serve as user friendly wrappers around the API. The links to their documentation can be found below:</p> <ul> <li>R package: <a href="https://bioconductor.org/packages/OmaDB/">OmaDB</a> bioconductor package; <a href="https://github.com/DessimozLab/OmaDB">project repository</a></li> <li>Python library: <a href="https://github.com/DessimozLab/pyomadb">OmaDB</a> python package</li> </ul> <h3>Pagination in the API</h3> <p style="text-align:justify">Note that some endpoints, such as the list of all Hierarchical Orthologous groups, return a very long list. In order to keep the response size and time manageable the API will take advantage of pagination, which is a mechanism for returning a subset of the results for a request (by default, we return the results in chunks of 100 objects) and allowing for subsequent requests to “page” through the rest of the results until the end is reached. This pagination is implemented with a "page" query parameter and a "per_page" parameter to specify the number of objects per page.</p> <p>Information about pagination is provided in the <a href="http://www.rfc-editor.org/rfc/rfc5988.txt">Link header</a> of an API call. This is a popular way how to implement pagination for APIs. In essence this strategy includes in the HTTP reply header a "Link" header with the urls to to next, previous, first and last page. Furthermore, we include in the "X-Total-Count" header the total number of objects that the request will return over all pages. Here is an example request:</p> <pre>curl -I "https://omabrowser.org/api/genome/?page=2"</pre> <pre>HTTP 200 OK Allow: GET, HEAD, OPTIONS Content-Type: application/json Link: <https://omabrowser.org/api/genomes/>; rel="first", <https://omabrowser.org/api/genomes/>; rel="prev", <https://omabrowser.org/api/genomes/?page=3>; rel="next", <https://omabrowser.org/api/genomes/?page=22>; rel="last" Vary: Accept X-Total-Count: 2198 </pre> <h3>HTTP status codes</h3> <table style="width:70%;border-collapse:collapse;border-spacing:0"><tr><th style="font-family:Arial, sans-serif;font-size:14px;font-weight:normal;padding:10px 5px;border-style:solid;border-width:1px;overflow:hidden;word-break:normal;background-color:#9fbd59;color:#000000;text-align:center;vertical-align:top">Status Code</th><th style="font-family:Arial, sans-serif;font-size:14px;font-weight:normal;padding:10px 5px;border-style:solid;border-width:1px;overflow:hidden;word-break:normal;background-color:#9fbd59;color:#000000;text-align:center;vertical-align:top"> Description</th></tr><tr><td style="font-family:Arial, sans-serif;font-size:14px;padding:10px 5px;border-style:solid;border-width:1px;overflow:hidden;word-break:normal;text-align:center;vertical-align:top"> 200</td><td style="font-family:Arial, sans-serif;font-size:14px;padding:10px 5px;border-style:solid;border-width:1px;overflow:hidden;word-break:normal;text-align:center;vertical-align:top"> OK. All is well.</td></tr><tr><td style="font-family:Arial, sans-serif;font-size:14px;padding:10px 5px;border-style:solid;border-width:1px;overflow:hidden;word-break:normal;text-align:center;vertical-align:top"> 400</td><td style="font-family:Arial, sans-serif;font-size:14px;padding:10px 5px;border-style:solid;border-width:1px;overflow:hidden;word-break:normal;text-align:center;vertical-align:top">Malformed request.</td></tr><tr><td style="font-family:Arial, sans-serif;font-size:14px;padding:10px 5px;border-style:solid;border-width:1px;overflow:hidden;word-break:normal;text-align:center;vertical-align:top"> 404</td><td style="font-family:Arial, sans-serif;font-size:14px;padding:10px 5px;border-style:solid;border-width:1px;overflow:hidden;word-break:normal;text-align:center;vertical-align:top"> Not found.</td></tr><tr><td style="font-family:Arial, sans-serif;font-size:14px;padding:10px 5px;border-style:solid;border-width:1px;overflow:hidden;word-break:normal;text-align:center;vertical-align:top"> 500</td><td style="font-family:Arial, sans-serif;font-size:14px;padding:10px 5px;border-style:solid;border-width:1px;overflow:hidden;word-break:normal;text-align:center;vertical-align:top"> Internal Server Error.</td></tr></table> <h2>Available API Endpoints</h2> <p>Below we list all the available endpoints together with a brief description of what they return and the parameters they take.</p></p> </div> <div class="col-md-6 intro-code"> <pre class="highlight shell hide" data-language="shell"><code><span class="c1"># Install the command line client</span> $<span class="w"> </span>pip<span class="w"> </span>install<span class="w"> </span>coreapi-cli </code></pre> <pre class="highlight javascript hide" data-language="javascript"><code><span class="cm"><!-- Load the JavaScript client library --></span> <span class="p"><</span><span class="nt">script</span> <span class="na">src</span><span class="o">=</span><span class="s">"/static/rest_framework/js/coreapi-0.1.1.js"</span><span class="p">></</span><span class="nt">script</span><span class="p">></span> <span class="p"><</span><span class="nt">script</span> <span class="na">src</span><span class="o">=</span><span class="s">"/api/docsschema.js"</span><span class="p">></</span><span class="nt">script</span><span class="p">></span> </code></pre> <pre class="highlight python hide" data-language="python"><code><span class="c1"># Install the Python client library</span> $<span class="w"> </span>pip<span class="w"> </span>install<span class="w"> </span>coreapi </code></pre> </div> </div> <h2 id="enrichment" class="coredocs-section-title">enrichment <a href="#enrichment"><i class="fa fa-link" aria-hidden="true"></i> </a></h2> <div class="row coredocs-link"> <div class="col-md-6 docs-content"> <button class="btn btn-sm btn-success" style="float: right; margin-top: 20px" data-toggle="modal" data-target="#enrichment_create_modal"> <i class="fa fa-exchange"></i> Interact </button> <h3 id="enrichment-create" class="coredocs-link-title">create <a href="#enrichment-create"><i class="fa fa-link" aria-hidden="true"></i> </a></h3> <div class="meta"> <span class="label label-primary">POST</span> <code>/api/enrichment/</code> </div> <p></p> <h4>Request Body</h4> <p>The request body should be a <code>"application/json"</code> encoded object, containing the following items.</p> <table class="parameters table table-bordered table-striped"> <thead> <tr><th>Parameter</th><th>Description</th></tr> </thead> <tbody> <tr><td class="parameter-name"><code>type</code> <span class="label label-warning">required</span></td><td></td></tr> <tr><td class="parameter-name"><code>foreground</code> <span class="label label-warning">required</span></td><td></td></tr> <tr><td class="parameter-name"><code>taxlevel</code></td><td></td></tr> <tr><td class="parameter-name"><code>name</code></td><td></td></tr> </tbody> </table> </div> <div class="col-md-6 code-samples"> <pre class="highlight shell hide" data-language="shell"><code><span class="c1"># Load the schema document</span> $<span class="w"> </span>coreapi<span class="w"> </span>get<span class="w"> </span>https://omabrowser.org/api/docs <span class="c1"># Interact with the API endpoint</span> $<span class="w"> </span>coreapi<span class="w"> </span>action<span class="w"> </span>enrichment<span class="w"> </span>create<span class="w"> </span>-p<span class="w"> </span><span class="nv">type</span><span class="o">=</span>...<span class="w"> </span>-p<span class="w"> </span><span class="nv">foreground</span><span class="o">=</span>...<span class="w"> </span>-p<span class="w"> </span><span class="nv">taxlevel</span><span class="o">=</span>...<span class="w"> </span>-p<span class="w"> </span><span class="nv">name</span><span class="o">=</span>... </code></pre> <pre class="highlight javascript hide" data-language="javascript"><code><span class="kd">var</span><span class="w"> </span><span class="nx">coreapi</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">coreapi</span><span class="w"> </span><span class="c1">// Loaded by `coreapi.js`</span> <span class="kd">var</span><span class="w"> </span><span class="nx">schema</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">schema</span><span class="w"> </span><span class="c1">// Loaded by `schema.js`</span> <span class="c1">// Initialize a client</span> <span class="kd">var</span><span class="w"> </span><span class="nx">client</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="ow">new</span><span class="w"> </span><span class="nx">coreapi</span><span class="p">.</span><span class="nx">Client</span><span class="p">()</span> <span class="c1">// Interact with the API endpoint</span> <span class="kd">var</span><span class="w"> </span><span class="nx">action</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">[</span><span class="s2">"enrichment"</span><span class="p">,</span><span class="w"> </span><span class="s2">"create"</span><span class="p">]</span> <span class="kd">var</span><span class="w"> </span><span class="nx">params</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="nx">type</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="w"> </span><span class="nx">foreground</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="w"> </span><span class="nx">taxlevel</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="w"> </span><span class="nx">name</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="p">}</span> <span class="nx">client</span><span class="p">.</span><span class="nx">action</span><span class="p">(</span><span class="nx">schema</span><span class="p">,</span><span class="w"> </span><span class="nx">action</span><span class="p">,</span><span class="w"> </span><span class="nx">params</span><span class="p">).</span><span class="nx">then</span><span class="p">(</span><span class="kd">function</span><span class="p">(</span><span class="nx">result</span><span class="p">)</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="c1">// Return value is in 'result'</span> <span class="p">})</span> </code></pre> <pre class="highlight python hide" data-language="python"><code><span class="kn">import</span> <span class="nn">coreapi</span> <span class="c1"># Initialize a client & load the schema document</span> <span class="n">client</span> <span class="o">=</span> <span class="n">coreapi</span><span class="o">.</span><span class="n">Client</span><span class="p">()</span> <span class="n">schema</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"https://omabrowser.org/api/docs"</span><span class="p">)</span> <span class="c1"># Interact with the API endpoint</span> <span class="n">action</span> <span class="o">=</span> <span class="p">[</span><span class="s2">"enrichment"</span><span class="p">,</span> <span class="s2">"create"</span><span class="p">]</span> <span class="n">params</span> <span class="o">=</span> <span class="p">{</span> <span class="s2">"type"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="s2">"foreground"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="s2">"taxlevel"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="s2">"name"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="p">}</span> <span class="n">result</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">action</span><span class="p">(</span><span class="n">schema</span><span class="p">,</span> <span class="n">action</span><span class="p">,</span> <span class="n">params</span><span class="o">=</span><span class="n">params</span><span class="p">)</span> </code></pre> </div> </div> <!-- Modal --> <div class="modal fade api-modal" id="enrichment_create_modal" tabindex="-1" role="dialog" aria-labelledby="api explorer modal"> <div class="modal-dialog modal-lg" role="document"> <div class="modal-content"> <div class="modal-header"> <div class="toggle-view hide"> <div class="btn-group" role="group"> <button type="button" data-display-toggle="data" class="btn btn-sm btn-info">Data</button> <button type="button" data-display-toggle="raw" class="btn btn-sm">Raw</button> </div> </div> <h3 class="modal-title"><i class="fa fa-exchange"></i> create</h3> </div> <form data-key='["enrichment", "create"]' class="api-interaction"> <div class="modal-body"> <div class="row"> <div class="col-lg-6 request"> <div class="form-group"> <label> Type </label> <select class="form-control" name="type" data-empty='' data-type='string'> <option></option> <option value="ancestral">ancestral</option> <option value="extant">extant</option> </select> </div> <div class="form-group"> <label for="foreground" class="control-label"> Foreground <span class="text-danger">*</span> </label> <textarea name="foreground" class="form-control" data-empty={} data-type='object' required>{ }</textarea> </div> <div class="form-group"> <label for="taxlevel" class="control-label"> Taxonomic level </label> <input name="taxlevel" class="form-control" data-empty='' data-type='string' > </div> <div class="form-group"> <label for="name" class="control-label"> Name of the enrichment analysis </label> <input name="name" class="form-control" data-empty='' data-type='string' > </div> </div> <hr class="hidden-lg hidden-xl" /> <div class="col-lg-6 response" id="response"> <div class="request-awaiting">Awaiting request</div> <div class="meta hide"> <span class="label label-primary request-method"></span> <code class="request-url"></code> <label class="label label-lg response-status-code pull-right"></label> </div> <pre class="well response-data hide"></pre> <pre class="well response-raw hide"><div class="response-raw-request"></div><div class="response-raw-response"></div></pre> </div> </div> </div> <div class="modal-footer"> <button type="button" class="btn btn-default" data-dismiss="modal">Close</button> <button type="submit" class="btn btn-primary">Send Request</button> </div> </form> </div> </div> </div> <div class="row coredocs-link"> <div class="col-md-6 docs-content"> <button class="btn btn-sm btn-success" style="float: right; margin-top: 20px" data-toggle="modal" data-target="#enrichment_status-read_modal"> <i class="fa fa-exchange"></i> Interact </button> <h3 id="enrichment-status-read" class="coredocs-link-title">status > read <a href="#enrichment-status-read"><i class="fa fa-link" aria-hidden="true"></i> </a></h3> <div class="meta"> <span class="label label-primary">GET</span> <code>/api/enrichment/status/{id}/</code> </div> <p></p> <h4>Path Parameters</h4> <p>The following parameters should be included in the URL path.</p> <table class="parameters table table-bordered table-striped"> <thead> <tr><th>Parameter</th><th>Description</th></tr> </thead> <tbody> <tr><td class="parameter-name"><code>id</code> <span class="label label-warning">required</span></td><td>A UUID string identifying this enrichment analysis model.</td></tr> </tbody> </table> </div> <div class="col-md-6 code-samples"> <pre class="highlight shell hide" data-language="shell"><code><span class="c1"># Load the schema document</span> $<span class="w"> </span>coreapi<span class="w"> </span>get<span class="w"> </span>https://omabrowser.org/api/docs <span class="c1"># Interact with the API endpoint</span> $<span class="w"> </span>coreapi<span class="w"> </span>action<span class="w"> </span>enrichment<span class="w"> </span>status<span class="w"> </span><span class="nb">read</span><span class="w"> </span>-p<span class="w"> </span><span class="nv">id</span><span class="o">=</span>... </code></pre> <pre class="highlight javascript hide" data-language="javascript"><code><span class="kd">var</span><span class="w"> </span><span class="nx">coreapi</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">coreapi</span><span class="w"> </span><span class="c1">// Loaded by `coreapi.js`</span> <span class="kd">var</span><span class="w"> </span><span class="nx">schema</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">schema</span><span class="w"> </span><span class="c1">// Loaded by `schema.js`</span> <span class="c1">// Initialize a client</span> <span class="kd">var</span><span class="w"> </span><span class="nx">client</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="ow">new</span><span class="w"> </span><span class="nx">coreapi</span><span class="p">.</span><span class="nx">Client</span><span class="p">()</span> <span class="c1">// Interact with the API endpoint</span> <span class="kd">var</span><span class="w"> </span><span class="nx">action</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">[</span><span class="s2">"enrichment"</span><span class="p">,</span><span class="w"> </span><span class="s2">"status &gt; read"</span><span class="p">]</span> <span class="kd">var</span><span class="w"> </span><span class="nx">params</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="nx">id</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="p">}</span> <span class="nx">client</span><span class="p">.</span><span class="nx">action</span><span class="p">(</span><span class="nx">schema</span><span class="p">,</span><span class="w"> </span><span class="nx">action</span><span class="p">,</span><span class="w"> </span><span class="nx">params</span><span class="p">).</span><span class="nx">then</span><span class="p">(</span><span class="kd">function</span><span class="p">(</span><span class="nx">result</span><span class="p">)</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="c1">// Return value is in 'result'</span> <span class="p">})</span> </code></pre> <pre class="highlight python hide" data-language="python"><code><span class="kn">import</span> <span class="nn">coreapi</span> <span class="c1"># Initialize a client & load the schema document</span> <span class="n">client</span> <span class="o">=</span> <span class="n">coreapi</span><span class="o">.</span><span class="n">Client</span><span class="p">()</span> <span class="n">schema</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"https://omabrowser.org/api/docs"</span><span class="p">)</span> <span class="c1"># Interact with the API endpoint</span> <span class="n">action</span> <span class="o">=</span> <span class="p">[</span><span class="s2">"enrichment"</span><span class="p">,</span> <span class="s2">"status &gt; read"</span><span class="p">]</span> <span class="n">params</span> <span class="o">=</span> <span class="p">{</span> <span class="s2">"id"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="p">}</span> <span class="n">result</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">action</span><span class="p">(</span><span class="n">schema</span><span class="p">,</span> <span class="n">action</span><span class="p">,</span> <span class="n">params</span><span class="o">=</span><span class="n">params</span><span class="p">)</span> </code></pre> </div> </div> <!-- Modal --> <div class="modal fade api-modal" id="enrichment_status-read_modal" tabindex="-1" role="dialog" aria-labelledby="api explorer modal"> <div class="modal-dialog modal-lg" role="document"> <div class="modal-content"> <div class="modal-header"> <div class="toggle-view hide"> <div class="btn-group" role="group"> <button type="button" data-display-toggle="data" class="btn btn-sm btn-info">Data</button> <button type="button" data-display-toggle="raw" class="btn btn-sm">Raw</button> </div> </div> <h3 class="modal-title"><i class="fa fa-exchange"></i> status > read</h3> </div> <form data-key='["enrichment", "status > read"]' class="api-interaction"> <div class="modal-body"> <div class="row"> <div class="col-lg-6 request"> <div class="form-group"> <label for="id" class="control-label"> id <span class="text-danger">*</span> </label> <input name="id" class="form-control" data-empty='' data-type='string' required> <p class="help-block">A UUID string identifying this enrichment analysis model.</p> </div> </div> <hr class="hidden-lg hidden-xl" /> <div class="col-lg-6 response" id="response"> <div class="request-awaiting">Awaiting request</div> <div class="meta hide"> <span class="label label-primary request-method"></span> <code class="request-url"></code> <label class="label label-lg response-status-code pull-right"></label> </div> <pre class="well response-data hide"></pre> <pre class="well response-raw hide"><div class="response-raw-request"></div><div class="response-raw-response"></div></pre> </div> </div> </div> <div class="modal-footer"> <button type="button" class="btn btn-default" data-dismiss="modal">Close</button> <button type="submit" class="btn btn-primary">Send Request</button> </div> </form> </div> </div> </div> <h2 id="function" class="coredocs-section-title">function <a href="#function"><i class="fa fa-link" aria-hidden="true"></i> </a></h2> <div class="row coredocs-link"> <div class="col-md-6 docs-content"> <button class="btn btn-sm btn-success" style="float: right; margin-top: 20px" data-toggle="modal" data-target="#function_list_modal"> <i class="fa fa-exchange"></i> Interact </button> <h3 id="function-list" class="coredocs-link-title">list <a href="#function-list"><i class="fa fa-link" aria-hidden="true"></i> </a></h3> <div class="meta"> <span class="label label-primary">GET</span> <code>/api/function/</code> </div> <p><p>Annotate a sequence with GO functions based on all annotations in OMA. The sequence is expected to be a simple string of amino acids and can be passed as a query parameter</p></p> <h4>Query Parameters</h4> <p>The following parameters should be included as part of a URL query string.</p> <table class="parameters table table-bordered table-striped"> <thead> <tr><th>Parameter</th><th>Description</th></tr> </thead> <tbody> <tr><td class="parameter-name"><code>query</code> <span class="label label-warning">required</span></td><td>the sequence to be annotated</td></tr> </tbody> </table> </div> <div class="col-md-6 code-samples"> <pre class="highlight shell hide" data-language="shell"><code><span class="c1"># Load the schema document</span> $<span class="w"> </span>coreapi<span class="w"> </span>get<span class="w"> </span>https://omabrowser.org/api/docs <span class="c1"># Interact with the API endpoint</span> $<span class="w"> </span>coreapi<span class="w"> </span>action<span class="w"> </span><span class="k">function</span><span class="w"> </span>list<span class="w"> </span>-p<span class="w"> </span><span class="nv">query</span><span class="o">=</span>... </code></pre> <pre class="highlight javascript hide" data-language="javascript"><code><span class="kd">var</span><span class="w"> </span><span class="nx">coreapi</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">coreapi</span><span class="w"> </span><span class="c1">// Loaded by `coreapi.js`</span> <span class="kd">var</span><span class="w"> </span><span class="nx">schema</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">schema</span><span class="w"> </span><span class="c1">// Loaded by `schema.js`</span> <span class="c1">// Initialize a client</span> <span class="kd">var</span><span class="w"> </span><span class="nx">client</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="ow">new</span><span class="w"> </span><span class="nx">coreapi</span><span class="p">.</span><span class="nx">Client</span><span class="p">()</span> <span class="c1">// Interact with the API endpoint</span> <span class="kd">var</span><span class="w"> </span><span class="nx">action</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">[</span><span class="s2">"function"</span><span class="p">,</span><span class="w"> </span><span class="s2">"list"</span><span class="p">]</span> <span class="kd">var</span><span class="w"> </span><span class="nx">params</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="nx">query</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="p">}</span> <span class="nx">client</span><span class="p">.</span><span class="nx">action</span><span class="p">(</span><span class="nx">schema</span><span class="p">,</span><span class="w"> </span><span class="nx">action</span><span class="p">,</span><span class="w"> </span><span class="nx">params</span><span class="p">).</span><span class="nx">then</span><span class="p">(</span><span class="kd">function</span><span class="p">(</span><span class="nx">result</span><span class="p">)</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="c1">// Return value is in 'result'</span> <span class="p">})</span> </code></pre> <pre class="highlight python hide" data-language="python"><code><span class="kn">import</span> <span class="nn">coreapi</span> <span class="c1"># Initialize a client & load the schema document</span> <span class="n">client</span> <span class="o">=</span> <span class="n">coreapi</span><span class="o">.</span><span class="n">Client</span><span class="p">()</span> <span class="n">schema</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"https://omabrowser.org/api/docs"</span><span class="p">)</span> <span class="c1"># Interact with the API endpoint</span> <span class="n">action</span> <span class="o">=</span> <span class="p">[</span><span class="s2">"function"</span><span class="p">,</span> <span class="s2">"list"</span><span class="p">]</span> <span class="n">params</span> <span class="o">=</span> <span class="p">{</span> <span class="s2">"query"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="p">}</span> <span class="n">result</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">action</span><span class="p">(</span><span class="n">schema</span><span class="p">,</span> <span class="n">action</span><span class="p">,</span> <span class="n">params</span><span class="o">=</span><span class="n">params</span><span class="p">)</span> </code></pre> </div> </div> <!-- Modal --> <div class="modal fade api-modal" id="function_list_modal" tabindex="-1" role="dialog" aria-labelledby="api explorer modal"> <div class="modal-dialog modal-lg" role="document"> <div class="modal-content"> <div class="modal-header"> <div class="toggle-view hide"> <div class="btn-group" role="group"> <button type="button" data-display-toggle="data" class="btn btn-sm btn-info">Data</button> <button type="button" data-display-toggle="raw" class="btn btn-sm">Raw</button> </div> </div> <h3 class="modal-title"><i class="fa fa-exchange"></i> list</h3> </div> <form data-key='["function", "list"]' class="api-interaction"> <div class="modal-body"> <div class="row"> <div class="col-lg-6 request"> <div class="form-group"> <label for="query" class="control-label"> query <span class="text-danger">*</span> </label> <input name="query" class="form-control" data-empty='' data-type='string' required> <p class="help-block">the sequence to be annotated</p> </div> </div> <hr class="hidden-lg hidden-xl" /> <div class="col-lg-6 response" id="response"> <div class="request-awaiting">Awaiting request</div> <div class="meta hide"> <span class="label label-primary request-method"></span> <code class="request-url"></code> <label class="label label-lg response-status-code pull-right"></label> </div> <pre class="well response-data hide"></pre> <pre class="well response-raw hide"><div class="response-raw-request"></div><div class="response-raw-response"></div></pre> </div> </div> </div> <div class="modal-footer"> <button type="button" class="btn btn-default" data-dismiss="modal">Close</button> <button type="submit" class="btn btn-primary">Send Request</button> </div> </form> </div> </div> </div> <h2 id="genome" class="coredocs-section-title">genome <a href="#genome"><i class="fa fa-link" aria-hidden="true"></i> </a></h2> <div class="row coredocs-link"> <div class="col-md-6 docs-content"> <button class="btn btn-sm btn-success" style="float: right; margin-top: 20px" data-toggle="modal" data-target="#genome_list_modal"> <i class="fa fa-exchange"></i> Interact </button> <h3 id="genome-list" class="coredocs-link-title">list <a href="#genome-list"><i class="fa fa-link" aria-hidden="true"></i> </a></h3> <div class="meta"> <span class="label label-primary">GET</span> <code>/api/genome/</code> </div> <p><p>List of all the genomes present in the current release.</p></p> <h4>Query Parameters</h4> <p>The following parameters should be included as part of a URL query string.</p> <table class="parameters table table-bordered table-striped"> <thead> <tr><th>Parameter</th><th>Description</th></tr> </thead> <tbody> <tr><td class="parameter-name"><code>page</code></td><td>A page number within the paginated result set.</td></tr> <tr><td class="parameter-name"><code>per_page</code></td><td>Number of results to return per page.</td></tr> </tbody> </table> </div> <div class="col-md-6 code-samples"> <pre class="highlight shell hide" data-language="shell"><code><span class="c1"># Load the schema document</span> $<span class="w"> </span>coreapi<span class="w"> </span>get<span class="w"> </span>https://omabrowser.org/api/docs <span class="c1"># Interact with the API endpoint</span> $<span class="w"> </span>coreapi<span class="w"> </span>action<span class="w"> </span>genome<span class="w"> </span>list<span class="w"> </span>-p<span class="w"> </span><span class="nv">page</span><span class="o">=</span>...<span class="w"> </span>-p<span class="w"> </span><span class="nv">per_page</span><span class="o">=</span>... </code></pre> <pre class="highlight javascript hide" data-language="javascript"><code><span class="kd">var</span><span class="w"> </span><span class="nx">coreapi</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">coreapi</span><span class="w"> </span><span class="c1">// Loaded by `coreapi.js`</span> <span class="kd">var</span><span class="w"> </span><span class="nx">schema</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">schema</span><span class="w"> </span><span class="c1">// Loaded by `schema.js`</span> <span class="c1">// Initialize a client</span> <span class="kd">var</span><span class="w"> </span><span class="nx">client</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="ow">new</span><span class="w"> </span><span class="nx">coreapi</span><span class="p">.</span><span class="nx">Client</span><span class="p">()</span> <span class="c1">// Interact with the API endpoint</span> <span class="kd">var</span><span class="w"> </span><span class="nx">action</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">[</span><span class="s2">"genome"</span><span class="p">,</span><span class="w"> </span><span class="s2">"list"</span><span class="p">]</span> <span class="kd">var</span><span class="w"> </span><span class="nx">params</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="nx">page</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="w"> </span><span class="nx">per_page</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="p">}</span> <span class="nx">client</span><span class="p">.</span><span class="nx">action</span><span class="p">(</span><span class="nx">schema</span><span class="p">,</span><span class="w"> </span><span class="nx">action</span><span class="p">,</span><span class="w"> </span><span class="nx">params</span><span class="p">).</span><span class="nx">then</span><span class="p">(</span><span class="kd">function</span><span class="p">(</span><span class="nx">result</span><span class="p">)</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="c1">// Return value is in 'result'</span> <span class="p">})</span> </code></pre> <pre class="highlight python hide" data-language="python"><code><span class="kn">import</span> <span class="nn">coreapi</span> <span class="c1"># Initialize a client & load the schema document</span> <span class="n">client</span> <span class="o">=</span> <span class="n">coreapi</span><span class="o">.</span><span class="n">Client</span><span class="p">()</span> <span class="n">schema</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"https://omabrowser.org/api/docs"</span><span class="p">)</span> <span class="c1"># Interact with the API endpoint</span> <span class="n">action</span> <span class="o">=</span> <span class="p">[</span><span class="s2">"genome"</span><span class="p">,</span> <span class="s2">"list"</span><span class="p">]</span> <span class="n">params</span> <span class="o">=</span> <span class="p">{</span> <span class="s2">"page"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="s2">"per_page"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="p">}</span> <span class="n">result</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">action</span><span class="p">(</span><span class="n">schema</span><span class="p">,</span> <span class="n">action</span><span class="p">,</span> <span class="n">params</span><span class="o">=</span><span class="n">params</span><span class="p">)</span> </code></pre> </div> </div> <!-- Modal --> <div class="modal fade api-modal" id="genome_list_modal" tabindex="-1" role="dialog" aria-labelledby="api explorer modal"> <div class="modal-dialog modal-lg" role="document"> <div class="modal-content"> <div class="modal-header"> <div class="toggle-view hide"> <div class="btn-group" role="group"> <button type="button" data-display-toggle="data" class="btn btn-sm btn-info">Data</button> <button type="button" data-display-toggle="raw" class="btn btn-sm">Raw</button> </div> </div> <h3 class="modal-title"><i class="fa fa-exchange"></i> list</h3> </div> <form data-key='["genome", "list"]' class="api-interaction"> <div class="modal-body"> <div class="row"> <div class="col-lg-6 request"> <div class="form-group"> <label for="page" class="control-label"> Page </label> <input name="page" class="form-control" data-empty=null data-type='integer' type='number' step=1 > <p class="help-block">A page number within the paginated result set.</p> </div> <div class="form-group"> <label for="per_page" class="control-label"> Page size </label> <input name="per_page" class="form-control" data-empty=null data-type='integer' type='number' step=1 > <p class="help-block">Number of results to return per page.</p> </div> </div> <hr class="hidden-lg hidden-xl" /> <div class="col-lg-6 response" id="response"> <div class="request-awaiting">Awaiting request</div> <div class="meta hide"> <span class="label label-primary request-method"></span> <code class="request-url"></code> <label class="label label-lg response-status-code pull-right"></label> </div> <pre class="well response-data hide"></pre> <pre class="well response-raw hide"><div class="response-raw-request"></div><div class="response-raw-response"></div></pre> </div> </div> </div> <div class="modal-footer"> <button type="button" class="btn btn-default" data-dismiss="modal">Close</button> <button type="submit" class="btn btn-primary">Send Request</button> </div> </form> </div> </div> </div> <div class="row coredocs-link"> <div class="col-md-6 docs-content"> <button class="btn btn-sm btn-success" style="float: right; margin-top: 20px" data-toggle="modal" data-target="#genome_read_modal"> <i class="fa fa-exchange"></i> Interact </button> <h3 id="genome-read" class="coredocs-link-title">read <a href="#genome-read"><i class="fa fa-link" aria-hidden="true"></i> </a></h3> <div class="meta"> <span class="label label-primary">GET</span> <code>/api/genome/{genome_id}/</code> </div> <p><p>Retrieve the information available for a given genome.</p></p> <h4>Path Parameters</h4> <p>The following parameters should be included in the URL path.</p> <table class="parameters table table-bordered table-striped"> <thead> <tr><th>Parameter</th><th>Description</th></tr> </thead> <tbody> <tr><td class="parameter-name"><code>genome_id</code> <span class="label label-warning">required</span></td><td>an unique identifier for a genome - either its ncbi taxon id or the UniProt species code</td></tr> </tbody> </table> </div> <div class="col-md-6 code-samples"> <pre class="highlight shell hide" data-language="shell"><code><span class="c1"># Load the schema document</span> $<span class="w"> </span>coreapi<span class="w"> </span>get<span class="w"> </span>https://omabrowser.org/api/docs <span class="c1"># Interact with the API endpoint</span> $<span class="w"> </span>coreapi<span class="w"> </span>action<span class="w"> </span>genome<span class="w"> </span><span class="nb">read</span><span class="w"> </span>-p<span class="w"> </span><span class="nv">genome_id</span><span class="o">=</span>... </code></pre> <pre class="highlight javascript hide" data-language="javascript"><code><span class="kd">var</span><span class="w"> </span><span class="nx">coreapi</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">coreapi</span><span class="w"> </span><span class="c1">// Loaded by `coreapi.js`</span> <span class="kd">var</span><span class="w"> </span><span class="nx">schema</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">schema</span><span class="w"> </span><span class="c1">// Loaded by `schema.js`</span> <span class="c1">// Initialize a client</span> <span class="kd">var</span><span class="w"> </span><span class="nx">client</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="ow">new</span><span class="w"> </span><span class="nx">coreapi</span><span class="p">.</span><span class="nx">Client</span><span class="p">()</span> <span class="c1">// Interact with the API endpoint</span> <span class="kd">var</span><span class="w"> </span><span class="nx">action</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">[</span><span class="s2">"genome"</span><span class="p">,</span><span class="w"> </span><span class="s2">"read"</span><span class="p">]</span> <span class="kd">var</span><span class="w"> </span><span class="nx">params</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="nx">genome_id</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="p">}</span> <span class="nx">client</span><span class="p">.</span><span class="nx">action</span><span class="p">(</span><span class="nx">schema</span><span class="p">,</span><span class="w"> </span><span class="nx">action</span><span class="p">,</span><span class="w"> </span><span class="nx">params</span><span class="p">).</span><span class="nx">then</span><span class="p">(</span><span class="kd">function</span><span class="p">(</span><span class="nx">result</span><span class="p">)</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="c1">// Return value is in 'result'</span> <span class="p">})</span> </code></pre> <pre class="highlight python hide" data-language="python"><code><span class="kn">import</span> <span class="nn">coreapi</span> <span class="c1"># Initialize a client & load the schema document</span> <span class="n">client</span> <span class="o">=</span> <span class="n">coreapi</span><span class="o">.</span><span class="n">Client</span><span class="p">()</span> <span class="n">schema</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"https://omabrowser.org/api/docs"</span><span class="p">)</span> <span class="c1"># Interact with the API endpoint</span> <span class="n">action</span> <span class="o">=</span> <span class="p">[</span><span class="s2">"genome"</span><span class="p">,</span> <span class="s2">"read"</span><span class="p">]</span> <span class="n">params</span> <span class="o">=</span> <span class="p">{</span> <span class="s2">"genome_id"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="p">}</span> <span class="n">result</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">action</span><span class="p">(</span><span class="n">schema</span><span class="p">,</span> <span class="n">action</span><span class="p">,</span> <span class="n">params</span><span class="o">=</span><span class="n">params</span><span class="p">)</span> </code></pre> </div> </div> <!-- Modal --> <div class="modal fade api-modal" id="genome_read_modal" tabindex="-1" role="dialog" aria-labelledby="api explorer modal"> <div class="modal-dialog modal-lg" role="document"> <div class="modal-content"> <div class="modal-header"> <div class="toggle-view hide"> <div class="btn-group" role="group"> <button type="button" data-display-toggle="data" class="btn btn-sm btn-info">Data</button> <button type="button" data-display-toggle="raw" class="btn btn-sm">Raw</button> </div> </div> <h3 class="modal-title"><i class="fa fa-exchange"></i> read</h3> </div> <form data-key='["genome", "read"]' class="api-interaction"> <div class="modal-body"> <div class="row"> <div class="col-lg-6 request"> <div class="form-group"> <label for="genome_id" class="control-label"> genome_id <span class="text-danger">*</span> </label> <input name="genome_id" class="form-control" data-empty='' data-type='string' required> <p class="help-block">an unique identifier for a genome - either its ncbi taxon id or the UniProt species code</p> </div> </div> <hr class="hidden-lg hidden-xl" /> <div class="col-lg-6 response" id="response"> <div class="request-awaiting">Awaiting request</div> <div class="meta hide"> <span class="label label-primary request-method"></span> <code class="request-url"></code> <label class="label label-lg response-status-code pull-right"></label> </div> <pre class="well response-data hide"></pre> <pre class="well response-raw hide"><div class="response-raw-request"></div><div class="response-raw-response"></div></pre> </div> </div> </div> <div class="modal-footer"> <button type="button" class="btn btn-default" data-dismiss="modal">Close</button> <button type="submit" class="btn btn-primary">Send Request</button> </div> </form> </div> </div> </div> <div class="row coredocs-link"> <div class="col-md-6 docs-content"> <button class="btn btn-sm btn-success" style="float: right; margin-top: 20px" data-toggle="modal" data-target="#genome_genes_modal"> <i class="fa fa-exchange"></i> Interact </button> <h3 id="genome-genes" class="coredocs-link-title">genes <a href="#genome-genes"><i class="fa fa-link" aria-hidden="true"></i> </a></h3> <div class="meta"> <span class="label label-primary">GET</span> <code>/api/genome/{genome_id}/genes/</code> </div> <p><p>Retrieve the list of all the genes available for a genome.</p> <p>This corresponds to the list of main isoform for genomes with multiple isoforms, or to all the proteins for the others.</p></p> <h4>Path Parameters</h4> <p>The following parameters should be included in the URL path.</p> <table class="parameters table table-bordered table-striped"> <thead> <tr><th>Parameter</th><th>Description</th></tr> </thead> <tbody> <tr><td class="parameter-name"><code>genome_id</code> <span class="label label-warning">required</span></td><td>an unique identifier for a genome - either its ncbi taxon id or the UniProt species code</td></tr> </tbody> </table> </div> <div class="col-md-6 code-samples"> <pre class="highlight shell hide" data-language="shell"><code><span class="c1"># Load the schema document</span> $<span class="w"> </span>coreapi<span class="w"> </span>get<span class="w"> </span>https://omabrowser.org/api/docs <span class="c1"># Interact with the API endpoint</span> $<span class="w"> </span>coreapi<span class="w"> </span>action<span class="w"> </span>genome<span class="w"> </span>genes<span class="w"> </span>-p<span class="w"> </span><span class="nv">genome_id</span><span class="o">=</span>... </code></pre> <pre class="highlight javascript hide" data-language="javascript"><code><span class="kd">var</span><span class="w"> </span><span class="nx">coreapi</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">coreapi</span><span class="w"> </span><span class="c1">// Loaded by `coreapi.js`</span> <span class="kd">var</span><span class="w"> </span><span class="nx">schema</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">schema</span><span class="w"> </span><span class="c1">// Loaded by `schema.js`</span> <span class="c1">// Initialize a client</span> <span class="kd">var</span><span class="w"> </span><span class="nx">client</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="ow">new</span><span class="w"> </span><span class="nx">coreapi</span><span class="p">.</span><span class="nx">Client</span><span class="p">()</span> <span class="c1">// Interact with the API endpoint</span> <span class="kd">var</span><span class="w"> </span><span class="nx">action</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">[</span><span class="s2">"genome"</span><span class="p">,</span><span class="w"> </span><span class="s2">"genes"</span><span class="p">]</span> <span class="kd">var</span><span class="w"> </span><span class="nx">params</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="nx">genome_id</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="p">}</span> <span class="nx">client</span><span class="p">.</span><span class="nx">action</span><span class="p">(</span><span class="nx">schema</span><span class="p">,</span><span class="w"> </span><span class="nx">action</span><span class="p">,</span><span class="w"> </span><span class="nx">params</span><span class="p">).</span><span class="nx">then</span><span class="p">(</span><span class="kd">function</span><span class="p">(</span><span class="nx">result</span><span class="p">)</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="c1">// Return value is in 'result'</span> <span class="p">})</span> </code></pre> <pre class="highlight python hide" data-language="python"><code><span class="kn">import</span> <span class="nn">coreapi</span> <span class="c1"># Initialize a client & load the schema document</span> <span class="n">client</span> <span class="o">=</span> <span class="n">coreapi</span><span class="o">.</span><span class="n">Client</span><span class="p">()</span> <span class="n">schema</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"https://omabrowser.org/api/docs"</span><span class="p">)</span> <span class="c1"># Interact with the API endpoint</span> <span class="n">action</span> <span class="o">=</span> <span class="p">[</span><span class="s2">"genome"</span><span class="p">,</span> <span class="s2">"genes"</span><span class="p">]</span> <span class="n">params</span> <span class="o">=</span> <span class="p">{</span> <span class="s2">"genome_id"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="p">}</span> <span class="n">result</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">action</span><span class="p">(</span><span class="n">schema</span><span class="p">,</span> <span class="n">action</span><span class="p">,</span> <span class="n">params</span><span class="o">=</span><span class="n">params</span><span class="p">)</span> </code></pre> </div> </div> <!-- Modal --> <div class="modal fade api-modal" id="genome_genes_modal" tabindex="-1" role="dialog" aria-labelledby="api explorer modal"> <div class="modal-dialog modal-lg" role="document"> <div class="modal-content"> <div class="modal-header"> <div class="toggle-view hide"> <div class="btn-group" role="group"> <button type="button" data-display-toggle="data" class="btn btn-sm btn-info">Data</button> <button type="button" data-display-toggle="raw" class="btn btn-sm">Raw</button> </div> </div> <h3 class="modal-title"><i class="fa fa-exchange"></i> genes</h3> </div> <form data-key='["genome", "genes"]' class="api-interaction"> <div class="modal-body"> <div class="row"> <div class="col-lg-6 request"> <div class="form-group"> <label for="genome_id" class="control-label"> genome_id <span class="text-danger">*</span> </label> <input name="genome_id" class="form-control" data-empty='' data-type='string' required> <p class="help-block">an unique identifier for a genome - either its ncbi taxon id or the UniProt species code</p> </div> </div> <hr class="hidden-lg hidden-xl" /> <div class="col-lg-6 response" id="response"> <div class="request-awaiting">Awaiting request</div> <div class="meta hide"> <span class="label label-primary request-method"></span> <code class="request-url"></code> <label class="label label-lg response-status-code pull-right"></label> </div> <pre class="well response-data hide"></pre> <pre class="well response-raw hide"><div class="response-raw-request"></div><div class="response-raw-response"></div></pre> </div> </div> </div> <div class="modal-footer"> <button type="button" class="btn btn-default" data-dismiss="modal">Close</button> <button type="submit" class="btn btn-primary">Send Request</button> </div> </form> </div> </div> </div> <div class="row coredocs-link"> <div class="col-md-6 docs-content"> <button class="btn btn-sm btn-success" style="float: right; margin-top: 20px" data-toggle="modal" data-target="#genome_proteins_modal"> <i class="fa fa-exchange"></i> Interact </button> <h3 id="genome-proteins" class="coredocs-link-title">proteins <a href="#genome-proteins"><i class="fa fa-link" aria-hidden="true"></i> </a></h3> <div class="meta"> <span class="label label-primary">GET</span> <code>/api/genome/{genome_id}/proteins/</code> </div> <p><p>Retrieve the list of all the protein entries available for a genome.</p></p> <h4>Path Parameters</h4> <p>The following parameters should be included in the URL path.</p> <table class="parameters table table-bordered table-striped"> <thead> <tr><th>Parameter</th><th>Description</th></tr> </thead> <tbody> <tr><td class="parameter-name"><code>genome_id</code> <span class="label label-warning">required</span></td><td>an unique identifier for a genome - either its ncbi taxon id or the UniProt species code</td></tr> </tbody> </table> </div> <div class="col-md-6 code-samples"> <pre class="highlight shell hide" data-language="shell"><code><span class="c1"># Load the schema document</span> $<span class="w"> </span>coreapi<span class="w"> </span>get<span class="w"> </span>https://omabrowser.org/api/docs <span class="c1"># Interact with the API endpoint</span> $<span class="w"> </span>coreapi<span class="w"> </span>action<span class="w"> </span>genome<span class="w"> </span>proteins<span class="w"> </span>-p<span class="w"> </span><span class="nv">genome_id</span><span class="o">=</span>... </code></pre> <pre class="highlight javascript hide" data-language="javascript"><code><span class="kd">var</span><span class="w"> </span><span class="nx">coreapi</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">coreapi</span><span class="w"> </span><span class="c1">// Loaded by `coreapi.js`</span> <span class="kd">var</span><span class="w"> </span><span class="nx">schema</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">schema</span><span class="w"> </span><span class="c1">// Loaded by `schema.js`</span> <span class="c1">// Initialize a client</span> <span class="kd">var</span><span class="w"> </span><span class="nx">client</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="ow">new</span><span class="w"> </span><span class="nx">coreapi</span><span class="p">.</span><span class="nx">Client</span><span class="p">()</span> <span class="c1">// Interact with the API endpoint</span> <span class="kd">var</span><span class="w"> </span><span class="nx">action</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">[</span><span class="s2">"genome"</span><span class="p">,</span><span class="w"> </span><span class="s2">"proteins"</span><span class="p">]</span> <span class="kd">var</span><span class="w"> </span><span class="nx">params</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="nx">genome_id</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="p">}</span> <span class="nx">client</span><span class="p">.</span><span class="nx">action</span><span class="p">(</span><span class="nx">schema</span><span class="p">,</span><span class="w"> </span><span class="nx">action</span><span class="p">,</span><span class="w"> </span><span class="nx">params</span><span class="p">).</span><span class="nx">then</span><span class="p">(</span><span class="kd">function</span><span class="p">(</span><span class="nx">result</span><span class="p">)</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="c1">// Return value is in 'result'</span> <span class="p">})</span> </code></pre> <pre class="highlight python hide" data-language="python"><code><span class="kn">import</span> <span class="nn">coreapi</span> <span class="c1"># Initialize a client & load the schema document</span> <span class="n">client</span> <span class="o">=</span> <span class="n">coreapi</span><span class="o">.</span><span class="n">Client</span><span class="p">()</span> <span class="n">schema</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"https://omabrowser.org/api/docs"</span><span class="p">)</span> <span class="c1"># Interact with the API endpoint</span> <span class="n">action</span> <span class="o">=</span> <span class="p">[</span><span class="s2">"genome"</span><span class="p">,</span> <span class="s2">"proteins"</span><span class="p">]</span> <span class="n">params</span> <span class="o">=</span> <span class="p">{</span> <span class="s2">"genome_id"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="p">}</span> <span class="n">result</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">action</span><span class="p">(</span><span class="n">schema</span><span class="p">,</span> <span class="n">action</span><span class="p">,</span> <span class="n">params</span><span class="o">=</span><span class="n">params</span><span class="p">)</span> </code></pre> </div> </div> <!-- Modal --> <div class="modal fade api-modal" id="genome_proteins_modal" tabindex="-1" role="dialog" aria-labelledby="api explorer modal"> <div class="modal-dialog modal-lg" role="document"> <div class="modal-content"> <div class="modal-header"> <div class="toggle-view hide"> <div class="btn-group" role="group"> <button type="button" data-display-toggle="data" class="btn btn-sm btn-info">Data</button> <button type="button" data-display-toggle="raw" class="btn btn-sm">Raw</button> </div> </div> <h3 class="modal-title"><i class="fa fa-exchange"></i> proteins</h3> </div> <form data-key='["genome", "proteins"]' class="api-interaction"> <div class="modal-body"> <div class="row"> <div class="col-lg-6 request"> <div class="form-group"> <label for="genome_id" class="control-label"> genome_id <span class="text-danger">*</span> </label> <input name="genome_id" class="form-control" data-empty='' data-type='string' required> <p class="help-block">an unique identifier for a genome - either its ncbi taxon id or the UniProt species code</p> </div> </div> <hr class="hidden-lg hidden-xl" /> <div class="col-lg-6 response" id="response"> <div class="request-awaiting">Awaiting request</div> <div class="meta hide"> <span class="label label-primary request-method"></span> <code class="request-url"></code> <label class="label label-lg response-status-code pull-right"></label> </div> <pre class="well response-data hide"></pre> <pre class="well response-raw hide"><div class="response-raw-request"></div><div class="response-raw-response"></div></pre> </div> </div> </div> <div class="modal-footer"> <button type="button" class="btn btn-default" data-dismiss="modal">Close</button> <button type="submit" class="btn btn-primary">Send Request</button> </div> </form> </div> </div> </div> <h2 id="group" class="coredocs-section-title">group <a href="#group"><i class="fa fa-link" aria-hidden="true"></i> </a></h2> <div class="row coredocs-link"> <div class="col-md-6 docs-content"> <button class="btn btn-sm btn-success" style="float: right; margin-top: 20px" data-toggle="modal" data-target="#group_list_modal"> <i class="fa fa-exchange"></i> Interact </button> <h3 id="group-list" class="coredocs-link-title">list <a href="#group-list"><i class="fa fa-link" aria-hidden="true"></i> </a></h3> <div class="meta"> <span class="label label-primary">GET</span> <code>/api/group/</code> </div> <p><p>List of all the OMA Groups in the current release.</p></p> <h4>Query Parameters</h4> <p>The following parameters should be included as part of a URL query string.</p> <table class="parameters table table-bordered table-striped"> <thead> <tr><th>Parameter</th><th>Description</th></tr> </thead> <tbody> <tr><td class="parameter-name"><code>page</code></td><td>A page number within the paginated result set.</td></tr> <tr><td class="parameter-name"><code>per_page</code></td><td>Number of results to return per page.</td></tr> </tbody> </table> </div> <div class="col-md-6 code-samples"> <pre class="highlight shell hide" data-language="shell"><code><span class="c1"># Load the schema document</span> $<span class="w"> </span>coreapi<span class="w"> </span>get<span class="w"> </span>https://omabrowser.org/api/docs <span class="c1"># Interact with the API endpoint</span> $<span class="w"> </span>coreapi<span class="w"> </span>action<span class="w"> </span>group<span class="w"> </span>list<span class="w"> </span>-p<span class="w"> </span><span class="nv">page</span><span class="o">=</span>...<span class="w"> </span>-p<span class="w"> </span><span class="nv">per_page</span><span class="o">=</span>... </code></pre> <pre class="highlight javascript hide" data-language="javascript"><code><span class="kd">var</span><span class="w"> </span><span class="nx">coreapi</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">coreapi</span><span class="w"> </span><span class="c1">// Loaded by `coreapi.js`</span> <span class="kd">var</span><span class="w"> </span><span class="nx">schema</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">schema</span><span class="w"> </span><span class="c1">// Loaded by `schema.js`</span> <span class="c1">// Initialize a client</span> <span class="kd">var</span><span class="w"> </span><span class="nx">client</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="ow">new</span><span class="w"> </span><span class="nx">coreapi</span><span class="p">.</span><span class="nx">Client</span><span class="p">()</span> <span class="c1">// Interact with the API endpoint</span> <span class="kd">var</span><span class="w"> </span><span class="nx">action</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">[</span><span class="s2">"group"</span><span class="p">,</span><span class="w"> </span><span class="s2">"list"</span><span class="p">]</span> <span class="kd">var</span><span class="w"> </span><span class="nx">params</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="nx">page</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="w"> </span><span class="nx">per_page</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="p">}</span> <span class="nx">client</span><span class="p">.</span><span class="nx">action</span><span class="p">(</span><span class="nx">schema</span><span class="p">,</span><span class="w"> </span><span class="nx">action</span><span class="p">,</span><span class="w"> </span><span class="nx">params</span><span class="p">).</span><span class="nx">then</span><span class="p">(</span><span class="kd">function</span><span class="p">(</span><span class="nx">result</span><span class="p">)</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="c1">// Return value is in 'result'</span> <span class="p">})</span> </code></pre> <pre class="highlight python hide" data-language="python"><code><span class="kn">import</span> <span class="nn">coreapi</span> <span class="c1"># Initialize a client & load the schema document</span> <span class="n">client</span> <span class="o">=</span> <span class="n">coreapi</span><span class="o">.</span><span class="n">Client</span><span class="p">()</span> <span class="n">schema</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"https://omabrowser.org/api/docs"</span><span class="p">)</span> <span class="c1"># Interact with the API endpoint</span> <span class="n">action</span> <span class="o">=</span> <span class="p">[</span><span class="s2">"group"</span><span class="p">,</span> <span class="s2">"list"</span><span class="p">]</span> <span class="n">params</span> <span class="o">=</span> <span class="p">{</span> <span class="s2">"page"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="s2">"per_page"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="p">}</span> <span class="n">result</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">action</span><span class="p">(</span><span class="n">schema</span><span class="p">,</span> <span class="n">action</span><span class="p">,</span> <span class="n">params</span><span class="o">=</span><span class="n">params</span><span class="p">)</span> </code></pre> </div> </div> <!-- Modal --> <div class="modal fade api-modal" id="group_list_modal" tabindex="-1" role="dialog" aria-labelledby="api explorer modal"> <div class="modal-dialog modal-lg" role="document"> <div class="modal-content"> <div class="modal-header"> <div class="toggle-view hide"> <div class="btn-group" role="group"> <button type="button" data-display-toggle="data" class="btn btn-sm btn-info">Data</button> <button type="button" data-display-toggle="raw" class="btn btn-sm">Raw</button> </div> </div> <h3 class="modal-title"><i class="fa fa-exchange"></i> list</h3> </div> <form data-key='["group", "list"]' class="api-interaction"> <div class="modal-body"> <div class="row"> <div class="col-lg-6 request"> <div class="form-group"> <label for="page" class="control-label"> Page </label> <input name="page" class="form-control" data-empty=null data-type='integer' type='number' step=1 > <p class="help-block">A page number within the paginated result set.</p> </div> <div class="form-group"> <label for="per_page" class="control-label"> Page size </label> <input name="per_page" class="form-control" data-empty=null data-type='integer' type='number' step=1 > <p class="help-block">Number of results to return per page.</p> </div> </div> <hr class="hidden-lg hidden-xl" /> <div class="col-lg-6 response" id="response"> <div class="request-awaiting">Awaiting request</div> <div class="meta hide"> <span class="label label-primary request-method"></span> <code class="request-url"></code> <label class="label label-lg response-status-code pull-right"></label> </div> <pre class="well response-data hide"></pre> <pre class="well response-raw hide"><div class="response-raw-request"></div><div class="response-raw-response"></div></pre> </div> </div> </div> <div class="modal-footer"> <button type="button" class="btn btn-default" data-dismiss="modal">Close</button> <button type="submit" class="btn btn-primary">Send Request</button> </div> </form> </div> </div> </div> <div class="row coredocs-link"> <div class="col-md-6 docs-content"> <button class="btn btn-sm btn-success" style="float: right; margin-top: 20px" data-toggle="modal" data-target="#group_read_modal"> <i class="fa fa-exchange"></i> Interact </button> <h3 id="group-read" class="coredocs-link-title">read <a href="#group-read"><i class="fa fa-link" aria-hidden="true"></i> </a></h3> <div class="meta"> <span class="label label-primary">GET</span> <code>/api/group/{group_id}/</code> </div> <p><p>Retrieve the information available for a given OMA group.</p></p> <h4>Path Parameters</h4> <p>The following parameters should be included in the URL path.</p> <table class="parameters table table-bordered table-striped"> <thead> <tr><th>Parameter</th><th>Description</th></tr> </thead> <tbody> <tr><td class="parameter-name"><code>group_id</code> <span class="label label-warning">required</span></td><td>an unique identifier for an OMA group - either its group number, its fingerprint or an entry id of one of its members</td></tr> </tbody> </table> </div> <div class="col-md-6 code-samples"> <pre class="highlight shell hide" data-language="shell"><code><span class="c1"># Load the schema document</span> $<span class="w"> </span>coreapi<span class="w"> </span>get<span class="w"> </span>https://omabrowser.org/api/docs <span class="c1"># Interact with the API endpoint</span> $<span class="w"> </span>coreapi<span class="w"> </span>action<span class="w"> </span>group<span class="w"> </span><span class="nb">read</span><span class="w"> </span>-p<span class="w"> </span><span class="nv">group_id</span><span class="o">=</span>... </code></pre> <pre class="highlight javascript hide" data-language="javascript"><code><span class="kd">var</span><span class="w"> </span><span class="nx">coreapi</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">coreapi</span><span class="w"> </span><span class="c1">// Loaded by `coreapi.js`</span> <span class="kd">var</span><span class="w"> </span><span class="nx">schema</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">schema</span><span class="w"> </span><span class="c1">// Loaded by `schema.js`</span> <span class="c1">// Initialize a client</span> <span class="kd">var</span><span class="w"> </span><span class="nx">client</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="ow">new</span><span class="w"> </span><span class="nx">coreapi</span><span class="p">.</span><span class="nx">Client</span><span class="p">()</span> <span class="c1">// Interact with the API endpoint</span> <span class="kd">var</span><span class="w"> </span><span class="nx">action</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">[</span><span class="s2">"group"</span><span class="p">,</span><span class="w"> </span><span class="s2">"read"</span><span class="p">]</span> <span class="kd">var</span><span class="w"> </span><span class="nx">params</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="nx">group_id</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="p">}</span> <span class="nx">client</span><span class="p">.</span><span class="nx">action</span><span class="p">(</span><span class="nx">schema</span><span class="p">,</span><span class="w"> </span><span class="nx">action</span><span class="p">,</span><span class="w"> </span><span class="nx">params</span><span class="p">).</span><span class="nx">then</span><span class="p">(</span><span class="kd">function</span><span class="p">(</span><span class="nx">result</span><span class="p">)</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="c1">// Return value is in 'result'</span> <span class="p">})</span> </code></pre> <pre class="highlight python hide" data-language="python"><code><span class="kn">import</span> <span class="nn">coreapi</span> <span class="c1"># Initialize a client & load the schema document</span> <span class="n">client</span> <span class="o">=</span> <span class="n">coreapi</span><span class="o">.</span><span class="n">Client</span><span class="p">()</span> <span class="n">schema</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"https://omabrowser.org/api/docs"</span><span class="p">)</span> <span class="c1"># Interact with the API endpoint</span> <span class="n">action</span> <span class="o">=</span> <span class="p">[</span><span class="s2">"group"</span><span class="p">,</span> <span class="s2">"read"</span><span class="p">]</span> <span class="n">params</span> <span class="o">=</span> <span class="p">{</span> <span class="s2">"group_id"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="p">}</span> <span class="n">result</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">action</span><span class="p">(</span><span class="n">schema</span><span class="p">,</span> <span class="n">action</span><span class="p">,</span> <span class="n">params</span><span class="o">=</span><span class="n">params</span><span class="p">)</span> </code></pre> </div> </div> <!-- Modal --> <div class="modal fade api-modal" id="group_read_modal" tabindex="-1" role="dialog" aria-labelledby="api explorer modal"> <div class="modal-dialog modal-lg" role="document"> <div class="modal-content"> <div class="modal-header"> <div class="toggle-view hide"> <div class="btn-group" role="group"> <button type="button" data-display-toggle="data" class="btn btn-sm btn-info">Data</button> <button type="button" data-display-toggle="raw" class="btn btn-sm">Raw</button> </div> </div> <h3 class="modal-title"><i class="fa fa-exchange"></i> read</h3> </div> <form data-key='["group", "read"]' class="api-interaction"> <div class="modal-body"> <div class="row"> <div class="col-lg-6 request"> <div class="form-group"> <label for="group_id" class="control-label"> group_id <span class="text-danger">*</span> </label> <input name="group_id" class="form-control" data-empty='' data-type='string' required> <p class="help-block">an unique identifier for an OMA group - either its group number, its fingerprint or an entry id of one of its members</p> </div> </div> <hr class="hidden-lg hidden-xl" /> <div class="col-lg-6 response" id="response"> <div class="request-awaiting">Awaiting request</div> <div class="meta hide"> <span class="label label-primary request-method"></span> <code class="request-url"></code> <label class="label label-lg response-status-code pull-right"></label> </div> <pre class="well response-data hide"></pre> <pre class="well response-raw hide"><div class="response-raw-request"></div><div class="response-raw-response"></div></pre> </div> </div> </div> <div class="modal-footer"> <button type="button" class="btn btn-default" data-dismiss="modal">Close</button> <button type="submit" class="btn btn-primary">Send Request</button> </div> </form> </div> </div> </div> <div class="row coredocs-link"> <div class="col-md-6 docs-content"> <button class="btn btn-sm btn-success" style="float: right; margin-top: 20px" data-toggle="modal" data-target="#group_close_groups_modal"> <i class="fa fa-exchange"></i> Interact </button> <h3 id="group-close_groups" class="coredocs-link-title">close_groups <a href="#group-close_groups"><i class="fa fa-link" aria-hidden="true"></i> </a></h3> <div class="meta"> <span class="label label-primary">GET</span> <code>/api/group/{group_id}/close_groups/</code> </div> <p><p>Retrieve the sorted list of closely related groups for a given OMA group.</p></p> <h4>Path Parameters</h4> <p>The following parameters should be included in the URL path.</p> <table class="parameters table table-bordered table-striped"> <thead> <tr><th>Parameter</th><th>Description</th></tr> </thead> <tbody> <tr><td class="parameter-name"><code>group_id</code> <span class="label label-warning">required</span></td><td>an unique identifier for an OMA group - either its group number, its fingerprint or an entry id of one of its members</td></tr> </tbody> </table> </div> <div class="col-md-6 code-samples"> <pre class="highlight shell hide" data-language="shell"><code><span class="c1"># Load the schema document</span> $<span class="w"> </span>coreapi<span class="w"> </span>get<span class="w"> </span>https://omabrowser.org/api/docs <span class="c1"># Interact with the API endpoint</span> $<span class="w"> </span>coreapi<span class="w"> </span>action<span class="w"> </span>group<span class="w"> </span>close_groups<span class="w"> </span>-p<span class="w"> </span><span class="nv">group_id</span><span class="o">=</span>... </code></pre> <pre class="highlight javascript hide" data-language="javascript"><code><span class="kd">var</span><span class="w"> </span><span class="nx">coreapi</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">coreapi</span><span class="w"> </span><span class="c1">// Loaded by `coreapi.js`</span> <span class="kd">var</span><span class="w"> </span><span class="nx">schema</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">schema</span><span class="w"> </span><span class="c1">// Loaded by `schema.js`</span> <span class="c1">// Initialize a client</span> <span class="kd">var</span><span class="w"> </span><span class="nx">client</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="ow">new</span><span class="w"> </span><span class="nx">coreapi</span><span class="p">.</span><span class="nx">Client</span><span class="p">()</span> <span class="c1">// Interact with the API endpoint</span> <span class="kd">var</span><span class="w"> </span><span class="nx">action</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">[</span><span class="s2">"group"</span><span class="p">,</span><span class="w"> </span><span class="s2">"close_groups"</span><span class="p">]</span> <span class="kd">var</span><span class="w"> </span><span class="nx">params</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="nx">group_id</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="p">}</span> <span class="nx">client</span><span class="p">.</span><span class="nx">action</span><span class="p">(</span><span class="nx">schema</span><span class="p">,</span><span class="w"> </span><span class="nx">action</span><span class="p">,</span><span class="w"> </span><span class="nx">params</span><span class="p">).</span><span class="nx">then</span><span class="p">(</span><span class="kd">function</span><span class="p">(</span><span class="nx">result</span><span class="p">)</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="c1">// Return value is in 'result'</span> <span class="p">})</span> </code></pre> <pre class="highlight python hide" data-language="python"><code><span class="kn">import</span> <span class="nn">coreapi</span> <span class="c1"># Initialize a client & load the schema document</span> <span class="n">client</span> <span class="o">=</span> <span class="n">coreapi</span><span class="o">.</span><span class="n">Client</span><span class="p">()</span> <span class="n">schema</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"https://omabrowser.org/api/docs"</span><span class="p">)</span> <span class="c1"># Interact with the API endpoint</span> <span class="n">action</span> <span class="o">=</span> <span class="p">[</span><span class="s2">"group"</span><span class="p">,</span> <span class="s2">"close_groups"</span><span class="p">]</span> <span class="n">params</span> <span class="o">=</span> <span class="p">{</span> <span class="s2">"group_id"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="p">}</span> <span class="n">result</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">action</span><span class="p">(</span><span class="n">schema</span><span class="p">,</span> <span class="n">action</span><span class="p">,</span> <span class="n">params</span><span class="o">=</span><span class="n">params</span><span class="p">)</span> </code></pre> </div> </div> <!-- Modal --> <div class="modal fade api-modal" id="group_close_groups_modal" tabindex="-1" role="dialog" aria-labelledby="api explorer modal"> <div class="modal-dialog modal-lg" role="document"> <div class="modal-content"> <div class="modal-header"> <div class="toggle-view hide"> <div class="btn-group" role="group"> <button type="button" data-display-toggle="data" class="btn btn-sm btn-info">Data</button> <button type="button" data-display-toggle="raw" class="btn btn-sm">Raw</button> </div> </div> <h3 class="modal-title"><i class="fa fa-exchange"></i> close_groups</h3> </div> <form data-key='["group", "close_groups"]' class="api-interaction"> <div class="modal-body"> <div class="row"> <div class="col-lg-6 request"> <div class="form-group"> <label for="group_id" class="control-label"> group_id <span class="text-danger">*</span> </label> <input name="group_id" class="form-control" data-empty='' data-type='string' required> <p class="help-block">an unique identifier for an OMA group - either its group number, its fingerprint or an entry id of one of its members</p> </div> </div> <hr class="hidden-lg hidden-xl" /> <div class="col-lg-6 response" id="response"> <div class="request-awaiting">Awaiting request</div> <div class="meta hide"> <span class="label label-primary request-method"></span> <code class="request-url"></code> <label class="label label-lg response-status-code pull-right"></label> </div> <pre class="well response-data hide"></pre> <pre class="well response-raw hide"><div class="response-raw-request"></div><div class="response-raw-response"></div></pre> </div> </div> </div> <div class="modal-footer"> <button type="button" class="btn btn-default" data-dismiss="modal">Close</button> <button type="submit" class="btn btn-primary">Send Request</button> </div> </form> </div> </div> </div> <h2 id="hog" class="coredocs-section-title">hog <a href="#hog"><i class="fa fa-link" aria-hidden="true"></i> </a></h2> <div class="row coredocs-link"> <div class="col-md-6 docs-content"> <button class="btn btn-sm btn-success" style="float: right; margin-top: 20px" data-toggle="modal" data-target="#hog_list_modal"> <i class="fa fa-exchange"></i> Interact </button> <h3 id="hog-list" class="coredocs-link-title">list <a href="#hog-list"><i class="fa fa-link" aria-hidden="true"></i> </a></h3> <div class="meta"> <span class="label label-primary">GET</span> <code>/api/hog/</code> </div> <p><p>List of all the HOGs identified by OMA.</p></p> <h4>Query Parameters</h4> <p>The following parameters should be included as part of a URL query string.</p> <table class="parameters table table-bordered table-striped"> <thead> <tr><th>Parameter</th><th>Description</th></tr> </thead> <tbody> <tr><td class="parameter-name"><code>level</code></td><td>filter the list of HOGs by a specific taxonomic level.</td></tr> <tr><td class="parameter-name"><code>compare_with</code></td><td>compares the hog at `level` with those passed with this argument (must be a parent level) and annotates all hogs with the evolutionary events that occured between the two points in time.</td></tr> <tr><td class="parameter-name"><code>page</code></td><td>A page number within the paginated result set.</td></tr> <tr><td class="parameter-name"><code>per_page</code></td><td>Number of results to return per page.</td></tr> </tbody> </table> </div> <div class="col-md-6 code-samples"> <pre class="highlight shell hide" data-language="shell"><code><span class="c1"># Load the schema document</span> $<span class="w"> </span>coreapi<span class="w"> </span>get<span class="w"> </span>https://omabrowser.org/api/docs <span class="c1"># Interact with the API endpoint</span> $<span class="w"> </span>coreapi<span class="w"> </span>action<span class="w"> </span>hog<span class="w"> </span>list<span class="w"> </span>-p<span class="w"> </span><span class="nv">level</span><span class="o">=</span>...<span class="w"> </span>-p<span class="w"> </span><span class="nv">compare_with</span><span class="o">=</span>...<span class="w"> </span>-p<span class="w"> </span><span class="nv">page</span><span class="o">=</span>...<span class="w"> </span>-p<span class="w"> </span><span class="nv">per_page</span><span class="o">=</span>... </code></pre> <pre class="highlight javascript hide" data-language="javascript"><code><span class="kd">var</span><span class="w"> </span><span class="nx">coreapi</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">coreapi</span><span class="w"> </span><span class="c1">// Loaded by `coreapi.js`</span> <span class="kd">var</span><span class="w"> </span><span class="nx">schema</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">schema</span><span class="w"> </span><span class="c1">// Loaded by `schema.js`</span> <span class="c1">// Initialize a client</span> <span class="kd">var</span><span class="w"> </span><span class="nx">client</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="ow">new</span><span class="w"> </span><span class="nx">coreapi</span><span class="p">.</span><span class="nx">Client</span><span class="p">()</span> <span class="c1">// Interact with the API endpoint</span> <span class="kd">var</span><span class="w"> </span><span class="nx">action</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">[</span><span class="s2">"hog"</span><span class="p">,</span><span class="w"> </span><span class="s2">"list"</span><span class="p">]</span> <span class="kd">var</span><span class="w"> </span><span class="nx">params</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="nx">level</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="w"> </span><span class="nx">compare_with</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="w"> </span><span class="nx">page</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="w"> </span><span class="nx">per_page</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="p">}</span> <span class="nx">client</span><span class="p">.</span><span class="nx">action</span><span class="p">(</span><span class="nx">schema</span><span class="p">,</span><span class="w"> </span><span class="nx">action</span><span class="p">,</span><span class="w"> </span><span class="nx">params</span><span class="p">).</span><span class="nx">then</span><span class="p">(</span><span class="kd">function</span><span class="p">(</span><span class="nx">result</span><span class="p">)</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="c1">// Return value is in 'result'</span> <span class="p">})</span> </code></pre> <pre class="highlight python hide" data-language="python"><code><span class="kn">import</span> <span class="nn">coreapi</span> <span class="c1"># Initialize a client & load the schema document</span> <span class="n">client</span> <span class="o">=</span> <span class="n">coreapi</span><span class="o">.</span><span class="n">Client</span><span class="p">()</span> <span class="n">schema</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"https://omabrowser.org/api/docs"</span><span class="p">)</span> <span class="c1"># Interact with the API endpoint</span> <span class="n">action</span> <span class="o">=</span> <span class="p">[</span><span class="s2">"hog"</span><span class="p">,</span> <span class="s2">"list"</span><span class="p">]</span> <span class="n">params</span> <span class="o">=</span> <span class="p">{</span> <span class="s2">"level"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="s2">"compare_with"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="s2">"page"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="s2">"per_page"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="p">}</span> <span class="n">result</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">action</span><span class="p">(</span><span class="n">schema</span><span class="p">,</span> <span class="n">action</span><span class="p">,</span> <span class="n">params</span><span class="o">=</span><span class="n">params</span><span class="p">)</span> </code></pre> </div> </div> <!-- Modal --> <div class="modal fade api-modal" id="hog_list_modal" tabindex="-1" role="dialog" aria-labelledby="api explorer modal"> <div class="modal-dialog modal-lg" role="document"> <div class="modal-content"> <div class="modal-header"> <div class="toggle-view hide"> <div class="btn-group" role="group"> <button type="button" data-display-toggle="data" class="btn btn-sm btn-info">Data</button> <button type="button" data-display-toggle="raw" class="btn btn-sm">Raw</button> </div> </div> <h3 class="modal-title"><i class="fa fa-exchange"></i> list</h3> </div> <form data-key='["hog", "list"]' class="api-interaction"> <div class="modal-body"> <div class="row"> <div class="col-lg-6 request"> <div class="form-group"> <label for="level" class="control-label"> level </label> <input name="level" class="form-control" data-empty='' data-type='string' > <p class="help-block">filter the list of HOGs by a specific taxonomic level.</p> </div> <div class="form-group"> <label for="compare_with" class="control-label"> compare_with </label> <input name="compare_with" class="form-control" data-empty='' data-type='string' > <p class="help-block">compares the hog at `level` with those passed with this argument (must be a parent level) and annotates all hogs with the evolutionary events that occured between the two points in time.</p> </div> <div class="form-group"> <label for="page" class="control-label"> Page </label> <input name="page" class="form-control" data-empty=null data-type='integer' type='number' step=1 > <p class="help-block">A page number within the paginated result set.</p> </div> <div class="form-group"> <label for="per_page" class="control-label"> Page size </label> <input name="per_page" class="form-control" data-empty=null data-type='integer' type='number' step=1 > <p class="help-block">Number of results to return per page.</p> </div> </div> <hr class="hidden-lg hidden-xl" /> <div class="col-lg-6 response" id="response"> <div class="request-awaiting">Awaiting request</div> <div class="meta hide"> <span class="label label-primary request-method"></span> <code class="request-url"></code> <label class="label label-lg response-status-code pull-right"></label> </div> <pre class="well response-data hide"></pre> <pre class="well response-raw hide"><div class="response-raw-request"></div><div class="response-raw-response"></div></pre> </div> </div> </div> <div class="modal-footer"> <button type="button" class="btn btn-default" data-dismiss="modal">Close</button> <button type="submit" class="btn btn-primary">Send Request</button> </div> </form> </div> </div> </div> <div class="row coredocs-link"> <div class="col-md-6 docs-content"> <button class="btn btn-sm btn-success" style="float: right; margin-top: 20px" data-toggle="modal" data-target="#hog_read_modal"> <i class="fa fa-exchange"></i> Interact </button> <h3 id="hog-read" class="coredocs-link-title">read <a href="#hog-read"><i class="fa fa-link" aria-hidden="true"></i> </a></h3> <div class="meta"> <span class="label label-primary">GET</span> <code>/api/hog/{hog_id}/</code> </div> <p><p>Retrieve the detail available for a given HOG, along with its deepest level (i.e. root level) as well as the list of all the taxonomic levels that the HOG spans through.</p> <p>For a given hog_id, the endpoint searches the deepest taxonomic level that has this ID, unless a more recent level has been chosen with the <code>level</code> query parameter in which case the following information is returned for all induced hogs.</p> <p>The endpoint returns an object per hog with the level, urls to the members and a list of parent and children hogs. The parent and children hogs are more ancient resp. more recent levels that involve at least one duplication event on the lineage from the query hog. So, in the parent_hogs, one can find hogs for which we infer a duplication event <em>to</em> the query hog level, where as for the children_hogs there happened at least one duplication event <em>after</em> the query hog level. In addition, we indicate alternative levels for which we infer that no event happened between those levels for this specific hog.</p></p> <h4>Path Parameters</h4> <p>The following parameters should be included in the URL path.</p> <table class="parameters table table-bordered table-striped"> <thead> <tr><th>Parameter</th><th>Description</th></tr> </thead> <tbody> <tr><td class="parameter-name"><code>hog_id</code> <span class="label label-warning">required</span></td><td>an unique identifier for a hog_group - either its hog id or one of its member proteins</td></tr> </tbody> </table> <h4>Query Parameters</h4> <p>The following parameters should be included as part of a URL query string.</p> <table class="parameters table table-bordered table-striped"> <thead> <tr><th>Parameter</th><th>Description</th></tr> </thead> <tbody> <tr><td class="parameter-name"><code>level</code></td><td>taxonomic level of restriction for a HOG. The special level 'root' can be used to identify the level at the roothog, i.e. the deepest level of that HOG.</td></tr> </tbody> </table> </div> <div class="col-md-6 code-samples"> <pre class="highlight shell hide" data-language="shell"><code><span class="c1"># Load the schema document</span> $<span class="w"> </span>coreapi<span class="w"> </span>get<span class="w"> </span>https://omabrowser.org/api/docs <span class="c1"># Interact with the API endpoint</span> $<span class="w"> </span>coreapi<span class="w"> </span>action<span class="w"> </span>hog<span class="w"> </span><span class="nb">read</span><span class="w"> </span>-p<span class="w"> </span><span class="nv">hog_id</span><span class="o">=</span>...<span class="w"> </span>-p<span class="w"> </span><span class="nv">level</span><span class="o">=</span>... </code></pre> <pre class="highlight javascript hide" data-language="javascript"><code><span class="kd">var</span><span class="w"> </span><span class="nx">coreapi</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">coreapi</span><span class="w"> </span><span class="c1">// Loaded by `coreapi.js`</span> <span class="kd">var</span><span class="w"> </span><span class="nx">schema</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">schema</span><span class="w"> </span><span class="c1">// Loaded by `schema.js`</span> <span class="c1">// Initialize a client</span> <span class="kd">var</span><span class="w"> </span><span class="nx">client</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="ow">new</span><span class="w"> </span><span class="nx">coreapi</span><span class="p">.</span><span class="nx">Client</span><span class="p">()</span> <span class="c1">// Interact with the API endpoint</span> <span class="kd">var</span><span class="w"> </span><span class="nx">action</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">[</span><span class="s2">"hog"</span><span class="p">,</span><span class="w"> </span><span class="s2">"read"</span><span class="p">]</span> <span class="kd">var</span><span class="w"> </span><span class="nx">params</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="nx">hog_id</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="w"> </span><span class="nx">level</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="p">}</span> <span class="nx">client</span><span class="p">.</span><span class="nx">action</span><span class="p">(</span><span class="nx">schema</span><span class="p">,</span><span class="w"> </span><span class="nx">action</span><span class="p">,</span><span class="w"> </span><span class="nx">params</span><span class="p">).</span><span class="nx">then</span><span class="p">(</span><span class="kd">function</span><span class="p">(</span><span class="nx">result</span><span class="p">)</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="c1">// Return value is in 'result'</span> <span class="p">})</span> </code></pre> <pre class="highlight python hide" data-language="python"><code><span class="kn">import</span> <span class="nn">coreapi</span> <span class="c1"># Initialize a client & load the schema document</span> <span class="n">client</span> <span class="o">=</span> <span class="n">coreapi</span><span class="o">.</span><span class="n">Client</span><span class="p">()</span> <span class="n">schema</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"https://omabrowser.org/api/docs"</span><span class="p">)</span> <span class="c1"># Interact with the API endpoint</span> <span class="n">action</span> <span class="o">=</span> <span class="p">[</span><span class="s2">"hog"</span><span class="p">,</span> <span class="s2">"read"</span><span class="p">]</span> <span class="n">params</span> <span class="o">=</span> <span class="p">{</span> <span class="s2">"hog_id"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="s2">"level"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="p">}</span> <span class="n">result</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">action</span><span class="p">(</span><span class="n">schema</span><span class="p">,</span> <span class="n">action</span><span class="p">,</span> <span class="n">params</span><span class="o">=</span><span class="n">params</span><span class="p">)</span> </code></pre> </div> </div> <!-- Modal --> <div class="modal fade api-modal" id="hog_read_modal" tabindex="-1" role="dialog" aria-labelledby="api explorer modal"> <div class="modal-dialog modal-lg" role="document"> <div class="modal-content"> <div class="modal-header"> <div class="toggle-view hide"> <div class="btn-group" role="group"> <button type="button" data-display-toggle="data" class="btn btn-sm btn-info">Data</button> <button type="button" data-display-toggle="raw" class="btn btn-sm">Raw</button> </div> </div> <h3 class="modal-title"><i class="fa fa-exchange"></i> read</h3> </div> <form data-key='["hog", "read"]' class="api-interaction"> <div class="modal-body"> <div class="row"> <div class="col-lg-6 request"> <div class="form-group"> <label for="hog_id" class="control-label"> hog_id <span class="text-danger">*</span> </label> <input name="hog_id" class="form-control" data-empty='' data-type='string' required> <p class="help-block">an unique identifier for a hog_group - either its hog id or one of its member proteins</p> </div> <div class="form-group"> <label for="level" class="control-label"> level </label> <input name="level" class="form-control" data-empty='' data-type='string' > <p class="help-block">taxonomic level of restriction for a HOG. The special level 'root' can be used to identify the level at the roothog, i.e. the deepest level of that HOG.</p> </div> </div> <hr class="hidden-lg hidden-xl" /> <div class="col-lg-6 response" id="response"> <div class="request-awaiting">Awaiting request</div> <div class="meta hide"> <span class="label label-primary request-method"></span> <code class="request-url"></code> <label class="label label-lg response-status-code pull-right"></label> </div> <pre class="well response-data hide"></pre> <pre class="well response-raw hide"><div class="response-raw-request"></div><div class="response-raw-response"></div></pre> </div> </div> </div> <div class="modal-footer"> <button type="button" class="btn btn-default" data-dismiss="modal">Close</button> <button type="submit" class="btn btn-primary">Send Request</button> </div> </form> </div> </div> </div> <div class="row coredocs-link"> <div class="col-md-6 docs-content"> <button class="btn btn-sm btn-success" style="float: right; margin-top: 20px" data-toggle="modal" data-target="#hog_gene_ontology_modal"> <i class="fa fa-exchange"></i> Interact </button> <h3 id="hog-gene_ontology" class="coredocs-link-title">gene_ontology <a href="#hog-gene_ontology"><i class="fa fa-link" aria-hidden="true"></i> </a></h3> <div class="meta"> <span class="label label-primary">GET</span> <code>/api/hog/{hog_id}/gene_ontology/</code> </div> <p><p>Gene ontology annotations for an ancestral gene (i.e. HOG).</p> <p>If a level is provided, the endpoint returns annotations with respect to this level. Note that if the level is a more ancient taxonomic level than the deepest level for the specified hog_id, the endpoint returns the annotations of that more ancient level (but adjusting the hog_id in the result object). The special level "root" will always return the members of the root HOG together with its deepest level.</p></p> <h4>Path Parameters</h4> <p>The following parameters should be included in the URL path.</p> <table class="parameters table table-bordered table-striped"> <thead> <tr><th>Parameter</th><th>Description</th></tr> </thead> <tbody> <tr><td class="parameter-name"><code>hog_id</code> <span class="label label-warning">required</span></td><td>a unique identifier for a hog_group - either its hog id starting with "HOG:" or one of its member proteins in which case the specific HOG ID of that protein is used. (Example: HOG:0001221.1a, P12345)</td></tr> </tbody> </table> <h4>Query Parameters</h4> <p>The following parameters should be included as part of a URL query string.</p> <table class="parameters table table-bordered table-striped"> <thead> <tr><th>Parameter</th><th>Description</th></tr> </thead> <tbody> <tr><td class="parameter-name"><code>level</code></td><td>taxonomic level of reference for a HOG - default is its deepest level for a given HOG ID. (Example: Mammalia)</td></tr> </tbody> </table> </div> <div class="col-md-6 code-samples"> <pre class="highlight shell hide" data-language="shell"><code><span class="c1"># Load the schema document</span> $<span class="w"> </span>coreapi<span class="w"> </span>get<span class="w"> </span>https://omabrowser.org/api/docs <span class="c1"># Interact with the API endpoint</span> $<span class="w"> </span>coreapi<span class="w"> </span>action<span class="w"> </span>hog<span class="w"> </span>gene_ontology<span class="w"> </span>-p<span class="w"> </span><span class="nv">hog_id</span><span class="o">=</span>...<span class="w"> </span>-p<span class="w"> </span><span class="nv">level</span><span class="o">=</span>... </code></pre> <pre class="highlight javascript hide" data-language="javascript"><code><span class="kd">var</span><span class="w"> </span><span class="nx">coreapi</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">coreapi</span><span class="w"> </span><span class="c1">// Loaded by `coreapi.js`</span> <span class="kd">var</span><span class="w"> </span><span class="nx">schema</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">schema</span><span class="w"> </span><span class="c1">// Loaded by `schema.js`</span> <span class="c1">// Initialize a client</span> <span class="kd">var</span><span class="w"> </span><span class="nx">client</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="ow">new</span><span class="w"> </span><span class="nx">coreapi</span><span class="p">.</span><span class="nx">Client</span><span class="p">()</span> <span class="c1">// Interact with the API endpoint</span> <span class="kd">var</span><span class="w"> </span><span class="nx">action</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">[</span><span class="s2">"hog"</span><span class="p">,</span><span class="w"> </span><span class="s2">"gene_ontology"</span><span class="p">]</span> <span class="kd">var</span><span class="w"> </span><span class="nx">params</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="nx">hog_id</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="w"> </span><span class="nx">level</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="p">}</span> <span class="nx">client</span><span class="p">.</span><span class="nx">action</span><span class="p">(</span><span class="nx">schema</span><span class="p">,</span><span class="w"> </span><span class="nx">action</span><span class="p">,</span><span class="w"> </span><span class="nx">params</span><span class="p">).</span><span class="nx">then</span><span class="p">(</span><span class="kd">function</span><span class="p">(</span><span class="nx">result</span><span class="p">)</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="c1">// Return value is in 'result'</span> <span class="p">})</span> </code></pre> <pre class="highlight python hide" data-language="python"><code><span class="kn">import</span> <span class="nn">coreapi</span> <span class="c1"># Initialize a client & load the schema document</span> <span class="n">client</span> <span class="o">=</span> <span class="n">coreapi</span><span class="o">.</span><span class="n">Client</span><span class="p">()</span> <span class="n">schema</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"https://omabrowser.org/api/docs"</span><span class="p">)</span> <span class="c1"># Interact with the API endpoint</span> <span class="n">action</span> <span class="o">=</span> <span class="p">[</span><span class="s2">"hog"</span><span class="p">,</span> <span class="s2">"gene_ontology"</span><span class="p">]</span> <span class="n">params</span> <span class="o">=</span> <span class="p">{</span> <span class="s2">"hog_id"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="s2">"level"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="p">}</span> <span class="n">result</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">action</span><span class="p">(</span><span class="n">schema</span><span class="p">,</span> <span class="n">action</span><span class="p">,</span> <span class="n">params</span><span class="o">=</span><span class="n">params</span><span class="p">)</span> </code></pre> </div> </div> <!-- Modal --> <div class="modal fade api-modal" id="hog_gene_ontology_modal" tabindex="-1" role="dialog" aria-labelledby="api explorer modal"> <div class="modal-dialog modal-lg" role="document"> <div class="modal-content"> <div class="modal-header"> <div class="toggle-view hide"> <div class="btn-group" role="group"> <button type="button" data-display-toggle="data" class="btn btn-sm btn-info">Data</button> <button type="button" data-display-toggle="raw" class="btn btn-sm">Raw</button> </div> </div> <h3 class="modal-title"><i class="fa fa-exchange"></i> gene_ontology</h3> </div> <form data-key='["hog", "gene_ontology"]' class="api-interaction"> <div class="modal-body"> <div class="row"> <div class="col-lg-6 request"> <div class="form-group"> <label for="hog_id" class="control-label"> hog_id <span class="text-danger">*</span> </label> <input name="hog_id" class="form-control" data-empty='' data-type='string' required> <p class="help-block">a unique identifier for a hog_group - either its hog id starting with "HOG:" or one of its member proteins in which case the specific HOG ID of that protein is used. (Example: HOG:0001221.1a, P12345)</p> </div> <div class="form-group"> <label for="level" class="control-label"> level </label> <input name="level" class="form-control" data-empty='' data-type='string' > <p class="help-block">taxonomic level of reference for a HOG - default is its deepest level for a given HOG ID. (Example: Mammalia)</p> </div> </div> <hr class="hidden-lg hidden-xl" /> <div class="col-lg-6 response" id="response"> <div class="request-awaiting">Awaiting request</div> <div class="meta hide"> <span class="label label-primary request-method"></span> <code class="request-url"></code> <label class="label label-lg response-status-code pull-right"></label> </div> <pre class="well response-data hide"></pre> <pre class="well response-raw hide"><div class="response-raw-request"></div><div class="response-raw-response"></div></pre> </div> </div> </div> <div class="modal-footer"> <button type="button" class="btn btn-default" data-dismiss="modal">Close</button> <button type="submit" class="btn btn-primary">Send Request</button> </div> </form> </div> </div> </div> <div class="row coredocs-link"> <div class="col-md-6 docs-content"> <button class="btn btn-sm btn-success" style="float: right; margin-top: 20px" data-toggle="modal" data-target="#hog_members_modal"> <i class="fa fa-exchange"></i> Interact </button> <h3 id="hog-members" class="coredocs-link-title">members <a href="#hog-members"><i class="fa fa-link" aria-hidden="true"></i> </a></h3> <div class="meta"> <span class="label label-primary">GET</span> <code>/api/hog/{hog_id}/members/</code> </div> <p><p>Retrieve a list of all the protein members for a given hog_id.</p> <p>The hog_id parameter uses an encoding of the inferred duplication events along the evolution of the family using the LOFT schema (see https://doi.org/10.1186/1471-2105-8-83).</p> <p>The hog_id changes only after duplication events and hence, the ID remains the same for potentially many taxonomic levels. If no level parameter is provided, this endpoint returns the deepest level that contains this specific ID.</p> <p>If a level is provided, the endpoint returns the members with respect to this level. Note that if the level is a more ancient taxonomic level than the deepest level for the specified hog_id, the endpoint retuns the members of for that more ancient level (but adjusting the hog_id in the result object). The special level "root" will always return the members of the root HOG together with its deepest level.</p></p> <h4>Path Parameters</h4> <p>The following parameters should be included in the URL path.</p> <table class="parameters table table-bordered table-striped"> <thead> <tr><th>Parameter</th><th>Description</th></tr> </thead> <tbody> <tr><td class="parameter-name"><code>hog_id</code> <span class="label label-warning">required</span></td><td>a unique identifier for a hog_group - either its hog id starting with "HOG:" or one of its member proteins in which case the specific HOG ID of that protein is used. (Example: HOG:0001221.1a, P12345)</td></tr> </tbody> </table> <h4>Query Parameters</h4> <p>The following parameters should be included as part of a URL query string.</p> <table class="parameters table table-bordered table-striped"> <thead> <tr><th>Parameter</th><th>Description</th></tr> </thead> <tbody> <tr><td class="parameter-name"><code>level</code></td><td>taxonomic level of restriction for a HOG - default is its deepest level for a given HOG ID. (Example: Mammalia)</td></tr> </tbody> </table> </div> <div class="col-md-6 code-samples"> <pre class="highlight shell hide" data-language="shell"><code><span class="c1"># Load the schema document</span> $<span class="w"> </span>coreapi<span class="w"> </span>get<span class="w"> </span>https://omabrowser.org/api/docs <span class="c1"># Interact with the API endpoint</span> $<span class="w"> </span>coreapi<span class="w"> </span>action<span class="w"> </span>hog<span class="w"> </span>members<span class="w"> </span>-p<span class="w"> </span><span class="nv">hog_id</span><span class="o">=</span>...<span class="w"> </span>-p<span class="w"> </span><span class="nv">level</span><span class="o">=</span>... </code></pre> <pre class="highlight javascript hide" data-language="javascript"><code><span class="kd">var</span><span class="w"> </span><span class="nx">coreapi</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">coreapi</span><span class="w"> </span><span class="c1">// Loaded by `coreapi.js`</span> <span class="kd">var</span><span class="w"> </span><span class="nx">schema</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">schema</span><span class="w"> </span><span class="c1">// Loaded by `schema.js`</span> <span class="c1">// Initialize a client</span> <span class="kd">var</span><span class="w"> </span><span class="nx">client</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="ow">new</span><span class="w"> </span><span class="nx">coreapi</span><span class="p">.</span><span class="nx">Client</span><span class="p">()</span> <span class="c1">// Interact with the API endpoint</span> <span class="kd">var</span><span class="w"> </span><span class="nx">action</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">[</span><span class="s2">"hog"</span><span class="p">,</span><span class="w"> </span><span class="s2">"members"</span><span class="p">]</span> <span class="kd">var</span><span class="w"> </span><span class="nx">params</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="nx">hog_id</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="w"> </span><span class="nx">level</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="p">}</span> <span class="nx">client</span><span class="p">.</span><span class="nx">action</span><span class="p">(</span><span class="nx">schema</span><span class="p">,</span><span class="w"> </span><span class="nx">action</span><span class="p">,</span><span class="w"> </span><span class="nx">params</span><span class="p">).</span><span class="nx">then</span><span class="p">(</span><span class="kd">function</span><span class="p">(</span><span class="nx">result</span><span class="p">)</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="c1">// Return value is in 'result'</span> <span class="p">})</span> </code></pre> <pre class="highlight python hide" data-language="python"><code><span class="kn">import</span> <span class="nn">coreapi</span> <span class="c1"># Initialize a client & load the schema document</span> <span class="n">client</span> <span class="o">=</span> <span class="n">coreapi</span><span class="o">.</span><span class="n">Client</span><span class="p">()</span> <span class="n">schema</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"https://omabrowser.org/api/docs"</span><span class="p">)</span> <span class="c1"># Interact with the API endpoint</span> <span class="n">action</span> <span class="o">=</span> <span class="p">[</span><span class="s2">"hog"</span><span class="p">,</span> <span class="s2">"members"</span><span class="p">]</span> <span class="n">params</span> <span class="o">=</span> <span class="p">{</span> <span class="s2">"hog_id"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="s2">"level"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="p">}</span> <span class="n">result</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">action</span><span class="p">(</span><span class="n">schema</span><span class="p">,</span> <span class="n">action</span><span class="p">,</span> <span class="n">params</span><span class="o">=</span><span class="n">params</span><span class="p">)</span> </code></pre> </div> </div> <!-- Modal --> <div class="modal fade api-modal" id="hog_members_modal" tabindex="-1" role="dialog" aria-labelledby="api explorer modal"> <div class="modal-dialog modal-lg" role="document"> <div class="modal-content"> <div class="modal-header"> <div class="toggle-view hide"> <div class="btn-group" role="group"> <button type="button" data-display-toggle="data" class="btn btn-sm btn-info">Data</button> <button type="button" data-display-toggle="raw" class="btn btn-sm">Raw</button> </div> </div> <h3 class="modal-title"><i class="fa fa-exchange"></i> members</h3> </div> <form data-key='["hog", "members"]' class="api-interaction"> <div class="modal-body"> <div class="row"> <div class="col-lg-6 request"> <div class="form-group"> <label for="hog_id" class="control-label"> hog_id <span class="text-danger">*</span> </label> <input name="hog_id" class="form-control" data-empty='' data-type='string' required> <p class="help-block">a unique identifier for a hog_group - either its hog id starting with "HOG:" or one of its member proteins in which case the specific HOG ID of that protein is used. (Example: HOG:0001221.1a, P12345)</p> </div> <div class="form-group"> <label for="level" class="control-label"> level </label> <input name="level" class="form-control" data-empty='' data-type='string' > <p class="help-block">taxonomic level of restriction for a HOG - default is its deepest level for a given HOG ID. (Example: Mammalia)</p> </div> </div> <hr class="hidden-lg hidden-xl" /> <div class="col-lg-6 response" id="response"> <div class="request-awaiting">Awaiting request</div> <div class="meta hide"> <span class="label label-primary request-method"></span> <code class="request-url"></code> <label class="label label-lg response-status-code pull-right"></label> </div> <pre class="well response-data hide"></pre> <pre class="well response-raw hide"><div class="response-raw-request"></div><div class="response-raw-response"></div></pre> </div> </div> </div> <div class="modal-footer"> <button type="button" class="btn btn-default" data-dismiss="modal">Close</button> <button type="submit" class="btn btn-primary">Send Request</button> </div> </form> </div> </div> </div> <div class="row coredocs-link"> <div class="col-md-6 docs-content"> <button class="btn btn-sm btn-success" style="float: right; margin-top: 20px" data-toggle="modal" data-target="#hog_similar_profile_hogs_modal"> <i class="fa fa-exchange"></i> Interact </button> <h3 id="hog-similar_profile_hogs" class="coredocs-link-title">similar_profile_hogs <a href="#hog-similar_profile_hogs"><i class="fa fa-link" aria-hidden="true"></i> </a></h3> <div class="meta"> <span class="label label-primary">GET</span> <code>/api/hog/{hog_id}/similar_profile_hogs/</code> </div> <p><p>Returns the HOGs with the most similar phylogenetic profiles.</p> <p>The profiles are based on the number of duplications, losses and retained genes along the phylogenetic tree. Hence, the profiles are computed on the deepest level only and all sub-hogs ids will return the same similar HOGs.</p> <p>Similar profile search is only useful for hogs that have a certain size, i.e. 100 species. For smaller query HOGs, the result will simply be empty.</p> <p>The result contains for both, the query HOG as well as the similar HOGs a field <code>in_species</code> that contains a list of all species in which at least one copy of the gene is present in the HOG.</p></p> <h4>Path Parameters</h4> <p>The following parameters should be included in the URL path.</p> <table class="parameters table table-bordered table-striped"> <thead> <tr><th>Parameter</th><th>Description</th></tr> </thead> <tbody> <tr><td class="parameter-name"><code>hog_id</code> <span class="label label-warning">required</span></td><td>an unique identifier for a hog_group - either its hog id starting with "HOG:" or one of its member proteins in which case the specific HOG ID of that protein is used. (Example: HOG:0450897, P12345)</td></tr> </tbody> </table> <h4>Query Parameters</h4> <p>The following parameters should be included as part of a URL query string.</p> <table class="parameters table table-bordered table-striped"> <thead> <tr><th>Parameter</th><th>Description</th></tr> </thead> <tbody> <tr><td class="parameter-name"><code>max_results</code></td><td>the number of similar profiles to return. Must be a positive number less than 50. By default the 10 most HOGs with the most similar profiles are returned. (Example: 20)</td></tr> </tbody> </table> </div> <div class="col-md-6 code-samples"> <pre class="highlight shell hide" data-language="shell"><code><span class="c1"># Load the schema document</span> $<span class="w"> </span>coreapi<span class="w"> </span>get<span class="w"> </span>https://omabrowser.org/api/docs <span class="c1"># Interact with the API endpoint</span> $<span class="w"> </span>coreapi<span class="w"> </span>action<span class="w"> </span>hog<span class="w"> </span>similar_profile_hogs<span class="w"> </span>-p<span class="w"> </span><span class="nv">hog_id</span><span class="o">=</span>...<span class="w"> </span>-p<span class="w"> </span><span class="nv">max_results</span><span class="o">=</span>... </code></pre> <pre class="highlight javascript hide" data-language="javascript"><code><span class="kd">var</span><span class="w"> </span><span class="nx">coreapi</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">coreapi</span><span class="w"> </span><span class="c1">// Loaded by `coreapi.js`</span> <span class="kd">var</span><span class="w"> </span><span class="nx">schema</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">schema</span><span class="w"> </span><span class="c1">// Loaded by `schema.js`</span> <span class="c1">// Initialize a client</span> <span class="kd">var</span><span class="w"> </span><span class="nx">client</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="ow">new</span><span class="w"> </span><span class="nx">coreapi</span><span class="p">.</span><span class="nx">Client</span><span class="p">()</span> <span class="c1">// Interact with the API endpoint</span> <span class="kd">var</span><span class="w"> </span><span class="nx">action</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">[</span><span class="s2">"hog"</span><span class="p">,</span><span class="w"> </span><span class="s2">"similar_profile_hogs"</span><span class="p">]</span> <span class="kd">var</span><span class="w"> </span><span class="nx">params</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="nx">hog_id</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="w"> </span><span class="nx">max_results</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="p">}</span> <span class="nx">client</span><span class="p">.</span><span class="nx">action</span><span class="p">(</span><span class="nx">schema</span><span class="p">,</span><span class="w"> </span><span class="nx">action</span><span class="p">,</span><span class="w"> </span><span class="nx">params</span><span class="p">).</span><span class="nx">then</span><span class="p">(</span><span class="kd">function</span><span class="p">(</span><span class="nx">result</span><span class="p">)</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="c1">// Return value is in 'result'</span> <span class="p">})</span> </code></pre> <pre class="highlight python hide" data-language="python"><code><span class="kn">import</span> <span class="nn">coreapi</span> <span class="c1"># Initialize a client & load the schema document</span> <span class="n">client</span> <span class="o">=</span> <span class="n">coreapi</span><span class="o">.</span><span class="n">Client</span><span class="p">()</span> <span class="n">schema</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"https://omabrowser.org/api/docs"</span><span class="p">)</span> <span class="c1"># Interact with the API endpoint</span> <span class="n">action</span> <span class="o">=</span> <span class="p">[</span><span class="s2">"hog"</span><span class="p">,</span> <span class="s2">"similar_profile_hogs"</span><span class="p">]</span> <span class="n">params</span> <span class="o">=</span> <span class="p">{</span> <span class="s2">"hog_id"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="s2">"max_results"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="p">}</span> <span class="n">result</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">action</span><span class="p">(</span><span class="n">schema</span><span class="p">,</span> <span class="n">action</span><span class="p">,</span> <span class="n">params</span><span class="o">=</span><span class="n">params</span><span class="p">)</span> </code></pre> </div> </div> <!-- Modal --> <div class="modal fade api-modal" id="hog_similar_profile_hogs_modal" tabindex="-1" role="dialog" aria-labelledby="api explorer modal"> <div class="modal-dialog modal-lg" role="document"> <div class="modal-content"> <div class="modal-header"> <div class="toggle-view hide"> <div class="btn-group" role="group"> <button type="button" data-display-toggle="data" class="btn btn-sm btn-info">Data</button> <button type="button" data-display-toggle="raw" class="btn btn-sm">Raw</button> </div> </div> <h3 class="modal-title"><i class="fa fa-exchange"></i> similar_profile_hogs</h3> </div> <form data-key='["hog", "similar_profile_hogs"]' class="api-interaction"> <div class="modal-body"> <div class="row"> <div class="col-lg-6 request"> <div class="form-group"> <label for="hog_id" class="control-label"> hog_id <span class="text-danger">*</span> </label> <input name="hog_id" class="form-control" data-empty='' data-type='string' required> <p class="help-block">an unique identifier for a hog_group - either its hog id starting with "HOG:" or one of its member proteins in which case the specific HOG ID of that protein is used. (Example: HOG:0450897, P12345)</p> </div> <div class="form-group"> <label for="max_results" class="control-label"> max_results </label> <input name="max_results" class="form-control" data-empty='' data-type='string' > <p class="help-block">the number of similar profiles to return. Must be a positive number less than 50. By default the 10 most HOGs with the most similar profiles are returned. (Example: 20)</p> </div> </div> <hr class="hidden-lg hidden-xl" /> <div class="col-lg-6 response" id="response"> <div class="request-awaiting">Awaiting request</div> <div class="meta hide"> <span class="label label-primary request-method"></span> <code class="request-url"></code> <label class="label label-lg response-status-code pull-right"></label> </div> <pre class="well response-data hide"></pre> <pre class="well response-raw hide"><div class="response-raw-request"></div><div class="response-raw-response"></div></pre> </div> </div> </div> <div class="modal-footer"> <button type="button" class="btn btn-default" data-dismiss="modal">Close</button> <button type="submit" class="btn btn-primary">Send Request</button> </div> </form> </div> </div> </div> <h2 id="pairs" class="coredocs-section-title">pairs <a href="#pairs"><i class="fa fa-link" aria-hidden="true"></i> </a></h2> <div class="row coredocs-link"> <div class="col-md-6 docs-content"> <button class="btn btn-sm btn-success" style="float: right; margin-top: 20px" data-toggle="modal" data-target="#pairs_read_modal"> <i class="fa fa-exchange"></i> Interact </button> <h3 id="pairs-read" class="coredocs-link-title">read <a href="#pairs-read"><i class="fa fa-link" aria-hidden="true"></i> </a></h3> <div class="meta"> <span class="label label-primary">GET</span> <code>/api/pairs/{genome_id1}/{genome_id2}/</code> </div> <p><p>List the pairwise relations among two genomes</p> <p>The relations are orthologs in case the genomes are different and close paralogs and homoeologs in case they are the same.</p> <p>By using the query_params 'chr1' and 'chr2', one can limit the relations to a certain chromosome for one or both genomes. The id of the chromosome corresponds to the ids returned by the genome endpoint.</p></p> <h4>Path Parameters</h4> <p>The following parameters should be included in the URL path.</p> <table class="parameters table table-bordered table-striped"> <thead> <tr><th>Parameter</th><th>Description</th></tr> </thead> <tbody> <tr><td class="parameter-name"><code>genome_id1</code> <span class="label label-warning">required</span></td><td>an unique identifier for the first genome - either its ncbi taxon id or the UniProt species code</td></tr> <tr><td class="parameter-name"><code>genome_id2</code> <span class="label label-warning">required</span></td><td>an unique identifier for the second genome - either its ncbi taxon id or the UniProt species code</td></tr> </tbody> </table> <h4>Query Parameters</h4> <p>The following parameters should be included as part of a URL query string.</p> <table class="parameters table table-bordered table-striped"> <thead> <tr><th>Parameter</th><th>Description</th></tr> </thead> <tbody> <tr><td class="parameter-name"><code>chr1</code></td><td>id of the chromosome of interest in the first genome</td></tr> <tr><td class="parameter-name"><code>chr2</code></td><td>id of the chromosome of interest in the second genome</td></tr> <tr><td class="parameter-name"><code>type</code></td><td>type of orthologs to use, can be either 'vps' or 'hogs' (default)</td></tr> <tr><td class="parameter-name"><code>xrefs</code></td><td>list of cross-references sources. Possible values are any subset of 'UniProtKB/SwissProt', UniProtKB/TrEMBL', 'EntrezGene', 'SourceID', 'SourceAC', 'Ensembl Gene' and 'RefSeq'. Default is no cross-references, but only OMA IDs.</td></tr> <tr><td class="parameter-name"><code>rel_type</code></td><td>limit relations to a certain type of relations, e.g. '1:1'.</td></tr> </tbody> </table> </div> <div class="col-md-6 code-samples"> <pre class="highlight shell hide" data-language="shell"><code><span class="c1"># Load the schema document</span> $<span class="w"> </span>coreapi<span class="w"> </span>get<span class="w"> </span>https://omabrowser.org/api/docs <span class="c1"># Interact with the API endpoint</span> $<span class="w"> </span>coreapi<span class="w"> </span>action<span class="w"> </span>pairs<span class="w"> </span><span class="nb">read</span><span class="w"> </span>-p<span class="w"> </span><span class="nv">genome_id1</span><span class="o">=</span>...<span class="w"> </span>-p<span class="w"> </span><span class="nv">genome_id2</span><span class="o">=</span>...<span class="w"> </span>-p<span class="w"> </span><span class="nv">chr1</span><span class="o">=</span>...<span class="w"> </span>-p<span class="w"> </span><span class="nv">chr2</span><span class="o">=</span>...<span class="w"> </span>-p<span class="w"> </span><span class="nv">type</span><span class="o">=</span>...<span class="w"> </span>-p<span class="w"> </span><span class="nv">xrefs</span><span class="o">=</span>...<span class="w"> </span>-p<span class="w"> </span><span class="nv">rel_type</span><span class="o">=</span>... </code></pre> <pre class="highlight javascript hide" data-language="javascript"><code><span class="kd">var</span><span class="w"> </span><span class="nx">coreapi</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">coreapi</span><span class="w"> </span><span class="c1">// Loaded by `coreapi.js`</span> <span class="kd">var</span><span class="w"> </span><span class="nx">schema</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">schema</span><span class="w"> </span><span class="c1">// Loaded by `schema.js`</span> <span class="c1">// Initialize a client</span> <span class="kd">var</span><span class="w"> </span><span class="nx">client</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="ow">new</span><span class="w"> </span><span class="nx">coreapi</span><span class="p">.</span><span class="nx">Client</span><span class="p">()</span> <span class="c1">// Interact with the API endpoint</span> <span class="kd">var</span><span class="w"> </span><span class="nx">action</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">[</span><span class="s2">"pairs"</span><span class="p">,</span><span class="w"> </span><span class="s2">"read"</span><span class="p">]</span> <span class="kd">var</span><span class="w"> </span><span class="nx">params</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="nx">genome_id1</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="w"> </span><span class="nx">genome_id2</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="w"> </span><span class="nx">chr1</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="w"> </span><span class="nx">chr2</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="w"> </span><span class="nx">type</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="w"> </span><span class="nx">xrefs</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="w"> </span><span class="nx">rel_type</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="p">}</span> <span class="nx">client</span><span class="p">.</span><span class="nx">action</span><span class="p">(</span><span class="nx">schema</span><span class="p">,</span><span class="w"> </span><span class="nx">action</span><span class="p">,</span><span class="w"> </span><span class="nx">params</span><span class="p">).</span><span class="nx">then</span><span class="p">(</span><span class="kd">function</span><span class="p">(</span><span class="nx">result</span><span class="p">)</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="c1">// Return value is in 'result'</span> <span class="p">})</span> </code></pre> <pre class="highlight python hide" data-language="python"><code><span class="kn">import</span> <span class="nn">coreapi</span> <span class="c1"># Initialize a client & load the schema document</span> <span class="n">client</span> <span class="o">=</span> <span class="n">coreapi</span><span class="o">.</span><span class="n">Client</span><span class="p">()</span> <span class="n">schema</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"https://omabrowser.org/api/docs"</span><span class="p">)</span> <span class="c1"># Interact with the API endpoint</span> <span class="n">action</span> <span class="o">=</span> <span class="p">[</span><span class="s2">"pairs"</span><span class="p">,</span> <span class="s2">"read"</span><span class="p">]</span> <span class="n">params</span> <span class="o">=</span> <span class="p">{</span> <span class="s2">"genome_id1"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="s2">"genome_id2"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="s2">"chr1"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="s2">"chr2"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="s2">"type"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="s2">"xrefs"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="s2">"rel_type"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="p">}</span> <span class="n">result</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">action</span><span class="p">(</span><span class="n">schema</span><span class="p">,</span> <span class="n">action</span><span class="p">,</span> <span class="n">params</span><span class="o">=</span><span class="n">params</span><span class="p">)</span> </code></pre> </div> </div> <!-- Modal --> <div class="modal fade api-modal" id="pairs_read_modal" tabindex="-1" role="dialog" aria-labelledby="api explorer modal"> <div class="modal-dialog modal-lg" role="document"> <div class="modal-content"> <div class="modal-header"> <div class="toggle-view hide"> <div class="btn-group" role="group"> <button type="button" data-display-toggle="data" class="btn btn-sm btn-info">Data</button> <button type="button" data-display-toggle="raw" class="btn btn-sm">Raw</button> </div> </div> <h3 class="modal-title"><i class="fa fa-exchange"></i> read</h3> </div> <form data-key='["pairs", "read"]' class="api-interaction"> <div class="modal-body"> <div class="row"> <div class="col-lg-6 request"> <div class="form-group"> <label for="genome_id1" class="control-label"> genome_id1 <span class="text-danger">*</span> </label> <input name="genome_id1" class="form-control" data-empty='' data-type='string' required> <p class="help-block">an unique identifier for the first genome - either its ncbi taxon id or the UniProt species code</p> </div> <div class="form-group"> <label for="genome_id2" class="control-label"> genome_id2 <span class="text-danger">*</span> </label> <input name="genome_id2" class="form-control" data-empty='' data-type='string' required> <p class="help-block">an unique identifier for the second genome - either its ncbi taxon id or the UniProt species code</p> </div> <div class="form-group"> <label for="chr1" class="control-label"> chr1 </label> <input name="chr1" class="form-control" data-empty='' data-type='string' > <p class="help-block">id of the chromosome of interest in the first genome</p> </div> <div class="form-group"> <label for="chr2" class="control-label"> chr2 </label> <input name="chr2" class="form-control" data-empty='' data-type='string' > <p class="help-block">id of the chromosome of interest in the second genome</p> </div> <div class="form-group"> <label for="type" class="control-label"> type </label> <input name="type" class="form-control" data-empty='' data-type='string' > <p class="help-block">type of orthologs to use, can be either 'vps' or 'hogs' (default)</p> </div> <div class="form-group"> <label for="xrefs" class="control-label"> xrefs </label> <input name="xrefs" class="form-control" data-empty='' data-type='string' > <p class="help-block">list of cross-references sources. Possible values are any subset of 'UniProtKB/SwissProt', UniProtKB/TrEMBL', 'EntrezGene', 'SourceID', 'SourceAC', 'Ensembl Gene' and 'RefSeq'. Default is no cross-references, but only OMA IDs.</p> </div> <div class="form-group"> <label for="rel_type" class="control-label"> rel_type </label> <input name="rel_type" class="form-control" data-empty='' data-type='string' > <p class="help-block">limit relations to a certain type of relations, e.g. '1:1'.</p> </div> </div> <hr class="hidden-lg hidden-xl" /> <div class="col-lg-6 response" id="response"> <div class="request-awaiting">Awaiting request</div> <div class="meta hide"> <span class="label label-primary request-method"></span> <code class="request-url"></code> <label class="label label-lg response-status-code pull-right"></label> </div> <pre class="well response-data hide"></pre> <pre class="well response-raw hide"><div class="response-raw-request"></div><div class="response-raw-response"></div></pre> </div> </div> </div> <div class="modal-footer"> <button type="button" class="btn btn-default" data-dismiss="modal">Close</button> <button type="submit" class="btn btn-primary">Send Request</button> </div> </form> </div> </div> </div> <h2 id="protein" class="coredocs-section-title">protein <a href="#protein"><i class="fa fa-link" aria-hidden="true"></i> </a></h2> <div class="row coredocs-link"> <div class="col-md-6 docs-content"> <button class="btn btn-sm btn-success" style="float: right; margin-top: 20px" data-toggle="modal" data-target="#protein_bulk_retrieve_modal"> <i class="fa fa-exchange"></i> Interact </button> <h3 id="protein-bulk_retrieve" class="coredocs-link-title">bulk_retrieve <a href="#protein-bulk_retrieve"><i class="fa fa-link" aria-hidden="true"></i> </a></h3> <div class="meta"> <span class="label label-primary">POST</span> <code>/api/protein/bulk_retrieve/</code> </div> <p><p>Retrieve the information available for multiple protein IDs at once.</p> <p>The POST request must contain a json-encoded list of IDs of up to 1000 IDs for which the information is returned.</p> <p>In case the ID is not unique or unknown, an empty element is returned for this query element.</p> <p>changed in verison 1.7: the endpoint returns now a list with tuples (query_id, target) instead of a simple list of proteins in the order of the query ids.</p></p> <h4>Request Body</h4> <p>The request body should be <code>"application/json"</code> encoded, and should contain a single item.</p> <table class="parameters table table-bordered table-striped"> <thead> <tr><th>Parameter</th><th>Description</th></tr> </thead> <tbody> <tr><td class="parameter-name"><code>ids</code> <span class="label label-warning">required</span></td><td>A list of ids of proteins to retrieve</td></tr> </tbody> </table> </div> <div class="col-md-6 code-samples"> <pre class="highlight shell hide" data-language="shell"><code><span class="c1"># Load the schema document</span> $<span class="w"> </span>coreapi<span class="w"> </span>get<span class="w"> </span>https://omabrowser.org/api/docs <span class="c1"># Interact with the API endpoint</span> $<span class="w"> </span>coreapi<span class="w"> </span>action<span class="w"> </span>protein<span class="w"> </span>bulk_retrieve<span class="w"> </span>-p<span class="w"> </span><span class="nv">ids</span><span class="o">=</span>... </code></pre> <pre class="highlight javascript hide" data-language="javascript"><code><span class="kd">var</span><span class="w"> </span><span class="nx">coreapi</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">coreapi</span><span class="w"> </span><span class="c1">// Loaded by `coreapi.js`</span> <span class="kd">var</span><span class="w"> </span><span class="nx">schema</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">schema</span><span class="w"> </span><span class="c1">// Loaded by `schema.js`</span> <span class="c1">// Initialize a client</span> <span class="kd">var</span><span class="w"> </span><span class="nx">client</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="ow">new</span><span class="w"> </span><span class="nx">coreapi</span><span class="p">.</span><span class="nx">Client</span><span class="p">()</span> <span class="c1">// Interact with the API endpoint</span> <span class="kd">var</span><span class="w"> </span><span class="nx">action</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">[</span><span class="s2">"protein"</span><span class="p">,</span><span class="w"> </span><span class="s2">"bulk_retrieve"</span><span class="p">]</span> <span class="kd">var</span><span class="w"> </span><span class="nx">params</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="nx">ids</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="p">}</span> <span class="nx">client</span><span class="p">.</span><span class="nx">action</span><span class="p">(</span><span class="nx">schema</span><span class="p">,</span><span class="w"> </span><span class="nx">action</span><span class="p">,</span><span class="w"> </span><span class="nx">params</span><span class="p">).</span><span class="nx">then</span><span class="p">(</span><span class="kd">function</span><span class="p">(</span><span class="nx">result</span><span class="p">)</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="c1">// Return value is in 'result'</span> <span class="p">})</span> </code></pre> <pre class="highlight python hide" data-language="python"><code><span class="kn">import</span> <span class="nn">coreapi</span> <span class="c1"># Initialize a client & load the schema document</span> <span class="n">client</span> <span class="o">=</span> <span class="n">coreapi</span><span class="o">.</span><span class="n">Client</span><span class="p">()</span> <span class="n">schema</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"https://omabrowser.org/api/docs"</span><span class="p">)</span> <span class="c1"># Interact with the API endpoint</span> <span class="n">action</span> <span class="o">=</span> <span class="p">[</span><span class="s2">"protein"</span><span class="p">,</span> <span class="s2">"bulk_retrieve"</span><span class="p">]</span> <span class="n">params</span> <span class="o">=</span> <span class="p">{</span> <span class="s2">"ids"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="p">}</span> <span class="n">result</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">action</span><span class="p">(</span><span class="n">schema</span><span class="p">,</span> <span class="n">action</span><span class="p">,</span> <span class="n">params</span><span class="o">=</span><span class="n">params</span><span class="p">)</span> </code></pre> </div> </div> <!-- Modal --> <div class="modal fade api-modal" id="protein_bulk_retrieve_modal" tabindex="-1" role="dialog" aria-labelledby="api explorer modal"> <div class="modal-dialog modal-lg" role="document"> <div class="modal-content"> <div class="modal-header"> <div class="toggle-view hide"> <div class="btn-group" role="group"> <button type="button" data-display-toggle="data" class="btn btn-sm btn-info">Data</button> <button type="button" data-display-toggle="raw" class="btn btn-sm">Raw</button> </div> </div> <h3 class="modal-title"><i class="fa fa-exchange"></i> bulk_retrieve</h3> </div> <form data-key='["protein", "bulk_retrieve"]' class="api-interaction"> <div class="modal-body"> <div class="row"> <div class="col-lg-6 request"> <div class="form-group"> <label for="ids" class="control-label"> ids <span class="text-danger">*</span> </label> <input name="ids" class="form-control" data-empty='' data-type='string' required> <p class="help-block">A list of ids of proteins to retrieve</p> </div> </div> <hr class="hidden-lg hidden-xl" /> <div class="col-lg-6 response" id="response"> <div class="request-awaiting">Awaiting request</div> <div class="meta hide"> <span class="label label-primary request-method"></span> <code class="request-url"></code> <label class="label label-lg response-status-code pull-right"></label> </div> <pre class="well response-data hide"></pre> <pre class="well response-raw hide"><div class="response-raw-request"></div><div class="response-raw-response"></div></pre> </div> </div> </div> <div class="modal-footer"> <button type="button" class="btn btn-default" data-dismiss="modal">Close</button> <button type="submit" class="btn btn-primary">Send Request</button> </div> </form> </div> </div> </div> <div class="row coredocs-link"> <div class="col-md-6 docs-content"> <button class="btn btn-sm btn-success" style="float: right; margin-top: 20px" data-toggle="modal" data-target="#protein_read_modal"> <i class="fa fa-exchange"></i> Interact </button> <h3 id="protein-read" class="coredocs-link-title">read <a href="#protein-read"><i class="fa fa-link" aria-hidden="true"></i> </a></h3> <div class="meta"> <span class="label label-primary">GET</span> <code>/api/protein/{entry_id}/</code> </div> <p><p>Retrieve the information available for a protein entry.</p></p> <h4>Path Parameters</h4> <p>The following parameters should be included in the URL path.</p> <table class="parameters table table-bordered table-striped"> <thead> <tr><th>Parameter</th><th>Description</th></tr> </thead> <tbody> <tr><td class="parameter-name"><code>entry_id</code> <span class="label label-warning">required</span></td><td>an unique identifier for a protein - either it entry number, omaid or its canonical id</td></tr> </tbody> </table> </div> <div class="col-md-6 code-samples"> <pre class="highlight shell hide" data-language="shell"><code><span class="c1"># Load the schema document</span> $<span class="w"> </span>coreapi<span class="w"> </span>get<span class="w"> </span>https://omabrowser.org/api/docs <span class="c1"># Interact with the API endpoint</span> $<span class="w"> </span>coreapi<span class="w"> </span>action<span class="w"> </span>protein<span class="w"> </span><span class="nb">read</span><span class="w"> </span>-p<span class="w"> </span><span class="nv">entry_id</span><span class="o">=</span>... </code></pre> <pre class="highlight javascript hide" data-language="javascript"><code><span class="kd">var</span><span class="w"> </span><span class="nx">coreapi</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">coreapi</span><span class="w"> </span><span class="c1">// Loaded by `coreapi.js`</span> <span class="kd">var</span><span class="w"> </span><span class="nx">schema</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">schema</span><span class="w"> </span><span class="c1">// Loaded by `schema.js`</span> <span class="c1">// Initialize a client</span> <span class="kd">var</span><span class="w"> </span><span class="nx">client</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="ow">new</span><span class="w"> </span><span class="nx">coreapi</span><span class="p">.</span><span class="nx">Client</span><span class="p">()</span> <span class="c1">// Interact with the API endpoint</span> <span class="kd">var</span><span class="w"> </span><span class="nx">action</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">[</span><span class="s2">"protein"</span><span class="p">,</span><span class="w"> </span><span class="s2">"read"</span><span class="p">]</span> <span class="kd">var</span><span class="w"> </span><span class="nx">params</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="nx">entry_id</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="p">}</span> <span class="nx">client</span><span class="p">.</span><span class="nx">action</span><span class="p">(</span><span class="nx">schema</span><span class="p">,</span><span class="w"> </span><span class="nx">action</span><span class="p">,</span><span class="w"> </span><span class="nx">params</span><span class="p">).</span><span class="nx">then</span><span class="p">(</span><span class="kd">function</span><span class="p">(</span><span class="nx">result</span><span class="p">)</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="c1">// Return value is in 'result'</span> <span class="p">})</span> </code></pre> <pre class="highlight python hide" data-language="python"><code><span class="kn">import</span> <span class="nn">coreapi</span> <span class="c1"># Initialize a client & load the schema document</span> <span class="n">client</span> <span class="o">=</span> <span class="n">coreapi</span><span class="o">.</span><span class="n">Client</span><span class="p">()</span> <span class="n">schema</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"https://omabrowser.org/api/docs"</span><span class="p">)</span> <span class="c1"># Interact with the API endpoint</span> <span class="n">action</span> <span class="o">=</span> <span class="p">[</span><span class="s2">"protein"</span><span class="p">,</span> <span class="s2">"read"</span><span class="p">]</span> <span class="n">params</span> <span class="o">=</span> <span class="p">{</span> <span class="s2">"entry_id"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="p">}</span> <span class="n">result</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">action</span><span class="p">(</span><span class="n">schema</span><span class="p">,</span> <span class="n">action</span><span class="p">,</span> <span class="n">params</span><span class="o">=</span><span class="n">params</span><span class="p">)</span> </code></pre> </div> </div> <!-- Modal --> <div class="modal fade api-modal" id="protein_read_modal" tabindex="-1" role="dialog" aria-labelledby="api explorer modal"> <div class="modal-dialog modal-lg" role="document"> <div class="modal-content"> <div class="modal-header"> <div class="toggle-view hide"> <div class="btn-group" role="group"> <button type="button" data-display-toggle="data" class="btn btn-sm btn-info">Data</button> <button type="button" data-display-toggle="raw" class="btn btn-sm">Raw</button> </div> </div> <h3 class="modal-title"><i class="fa fa-exchange"></i> read</h3> </div> <form data-key='["protein", "read"]' class="api-interaction"> <div class="modal-body"> <div class="row"> <div class="col-lg-6 request"> <div class="form-group"> <label for="entry_id" class="control-label"> entry_id <span class="text-danger">*</span> </label> <input name="entry_id" class="form-control" data-empty='' data-type='string' required> <p class="help-block">an unique identifier for a protein - either it entry number, omaid or its canonical id</p> </div> </div> <hr class="hidden-lg hidden-xl" /> <div class="col-lg-6 response" id="response"> <div class="request-awaiting">Awaiting request</div> <div class="meta hide"> <span class="label label-primary request-method"></span> <code class="request-url"></code> <label class="label label-lg response-status-code pull-right"></label> </div> <pre class="well response-data hide"></pre> <pre class="well response-raw hide"><div class="response-raw-request"></div><div class="response-raw-response"></div></pre> </div> </div> </div> <div class="modal-footer"> <button type="button" class="btn btn-default" data-dismiss="modal">Close</button> <button type="submit" class="btn btn-primary">Send Request</button> </div> </form> </div> </div> </div> <div class="row coredocs-link"> <div class="col-md-6 docs-content"> <button class="btn btn-sm btn-success" style="float: right; margin-top: 20px" data-toggle="modal" data-target="#protein_domains_modal"> <i class="fa fa-exchange"></i> Interact </button> <h3 id="protein-domains" class="coredocs-link-title">domains <a href="#protein-domains"><i class="fa fa-link" aria-hidden="true"></i> </a></h3> <div class="meta"> <span class="label label-primary">GET</span> <code>/api/protein/{entry_id}/domains/</code> </div> <p><p>List of the domains present in a protein.</p></p> <h4>Path Parameters</h4> <p>The following parameters should be included in the URL path.</p> <table class="parameters table table-bordered table-striped"> <thead> <tr><th>Parameter</th><th>Description</th></tr> </thead> <tbody> <tr><td class="parameter-name"><code>entry_id</code> <span class="label label-warning">required</span></td><td>an unique identifier for a protein - either it entry number, omaid or its canonical id</td></tr> </tbody> </table> </div> <div class="col-md-6 code-samples"> <pre class="highlight shell hide" data-language="shell"><code><span class="c1"># Load the schema document</span> $<span class="w"> </span>coreapi<span class="w"> </span>get<span class="w"> </span>https://omabrowser.org/api/docs <span class="c1"># Interact with the API endpoint</span> $<span class="w"> </span>coreapi<span class="w"> </span>action<span class="w"> </span>protein<span class="w"> </span>domains<span class="w"> </span>-p<span class="w"> </span><span class="nv">entry_id</span><span class="o">=</span>... </code></pre> <pre class="highlight javascript hide" data-language="javascript"><code><span class="kd">var</span><span class="w"> </span><span class="nx">coreapi</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">coreapi</span><span class="w"> </span><span class="c1">// Loaded by `coreapi.js`</span> <span class="kd">var</span><span class="w"> </span><span class="nx">schema</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">schema</span><span class="w"> </span><span class="c1">// Loaded by `schema.js`</span> <span class="c1">// Initialize a client</span> <span class="kd">var</span><span class="w"> </span><span class="nx">client</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="ow">new</span><span class="w"> </span><span class="nx">coreapi</span><span class="p">.</span><span class="nx">Client</span><span class="p">()</span> <span class="c1">// Interact with the API endpoint</span> <span class="kd">var</span><span class="w"> </span><span class="nx">action</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">[</span><span class="s2">"protein"</span><span class="p">,</span><span class="w"> </span><span class="s2">"domains"</span><span class="p">]</span> <span class="kd">var</span><span class="w"> </span><span class="nx">params</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="nx">entry_id</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="p">}</span> <span class="nx">client</span><span class="p">.</span><span class="nx">action</span><span class="p">(</span><span class="nx">schema</span><span class="p">,</span><span class="w"> </span><span class="nx">action</span><span class="p">,</span><span class="w"> </span><span class="nx">params</span><span class="p">).</span><span class="nx">then</span><span class="p">(</span><span class="kd">function</span><span class="p">(</span><span class="nx">result</span><span class="p">)</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="c1">// Return value is in 'result'</span> <span class="p">})</span> </code></pre> <pre class="highlight python hide" data-language="python"><code><span class="kn">import</span> <span class="nn">coreapi</span> <span class="c1"># Initialize a client & load the schema document</span> <span class="n">client</span> <span class="o">=</span> <span class="n">coreapi</span><span class="o">.</span><span class="n">Client</span><span class="p">()</span> <span class="n">schema</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"https://omabrowser.org/api/docs"</span><span class="p">)</span> <span class="c1"># Interact with the API endpoint</span> <span class="n">action</span> <span class="o">=</span> <span class="p">[</span><span class="s2">"protein"</span><span class="p">,</span> <span class="s2">"domains"</span><span class="p">]</span> <span class="n">params</span> <span class="o">=</span> <span class="p">{</span> <span class="s2">"entry_id"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="p">}</span> <span class="n">result</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">action</span><span class="p">(</span><span class="n">schema</span><span class="p">,</span> <span class="n">action</span><span class="p">,</span> <span class="n">params</span><span class="o">=</span><span class="n">params</span><span class="p">)</span> </code></pre> </div> </div> <!-- Modal --> <div class="modal fade api-modal" id="protein_domains_modal" tabindex="-1" role="dialog" aria-labelledby="api explorer modal"> <div class="modal-dialog modal-lg" role="document"> <div class="modal-content"> <div class="modal-header"> <div class="toggle-view hide"> <div class="btn-group" role="group"> <button type="button" data-display-toggle="data" class="btn btn-sm btn-info">Data</button> <button type="button" data-display-toggle="raw" class="btn btn-sm">Raw</button> </div> </div> <h3 class="modal-title"><i class="fa fa-exchange"></i> domains</h3> </div> <form data-key='["protein", "domains"]' class="api-interaction"> <div class="modal-body"> <div class="row"> <div class="col-lg-6 request"> <div class="form-group"> <label for="entry_id" class="control-label"> entry_id <span class="text-danger">*</span> </label> <input name="entry_id" class="form-control" data-empty='' data-type='string' required> <p class="help-block">an unique identifier for a protein - either it entry number, omaid or its canonical id</p> </div> </div> <hr class="hidden-lg hidden-xl" /> <div class="col-lg-6 response" id="response"> <div class="request-awaiting">Awaiting request</div> <div class="meta hide"> <span class="label label-primary request-method"></span> <code class="request-url"></code> <label class="label label-lg response-status-code pull-right"></label> </div> <pre class="well response-data hide"></pre> <pre class="well response-raw hide"><div class="response-raw-request"></div><div class="response-raw-response"></div></pre> </div> </div> </div> <div class="modal-footer"> <button type="button" class="btn btn-default" data-dismiss="modal">Close</button> <button type="submit" class="btn btn-primary">Send Request</button> </div> </form> </div> </div> </div> <div class="row coredocs-link"> <div class="col-md-6 docs-content"> <button class="btn btn-sm btn-success" style="float: right; margin-top: 20px" data-toggle="modal" data-target="#protein_gene_ontology_modal"> <i class="fa fa-exchange"></i> Interact </button> <h3 id="protein-gene_ontology" class="coredocs-link-title">gene_ontology <a href="#protein-gene_ontology"><i class="fa fa-link" aria-hidden="true"></i> </a></h3> <div class="meta"> <span class="label label-primary">GET</span> <code>/api/protein/{entry_id}/gene_ontology/</code> </div> <p><p>Gene ontology information available for a protein.</p></p> <h4>Path Parameters</h4> <p>The following parameters should be included in the URL path.</p> <table class="parameters table table-bordered table-striped"> <thead> <tr><th>Parameter</th><th>Description</th></tr> </thead> <tbody> <tr><td class="parameter-name"><code>entry_id</code> <span class="label label-warning">required</span></td><td>an unique identifier for a protein - either its entry number, omaid or its canonical id</td></tr> </tbody> </table> </div> <div class="col-md-6 code-samples"> <pre class="highlight shell hide" data-language="shell"><code><span class="c1"># Load the schema document</span> $<span class="w"> </span>coreapi<span class="w"> </span>get<span class="w"> </span>https://omabrowser.org/api/docs <span class="c1"># Interact with the API endpoint</span> $<span class="w"> </span>coreapi<span class="w"> </span>action<span class="w"> </span>protein<span class="w"> </span>gene_ontology<span class="w"> </span>-p<span class="w"> </span><span class="nv">entry_id</span><span class="o">=</span>... </code></pre> <pre class="highlight javascript hide" data-language="javascript"><code><span class="kd">var</span><span class="w"> </span><span class="nx">coreapi</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">coreapi</span><span class="w"> </span><span class="c1">// Loaded by `coreapi.js`</span> <span class="kd">var</span><span class="w"> </span><span class="nx">schema</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">schema</span><span class="w"> </span><span class="c1">// Loaded by `schema.js`</span> <span class="c1">// Initialize a client</span> <span class="kd">var</span><span class="w"> </span><span class="nx">client</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="ow">new</span><span class="w"> </span><span class="nx">coreapi</span><span class="p">.</span><span class="nx">Client</span><span class="p">()</span> <span class="c1">// Interact with the API endpoint</span> <span class="kd">var</span><span class="w"> </span><span class="nx">action</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">[</span><span class="s2">"protein"</span><span class="p">,</span><span class="w"> </span><span class="s2">"gene_ontology"</span><span class="p">]</span> <span class="kd">var</span><span class="w"> </span><span class="nx">params</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="nx">entry_id</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="p">}</span> <span class="nx">client</span><span class="p">.</span><span class="nx">action</span><span class="p">(</span><span class="nx">schema</span><span class="p">,</span><span class="w"> </span><span class="nx">action</span><span class="p">,</span><span class="w"> </span><span class="nx">params</span><span class="p">).</span><span class="nx">then</span><span class="p">(</span><span class="kd">function</span><span class="p">(</span><span class="nx">result</span><span class="p">)</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="c1">// Return value is in 'result'</span> <span class="p">})</span> </code></pre> <pre class="highlight python hide" data-language="python"><code><span class="kn">import</span> <span class="nn">coreapi</span> <span class="c1"># Initialize a client & load the schema document</span> <span class="n">client</span> <span class="o">=</span> <span class="n">coreapi</span><span class="o">.</span><span class="n">Client</span><span class="p">()</span> <span class="n">schema</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"https://omabrowser.org/api/docs"</span><span class="p">)</span> <span class="c1"># Interact with the API endpoint</span> <span class="n">action</span> <span class="o">=</span> <span class="p">[</span><span class="s2">"protein"</span><span class="p">,</span> <span class="s2">"gene_ontology"</span><span class="p">]</span> <span class="n">params</span> <span class="o">=</span> <span class="p">{</span> <span class="s2">"entry_id"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="p">}</span> <span class="n">result</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">action</span><span class="p">(</span><span class="n">schema</span><span class="p">,</span> <span class="n">action</span><span class="p">,</span> <span class="n">params</span><span class="o">=</span><span class="n">params</span><span class="p">)</span> </code></pre> </div> </div> <!-- Modal --> <div class="modal fade api-modal" id="protein_gene_ontology_modal" tabindex="-1" role="dialog" aria-labelledby="api explorer modal"> <div class="modal-dialog modal-lg" role="document"> <div class="modal-content"> <div class="modal-header"> <div class="toggle-view hide"> <div class="btn-group" role="group"> <button type="button" data-display-toggle="data" class="btn btn-sm btn-info">Data</button> <button type="button" data-display-toggle="raw" class="btn btn-sm">Raw</button> </div> </div> <h3 class="modal-title"><i class="fa fa-exchange"></i> gene_ontology</h3> </div> <form data-key='["protein", "gene_ontology"]' class="api-interaction"> <div class="modal-body"> <div class="row"> <div class="col-lg-6 request"> <div class="form-group"> <label for="entry_id" class="control-label"> entry_id <span class="text-danger">*</span> </label> <input name="entry_id" class="form-control" data-empty='' data-type='string' required> <p class="help-block">an unique identifier for a protein - either its entry number, omaid or its canonical id</p> </div> </div> <hr class="hidden-lg hidden-xl" /> <div class="col-lg-6 response" id="response"> <div class="request-awaiting">Awaiting request</div> <div class="meta hide"> <span class="label label-primary request-method"></span> <code class="request-url"></code> <label class="label label-lg response-status-code pull-right"></label> </div> <pre class="well response-data hide"></pre> <pre class="well response-raw hide"><div class="response-raw-request"></div><div class="response-raw-response"></div></pre> </div> </div> </div> <div class="modal-footer"> <button type="button" class="btn btn-default" data-dismiss="modal">Close</button> <button type="submit" class="btn btn-primary">Send Request</button> </div> </form> </div> </div> </div> <div class="row coredocs-link"> <div class="col-md-6 docs-content"> <button class="btn btn-sm btn-success" style="float: right; margin-top: 20px" data-toggle="modal" data-target="#protein_hog_derived_orthologs_modal"> <i class="fa fa-exchange"></i> Interact </button> <h3 id="protein-hog_derived_orthologs" class="coredocs-link-title">hog_derived_orthologs <a href="#protein-hog_derived_orthologs"><i class="fa fa-link" aria-hidden="true"></i> </a></h3> <div class="meta"> <span class="label label-primary">GET</span> <code>/api/protein/{entry_id}/hog_derived_orthologs/</code> </div> <p><p>List of the orthologs derived from the hog for a given protein.</p></p> <h4>Path Parameters</h4> <p>The following parameters should be included in the URL path.</p> <table class="parameters table table-bordered table-striped"> <thead> <tr><th>Parameter</th><th>Description</th></tr> </thead> <tbody> <tr><td class="parameter-name"><code>entry_id</code> <span class="label label-warning">required</span></td><td>an unique identifier for a protein - either it entry number, omaid or its canonical id</td></tr> </tbody> </table> </div> <div class="col-md-6 code-samples"> <pre class="highlight shell hide" data-language="shell"><code><span class="c1"># Load the schema document</span> $<span class="w"> </span>coreapi<span class="w"> </span>get<span class="w"> </span>https://omabrowser.org/api/docs <span class="c1"># Interact with the API endpoint</span> $<span class="w"> </span>coreapi<span class="w"> </span>action<span class="w"> </span>protein<span class="w"> </span>hog_derived_orthologs<span class="w"> </span>-p<span class="w"> </span><span class="nv">entry_id</span><span class="o">=</span>... </code></pre> <pre class="highlight javascript hide" data-language="javascript"><code><span class="kd">var</span><span class="w"> </span><span class="nx">coreapi</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">coreapi</span><span class="w"> </span><span class="c1">// Loaded by `coreapi.js`</span> <span class="kd">var</span><span class="w"> </span><span class="nx">schema</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">schema</span><span class="w"> </span><span class="c1">// Loaded by `schema.js`</span> <span class="c1">// Initialize a client</span> <span class="kd">var</span><span class="w"> </span><span class="nx">client</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="ow">new</span><span class="w"> </span><span class="nx">coreapi</span><span class="p">.</span><span class="nx">Client</span><span class="p">()</span> <span class="c1">// Interact with the API endpoint</span> <span class="kd">var</span><span class="w"> </span><span class="nx">action</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">[</span><span class="s2">"protein"</span><span class="p">,</span><span class="w"> </span><span class="s2">"hog_derived_orthologs"</span><span class="p">]</span> <span class="kd">var</span><span class="w"> </span><span class="nx">params</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="nx">entry_id</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="p">}</span> <span class="nx">client</span><span class="p">.</span><span class="nx">action</span><span class="p">(</span><span class="nx">schema</span><span class="p">,</span><span class="w"> </span><span class="nx">action</span><span class="p">,</span><span class="w"> </span><span class="nx">params</span><span class="p">).</span><span class="nx">then</span><span class="p">(</span><span class="kd">function</span><span class="p">(</span><span class="nx">result</span><span class="p">)</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="c1">// Return value is in 'result'</span> <span class="p">})</span> </code></pre> <pre class="highlight python hide" data-language="python"><code><span class="kn">import</span> <span class="nn">coreapi</span> <span class="c1"># Initialize a client & load the schema document</span> <span class="n">client</span> <span class="o">=</span> <span class="n">coreapi</span><span class="o">.</span><span class="n">Client</span><span class="p">()</span> <span class="n">schema</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"https://omabrowser.org/api/docs"</span><span class="p">)</span> <span class="c1"># Interact with the API endpoint</span> <span class="n">action</span> <span class="o">=</span> <span class="p">[</span><span class="s2">"protein"</span><span class="p">,</span> <span class="s2">"hog_derived_orthologs"</span><span class="p">]</span> <span class="n">params</span> <span class="o">=</span> <span class="p">{</span> <span class="s2">"entry_id"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="p">}</span> <span class="n">result</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">action</span><span class="p">(</span><span class="n">schema</span><span class="p">,</span> <span class="n">action</span><span class="p">,</span> <span class="n">params</span><span class="o">=</span><span class="n">params</span><span class="p">)</span> </code></pre> </div> </div> <!-- Modal --> <div class="modal fade api-modal" id="protein_hog_derived_orthologs_modal" tabindex="-1" role="dialog" aria-labelledby="api explorer modal"> <div class="modal-dialog modal-lg" role="document"> <div class="modal-content"> <div class="modal-header"> <div class="toggle-view hide"> <div class="btn-group" role="group"> <button type="button" data-display-toggle="data" class="btn btn-sm btn-info">Data</button> <button type="button" data-display-toggle="raw" class="btn btn-sm">Raw</button> </div> </div> <h3 class="modal-title"><i class="fa fa-exchange"></i> hog_derived_orthologs</h3> </div> <form data-key='["protein", "hog_derived_orthologs"]' class="api-interaction"> <div class="modal-body"> <div class="row"> <div class="col-lg-6 request"> <div class="form-group"> <label for="entry_id" class="control-label"> entry_id <span class="text-danger">*</span> </label> <input name="entry_id" class="form-control" data-empty='' data-type='string' required> <p class="help-block">an unique identifier for a protein - either it entry number, omaid or its canonical id</p> </div> </div> <hr class="hidden-lg hidden-xl" /> <div class="col-lg-6 response" id="response"> <div class="request-awaiting">Awaiting request</div> <div class="meta hide"> <span class="label label-primary request-method"></span> <code class="request-url"></code> <label class="label label-lg response-status-code pull-right"></label> </div> <pre class="well response-data hide"></pre> <pre class="well response-raw hide"><div class="response-raw-request"></div><div class="response-raw-response"></div></pre> </div> </div> </div> <div class="modal-footer"> <button type="button" class="btn btn-default" data-dismiss="modal">Close</button> <button type="submit" class="btn btn-primary">Send Request</button> </div> </form> </div> </div> </div> <div class="row coredocs-link"> <div class="col-md-6 docs-content"> <button class="btn btn-sm btn-success" style="float: right; margin-top: 20px" data-toggle="modal" data-target="#protein_homoeologs_modal"> <i class="fa fa-exchange"></i> Interact </button> <h3 id="protein-homoeologs" class="coredocs-link-title">homoeologs <a href="#protein-homoeologs"><i class="fa fa-link" aria-hidden="true"></i> </a></h3> <div class="meta"> <span class="label label-primary">GET</span> <code>/api/protein/{entry_id}/homoeologs/</code> </div> <p><p>List of all the homoeologs for a given protein.</p></p> <h4>Path Parameters</h4> <p>The following parameters should be included in the URL path.</p> <table class="parameters table table-bordered table-striped"> <thead> <tr><th>Parameter</th><th>Description</th></tr> </thead> <tbody> <tr><td class="parameter-name"><code>entry_id</code> <span class="label label-warning">required</span></td><td>an unique identifier for a protein - either its entry number, omaid or canonical id.</td></tr> </tbody> </table> </div> <div class="col-md-6 code-samples"> <pre class="highlight shell hide" data-language="shell"><code><span class="c1"># Load the schema document</span> $<span class="w"> </span>coreapi<span class="w"> </span>get<span class="w"> </span>https://omabrowser.org/api/docs <span class="c1"># Interact with the API endpoint</span> $<span class="w"> </span>coreapi<span class="w"> </span>action<span class="w"> </span>protein<span class="w"> </span>homoeologs<span class="w"> </span>-p<span class="w"> </span><span class="nv">entry_id</span><span class="o">=</span>... </code></pre> <pre class="highlight javascript hide" data-language="javascript"><code><span class="kd">var</span><span class="w"> </span><span class="nx">coreapi</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">coreapi</span><span class="w"> </span><span class="c1">// Loaded by `coreapi.js`</span> <span class="kd">var</span><span class="w"> </span><span class="nx">schema</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">schema</span><span class="w"> </span><span class="c1">// Loaded by `schema.js`</span> <span class="c1">// Initialize a client</span> <span class="kd">var</span><span class="w"> </span><span class="nx">client</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="ow">new</span><span class="w"> </span><span class="nx">coreapi</span><span class="p">.</span><span class="nx">Client</span><span class="p">()</span> <span class="c1">// Interact with the API endpoint</span> <span class="kd">var</span><span class="w"> </span><span class="nx">action</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">[</span><span class="s2">"protein"</span><span class="p">,</span><span class="w"> </span><span class="s2">"homoeologs"</span><span class="p">]</span> <span class="kd">var</span><span class="w"> </span><span class="nx">params</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="nx">entry_id</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="p">}</span> <span class="nx">client</span><span class="p">.</span><span class="nx">action</span><span class="p">(</span><span class="nx">schema</span><span class="p">,</span><span class="w"> </span><span class="nx">action</span><span class="p">,</span><span class="w"> </span><span class="nx">params</span><span class="p">).</span><span class="nx">then</span><span class="p">(</span><span class="kd">function</span><span class="p">(</span><span class="nx">result</span><span class="p">)</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="c1">// Return value is in 'result'</span> <span class="p">})</span> </code></pre> <pre class="highlight python hide" data-language="python"><code><span class="kn">import</span> <span class="nn">coreapi</span> <span class="c1"># Initialize a client & load the schema document</span> <span class="n">client</span> <span class="o">=</span> <span class="n">coreapi</span><span class="o">.</span><span class="n">Client</span><span class="p">()</span> <span class="n">schema</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"https://omabrowser.org/api/docs"</span><span class="p">)</span> <span class="c1"># Interact with the API endpoint</span> <span class="n">action</span> <span class="o">=</span> <span class="p">[</span><span class="s2">"protein"</span><span class="p">,</span> <span class="s2">"homoeologs"</span><span class="p">]</span> <span class="n">params</span> <span class="o">=</span> <span class="p">{</span> <span class="s2">"entry_id"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="p">}</span> <span class="n">result</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">action</span><span class="p">(</span><span class="n">schema</span><span class="p">,</span> <span class="n">action</span><span class="p">,</span> <span class="n">params</span><span class="o">=</span><span class="n">params</span><span class="p">)</span> </code></pre> </div> </div> <!-- Modal --> <div class="modal fade api-modal" id="protein_homoeologs_modal" tabindex="-1" role="dialog" aria-labelledby="api explorer modal"> <div class="modal-dialog modal-lg" role="document"> <div class="modal-content"> <div class="modal-header"> <div class="toggle-view hide"> <div class="btn-group" role="group"> <button type="button" data-display-toggle="data" class="btn btn-sm btn-info">Data</button> <button type="button" data-display-toggle="raw" class="btn btn-sm">Raw</button> </div> </div> <h3 class="modal-title"><i class="fa fa-exchange"></i> homoeologs</h3> </div> <form data-key='["protein", "homoeologs"]' class="api-interaction"> <div class="modal-body"> <div class="row"> <div class="col-lg-6 request"> <div class="form-group"> <label for="entry_id" class="control-label"> entry_id <span class="text-danger">*</span> </label> <input name="entry_id" class="form-control" data-empty='' data-type='string' required> <p class="help-block">an unique identifier for a protein - either its entry number, omaid or canonical id.</p> </div> </div> <hr class="hidden-lg hidden-xl" /> <div class="col-lg-6 response" id="response"> <div class="request-awaiting">Awaiting request</div> <div class="meta hide"> <span class="label label-primary request-method"></span> <code class="request-url"></code> <label class="label label-lg response-status-code pull-right"></label> </div> <pre class="well response-data hide"></pre> <pre class="well response-raw hide"><div class="response-raw-request"></div><div class="response-raw-response"></div></pre> </div> </div> </div> <div class="modal-footer"> <button type="button" class="btn btn-default" data-dismiss="modal">Close</button> <button type="submit" class="btn btn-primary">Send Request</button> </div> </form> </div> </div> </div> <div class="row coredocs-link"> <div class="col-md-6 docs-content"> <button class="btn btn-sm btn-success" style="float: right; margin-top: 20px" data-toggle="modal" data-target="#protein_isoforms_modal"> <i class="fa fa-exchange"></i> Interact </button> <h3 id="protein-isoforms" class="coredocs-link-title">isoforms <a href="#protein-isoforms"><i class="fa fa-link" aria-hidden="true"></i> </a></h3> <div class="meta"> <span class="label label-primary">GET</span> <code>/api/protein/{entry_id}/isoforms/</code> </div> <p><p>List of isoforms for a protein.</p> <p>The result contains a list of proteins with information on their locus and and exon structure for all the isoforms recored in OMA belonging to the gene of the query protein.</p></p> <h4>Path Parameters</h4> <p>The following parameters should be included in the URL path.</p> <table class="parameters table table-bordered table-striped"> <thead> <tr><th>Parameter</th><th>Description</th></tr> </thead> <tbody> <tr><td class="parameter-name"><code>entry_id</code> <span class="label label-warning">required</span></td><td>an unique identifier for a protein - either it entry number, omaid or its canonical id</td></tr> </tbody> </table> </div> <div class="col-md-6 code-samples"> <pre class="highlight shell hide" data-language="shell"><code><span class="c1"># Load the schema document</span> $<span class="w"> </span>coreapi<span class="w"> </span>get<span class="w"> </span>https://omabrowser.org/api/docs <span class="c1"># Interact with the API endpoint</span> $<span class="w"> </span>coreapi<span class="w"> </span>action<span class="w"> </span>protein<span class="w"> </span>isoforms<span class="w"> </span>-p<span class="w"> </span><span class="nv">entry_id</span><span class="o">=</span>... </code></pre> <pre class="highlight javascript hide" data-language="javascript"><code><span class="kd">var</span><span class="w"> </span><span class="nx">coreapi</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">coreapi</span><span class="w"> </span><span class="c1">// Loaded by `coreapi.js`</span> <span class="kd">var</span><span class="w"> </span><span class="nx">schema</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">schema</span><span class="w"> </span><span class="c1">// Loaded by `schema.js`</span> <span class="c1">// Initialize a client</span> <span class="kd">var</span><span class="w"> </span><span class="nx">client</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="ow">new</span><span class="w"> </span><span class="nx">coreapi</span><span class="p">.</span><span class="nx">Client</span><span class="p">()</span> <span class="c1">// Interact with the API endpoint</span> <span class="kd">var</span><span class="w"> </span><span class="nx">action</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">[</span><span class="s2">"protein"</span><span class="p">,</span><span class="w"> </span><span class="s2">"isoforms"</span><span class="p">]</span> <span class="kd">var</span><span class="w"> </span><span class="nx">params</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="nx">entry_id</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="p">}</span> <span class="nx">client</span><span class="p">.</span><span class="nx">action</span><span class="p">(</span><span class="nx">schema</span><span class="p">,</span><span class="w"> </span><span class="nx">action</span><span class="p">,</span><span class="w"> </span><span class="nx">params</span><span class="p">).</span><span class="nx">then</span><span class="p">(</span><span class="kd">function</span><span class="p">(</span><span class="nx">result</span><span class="p">)</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="c1">// Return value is in 'result'</span> <span class="p">})</span> </code></pre> <pre class="highlight python hide" data-language="python"><code><span class="kn">import</span> <span class="nn">coreapi</span> <span class="c1"># Initialize a client & load the schema document</span> <span class="n">client</span> <span class="o">=</span> <span class="n">coreapi</span><span class="o">.</span><span class="n">Client</span><span class="p">()</span> <span class="n">schema</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"https://omabrowser.org/api/docs"</span><span class="p">)</span> <span class="c1"># Interact with the API endpoint</span> <span class="n">action</span> <span class="o">=</span> <span class="p">[</span><span class="s2">"protein"</span><span class="p">,</span> <span class="s2">"isoforms"</span><span class="p">]</span> <span class="n">params</span> <span class="o">=</span> <span class="p">{</span> <span class="s2">"entry_id"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="p">}</span> <span class="n">result</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">action</span><span class="p">(</span><span class="n">schema</span><span class="p">,</span> <span class="n">action</span><span class="p">,</span> <span class="n">params</span><span class="o">=</span><span class="n">params</span><span class="p">)</span> </code></pre> </div> </div> <!-- Modal --> <div class="modal fade api-modal" id="protein_isoforms_modal" tabindex="-1" role="dialog" aria-labelledby="api explorer modal"> <div class="modal-dialog modal-lg" role="document"> <div class="modal-content"> <div class="modal-header"> <div class="toggle-view hide"> <div class="btn-group" role="group"> <button type="button" data-display-toggle="data" class="btn btn-sm btn-info">Data</button> <button type="button" data-display-toggle="raw" class="btn btn-sm">Raw</button> </div> </div> <h3 class="modal-title"><i class="fa fa-exchange"></i> isoforms</h3> </div> <form data-key='["protein", "isoforms"]' class="api-interaction"> <div class="modal-body"> <div class="row"> <div class="col-lg-6 request"> <div class="form-group"> <label for="entry_id" class="control-label"> entry_id <span class="text-danger">*</span> </label> <input name="entry_id" class="form-control" data-empty='' data-type='string' required> <p class="help-block">an unique identifier for a protein - either it entry number, omaid or its canonical id</p> </div> </div> <hr class="hidden-lg hidden-xl" /> <div class="col-lg-6 response" id="response"> <div class="request-awaiting">Awaiting request</div> <div class="meta hide"> <span class="label label-primary request-method"></span> <code class="request-url"></code> <label class="label label-lg response-status-code pull-right"></label> </div> <pre class="well response-data hide"></pre> <pre class="well response-raw hide"><div class="response-raw-request"></div><div class="response-raw-response"></div></pre> </div> </div> </div> <div class="modal-footer"> <button type="button" class="btn btn-default" data-dismiss="modal">Close</button> <button type="submit" class="btn btn-primary">Send Request</button> </div> </form> </div> </div> </div> <div class="row coredocs-link"> <div class="col-md-6 docs-content"> <button class="btn btn-sm btn-success" style="float: right; margin-top: 20px" data-toggle="modal" data-target="#protein_ontology_modal"> <i class="fa fa-exchange"></i> Interact </button> <h3 id="protein-ontology" class="coredocs-link-title">ontology <a href="#protein-ontology"><i class="fa fa-link" aria-hidden="true"></i> </a></h3> <div class="meta"> <span class="label label-primary">GET</span> <code>/api/protein/{entry_id}/ontology/</code> </div> <p><p>Deprecated: use gene_ontology endpoint instead</p></p> </div> <div class="col-md-6 code-samples"> <pre class="highlight shell hide" data-language="shell"><code><span class="c1"># Load the schema document</span> $<span class="w"> </span>coreapi<span class="w"> </span>get<span class="w"> </span>https://omabrowser.org/api/docs <span class="c1"># Interact with the API endpoint</span> $<span class="w"> </span>coreapi<span class="w"> </span>action<span class="w"> </span>protein<span class="w"> </span>ontology </code></pre> <pre class="highlight javascript hide" data-language="javascript"><code><span class="kd">var</span><span class="w"> </span><span class="nx">coreapi</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">coreapi</span><span class="w"> </span><span class="c1">// Loaded by `coreapi.js`</span> <span class="kd">var</span><span class="w"> </span><span class="nx">schema</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">schema</span><span class="w"> </span><span class="c1">// Loaded by `schema.js`</span> <span class="c1">// Initialize a client</span> <span class="kd">var</span><span class="w"> </span><span class="nx">client</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="ow">new</span><span class="w"> </span><span class="nx">coreapi</span><span class="p">.</span><span class="nx">Client</span><span class="p">()</span> <span class="c1">// Interact with the API endpoint</span> <span class="kd">var</span><span class="w"> </span><span class="nx">action</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">[</span><span class="s2">"protein"</span><span class="p">,</span><span class="w"> </span><span class="s2">"ontology"</span><span class="p">]</span> <span class="nx">client</span><span class="p">.</span><span class="nx">action</span><span class="p">(</span><span class="nx">schema</span><span class="p">,</span><span class="w"> </span><span class="nx">action</span><span class="p">).</span><span class="nx">then</span><span class="p">(</span><span class="kd">function</span><span class="p">(</span><span class="nx">result</span><span class="p">)</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="c1">// Return value is in 'result'</span> <span class="p">})</span> </code></pre> <pre class="highlight python hide" data-language="python"><code><span class="kn">import</span> <span class="nn">coreapi</span> <span class="c1"># Initialize a client & load the schema document</span> <span class="n">client</span> <span class="o">=</span> <span class="n">coreapi</span><span class="o">.</span><span class="n">Client</span><span class="p">()</span> <span class="n">schema</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"https://omabrowser.org/api/docs"</span><span class="p">)</span> <span class="c1"># Interact with the API endpoint</span> <span class="n">action</span> <span class="o">=</span> <span class="p">[</span><span class="s2">"protein"</span><span class="p">,</span> <span class="s2">"ontology"</span><span class="p">]</span> <span class="n">result</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">action</span><span class="p">(</span><span class="n">schema</span><span class="p">,</span> <span class="n">action</span><span class="p">)</span> </code></pre> </div> </div> <!-- Modal --> <div class="modal fade api-modal" id="protein_ontology_modal" tabindex="-1" role="dialog" aria-labelledby="api explorer modal"> <div class="modal-dialog modal-lg" role="document"> <div class="modal-content"> <div class="modal-header"> <div class="toggle-view hide"> <div class="btn-group" role="group"> <button type="button" data-display-toggle="data" class="btn btn-sm btn-info">Data</button> <button type="button" data-display-toggle="raw" class="btn btn-sm">Raw</button> </div> </div> <h3 class="modal-title"><i class="fa fa-exchange"></i> ontology</h3> </div> <form data-key='["protein", "ontology"]' class="api-interaction"> <div class="modal-body"> <div class="row"> <div class="col-lg-6 request"> </div> <hr class="hidden-lg hidden-xl" /> <div class="col-lg-6 response" id="response"> <div class="request-awaiting">Awaiting request</div> <div class="meta hide"> <span class="label label-primary request-method"></span> <code class="request-url"></code> <label class="label label-lg response-status-code pull-right"></label> </div> <pre class="well response-data hide"></pre> <pre class="well response-raw hide"><div class="response-raw-request"></div><div class="response-raw-response"></div></pre> </div> </div> </div> <div class="modal-footer"> <button type="button" class="btn btn-default" data-dismiss="modal">Close</button> <button type="submit" class="btn btn-primary">Send Request</button> </div> </form> </div> </div> </div> <div class="row coredocs-link"> <div class="col-md-6 docs-content"> <button class="btn btn-sm btn-success" style="float: right; margin-top: 20px" data-toggle="modal" data-target="#protein_orthologs_modal"> <i class="fa fa-exchange"></i> Interact </button> <h3 id="protein-orthologs" class="coredocs-link-title">orthologs <a href="#protein-orthologs"><i class="fa fa-link" aria-hidden="true"></i> </a></h3> <div class="meta"> <span class="label label-primary">GET</span> <code>/api/protein/{entry_id}/orthologs/</code> </div> <p><p>List of all the identified pairwise orthologues for a protein. Filtering specific subtypes of orthology is possible by specifying a rel_type query parameter.</p></p> <h4>Path Parameters</h4> <p>The following parameters should be included in the URL path.</p> <table class="parameters table table-bordered table-striped"> <thead> <tr><th>Parameter</th><th>Description</th></tr> </thead> <tbody> <tr><td class="parameter-name"><code>entry_id</code> <span class="label label-warning">required</span></td><td>an unique identifier for a protein - either it entry number, omaid or its canonical id</td></tr> </tbody> </table> <h4>Query Parameters</h4> <p>The following parameters should be included as part of a URL query string.</p> <table class="parameters table table-bordered table-striped"> <thead> <tr><th>Parameter</th><th>Description</th></tr> </thead> <tbody> <tr><td class="parameter-name"><code>rel_type</code></td><td>filter for orthologs of a specific relationship type only (Example: 1:1)</td></tr> </tbody> </table> </div> <div class="col-md-6 code-samples"> <pre class="highlight shell hide" data-language="shell"><code><span class="c1"># Load the schema document</span> $<span class="w"> </span>coreapi<span class="w"> </span>get<span class="w"> </span>https://omabrowser.org/api/docs <span class="c1"># Interact with the API endpoint</span> $<span class="w"> </span>coreapi<span class="w"> </span>action<span class="w"> </span>protein<span class="w"> </span>orthologs<span class="w"> </span>-p<span class="w"> </span><span class="nv">entry_id</span><span class="o">=</span>...<span class="w"> </span>-p<span class="w"> </span><span class="nv">rel_type</span><span class="o">=</span>... </code></pre> <pre class="highlight javascript hide" data-language="javascript"><code><span class="kd">var</span><span class="w"> </span><span class="nx">coreapi</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">coreapi</span><span class="w"> </span><span class="c1">// Loaded by `coreapi.js`</span> <span class="kd">var</span><span class="w"> </span><span class="nx">schema</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">schema</span><span class="w"> </span><span class="c1">// Loaded by `schema.js`</span> <span class="c1">// Initialize a client</span> <span class="kd">var</span><span class="w"> </span><span class="nx">client</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="ow">new</span><span class="w"> </span><span class="nx">coreapi</span><span class="p">.</span><span class="nx">Client</span><span class="p">()</span> <span class="c1">// Interact with the API endpoint</span> <span class="kd">var</span><span class="w"> </span><span class="nx">action</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">[</span><span class="s2">"protein"</span><span class="p">,</span><span class="w"> </span><span class="s2">"orthologs"</span><span class="p">]</span> <span class="kd">var</span><span class="w"> </span><span class="nx">params</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="nx">entry_id</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="w"> </span><span class="nx">rel_type</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="p">}</span> <span class="nx">client</span><span class="p">.</span><span class="nx">action</span><span class="p">(</span><span class="nx">schema</span><span class="p">,</span><span class="w"> </span><span class="nx">action</span><span class="p">,</span><span class="w"> </span><span class="nx">params</span><span class="p">).</span><span class="nx">then</span><span class="p">(</span><span class="kd">function</span><span class="p">(</span><span class="nx">result</span><span class="p">)</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="c1">// Return value is in 'result'</span> <span class="p">})</span> </code></pre> <pre class="highlight python hide" data-language="python"><code><span class="kn">import</span> <span class="nn">coreapi</span> <span class="c1"># Initialize a client & load the schema document</span> <span class="n">client</span> <span class="o">=</span> <span class="n">coreapi</span><span class="o">.</span><span class="n">Client</span><span class="p">()</span> <span class="n">schema</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"https://omabrowser.org/api/docs"</span><span class="p">)</span> <span class="c1"># Interact with the API endpoint</span> <span class="n">action</span> <span class="o">=</span> <span class="p">[</span><span class="s2">"protein"</span><span class="p">,</span> <span class="s2">"orthologs"</span><span class="p">]</span> <span class="n">params</span> <span class="o">=</span> <span class="p">{</span> <span class="s2">"entry_id"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="s2">"rel_type"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="p">}</span> <span class="n">result</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">action</span><span class="p">(</span><span class="n">schema</span><span class="p">,</span> <span class="n">action</span><span class="p">,</span> <span class="n">params</span><span class="o">=</span><span class="n">params</span><span class="p">)</span> </code></pre> </div> </div> <!-- Modal --> <div class="modal fade api-modal" id="protein_orthologs_modal" tabindex="-1" role="dialog" aria-labelledby="api explorer modal"> <div class="modal-dialog modal-lg" role="document"> <div class="modal-content"> <div class="modal-header"> <div class="toggle-view hide"> <div class="btn-group" role="group"> <button type="button" data-display-toggle="data" class="btn btn-sm btn-info">Data</button> <button type="button" data-display-toggle="raw" class="btn btn-sm">Raw</button> </div> </div> <h3 class="modal-title"><i class="fa fa-exchange"></i> orthologs</h3> </div> <form data-key='["protein", "orthologs"]' class="api-interaction"> <div class="modal-body"> <div class="row"> <div class="col-lg-6 request"> <div class="form-group"> <label for="entry_id" class="control-label"> entry_id <span class="text-danger">*</span> </label> <input name="entry_id" class="form-control" data-empty='' data-type='string' required> <p class="help-block">an unique identifier for a protein - either it entry number, omaid or its canonical id</p> </div> <div class="form-group"> <label for="rel_type" class="control-label"> rel_type </label> <input name="rel_type" class="form-control" data-empty='' data-type='string' > <p class="help-block">filter for orthologs of a specific relationship type only (Example: 1:1)</p> </div> </div> <hr class="hidden-lg hidden-xl" /> <div class="col-lg-6 response" id="response"> <div class="request-awaiting">Awaiting request</div> <div class="meta hide"> <span class="label label-primary request-method"></span> <code class="request-url"></code> <label class="label label-lg response-status-code pull-right"></label> </div> <pre class="well response-data hide"></pre> <pre class="well response-raw hide"><div class="response-raw-request"></div><div class="response-raw-response"></div></pre> </div> </div> </div> <div class="modal-footer"> <button type="button" class="btn btn-default" data-dismiss="modal">Close</button> <button type="submit" class="btn btn-primary">Send Request</button> </div> </form> </div> </div> </div> <div class="row coredocs-link"> <div class="col-md-6 docs-content"> <button class="btn btn-sm btn-success" style="float: right; margin-top: 20px" data-toggle="modal" data-target="#protein_xref_modal"> <i class="fa fa-exchange"></i> Interact </button> <h3 id="protein-xref" class="coredocs-link-title">xref <a href="#protein-xref"><i class="fa fa-link" aria-hidden="true"></i> </a></h3> <div class="meta"> <span class="label label-primary">GET</span> <code>/api/protein/{entry_id}/xref/</code> </div> <p><p>List of cross-references for a protein.</p></p> <h4>Path Parameters</h4> <p>The following parameters should be included in the URL path.</p> <table class="parameters table table-bordered table-striped"> <thead> <tr><th>Parameter</th><th>Description</th></tr> </thead> <tbody> <tr><td class="parameter-name"><code>entry_id</code> <span class="label label-warning">required</span></td><td>an unique identifier for a protein - either it entry number, omaid or its canonical id</td></tr> </tbody> </table> <h4>Query Parameters</h4> <p>The following parameters should be included as part of a URL query string.</p> <table class="parameters table table-bordered table-striped"> <thead> <tr><th>Parameter</th><th>Description</th></tr> </thead> <tbody> <tr><td class="parameter-name"><code>filter</code></td><td>a filter name to exclude some cross-references that are not relevant. Possible values are `all`, `exact`, `maindb`. - `all` does not apply any filter and returns all cross-references (default). - `exact` ignores all cross-references for which the protein sequence is not exactly the same as the one in the OMA browser. - `maindb` returns only the GeneName, UniProtKB, Ensembl Genes, RefSeq and EntrezGene and the SourceID cross-references.</td></tr> </tbody> </table> </div> <div class="col-md-6 code-samples"> <pre class="highlight shell hide" data-language="shell"><code><span class="c1"># Load the schema document</span> $<span class="w"> </span>coreapi<span class="w"> </span>get<span class="w"> </span>https://omabrowser.org/api/docs <span class="c1"># Interact with the API endpoint</span> $<span class="w"> </span>coreapi<span class="w"> </span>action<span class="w"> </span>protein<span class="w"> </span>xref<span class="w"> </span>-p<span class="w"> </span><span class="nv">entry_id</span><span class="o">=</span>...<span class="w"> </span>-p<span class="w"> </span><span class="nv">filter</span><span class="o">=</span>... </code></pre> <pre class="highlight javascript hide" data-language="javascript"><code><span class="kd">var</span><span class="w"> </span><span class="nx">coreapi</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">coreapi</span><span class="w"> </span><span class="c1">// Loaded by `coreapi.js`</span> <span class="kd">var</span><span class="w"> </span><span class="nx">schema</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">schema</span><span class="w"> </span><span class="c1">// Loaded by `schema.js`</span> <span class="c1">// Initialize a client</span> <span class="kd">var</span><span class="w"> </span><span class="nx">client</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="ow">new</span><span class="w"> </span><span class="nx">coreapi</span><span class="p">.</span><span class="nx">Client</span><span class="p">()</span> <span class="c1">// Interact with the API endpoint</span> <span class="kd">var</span><span class="w"> </span><span class="nx">action</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">[</span><span class="s2">"protein"</span><span class="p">,</span><span class="w"> </span><span class="s2">"xref"</span><span class="p">]</span> <span class="kd">var</span><span class="w"> </span><span class="nx">params</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="nx">entry_id</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="w"> </span><span class="nx">filter</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="p">}</span> <span class="nx">client</span><span class="p">.</span><span class="nx">action</span><span class="p">(</span><span class="nx">schema</span><span class="p">,</span><span class="w"> </span><span class="nx">action</span><span class="p">,</span><span class="w"> </span><span class="nx">params</span><span class="p">).</span><span class="nx">then</span><span class="p">(</span><span class="kd">function</span><span class="p">(</span><span class="nx">result</span><span class="p">)</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="c1">// Return value is in 'result'</span> <span class="p">})</span> </code></pre> <pre class="highlight python hide" data-language="python"><code><span class="kn">import</span> <span class="nn">coreapi</span> <span class="c1"># Initialize a client & load the schema document</span> <span class="n">client</span> <span class="o">=</span> <span class="n">coreapi</span><span class="o">.</span><span class="n">Client</span><span class="p">()</span> <span class="n">schema</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"https://omabrowser.org/api/docs"</span><span class="p">)</span> <span class="c1"># Interact with the API endpoint</span> <span class="n">action</span> <span class="o">=</span> <span class="p">[</span><span class="s2">"protein"</span><span class="p">,</span> <span class="s2">"xref"</span><span class="p">]</span> <span class="n">params</span> <span class="o">=</span> <span class="p">{</span> <span class="s2">"entry_id"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="s2">"filter"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="p">}</span> <span class="n">result</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">action</span><span class="p">(</span><span class="n">schema</span><span class="p">,</span> <span class="n">action</span><span class="p">,</span> <span class="n">params</span><span class="o">=</span><span class="n">params</span><span class="p">)</span> </code></pre> </div> </div> <!-- Modal --> <div class="modal fade api-modal" id="protein_xref_modal" tabindex="-1" role="dialog" aria-labelledby="api explorer modal"> <div class="modal-dialog modal-lg" role="document"> <div class="modal-content"> <div class="modal-header"> <div class="toggle-view hide"> <div class="btn-group" role="group"> <button type="button" data-display-toggle="data" class="btn btn-sm btn-info">Data</button> <button type="button" data-display-toggle="raw" class="btn btn-sm">Raw</button> </div> </div> <h3 class="modal-title"><i class="fa fa-exchange"></i> xref</h3> </div> <form data-key='["protein", "xref"]' class="api-interaction"> <div class="modal-body"> <div class="row"> <div class="col-lg-6 request"> <div class="form-group"> <label for="entry_id" class="control-label"> entry_id <span class="text-danger">*</span> </label> <input name="entry_id" class="form-control" data-empty='' data-type='string' required> <p class="help-block">an unique identifier for a protein - either it entry number, omaid or its canonical id</p> </div> <div class="form-group"> <label for="filter" class="control-label"> filter </label> <input name="filter" class="form-control" data-empty='' data-type='string' > <p class="help-block">a filter name to exclude some cross-references that are not relevant. Possible values are `all`, `exact`, `maindb`. - `all` does not apply any filter and returns all cross-references (default). - `exact` ignores all cross-references for which the protein sequence is not exactly the same as the one in the OMA browser. - `maindb` returns only the GeneName, UniProtKB, Ensembl Genes, RefSeq and EntrezGene and the SourceID cross-references.</p> </div> </div> <hr class="hidden-lg hidden-xl" /> <div class="col-lg-6 response" id="response"> <div class="request-awaiting">Awaiting request</div> <div class="meta hide"> <span class="label label-primary request-method"></span> <code class="request-url"></code> <label class="label label-lg response-status-code pull-right"></label> </div> <pre class="well response-data hide"></pre> <pre class="well response-raw hide"><div class="response-raw-request"></div><div class="response-raw-response"></div></pre> </div> </div> </div> <div class="modal-footer"> <button type="button" class="btn btn-default" data-dismiss="modal">Close</button> <button type="submit" class="btn btn-primary">Send Request</button> </div> </form> </div> </div> </div> <h2 id="sequence" class="coredocs-section-title">sequence <a href="#sequence"><i class="fa fa-link" aria-hidden="true"></i> </a></h2> <div class="row coredocs-link"> <div class="col-md-6 docs-content"> <button class="btn btn-sm btn-success" style="float: right; margin-top: 20px" data-toggle="modal" data-target="#sequence_list_modal"> <i class="fa fa-exchange"></i> Interact </button> <h3 id="sequence-list" class="coredocs-link-title">list <a href="#sequence-list"><i class="fa fa-link" aria-hidden="true"></i> </a></h3> <div class="meta"> <span class="label label-primary">GET</span> <code>/api/sequence/</code> </div> <p><p>Identify a protein sequence.</p></p> <h4>Query Parameters</h4> <p>The following parameters should be included as part of a URL query string.</p> <table class="parameters table table-bordered table-striped"> <thead> <tr><th>Parameter</th><th>Description</th></tr> </thead> <tbody> <tr><td class="parameter-name"><code>query</code> <span class="label label-warning">required</span></td><td>the sequence to be searched.</td></tr> <tr><td class="parameter-name"><code>search</code></td><td>argument to choose search strategy. Can be set to 'exact', 'approximate' or 'mixed'. Defaults to 'mixed', meaning first tries to find exact match. If no target can be found, uses approximate search strategy to identify query sequence in database.</td></tr> <tr><td class="parameter-name"><code>full_length</code></td><td>a boolean indicating whether or not for exact matches, the query sequence must be matching the full target sequence. By default, a partial exact match is also reported as exact match.</td></tr> </tbody> </table> </div> <div class="col-md-6 code-samples"> <pre class="highlight shell hide" data-language="shell"><code><span class="c1"># Load the schema document</span> $<span class="w"> </span>coreapi<span class="w"> </span>get<span class="w"> </span>https://omabrowser.org/api/docs <span class="c1"># Interact with the API endpoint</span> $<span class="w"> </span>coreapi<span class="w"> </span>action<span class="w"> </span>sequence<span class="w"> </span>list<span class="w"> </span>-p<span class="w"> </span><span class="nv">query</span><span class="o">=</span>...<span class="w"> </span>-p<span class="w"> </span><span class="nv">search</span><span class="o">=</span>...<span class="w"> </span>-p<span class="w"> </span><span class="nv">full_length</span><span class="o">=</span>... </code></pre> <pre class="highlight javascript hide" data-language="javascript"><code><span class="kd">var</span><span class="w"> </span><span class="nx">coreapi</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">coreapi</span><span class="w"> </span><span class="c1">// Loaded by `coreapi.js`</span> <span class="kd">var</span><span class="w"> </span><span class="nx">schema</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">schema</span><span class="w"> </span><span class="c1">// Loaded by `schema.js`</span> <span class="c1">// Initialize a client</span> <span class="kd">var</span><span class="w"> </span><span class="nx">client</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="ow">new</span><span class="w"> </span><span class="nx">coreapi</span><span class="p">.</span><span class="nx">Client</span><span class="p">()</span> <span class="c1">// Interact with the API endpoint</span> <span class="kd">var</span><span class="w"> </span><span class="nx">action</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">[</span><span class="s2">"sequence"</span><span class="p">,</span><span class="w"> </span><span class="s2">"list"</span><span class="p">]</span> <span class="kd">var</span><span class="w"> </span><span class="nx">params</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="nx">query</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="w"> </span><span class="nx">search</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="w"> </span><span class="nx">full_length</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="p">}</span> <span class="nx">client</span><span class="p">.</span><span class="nx">action</span><span class="p">(</span><span class="nx">schema</span><span class="p">,</span><span class="w"> </span><span class="nx">action</span><span class="p">,</span><span class="w"> </span><span class="nx">params</span><span class="p">).</span><span class="nx">then</span><span class="p">(</span><span class="kd">function</span><span class="p">(</span><span class="nx">result</span><span class="p">)</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="c1">// Return value is in 'result'</span> <span class="p">})</span> </code></pre> <pre class="highlight python hide" data-language="python"><code><span class="kn">import</span> <span class="nn">coreapi</span> <span class="c1"># Initialize a client & load the schema document</span> <span class="n">client</span> <span class="o">=</span> <span class="n">coreapi</span><span class="o">.</span><span class="n">Client</span><span class="p">()</span> <span class="n">schema</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"https://omabrowser.org/api/docs"</span><span class="p">)</span> <span class="c1"># Interact with the API endpoint</span> <span class="n">action</span> <span class="o">=</span> <span class="p">[</span><span class="s2">"sequence"</span><span class="p">,</span> <span class="s2">"list"</span><span class="p">]</span> <span class="n">params</span> <span class="o">=</span> <span class="p">{</span> <span class="s2">"query"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="s2">"search"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="s2">"full_length"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="p">}</span> <span class="n">result</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">action</span><span class="p">(</span><span class="n">schema</span><span class="p">,</span> <span class="n">action</span><span class="p">,</span> <span class="n">params</span><span class="o">=</span><span class="n">params</span><span class="p">)</span> </code></pre> </div> </div> <!-- Modal --> <div class="modal fade api-modal" id="sequence_list_modal" tabindex="-1" role="dialog" aria-labelledby="api explorer modal"> <div class="modal-dialog modal-lg" role="document"> <div class="modal-content"> <div class="modal-header"> <div class="toggle-view hide"> <div class="btn-group" role="group"> <button type="button" data-display-toggle="data" class="btn btn-sm btn-info">Data</button> <button type="button" data-display-toggle="raw" class="btn btn-sm">Raw</button> </div> </div> <h3 class="modal-title"><i class="fa fa-exchange"></i> list</h3> </div> <form data-key='["sequence", "list"]' class="api-interaction"> <div class="modal-body"> <div class="row"> <div class="col-lg-6 request"> <div class="form-group"> <label for="query" class="control-label"> query <span class="text-danger">*</span> </label> <input name="query" class="form-control" data-empty='' data-type='string' required> <p class="help-block">the sequence to be searched.</p> </div> <div class="form-group"> <label for="search" class="control-label"> search </label> <input name="search" class="form-control" data-empty='' data-type='string' > <p class="help-block">argument to choose search strategy. Can be set to 'exact', 'approximate' or 'mixed'. Defaults to 'mixed', meaning first tries to find exact match. If no target can be found, uses approximate search strategy to identify query sequence in database.</p> </div> <div class="form-group"> <div class="checkbox"> <label class="control-label"> <input type="checkbox" name="full_length" value="true" data-empty=false data-type='boolean'> full_length </label> </div> <span class="help-block">a boolean indicating whether or not for exact matches, the query sequence must be matching the full target sequence. By default, a partial exact match is also reported as exact match.</span> </div> </div> <hr class="hidden-lg hidden-xl" /> <div class="col-lg-6 response" id="response"> <div class="request-awaiting">Awaiting request</div> <div class="meta hide"> <span class="label label-primary request-method"></span> <code class="request-url"></code> <label class="label label-lg response-status-code pull-right"></label> </div> <pre class="well response-data hide"></pre> <pre class="well response-raw hide"><div class="response-raw-request"></div><div class="response-raw-response"></div></pre> </div> </div> </div> <div class="modal-footer"> <button type="button" class="btn btn-default" data-dismiss="modal">Close</button> <button type="submit" class="btn btn-primary">Send Request</button> </div> </form> </div> </div> </div> <h2 id="summary" class="coredocs-section-title">summary <a href="#summary"><i class="fa fa-link" aria-hidden="true"></i> </a></h2> <div class="row coredocs-link"> <div class="col-md-6 docs-content"> <button class="btn btn-sm btn-success" style="float: right; margin-top: 20px" data-toggle="modal" data-target="#summary_shared_ancestry-read_modal"> <i class="fa fa-exchange"></i> Interact </button> <h3 id="summary-shared_ancestry-read" class="coredocs-link-title">shared_ancestry > read <a href="#summary-shared_ancestry-read"><i class="fa fa-link" aria-hidden="true"></i> </a></h3> <div class="meta"> <span class="label label-primary">GET</span> <code>/api/summary/shared_ancestry/{genome_id1}/{genome_id2}/</code> </div> <p><p>Returns the fraction of shared ancestry between to species of interest.</p></p> <h4>Path Parameters</h4> <p>The following parameters should be included in the URL path.</p> <table class="parameters table table-bordered table-striped"> <thead> <tr><th>Parameter</th><th>Description</th></tr> </thead> <tbody> <tr><td class="parameter-name"><code>genome_id1</code> <span class="label label-warning">required</span></td><td>a unique identifier for the first genome - either its ncbi taxon id or the UniProt species code</td></tr> <tr><td class="parameter-name"><code>genome_id2</code> <span class="label label-warning">required</span></td><td>a unique identifier for the second genome - either its ncbi taxon id or the UniProt species code</td></tr> </tbody> </table> <h4>Query Parameters</h4> <p>The following parameters should be included as part of a URL query string.</p> <table class="parameters table table-bordered table-striped"> <thead> <tr><th>Parameter</th><th>Description</th></tr> </thead> <tbody> <tr><td class="parameter-name"><code>type</code></td><td>type of orthology information to compute the fraction of shared ancestry, either 'hogs' (default) or 'vps'.</td></tr> </tbody> </table> </div> <div class="col-md-6 code-samples"> <pre class="highlight shell hide" data-language="shell"><code><span class="c1"># Load the schema document</span> $<span class="w"> </span>coreapi<span class="w"> </span>get<span class="w"> </span>https://omabrowser.org/api/docs <span class="c1"># Interact with the API endpoint</span> $<span class="w"> </span>coreapi<span class="w"> </span>action<span class="w"> </span>summary<span class="w"> </span>shared_ancestry<span class="w"> </span><span class="nb">read</span><span class="w"> </span>-p<span class="w"> </span><span class="nv">genome_id1</span><span class="o">=</span>...<span class="w"> </span>-p<span class="w"> </span><span class="nv">genome_id2</span><span class="o">=</span>...<span class="w"> </span>-p<span class="w"> </span><span class="nv">type</span><span class="o">=</span>... </code></pre> <pre class="highlight javascript hide" data-language="javascript"><code><span class="kd">var</span><span class="w"> </span><span class="nx">coreapi</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">coreapi</span><span class="w"> </span><span class="c1">// Loaded by `coreapi.js`</span> <span class="kd">var</span><span class="w"> </span><span class="nx">schema</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">schema</span><span class="w"> </span><span class="c1">// Loaded by `schema.js`</span> <span class="c1">// Initialize a client</span> <span class="kd">var</span><span class="w"> </span><span class="nx">client</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="ow">new</span><span class="w"> </span><span class="nx">coreapi</span><span class="p">.</span><span class="nx">Client</span><span class="p">()</span> <span class="c1">// Interact with the API endpoint</span> <span class="kd">var</span><span class="w"> </span><span class="nx">action</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">[</span><span class="s2">"summary"</span><span class="p">,</span><span class="w"> </span><span class="s2">"shared_ancestry &gt; read"</span><span class="p">]</span> <span class="kd">var</span><span class="w"> </span><span class="nx">params</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="nx">genome_id1</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="w"> </span><span class="nx">genome_id2</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="w"> </span><span class="nx">type</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="p">}</span> <span class="nx">client</span><span class="p">.</span><span class="nx">action</span><span class="p">(</span><span class="nx">schema</span><span class="p">,</span><span class="w"> </span><span class="nx">action</span><span class="p">,</span><span class="w"> </span><span class="nx">params</span><span class="p">).</span><span class="nx">then</span><span class="p">(</span><span class="kd">function</span><span class="p">(</span><span class="nx">result</span><span class="p">)</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="c1">// Return value is in 'result'</span> <span class="p">})</span> </code></pre> <pre class="highlight python hide" data-language="python"><code><span class="kn">import</span> <span class="nn">coreapi</span> <span class="c1"># Initialize a client & load the schema document</span> <span class="n">client</span> <span class="o">=</span> <span class="n">coreapi</span><span class="o">.</span><span class="n">Client</span><span class="p">()</span> <span class="n">schema</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"https://omabrowser.org/api/docs"</span><span class="p">)</span> <span class="c1"># Interact with the API endpoint</span> <span class="n">action</span> <span class="o">=</span> <span class="p">[</span><span class="s2">"summary"</span><span class="p">,</span> <span class="s2">"shared_ancestry &gt; read"</span><span class="p">]</span> <span class="n">params</span> <span class="o">=</span> <span class="p">{</span> <span class="s2">"genome_id1"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="s2">"genome_id2"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="s2">"type"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="p">}</span> <span class="n">result</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">action</span><span class="p">(</span><span class="n">schema</span><span class="p">,</span> <span class="n">action</span><span class="p">,</span> <span class="n">params</span><span class="o">=</span><span class="n">params</span><span class="p">)</span> </code></pre> </div> </div> <!-- Modal --> <div class="modal fade api-modal" id="summary_shared_ancestry-read_modal" tabindex="-1" role="dialog" aria-labelledby="api explorer modal"> <div class="modal-dialog modal-lg" role="document"> <div class="modal-content"> <div class="modal-header"> <div class="toggle-view hide"> <div class="btn-group" role="group"> <button type="button" data-display-toggle="data" class="btn btn-sm btn-info">Data</button> <button type="button" data-display-toggle="raw" class="btn btn-sm">Raw</button> </div> </div> <h3 class="modal-title"><i class="fa fa-exchange"></i> shared_ancestry > read</h3> </div> <form data-key='["summary", "shared_ancestry > read"]' class="api-interaction"> <div class="modal-body"> <div class="row"> <div class="col-lg-6 request"> <div class="form-group"> <label for="genome_id1" class="control-label"> genome_id1 <span class="text-danger">*</span> </label> <input name="genome_id1" class="form-control" data-empty='' data-type='string' required> <p class="help-block">a unique identifier for the first genome - either its ncbi taxon id or the UniProt species code</p> </div> <div class="form-group"> <label for="genome_id2" class="control-label"> genome_id2 <span class="text-danger">*</span> </label> <input name="genome_id2" class="form-control" data-empty='' data-type='string' required> <p class="help-block">a unique identifier for the second genome - either its ncbi taxon id or the UniProt species code</p> </div> <div class="form-group"> <label for="type" class="control-label"> type </label> <input name="type" class="form-control" data-empty='' data-type='string' > <p class="help-block">type of orthology information to compute the fraction of shared ancestry, either 'hogs' (default) or 'vps'.</p> </div> </div> <hr class="hidden-lg hidden-xl" /> <div class="col-lg-6 response" id="response"> <div class="request-awaiting">Awaiting request</div> <div class="meta hide"> <span class="label label-primary request-method"></span> <code class="request-url"></code> <label class="label label-lg response-status-code pull-right"></label> </div> <pre class="well response-data hide"></pre> <pre class="well response-raw hide"><div class="response-raw-request"></div><div class="response-raw-response"></div></pre> </div> </div> </div> <div class="modal-footer"> <button type="button" class="btn btn-default" data-dismiss="modal">Close</button> <button type="submit" class="btn btn-primary">Send Request</button> </div> </form> </div> </div> </div> <h2 id="synteny" class="coredocs-section-title">synteny <a href="#synteny"><i class="fa fa-link" aria-hidden="true"></i> </a></h2> <div class="row coredocs-link"> <div class="col-md-6 docs-content"> <button class="btn btn-sm btn-success" style="float: right; margin-top: 20px" data-toggle="modal" data-target="#synteny_list_modal"> <i class="fa fa-exchange"></i> Interact </button> <h3 id="synteny-list" class="coredocs-link-title">list <a href="#synteny-list"><i class="fa fa-link" aria-hidden="true"></i> </a></h3> <div class="meta"> <span class="label label-primary">GET</span> <code>/api/synteny/</code> </div> <p><p>List of all the ancestral / extant "contigs" of an ancestral / extant genome.</p> <p>Each contig will contain a graph with all the ancestral genes (HOGs) or the extant genes and their neighbors as edges (order of ancestral/extant genes on "scaffolds/chromosomes")</p> <p>The return value is a list of graph objects that consist of 'nodes' and 'links' attributes.</p> <pre><code>{"nodes": [{"id":"HOG:C0594134.1a", ...}, {"id":"HOG:C0594135.3c", ...}, {"id":"HOG:C0600830.1c.3b", ...}], "links": [{"weight":15,"source":"HOG:C0594134.1a","target":"HOG:C0594135.3c"}, {"weight":15,"source":"HOG:C0594134.1a","target":"HOG:C0600830.1c.3b"}] } </code></pre> <p>For extant genes, the gene IDs are the OMA IDs (e.g. <code>HUMAN00007</code>)</p></p> <h4>Query Parameters</h4> <p>The following parameters should be included as part of a URL query string.</p> <table class="parameters table table-bordered table-striped"> <thead> <tr><th>Parameter</th><th>Description</th></tr> </thead> <tbody> <tr><td class="parameter-name"><code>level</code> <span class="label label-warning">required</span></td><td>The taxonomic level at which the ancestral synteny should be retrieved. The level can be specified with its numeric taxid or the scientific name. For extant genomes, also the UniProt mnemonic species code can be used.</td></tr> <tr><td class="parameter-name"><code>evidence</code></td><td>The evidence value for the ancestral synteny graph. This is used for filtering. The evidence values are `linearized` < `parsimonious` < `any` By default, we only show the linearized graph (Example: linearized, parsimonious, any)</td></tr> <tr><td class="parameter-name"><code>break_circular_contigs</code></td><td>Some ancestral contigs end up being circles. For certain applications this poses a problem. By setting this argument to "yes" (default), the function will break the circle on the weakest edge, with "no" it will return the full linearized graph. Note that this parameter has no effect if the `evidence` parameter is not equal to "linearized".</td></tr> </tbody> </table> </div> <div class="col-md-6 code-samples"> <pre class="highlight shell hide" data-language="shell"><code><span class="c1"># Load the schema document</span> $<span class="w"> </span>coreapi<span class="w"> </span>get<span class="w"> </span>https://omabrowser.org/api/docs <span class="c1"># Interact with the API endpoint</span> $<span class="w"> </span>coreapi<span class="w"> </span>action<span class="w"> </span>synteny<span class="w"> </span>list<span class="w"> </span>-p<span class="w"> </span><span class="nv">level</span><span class="o">=</span>...<span class="w"> </span>-p<span class="w"> </span><span class="nv">evidence</span><span class="o">=</span>...<span class="w"> </span>-p<span class="w"> </span><span class="nv">break_circular_contigs</span><span class="o">=</span>... </code></pre> <pre class="highlight javascript hide" data-language="javascript"><code><span class="kd">var</span><span class="w"> </span><span class="nx">coreapi</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">coreapi</span><span class="w"> </span><span class="c1">// Loaded by `coreapi.js`</span> <span class="kd">var</span><span class="w"> </span><span class="nx">schema</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">schema</span><span class="w"> </span><span class="c1">// Loaded by `schema.js`</span> <span class="c1">// Initialize a client</span> <span class="kd">var</span><span class="w"> </span><span class="nx">client</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="ow">new</span><span class="w"> </span><span class="nx">coreapi</span><span class="p">.</span><span class="nx">Client</span><span class="p">()</span> <span class="c1">// Interact with the API endpoint</span> <span class="kd">var</span><span class="w"> </span><span class="nx">action</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">[</span><span class="s2">"synteny"</span><span class="p">,</span><span class="w"> </span><span class="s2">"list"</span><span class="p">]</span> <span class="kd">var</span><span class="w"> </span><span class="nx">params</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="nx">level</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="w"> </span><span class="nx">evidence</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="w"> </span><span class="nx">break_circular_contigs</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="p">}</span> <span class="nx">client</span><span class="p">.</span><span class="nx">action</span><span class="p">(</span><span class="nx">schema</span><span class="p">,</span><span class="w"> </span><span class="nx">action</span><span class="p">,</span><span class="w"> </span><span class="nx">params</span><span class="p">).</span><span class="nx">then</span><span class="p">(</span><span class="kd">function</span><span class="p">(</span><span class="nx">result</span><span class="p">)</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="c1">// Return value is in 'result'</span> <span class="p">})</span> </code></pre> <pre class="highlight python hide" data-language="python"><code><span class="kn">import</span> <span class="nn">coreapi</span> <span class="c1"># Initialize a client & load the schema document</span> <span class="n">client</span> <span class="o">=</span> <span class="n">coreapi</span><span class="o">.</span><span class="n">Client</span><span class="p">()</span> <span class="n">schema</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"https://omabrowser.org/api/docs"</span><span class="p">)</span> <span class="c1"># Interact with the API endpoint</span> <span class="n">action</span> <span class="o">=</span> <span class="p">[</span><span class="s2">"synteny"</span><span class="p">,</span> <span class="s2">"list"</span><span class="p">]</span> <span class="n">params</span> <span class="o">=</span> <span class="p">{</span> <span class="s2">"level"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="s2">"evidence"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="s2">"break_circular_contigs"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="p">}</span> <span class="n">result</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">action</span><span class="p">(</span><span class="n">schema</span><span class="p">,</span> <span class="n">action</span><span class="p">,</span> <span class="n">params</span><span class="o">=</span><span class="n">params</span><span class="p">)</span> </code></pre> </div> </div> <!-- Modal --> <div class="modal fade api-modal" id="synteny_list_modal" tabindex="-1" role="dialog" aria-labelledby="api explorer modal"> <div class="modal-dialog modal-lg" role="document"> <div class="modal-content"> <div class="modal-header"> <div class="toggle-view hide"> <div class="btn-group" role="group"> <button type="button" data-display-toggle="data" class="btn btn-sm btn-info">Data</button> <button type="button" data-display-toggle="raw" class="btn btn-sm">Raw</button> </div> </div> <h3 class="modal-title"><i class="fa fa-exchange"></i> list</h3> </div> <form data-key='["synteny", "list"]' class="api-interaction"> <div class="modal-body"> <div class="row"> <div class="col-lg-6 request"> <div class="form-group"> <label for="level" class="control-label"> level <span class="text-danger">*</span> </label> <input name="level" class="form-control" data-empty='' data-type='string' required> <p class="help-block">The taxonomic level at which the ancestral synteny should be retrieved. The level can be specified with its numeric taxid or the scientific name. For extant genomes, also the UniProt mnemonic species code can be used.</p> </div> <div class="form-group"> <label for="evidence" class="control-label"> evidence </label> <input name="evidence" class="form-control" data-empty='' data-type='string' > <p class="help-block">The evidence value for the ancestral synteny graph. This is used for filtering. The evidence values are `linearized` < `parsimonious` < `any` By default, we only show the linearized graph (Example: linearized, parsimonious, any)</p> </div> <div class="form-group"> <label for="break_circular_contigs" class="control-label"> break_circular_contigs </label> <input name="break_circular_contigs" class="form-control" data-empty='' data-type='string' > <p class="help-block">Some ancestral contigs end up being circles. For certain applications this poses a problem. By setting this argument to "yes" (default), the function will break the circle on the weakest edge, with "no" it will return the full linearized graph. Note that this parameter has no effect if the `evidence` parameter is not equal to "linearized".</p> </div> </div> <hr class="hidden-lg hidden-xl" /> <div class="col-lg-6 response" id="response"> <div class="request-awaiting">Awaiting request</div> <div class="meta hide"> <span class="label label-primary request-method"></span> <code class="request-url"></code> <label class="label label-lg response-status-code pull-right"></label> </div> <pre class="well response-data hide"></pre> <pre class="well response-raw hide"><div class="response-raw-request"></div><div class="response-raw-response"></div></pre> </div> </div> </div> <div class="modal-footer"> <button type="button" class="btn btn-default" data-dismiss="modal">Close</button> <button type="submit" class="btn btn-primary">Send Request</button> </div> </form> </div> </div> </div> <div class="row coredocs-link"> <div class="col-md-6 docs-content"> <button class="btn btn-sm btn-success" style="float: right; margin-top: 20px" data-toggle="modal" data-target="#synteny_read_modal"> <i class="fa fa-exchange"></i> Interact </button> <h3 id="synteny-read" class="coredocs-link-title">read <a href="#synteny-read"><i class="fa fa-link" aria-hidden="true"></i> </a></h3> <div class="meta"> <span class="label label-primary">GET</span> <code>/api/synteny/{hog_id}/</code> </div> <p><p>Returns the ancestral synteny graph around a reference hog at a given taxonomic level.</p></p> <h4>Path Parameters</h4> <p>The following parameters should be included in the URL path.</p> <table class="parameters table table-bordered table-striped"> <thead> <tr><th>Parameter</th><th>Description</th></tr> </thead> <tbody> <tr><td class="parameter-name"><code>hog_id / protein_id</code> <span class="label label-warning">required</span></td><td>a unique identifier for a hog_group starting with "HOG:" for ancestral synteny levels, or a unique protein ID (e.g. YEAST00012) for an extant species synteny query. (Example: HOG:0450897, HUMAN01330)</td></tr> </tbody> </table> <h4>Query Parameters</h4> <p>The following parameters should be included as part of a URL query string.</p> <table class="parameters table table-bordered table-striped"> <thead> <tr><th>Parameter</th><th>Description</th></tr> </thead> <tbody> <tr><td class="parameter-name"><code>level</code></td><td>the taxonomic level at which the synteny graph should be extracted. If not specified, the deepest level of the given HOG is used. The level can bei either a scientific name or the numeric taxonomy identifier (Example: Primates, 9604)</td></tr> <tr><td class="parameter-name"><code>evidence</code></td><td>The evidence value for the ancestral synteny graph. This is used for filtering. The evidence values are `linearized` < `parsimonious` < `any` (Example: parsimonious)</td></tr> <tr><td class="parameter-name"><code>context</code></td><td>the size of the graph around the query HOG. By default the HOGs which are at most 2 edges apart from the query HOG are returned.</td></tr> <tr><td class="parameter-name"><code>break_circular_contigs</code></td><td>Some ancestral contigs end up being circles. For certain applications this poses a problem. By setting this argument to "yes" (default), the function will break the circle on the weakest edge, with "no" it will return the full linearized graph. Note that this parameter has no effect if the `evidence` parameter is not equal to "linearized".</td></tr> </tbody> </table> </div> <div class="col-md-6 code-samples"> <pre class="highlight shell hide" data-language="shell"><code><span class="c1"># Load the schema document</span> $<span class="w"> </span>coreapi<span class="w"> </span>get<span class="w"> </span>https://omabrowser.org/api/docs <span class="c1"># Interact with the API endpoint</span> $<span class="w"> </span>coreapi<span class="w"> </span>action<span class="w"> </span>synteny<span class="w"> </span><span class="nb">read</span><span class="w"> </span>-p<span class="w"> </span>hog_id<span class="w"> </span>/<span class="w"> </span><span class="nv">protein_id</span><span class="o">=</span>...<span class="w"> </span>-p<span class="w"> </span><span class="nv">level</span><span class="o">=</span>...<span class="w"> </span>-p<span class="w"> </span><span class="nv">evidence</span><span class="o">=</span>...<span class="w"> </span>-p<span class="w"> </span><span class="nv">context</span><span class="o">=</span>...<span class="w"> </span>-p<span class="w"> </span><span class="nv">break_circular_contigs</span><span class="o">=</span>... </code></pre> <pre class="highlight javascript hide" data-language="javascript"><code><span class="kd">var</span><span class="w"> </span><span class="nx">coreapi</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">coreapi</span><span class="w"> </span><span class="c1">// Loaded by `coreapi.js`</span> <span class="kd">var</span><span class="w"> </span><span class="nx">schema</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">schema</span><span class="w"> </span><span class="c1">// Loaded by `schema.js`</span> <span class="c1">// Initialize a client</span> <span class="kd">var</span><span class="w"> </span><span class="nx">client</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="ow">new</span><span class="w"> </span><span class="nx">coreapi</span><span class="p">.</span><span class="nx">Client</span><span class="p">()</span> <span class="c1">// Interact with the API endpoint</span> <span class="kd">var</span><span class="w"> </span><span class="nx">action</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">[</span><span class="s2">"synteny"</span><span class="p">,</span><span class="w"> </span><span class="s2">"read"</span><span class="p">]</span> <span class="kd">var</span><span class="w"> </span><span class="nx">params</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="nx">hog_id</span><span class="w"> </span><span class="o">/</span><span class="w"> </span><span class="nx">protein_id</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="w"> </span><span class="nx">level</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="w"> </span><span class="nx">evidence</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="w"> </span><span class="nx">context</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="w"> </span><span class="nx">break_circular_contigs</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="p">}</span> <span class="nx">client</span><span class="p">.</span><span class="nx">action</span><span class="p">(</span><span class="nx">schema</span><span class="p">,</span><span class="w"> </span><span class="nx">action</span><span class="p">,</span><span class="w"> </span><span class="nx">params</span><span class="p">).</span><span class="nx">then</span><span class="p">(</span><span class="kd">function</span><span class="p">(</span><span class="nx">result</span><span class="p">)</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="c1">// Return value is in 'result'</span> <span class="p">})</span> </code></pre> <pre class="highlight python hide" data-language="python"><code><span class="kn">import</span> <span class="nn">coreapi</span> <span class="c1"># Initialize a client & load the schema document</span> <span class="n">client</span> <span class="o">=</span> <span class="n">coreapi</span><span class="o">.</span><span class="n">Client</span><span class="p">()</span> <span class="n">schema</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"https://omabrowser.org/api/docs"</span><span class="p">)</span> <span class="c1"># Interact with the API endpoint</span> <span class="n">action</span> <span class="o">=</span> <span class="p">[</span><span class="s2">"synteny"</span><span class="p">,</span> <span class="s2">"read"</span><span class="p">]</span> <span class="n">params</span> <span class="o">=</span> <span class="p">{</span> <span class="s2">"hog_id / protein_id"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="s2">"level"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="s2">"evidence"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="s2">"context"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="s2">"break_circular_contigs"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="p">}</span> <span class="n">result</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">action</span><span class="p">(</span><span class="n">schema</span><span class="p">,</span> <span class="n">action</span><span class="p">,</span> <span class="n">params</span><span class="o">=</span><span class="n">params</span><span class="p">)</span> </code></pre> </div> </div> <!-- Modal --> <div class="modal fade api-modal" id="synteny_read_modal" tabindex="-1" role="dialog" aria-labelledby="api explorer modal"> <div class="modal-dialog modal-lg" role="document"> <div class="modal-content"> <div class="modal-header"> <div class="toggle-view hide"> <div class="btn-group" role="group"> <button type="button" data-display-toggle="data" class="btn btn-sm btn-info">Data</button> <button type="button" data-display-toggle="raw" class="btn btn-sm">Raw</button> </div> </div> <h3 class="modal-title"><i class="fa fa-exchange"></i> read</h3> </div> <form data-key='["synteny", "read"]' class="api-interaction"> <div class="modal-body"> <div class="row"> <div class="col-lg-6 request"> <div class="form-group"> <label for="hog_id / protein_id" class="control-label"> hog_id / protein_id <span class="text-danger">*</span> </label> <input name="hog_id / protein_id" class="form-control" data-empty='' data-type='string' required> <p class="help-block">a unique identifier for a hog_group starting with "HOG:" for ancestral synteny levels, or a unique protein ID (e.g. YEAST00012) for an extant species synteny query. (Example: HOG:0450897, HUMAN01330)</p> </div> <div class="form-group"> <label for="level" class="control-label"> level </label> <input name="level" class="form-control" data-empty='' data-type='string' > <p class="help-block">the taxonomic level at which the synteny graph should be extracted. If not specified, the deepest level of the given HOG is used. The level can bei either a scientific name or the numeric taxonomy identifier (Example: Primates, 9604)</p> </div> <div class="form-group"> <label for="evidence" class="control-label"> evidence </label> <input name="evidence" class="form-control" data-empty='' data-type='string' > <p class="help-block">The evidence value for the ancestral synteny graph. This is used for filtering. The evidence values are `linearized` < `parsimonious` < `any` (Example: parsimonious)</p> </div> <div class="form-group"> <label for="context" class="control-label"> context </label> <input name="context" class="form-control" data-empty='' data-type='string' > <p class="help-block">the size of the graph around the query HOG. By default the HOGs which are at most 2 edges apart from the query HOG are returned.</p> </div> <div class="form-group"> <label for="break_circular_contigs" class="control-label"> break_circular_contigs </label> <input name="break_circular_contigs" class="form-control" data-empty='' data-type='string' > <p class="help-block">Some ancestral contigs end up being circles. For certain applications this poses a problem. By setting this argument to "yes" (default), the function will break the circle on the weakest edge, with "no" it will return the full linearized graph. Note that this parameter has no effect if the `evidence` parameter is not equal to "linearized".</p> </div> </div> <hr class="hidden-lg hidden-xl" /> <div class="col-lg-6 response" id="response"> <div class="request-awaiting">Awaiting request</div> <div class="meta hide"> <span class="label label-primary request-method"></span> <code class="request-url"></code> <label class="label label-lg response-status-code pull-right"></label> </div> <pre class="well response-data hide"></pre> <pre class="well response-raw hide"><div class="response-raw-request"></div><div class="response-raw-response"></div></pre> </div> </div> </div> <div class="modal-footer"> <button type="button" class="btn btn-default" data-dismiss="modal">Close</button> <button type="submit" class="btn btn-primary">Send Request</button> </div> </form> </div> </div> </div> <h2 id="taxonomy" class="coredocs-section-title">taxonomy <a href="#taxonomy"><i class="fa fa-link" aria-hidden="true"></i> </a></h2> <div class="row coredocs-link"> <div class="col-md-6 docs-content"> <button class="btn btn-sm btn-success" style="float: right; margin-top: 20px" data-toggle="modal" data-target="#taxonomy_list_modal"> <i class="fa fa-exchange"></i> Interact </button> <h3 id="taxonomy-list" class="coredocs-link-title">list <a href="#taxonomy-list"><i class="fa fa-link" aria-hidden="true"></i> </a></h3> <div class="meta"> <span class="label label-primary">GET</span> <code>/api/taxonomy/</code> </div> <p><p>Retrieve the taxonomic tree that is available in the current release.</p></p> <h4>Query Parameters</h4> <p>The following parameters should be included as part of a URL query string.</p> <table class="parameters table table-bordered table-striped"> <thead> <tr><th>Parameter</th><th>Description</th></tr> </thead> <tbody> <tr><td class="parameter-name"><code>type</code></td><td>the type of the returned data - either dictionary (default), newick or phyloxml.</td></tr> <tr><td class="parameter-name"><code>members</code></td><td>list of members to get the induced taxonomy from. The list is supposed to be a comma-separated list. Member IDs can be either their ncbi taxon IDs or their UniProt species codes - they just have to be consistent.</td></tr> <tr><td class="parameter-name"><code>collapse</code></td><td>whether or not taxonomic levels with a single child should be collapsed or not. Defaults to yes.</td></tr> <tr><td class="parameter-name"><code>newick_leaf_label</code></td><td>type of data to store in the leaf nodes of the newick tree. Must be one of ("sciname", "species_code") Defaults to "sciname" if not specified.</td></tr> <tr><td class="parameter-name"><code>newick_internal_label</code></td><td>type of data to store in the internal nodes of the newick tree. Must be one of ("sciname", "taxid" or "None"). Defaults to "sciname" if not specified.</td></tr> <tr><td class="parameter-name"><code>newick_quote_labels</code></td><td>Whether or not to quote the labels in the newick tree. If not, spaces are replaced by '_' characters. Defaults to no.</td></tr> </tbody> </table> </div> <div class="col-md-6 code-samples"> <pre class="highlight shell hide" data-language="shell"><code><span class="c1"># Load the schema document</span> $<span class="w"> </span>coreapi<span class="w"> </span>get<span class="w"> </span>https://omabrowser.org/api/docs <span class="c1"># Interact with the API endpoint</span> $<span class="w"> </span>coreapi<span class="w"> </span>action<span class="w"> </span>taxonomy<span class="w"> </span>list<span class="w"> </span>-p<span class="w"> </span><span class="nv">type</span><span class="o">=</span>...<span class="w"> </span>-p<span class="w"> </span><span class="nv">members</span><span class="o">=</span>...<span class="w"> </span>-p<span class="w"> </span><span class="nv">collapse</span><span class="o">=</span>...<span class="w"> </span>-p<span class="w"> </span><span class="nv">newick_leaf_label</span><span class="o">=</span>...<span class="w"> </span>-p<span class="w"> </span><span class="nv">newick_internal_label</span><span class="o">=</span>...<span class="w"> </span>-p<span class="w"> </span><span class="nv">newick_quote_labels</span><span class="o">=</span>... </code></pre> <pre class="highlight javascript hide" data-language="javascript"><code><span class="kd">var</span><span class="w"> </span><span class="nx">coreapi</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">coreapi</span><span class="w"> </span><span class="c1">// Loaded by `coreapi.js`</span> <span class="kd">var</span><span class="w"> </span><span class="nx">schema</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">schema</span><span class="w"> </span><span class="c1">// Loaded by `schema.js`</span> <span class="c1">// Initialize a client</span> <span class="kd">var</span><span class="w"> </span><span class="nx">client</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="ow">new</span><span class="w"> </span><span class="nx">coreapi</span><span class="p">.</span><span class="nx">Client</span><span class="p">()</span> <span class="c1">// Interact with the API endpoint</span> <span class="kd">var</span><span class="w"> </span><span class="nx">action</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">[</span><span class="s2">"taxonomy"</span><span class="p">,</span><span class="w"> </span><span class="s2">"list"</span><span class="p">]</span> <span class="kd">var</span><span class="w"> </span><span class="nx">params</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="nx">type</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="w"> </span><span class="nx">members</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="w"> </span><span class="nx">collapse</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="w"> </span><span class="nx">newick_leaf_label</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="w"> </span><span class="nx">newick_internal_label</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="w"> </span><span class="nx">newick_quote_labels</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="p">}</span> <span class="nx">client</span><span class="p">.</span><span class="nx">action</span><span class="p">(</span><span class="nx">schema</span><span class="p">,</span><span class="w"> </span><span class="nx">action</span><span class="p">,</span><span class="w"> </span><span class="nx">params</span><span class="p">).</span><span class="nx">then</span><span class="p">(</span><span class="kd">function</span><span class="p">(</span><span class="nx">result</span><span class="p">)</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="c1">// Return value is in 'result'</span> <span class="p">})</span> </code></pre> <pre class="highlight python hide" data-language="python"><code><span class="kn">import</span> <span class="nn">coreapi</span> <span class="c1"># Initialize a client & load the schema document</span> <span class="n">client</span> <span class="o">=</span> <span class="n">coreapi</span><span class="o">.</span><span class="n">Client</span><span class="p">()</span> <span class="n">schema</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"https://omabrowser.org/api/docs"</span><span class="p">)</span> <span class="c1"># Interact with the API endpoint</span> <span class="n">action</span> <span class="o">=</span> <span class="p">[</span><span class="s2">"taxonomy"</span><span class="p">,</span> <span class="s2">"list"</span><span class="p">]</span> <span class="n">params</span> <span class="o">=</span> <span class="p">{</span> <span class="s2">"type"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="s2">"members"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="s2">"collapse"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="s2">"newick_leaf_label"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="s2">"newick_internal_label"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="s2">"newick_quote_labels"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="p">}</span> <span class="n">result</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">action</span><span class="p">(</span><span class="n">schema</span><span class="p">,</span> <span class="n">action</span><span class="p">,</span> <span class="n">params</span><span class="o">=</span><span class="n">params</span><span class="p">)</span> </code></pre> </div> </div> <!-- Modal --> <div class="modal fade api-modal" id="taxonomy_list_modal" tabindex="-1" role="dialog" aria-labelledby="api explorer modal"> <div class="modal-dialog modal-lg" role="document"> <div class="modal-content"> <div class="modal-header"> <div class="toggle-view hide"> <div class="btn-group" role="group"> <button type="button" data-display-toggle="data" class="btn btn-sm btn-info">Data</button> <button type="button" data-display-toggle="raw" class="btn btn-sm">Raw</button> </div> </div> <h3 class="modal-title"><i class="fa fa-exchange"></i> list</h3> </div> <form data-key='["taxonomy", "list"]' class="api-interaction"> <div class="modal-body"> <div class="row"> <div class="col-lg-6 request"> <div class="form-group"> <label for="type" class="control-label"> type </label> <input name="type" class="form-control" data-empty='' data-type='string' > <p class="help-block">the type of the returned data - either dictionary (default), newick or phyloxml.</p> </div> <div class="form-group"> <label for="members" class="control-label"> members </label> <input name="members" class="form-control" data-empty='' data-type='string' > <p class="help-block">list of members to get the induced taxonomy from. The list is supposed to be a comma-separated list. Member IDs can be either their ncbi taxon IDs or their UniProt species codes - they just have to be consistent.</p> </div> <div class="form-group"> <div class="checkbox"> <label class="control-label"> <input type="checkbox" name="collapse" value="true" data-empty=false data-type='boolean'> collapse </label> </div> <span class="help-block">whether or not taxonomic levels with a single child should be collapsed or not. Defaults to yes.</span> </div> <div class="form-group"> <label for="newick_leaf_label" class="control-label"> newick_leaf_label </label> <input name="newick_leaf_label" class="form-control" data-empty='' data-type='string' > <p class="help-block">type of data to store in the leaf nodes of the newick tree. Must be one of ("sciname", "species_code") Defaults to "sciname" if not specified.</p> </div> <div class="form-group"> <label for="newick_internal_label" class="control-label"> newick_internal_label </label> <input name="newick_internal_label" class="form-control" data-empty='' data-type='string' > <p class="help-block">type of data to store in the internal nodes of the newick tree. Must be one of ("sciname", "taxid" or "None"). Defaults to "sciname" if not specified.</p> </div> <div class="form-group"> <div class="checkbox"> <label class="control-label"> <input type="checkbox" name="newick_quote_labels" value="true" data-empty=false data-type='boolean'> newick_quote_labels </label> </div> <span class="help-block">Whether or not to quote the labels in the newick tree. If not, spaces are replaced by '_' characters. Defaults to no.</span> </div> </div> <hr class="hidden-lg hidden-xl" /> <div class="col-lg-6 response" id="response"> <div class="request-awaiting">Awaiting request</div> <div class="meta hide"> <span class="label label-primary request-method"></span> <code class="request-url"></code> <label class="label label-lg response-status-code pull-right"></label> </div> <pre class="well response-data hide"></pre> <pre class="well response-raw hide"><div class="response-raw-request"></div><div class="response-raw-response"></div></pre> </div> </div> </div> <div class="modal-footer"> <button type="button" class="btn btn-default" data-dismiss="modal">Close</button> <button type="submit" class="btn btn-primary">Send Request</button> </div> </form> </div> </div> </div> <div class="row coredocs-link"> <div class="col-md-6 docs-content"> <button class="btn btn-sm btn-success" style="float: right; margin-top: 20px" data-toggle="modal" data-target="#taxonomy_read_modal"> <i class="fa fa-exchange"></i> Interact </button> <h3 id="taxonomy-read" class="coredocs-link-title">read <a href="#taxonomy-read"><i class="fa fa-link" aria-hidden="true"></i> </a></h3> <div class="meta"> <span class="label label-primary">GET</span> <code>/api/taxonomy/{root_id}/</code> </div> <p><p>Retrieve the subtree rooted at the taxonomic level indicated.</p></p> <h4>Path Parameters</h4> <p>The following parameters should be included in the URL path.</p> <table class="parameters table table-bordered table-striped"> <thead> <tr><th>Parameter</th><th>Description</th></tr> </thead> <tbody> <tr><td class="parameter-name"><code>root_id</code> <span class="label label-warning">required</span></td><td>either the taxon id, species name or the 5 letter UniProt species code for a root taxonomic level</td></tr> </tbody> </table> <h4>Query Parameters</h4> <p>The following parameters should be included as part of a URL query string.</p> <table class="parameters table table-bordered table-striped"> <thead> <tr><th>Parameter</th><th>Description</th></tr> </thead> <tbody> <tr><td class="parameter-name"><code>type</code></td><td>the type of the returned data - either dictionary (default) or newick.</td></tr> <tr><td class="parameter-name"><code>collapse</code></td><td>whether or not taxonomic levels with a single child should be collapsed or not. Defaults to yes.</td></tr> </tbody> </table> </div> <div class="col-md-6 code-samples"> <pre class="highlight shell hide" data-language="shell"><code><span class="c1"># Load the schema document</span> $<span class="w"> </span>coreapi<span class="w"> </span>get<span class="w"> </span>https://omabrowser.org/api/docs <span class="c1"># Interact with the API endpoint</span> $<span class="w"> </span>coreapi<span class="w"> </span>action<span class="w"> </span>taxonomy<span class="w"> </span><span class="nb">read</span><span class="w"> </span>-p<span class="w"> </span><span class="nv">root_id</span><span class="o">=</span>...<span class="w"> </span>-p<span class="w"> </span><span class="nv">type</span><span class="o">=</span>...<span class="w"> </span>-p<span class="w"> </span><span class="nv">collapse</span><span class="o">=</span>... </code></pre> <pre class="highlight javascript hide" data-language="javascript"><code><span class="kd">var</span><span class="w"> </span><span class="nx">coreapi</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">coreapi</span><span class="w"> </span><span class="c1">// Loaded by `coreapi.js`</span> <span class="kd">var</span><span class="w"> </span><span class="nx">schema</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">schema</span><span class="w"> </span><span class="c1">// Loaded by `schema.js`</span> <span class="c1">// Initialize a client</span> <span class="kd">var</span><span class="w"> </span><span class="nx">client</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="ow">new</span><span class="w"> </span><span class="nx">coreapi</span><span class="p">.</span><span class="nx">Client</span><span class="p">()</span> <span class="c1">// Interact with the API endpoint</span> <span class="kd">var</span><span class="w"> </span><span class="nx">action</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">[</span><span class="s2">"taxonomy"</span><span class="p">,</span><span class="w"> </span><span class="s2">"read"</span><span class="p">]</span> <span class="kd">var</span><span class="w"> </span><span class="nx">params</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="nx">root_id</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="w"> </span><span class="nx">type</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="w"> </span><span class="nx">collapse</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="p">}</span> <span class="nx">client</span><span class="p">.</span><span class="nx">action</span><span class="p">(</span><span class="nx">schema</span><span class="p">,</span><span class="w"> </span><span class="nx">action</span><span class="p">,</span><span class="w"> </span><span class="nx">params</span><span class="p">).</span><span class="nx">then</span><span class="p">(</span><span class="kd">function</span><span class="p">(</span><span class="nx">result</span><span class="p">)</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="c1">// Return value is in 'result'</span> <span class="p">})</span> </code></pre> <pre class="highlight python hide" data-language="python"><code><span class="kn">import</span> <span class="nn">coreapi</span> <span class="c1"># Initialize a client & load the schema document</span> <span class="n">client</span> <span class="o">=</span> <span class="n">coreapi</span><span class="o">.</span><span class="n">Client</span><span class="p">()</span> <span class="n">schema</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"https://omabrowser.org/api/docs"</span><span class="p">)</span> <span class="c1"># Interact with the API endpoint</span> <span class="n">action</span> <span class="o">=</span> <span class="p">[</span><span class="s2">"taxonomy"</span><span class="p">,</span> <span class="s2">"read"</span><span class="p">]</span> <span class="n">params</span> <span class="o">=</span> <span class="p">{</span> <span class="s2">"root_id"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="s2">"type"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="s2">"collapse"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="p">}</span> <span class="n">result</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">action</span><span class="p">(</span><span class="n">schema</span><span class="p">,</span> <span class="n">action</span><span class="p">,</span> <span class="n">params</span><span class="o">=</span><span class="n">params</span><span class="p">)</span> </code></pre> </div> </div> <!-- Modal --> <div class="modal fade api-modal" id="taxonomy_read_modal" tabindex="-1" role="dialog" aria-labelledby="api explorer modal"> <div class="modal-dialog modal-lg" role="document"> <div class="modal-content"> <div class="modal-header"> <div class="toggle-view hide"> <div class="btn-group" role="group"> <button type="button" data-display-toggle="data" class="btn btn-sm btn-info">Data</button> <button type="button" data-display-toggle="raw" class="btn btn-sm">Raw</button> </div> </div> <h3 class="modal-title"><i class="fa fa-exchange"></i> read</h3> </div> <form data-key='["taxonomy", "read"]' class="api-interaction"> <div class="modal-body"> <div class="row"> <div class="col-lg-6 request"> <div class="form-group"> <label for="root_id" class="control-label"> root_id <span class="text-danger">*</span> </label> <input name="root_id" class="form-control" data-empty='' data-type='string' required> <p class="help-block">either the taxon id, species name or the 5 letter UniProt species code for a root taxonomic level</p> </div> <div class="form-group"> <label for="type" class="control-label"> type </label> <input name="type" class="form-control" data-empty='' data-type='string' > <p class="help-block">the type of the returned data - either dictionary (default) or newick.</p> </div> <div class="form-group"> <div class="checkbox"> <label class="control-label"> <input type="checkbox" name="collapse" value="true" data-empty=false data-type='boolean'> collapse </label> </div> <span class="help-block">whether or not taxonomic levels with a single child should be collapsed or not. Defaults to yes.</span> </div> </div> <hr class="hidden-lg hidden-xl" /> <div class="col-lg-6 response" id="response"> <div class="request-awaiting">Awaiting request</div> <div class="meta hide"> <span class="label label-primary request-method"></span> <code class="request-url"></code> <label class="label label-lg response-status-code pull-right"></label> </div> <pre class="well response-data hide"></pre> <pre class="well response-raw hide"><div class="response-raw-request"></div><div class="response-raw-response"></div></pre> </div> </div> </div> <div class="modal-footer"> <button type="button" class="btn btn-default" data-dismiss="modal">Close</button> <button type="submit" class="btn btn-primary">Send Request</button> </div> </form> </div> </div> </div> <h2 id="version" class="coredocs-section-title">version <a href="#version"><i class="fa fa-link" aria-hidden="true"></i> </a></h2> <div class="row coredocs-link"> <div class="col-md-6 docs-content"> <button class="btn btn-sm btn-success" style="float: right; margin-top: 20px" data-toggle="modal" data-target="#version_list_modal"> <i class="fa fa-exchange"></i> Interact </button> <h3 id="version-list" class="coredocs-link-title">list <a href="#version-list"><i class="fa fa-link" aria-hidden="true"></i> </a></h3> <div class="meta"> <span class="label label-primary">GET</span> <code>/api/version/</code> </div> <p><p>Returns the version information of the api and the underlying oma browser database release.</p></p> </div> <div class="col-md-6 code-samples"> <pre class="highlight shell hide" data-language="shell"><code><span class="c1"># Load the schema document</span> $<span class="w"> </span>coreapi<span class="w"> </span>get<span class="w"> </span>https://omabrowser.org/api/docs <span class="c1"># Interact with the API endpoint</span> $<span class="w"> </span>coreapi<span class="w"> </span>action<span class="w"> </span>version<span class="w"> </span>list </code></pre> <pre class="highlight javascript hide" data-language="javascript"><code><span class="kd">var</span><span class="w"> </span><span class="nx">coreapi</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">coreapi</span><span class="w"> </span><span class="c1">// Loaded by `coreapi.js`</span> <span class="kd">var</span><span class="w"> </span><span class="nx">schema</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">schema</span><span class="w"> </span><span class="c1">// Loaded by `schema.js`</span> <span class="c1">// Initialize a client</span> <span class="kd">var</span><span class="w"> </span><span class="nx">client</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="ow">new</span><span class="w"> </span><span class="nx">coreapi</span><span class="p">.</span><span class="nx">Client</span><span class="p">()</span> <span class="c1">// Interact with the API endpoint</span> <span class="kd">var</span><span class="w"> </span><span class="nx">action</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">[</span><span class="s2">"version"</span><span class="p">,</span><span class="w"> </span><span class="s2">"list"</span><span class="p">]</span> <span class="nx">client</span><span class="p">.</span><span class="nx">action</span><span class="p">(</span><span class="nx">schema</span><span class="p">,</span><span class="w"> </span><span class="nx">action</span><span class="p">).</span><span class="nx">then</span><span class="p">(</span><span class="kd">function</span><span class="p">(</span><span class="nx">result</span><span class="p">)</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="c1">// Return value is in 'result'</span> <span class="p">})</span> </code></pre> <pre class="highlight python hide" data-language="python"><code><span class="kn">import</span> <span class="nn">coreapi</span> <span class="c1"># Initialize a client & load the schema document</span> <span class="n">client</span> <span class="o">=</span> <span class="n">coreapi</span><span class="o">.</span><span class="n">Client</span><span class="p">()</span> <span class="n">schema</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"https://omabrowser.org/api/docs"</span><span class="p">)</span> <span class="c1"># Interact with the API endpoint</span> <span class="n">action</span> <span class="o">=</span> <span class="p">[</span><span class="s2">"version"</span><span class="p">,</span> <span class="s2">"list"</span><span class="p">]</span> <span class="n">result</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">action</span><span class="p">(</span><span class="n">schema</span><span class="p">,</span> <span class="n">action</span><span class="p">)</span> </code></pre> </div> </div> <!-- Modal --> <div class="modal fade api-modal" id="version_list_modal" tabindex="-1" role="dialog" aria-labelledby="api explorer modal"> <div class="modal-dialog modal-lg" role="document"> <div class="modal-content"> <div class="modal-header"> <div class="toggle-view hide"> <div class="btn-group" role="group"> <button type="button" data-display-toggle="data" class="btn btn-sm btn-info">Data</button> <button type="button" data-display-toggle="raw" class="btn btn-sm">Raw</button> </div> </div> <h3 class="modal-title"><i class="fa fa-exchange"></i> list</h3> </div> <form data-key='["version", "list"]' class="api-interaction"> <div class="modal-body"> <div class="row"> <div class="col-lg-6 request"> </div> <hr class="hidden-lg hidden-xl" /> <div class="col-lg-6 response" id="response"> <div class="request-awaiting">Awaiting request</div> <div class="meta hide"> <span class="label label-primary request-method"></span> <code class="request-url"></code> <label class="label label-lg response-status-code pull-right"></label> </div> <pre class="well response-data hide"></pre> <pre class="well response-raw hide"><div class="response-raw-request"></div><div class="response-raw-response"></div></pre> </div> </div> </div> <div class="modal-footer"> <button type="button" class="btn btn-default" data-dismiss="modal">Close</button> <button type="submit" class="btn btn-primary">Send Request</button> </div> </form> </div> </div> </div> <h2 id="xref" class="coredocs-section-title">xref <a href="#xref"><i class="fa fa-link" aria-hidden="true"></i> </a></h2> <div class="row coredocs-link"> <div class="col-md-6 docs-content"> <button class="btn btn-sm btn-success" style="float: right; margin-top: 20px" data-toggle="modal" data-target="#xref_list_modal"> <i class="fa fa-exchange"></i> Interact </button> <h3 id="xref-list" class="coredocs-link-title">list <a href="#xref-list"><i class="fa fa-link" aria-hidden="true"></i> </a></h3> <div class="meta"> <span class="label label-primary">GET</span> <code>/api/xref/</code> </div> <p><p>List all the crossreferences that match a certain pattern.</p></p> <h4>Query Parameters</h4> <p>The following parameters should be included as part of a URL query string.</p> <table class="parameters table table-bordered table-striped"> <thead> <tr><th>Parameter</th><th>Description</th></tr> </thead> <tbody> <tr><td class="parameter-name"><code>search</code></td><td>the pattern to be searched for. The pattern must be at least 3 characters long in order to return a hit.</td></tr> </tbody> </table> </div> <div class="col-md-6 code-samples"> <pre class="highlight shell hide" data-language="shell"><code><span class="c1"># Load the schema document</span> $<span class="w"> </span>coreapi<span class="w"> </span>get<span class="w"> </span>https://omabrowser.org/api/docs <span class="c1"># Interact with the API endpoint</span> $<span class="w"> </span>coreapi<span class="w"> </span>action<span class="w"> </span>xref<span class="w"> </span>list<span class="w"> </span>-p<span class="w"> </span><span class="nv">search</span><span class="o">=</span>... </code></pre> <pre class="highlight javascript hide" data-language="javascript"><code><span class="kd">var</span><span class="w"> </span><span class="nx">coreapi</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">coreapi</span><span class="w"> </span><span class="c1">// Loaded by `coreapi.js`</span> <span class="kd">var</span><span class="w"> </span><span class="nx">schema</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nb">window</span><span class="p">.</span><span class="nx">schema</span><span class="w"> </span><span class="c1">// Loaded by `schema.js`</span> <span class="c1">// Initialize a client</span> <span class="kd">var</span><span class="w"> </span><span class="nx">client</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="ow">new</span><span class="w"> </span><span class="nx">coreapi</span><span class="p">.</span><span class="nx">Client</span><span class="p">()</span> <span class="c1">// Interact with the API endpoint</span> <span class="kd">var</span><span class="w"> </span><span class="nx">action</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">[</span><span class="s2">"xref"</span><span class="p">,</span><span class="w"> </span><span class="s2">"list"</span><span class="p">]</span> <span class="kd">var</span><span class="w"> </span><span class="nx">params</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="nx">search</span><span class="o">:</span><span class="w"> </span><span class="p">...,</span> <span class="p">}</span> <span class="nx">client</span><span class="p">.</span><span class="nx">action</span><span class="p">(</span><span class="nx">schema</span><span class="p">,</span><span class="w"> </span><span class="nx">action</span><span class="p">,</span><span class="w"> </span><span class="nx">params</span><span class="p">).</span><span class="nx">then</span><span class="p">(</span><span class="kd">function</span><span class="p">(</span><span class="nx">result</span><span class="p">)</span><span class="w"> </span><span class="p">{</span> <span class="w"> </span><span class="c1">// Return value is in 'result'</span> <span class="p">})</span> </code></pre> <pre class="highlight python hide" data-language="python"><code><span class="kn">import</span> <span class="nn">coreapi</span> <span class="c1"># Initialize a client & load the schema document</span> <span class="n">client</span> <span class="o">=</span> <span class="n">coreapi</span><span class="o">.</span><span class="n">Client</span><span class="p">()</span> <span class="n">schema</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"https://omabrowser.org/api/docs"</span><span class="p">)</span> <span class="c1"># Interact with the API endpoint</span> <span class="n">action</span> <span class="o">=</span> <span class="p">[</span><span class="s2">"xref"</span><span class="p">,</span> <span class="s2">"list"</span><span class="p">]</span> <span class="n">params</span> <span class="o">=</span> <span class="p">{</span> <span class="s2">"search"</span><span class="p">:</span> <span class="o">...</span><span class="p">,</span> <span class="p">}</span> <span class="n">result</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">action</span><span class="p">(</span><span class="n">schema</span><span class="p">,</span> <span class="n">action</span><span class="p">,</span> <span class="n">params</span><span class="o">=</span><span class="n">params</span><span class="p">)</span> </code></pre> </div> </div> <!-- Modal --> <div class="modal fade api-modal" id="xref_list_modal" tabindex="-1" role="dialog" aria-labelledby="api explorer modal"> <div class="modal-dialog modal-lg" role="document"> <div class="modal-content"> <div class="modal-header"> <div class="toggle-view hide"> <div class="btn-group" role="group"> <button type="button" data-display-toggle="data" class="btn btn-sm btn-info">Data</button> <button type="button" data-display-toggle="raw" class="btn btn-sm">Raw</button> </div> </div> <h3 class="modal-title"><i class="fa fa-exchange"></i> list</h3> </div> <form data-key='["xref", "list"]' class="api-interaction"> <div class="modal-body"> <div class="row"> <div class="col-lg-6 request"> <div class="form-group"> <label for="search" class="control-label"> search </label> <input name="search" class="form-control" data-empty='' data-type='string' > <p class="help-block">the pattern to be searched for. The pattern must be at least 3 characters long in order to return a hit.</p> </div> </div> <hr class="hidden-lg hidden-xl" /> <div class="col-lg-6 response" id="response"> <div class="request-awaiting">Awaiting request</div> <div class="meta hide"> <span class="label label-primary request-method"></span> <code class="request-url"></code> <label class="label label-lg response-status-code pull-right"></label> </div> <pre class="well response-data hide"></pre> <pre class="well response-raw hide"><div class="response-raw-request"></div><div class="response-raw-response"></div></pre> </div> </div> </div> <div class="modal-footer"> <button type="button" class="btn btn-default" data-dismiss="modal">Close</button> <button type="submit" class="btn btn-primary">Send Request</button> </div> </form> </div> </div> </div> </div> </div> </div> <!-- Modal --> <div class="modal fade auth-modal auth-token" id="auth_token_modal" tabindex="-1" role="dialog" aria-labelledby="token authentication modal"> <div class="modal-dialog modal-md" role="document"> <div class="modal-content"> <div class="modal-header"> <h3 class="modal-title"><i class="fa fa-key"></i> Token Authentication</h3> </div> <form class="form-horizontal authentication-token-form"> <div class="modal-body"> <div class="form-group"> <label for="prefix" class="col-sm-2 control-label">Scheme:</label> <div class="col-sm-10"> <input type="text" class="form-control" id="scheme" placeholder="Bearer" aria-describedby="schemeHelpBlock" required> <span id="schemeHelpBlock" class="help-block">Either a registered authentication scheme such as <code>Bearer</code>, or a custom schema such as <code>Token</code> or <code>JWT</code>.</span> </div> </div> <div class="form-group"> <label for="token" class="col-sm-2 control-label">Token:</label> <div class="col-sm-10"> <input type="text" class="form-control" id="token" placeholder="XXXX-XXXX-XXXX-XXXX" aria-describedby="helpBlock" required> <span id="tokenHelpBlock" class="help-block">A valid API token.</span> </div> </div> </div> <div class="modal-footer"> <button type="button" class="btn btn-default" data-dismiss="modal">Close</button> <button type="submit" class="btn btn-primary">Use Token Authentication</button> </div> </form> </div> </div> </div> <!-- Modal --> <div class="modal fade auth-modal auth-basic" id="auth_basic_modal" tabindex="-1" role="dialog" aria-labelledby="basic authentication modal"> <div class="modal-dialog modal-md" role="document"> <div class="modal-content"> <div class="modal-header"> <h3 class="modal-title"><i class="fa fa-key"></i> Basic Authentication</h3> </div> <form class="form-horizontal authentication-basic-form"> <div class="modal-body"> <div class="form-group"> <label for="authorization" class="col-sm-2 control-label">Username:</label> <div class="col-sm-10"> <input type="text" class="form-control" id="username" required> </div> </div> <div class="form-group"> <label for="authorization" class="col-sm-2 control-label">Password:</label> <div class="col-sm-10"> <input type="password" class="form-control" id="password" required> </div> </div> </div> <div class="modal-footer"> <button type="button" class="btn btn-default" data-dismiss="modal">Close</button> <button type="submit" class="btn btn-primary">Use Basic Authentication</button> </div> </form> </div> </div> </div> <!-- Modal --> <div class="modal fade auth-modal auth-session" id="auth_session_modal" tabindex="-1" role="dialog" aria-labelledby="session authentication modal"> <div class="modal-dialog modal-md" role="document"> <div class="modal-content"> <div class="modal-header"> <h3 class="modal-title"><i class="fa fa-key"></i> Session Authentication</h3> </div> <form class="form-horizontal authentication-session-form"> <div class="modal-body"> <div class="text-center"> <h4 class="text-center">You need to log in to enable Session Authentication.</h4> </div> </div> <div class="modal-footer"> <button type="button" class="btn btn-default" data-dismiss="modal">Close</button> </div> </form> </div> </div> </div> <script src="/static/rest_framework/js/jquery-3.5.1.min.js"></script> <script src="/static/rest_framework/js/bootstrap.min.js"></script> <script src="/static/rest_framework/docs/js/jquery.json-view.min.js"></script> <script src="/static/rest_framework/docs/js/api.js"></script> <script> $('pre.highlight').filter('[data-language="shell"]').removeClass('hide'); </script> </body> </html>