667 lines
No EOL
35 KiB
HTML
667 lines
No EOL
35 KiB
HTML
<!DOCTYPE html>
|
||
|
||
|
||
|
||
|
||
<html lang="en" >
|
||
<head >
|
||
<meta charset="UTF-8">
|
||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||
|
||
<!-- Mobile properties -->
|
||
<meta name="HandheldFriendly" content="True">
|
||
<meta name="MobileOptimized" content="320">
|
||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||
|
||
|
||
<!-- Stylesheets -->
|
||
|
||
<link href="/pathogens/static/django_uswds/uswds/css/uswds.css" rel="stylesheet" />
|
||
|
||
|
||
|
||
<link rel="stylesheet" href="/pathogens/static/nwds/css/nwds.css" />
|
||
<link rel="stylesheet" href="/pathogens/static/nwds/css/header.css" />
|
||
<link rel="stylesheet" href="/pathogens/static/nwds/css/footer.css" />
|
||
<link rel="stylesheet" href="/pathogens/static/nwds/css/form.css" />
|
||
|
||
|
||
|
||
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/font-awesome/4.7.0/css/font-awesome.min.css"/>
|
||
|
||
|
||
|
||
<title>
|
||
Getting started with BigQuery -
|
||
Pathogen Detection - NCBI
|
||
|
||
</title>
|
||
|
||
|
||
|
||
<!-- extra head -->
|
||
|
||
<!-- Favicons -->
|
||
<link rel="shortcut icon" type="image/ico" href="https://www.ncbi.nlm.nih.gov/coreutils/nwds/img/favicons/favicon.ico" />
|
||
<link rel="icon" type="image/png" href="https://www.ncbi.nlm.nih.gov/coreutils/nwds/img/favicons/favicon.png" />
|
||
|
||
<!-- 192x192, as recommended for Android
|
||
http://updates.html5rocks.com/2014/11/Support-for-theme-color-in-Chrome-39-for-Android
|
||
-->
|
||
<link rel="icon" type="image/png" sizes="192x192" href="https://www.ncbi.nlm.nih.gov/coreutils/nwds/img/favicons/favicon-192.png" />
|
||
|
||
<!-- 57x57 (precomposed) for iPhone 3GS, pre-2011 iPod Touch and older Android devices -->
|
||
<link rel="apple-touch-icon-precomposed" href="https://www.ncbi.nlm.nih.gov/coreutils/nwds/img/favicons/favicon-57.png">
|
||
<!-- 72x72 (precomposed) for 1st generation iPad, iPad 2 and iPad mini -->
|
||
<link rel="apple-touch-icon-precomposed" sizes="72x72" href="https://www.ncbi.nlm.nih.gov/coreutils/nwds/img/favicons/favicon-72.png">
|
||
<!-- 114x114 (precomposed) for iPhone 4, 4S, 5 and post-2011 iPod Touch -->
|
||
<link rel="apple-touch-icon-precomposed" sizes="114x114" href="https://www.ncbi.nlm.nih.gov/coreutils/nwds/img/favicons/favicon-114.png">
|
||
<!-- 144x144 (precomposed) for iPad 3rd and 4th generation -->
|
||
<link rel="apple-touch-icon-precomposed" sizes="144x144" href="https://www.ncbi.nlm.nih.gov/coreutils/nwds/img/favicons/favicon-144.png">
|
||
|
||
|
||
<link rel="stylesheet" href="/pathogens/static/main/styles/app.css" type="text/css" media="screen">
|
||
<link rel="stylesheet" href="/pathogens/static/main/styles/breadcrumbs.css" type="text/css" media="screen">
|
||
<style type="text/css">
|
||
a { text-decoration: underline }
|
||
</style>
|
||
<!-- Logging params: Pinger defaults -->
|
||
|
||
<meta name="ncbi_app" content="labs_pathogens" />
|
||
|
||
<meta name="ncbi_pdid" content="static" />
|
||
|
||
<meta name="ncbi_phid" content="322C300D9B303815000060937E9F8648.1.m_9" />
|
||
|
||
|
||
<!-- /extra head -->
|
||
|
||
<link rel="stylesheet" href="/pathogens/static/main/styles/page-search.css" type="text/css">
|
||
|
||
|
||
</head>
|
||
<body >
|
||
|
||
|
||
<a class="usa-skipnav" href="#main_content">Skip to main page content</a>
|
||
|
||
<!-- ========== BEGIN HEADER ========== -->
|
||
<section class="usa-banner">
|
||
<div class="usa-accordion">
|
||
<header class="usa-banner-header">
|
||
<div class="usa-grid usa-banner-inner">
|
||
<img src="https://www.ncbi.nlm.nih.gov/coreutils/uswds/img/favicons/favicon-57.png" alt="U.S. flag" />
|
||
<p>An official website of the United States government</p>
|
||
<button
|
||
class="usa-accordion-button usa-banner-button"
|
||
aria-expanded="false"
|
||
aria-controls="gov-banner-top"
|
||
>
|
||
<span class="usa-banner-button-text">Here's how you know</span>
|
||
</button>
|
||
</div>
|
||
</header>
|
||
<div
|
||
class="usa-banner-content usa-grid usa-accordion-content"
|
||
id="gov-banner-top"
|
||
>
|
||
<div class="usa-banner-guidance-gov usa-width-one-half">
|
||
<img
|
||
class="usa-banner-icon usa-media_block-img"
|
||
src="https://www.ncbi.nlm.nih.gov/coreutils/uswds/img/icon-dot-gov.svg"
|
||
alt="Dot gov"
|
||
/>
|
||
<div class="usa-media_block-body">
|
||
<p>
|
||
<strong>The .gov means it’s official.</strong>
|
||
<br />
|
||
Federal government websites often end in .gov or .mil. Before
|
||
sharing sensitive information, make sure you’re on a federal
|
||
government site.
|
||
</p>
|
||
</div>
|
||
</div>
|
||
<div class="usa-banner-guidance-ssl usa-width-one-half">
|
||
<img
|
||
class="usa-banner-icon usa-media_block-img"
|
||
src="https://www.ncbi.nlm.nih.gov/coreutils/uswds/img/icon-https.svg"
|
||
alt="Https"
|
||
/>
|
||
<div class="usa-media_block-body">
|
||
<p>
|
||
<strong>The site is secure.</strong>
|
||
<br />
|
||
The <strong>https://</strong> ensures that you are connecting to the
|
||
official website and that any information you provide is encrypted
|
||
and transmitted securely.
|
||
</p>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
</section>
|
||
<div class="usa-overlay"></div>
|
||
<header class="ncbi-header" role="banner" data-section="Header">
|
||
|
||
<div class="usa-grid">
|
||
<div class="usa-width-one-whole">
|
||
|
||
<div class="ncbi-header__logo">
|
||
<a href="https://www.ncbi.nlm.nih.gov/" class="logo" aria-label="NCBI Logo" data-ga-action="click_image" data-ga-label="NIH NLM Logo">
|
||
<img src="https://www.ncbi.nlm.nih.gov/coreutils/nwds/img/logos/AgencyLogo.svg" alt="NIH NLM Logo" />
|
||
</a>
|
||
</div>
|
||
|
||
<div class="ncbi-header__account">
|
||
<a id="account_login" href="https://account.ncbi.nlm.nih.gov" class="usa-button header-button" style="display:none" data-ga-action="open_menu" data-ga-label="account_menu">Log in</a>
|
||
<button id="account_info" class="header-button" style="display:none"
|
||
aria-controls="account_popup">
|
||
<span class="fa fa-user" aria-hidden="true"></span>
|
||
<span class="username desktop-only" aria-hidden="true" id="uname_short"></span>
|
||
<span class="sr-only">Show account info</span>
|
||
</button>
|
||
</div>
|
||
|
||
<div class="ncbi-popup-anchor">
|
||
<div class="ncbi-popup account-popup" id="account_popup" aria-hidden="true">
|
||
<div class="ncbi-popup-head">
|
||
<button class="ncbi-close-button" data-ga-action="close_menu" data-ga-label="account_menu"><span class="fa fa-times"></span><span class="usa-sr-only">Close</span></button>
|
||
<h4>Account</h4>
|
||
</div>
|
||
<div class="account-user-info">
|
||
Logged in as:<br/>
|
||
<b><span class="username" id="uname_long">username</span></b>
|
||
</div>
|
||
<div class="account-links">
|
||
<ul class="usa-unstyled-list">
|
||
<li><a id="account_myncbi" href="/myncbi/" class="set-base-url" data-ga-action="click_menu_item" data-ga-label="account_myncbi">Dashboard</a></li>
|
||
<li><a id="account_pubs" href="/myncbi/collections/bibliography/" class="set-base-url" data-ga-action="click_menu_item" data-ga-label="account_pubs">Publications</a></li>
|
||
<li><a id="account_settings" href="/account/settings/" class="set-base-url" data-ga-action="click_menu_item" data-ga-label="account_settings">Account settings</a></li>
|
||
<li><a id="account_logout" href="/account/signout/" class="set-base-url" data-ga-action="click_menu_item" data-ga-label="account_logout">Log out</a></li>
|
||
</ul>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
|
||
</div>
|
||
</div>
|
||
</header>
|
||
<div role="navigation" aria-label="access keys">
|
||
<a id="nws_header_accesskey_0" href="https://www.ncbi.nlm.nih.gov/guide/browsers/#ncbi_accesskeys" class="usa-sr-only" accesskey="0" tabindex="-1">Access keys</a>
|
||
<a id="nws_header_accesskey_1" href="https://www.ncbi.nlm.nih.gov" class="usa-sr-only" accesskey="1" tabindex="-1">NCBI Homepage</a>
|
||
<a id="nws_header_accesskey_2" href="/myncbi/" class="set-base-url usa-sr-only" accesskey="2" tabindex="-1">MyNCBI Homepage</a>
|
||
<a id="nws_header_accesskey_3" href="#maincontent" class="usa-sr-only" accesskey="3" tabindex="-1">Main Content</a>
|
||
<a id="nws_header_accesskey_4" href="#" class="usa-sr-only" accesskey="4" tabindex="-1">Main Navigation</a>
|
||
</div>
|
||
<section data-section="Alerts">
|
||
<div class="ncbi-alerts-placeholder"></div>
|
||
</section>
|
||
<!-- ========== END HEADER ========== -->
|
||
|
||
|
||
|
||
|
||
|
||
<main id="main_content" accesskey="3">
|
||
|
||
<section class="pathogens-content-page usa-grid">
|
||
|
||
<div class="usa-width-one-whole ptg-top">
|
||
<div><ul id="breadcrumbs" class="usa-unstyled-list breadcrumbs">
|
||
<li><a href="https://www.ncbi.nlm.nih.gov/home/health.shtml">Health</a></li>
|
||
|
||
<li><a href=/pathogens/>Pathogen Detection</a></li>
|
||
|
||
<li><a href="/pathogens/pathogens_help/">Help</a></li>
|
||
|
||
|
||
|
||
<li><a href="/pathogens/docs/gcp/">GCP</a></li>
|
||
|
||
|
||
|
||
<li>Getting started with BigQuery</li>
|
||
</ul>
|
||
|
||
</div>
|
||
<div class="ptg-search">
|
||
<input placeholder="Search page" type="search"/><button title="Previous" disabled="disabled"></button><button title="Next" disabled="disabled"></button>
|
||
</div>
|
||
</div>
|
||
<div>
|
||
<p><a name="TOC"> </a></p>
|
||
|
||
<h1 id="getting-started-with-bigquery">Getting started with BigQuery</h1>
|
||
|
||
<div class="toc">
|
||
<ul>
|
||
<li><a href="#pathogen-detection-resources-at-">Pathogen Detection Resources at Google Cloud Platform</a></li>
|
||
<li><a href="#set-up-account">Set up account</a></li>
|
||
<li><a href="#payment">Payment</a></li>
|
||
<li><a href="#access-methods">Access methods</a></li>
|
||
<li><a href="#using-the-sql-workspace">Using the SQL Workspace</a><ul>
|
||
<li><a href="#add-ncbipathogendetect-to-the-da">Add ncbi-pathogen-detect to the Data Explorer</a></li>
|
||
<li><a href="#search-in-bigquery">Search in BigQuery</a></li>
|
||
</ul>
|
||
</li>
|
||
<li><a href="#commandline">Using the bq command-line tool</a></li>
|
||
<li><a href="#exporting-large-tables">Exporting large tables</a></li>
|
||
<li><a href="#what-pathogen-detection-pipeline">What Pathogen Detection Pipeline data is available at BigQuery?</a></li>
|
||
</ul>
|
||
</div>
|
||
|
||
<h3 id="pathogen-detection-resources-at-">Pathogen Detection Resources at Google Cloud Platform</h3>
|
||
|
||
<ul>
|
||
<li><a href="/pathogens/docs/gcp/">Pathogen Detection Resources at Google Cloud Platform</a></li>
|
||
<li><a href="/pathogens/docs/microbigge_gcp">MicroBIGG-E table in BigQuery</a></li>
|
||
<li><a href="/pathogens/docs/microbigge_gcp#contig-sequences">MicroBIGG-E contig sequences in Google Storage buckets</a></li>
|
||
<li><a href="/pathogens/docs/microbigge_gcp#protein-sequences">MicroBIGG-E protein sequences in Google Storage buckets</a></li>
|
||
<li><a href="/pathogens/docs/isolates_gcp">Isolates Browser table in BigQuery</a></li>
|
||
<li><a href="/pathogens/docs/isolates_gcp#isolate_exceptions">Isolate Exceptions table in BigQuery</a></li>
|
||
</ul>
|
||
|
||
<h3 id="set-up-account">Set up account <a href="#TOC"><img alt="MicroBIGG-E at Google Cloud Platform TOC" src="/core/assets/pathogens/images/toc_icon.png"/></a> <a href="/pathogens/pathogens_help/"><img alt="Main documentation page" src="/core/assets/pathogens/images/arrowup_blue.gif"/></a></h3>
|
||
|
||
<p>To access BigQuery, you will need to set up a Google cloud account:
|
||
<a href="https://cloud.google.com/">https://cloud.google.com/</a></p>
|
||
|
||
<p>Once you have set up the account, you will need to create your project:
|
||
<a href="https://cloud.google.com/resource-manager/docs/creating-managing-projects">https://cloud.google.com/resource-manager/docs/creating-managing-projects</a></p>
|
||
|
||
<h3 id="payment">Payment <a href="#TOC"><img alt="MicroBIGG-E at Google Cloud Platform TOC" src="/core/assets/pathogens/images/toc_icon.png"/></a> <a href="/pathogens/pathogens_help/"><img alt="Main documentation page" src="/core/assets/pathogens/images/arrowup_blue.gif"/></a></h3>
|
||
|
||
<p>The user pays for running queries against public data sets and you should review the payment requirements for on-demand queries from Google BigQuery. Google BigQuery provides 1TB per month free for querying data. </p>
|
||
|
||
<h3 id="access-methods">Access methods <a href="#TOC"><img alt="MicroBIGG-E at Google Cloud Platform TOC" src="/core/assets/pathogens/images/toc_icon.png"/></a> <a href="/pathogens/pathogens_help/"><img alt="Main documentation page" src="/core/assets/pathogens/images/arrowup_blue.gif"/></a></h3>
|
||
|
||
<p>We recommend starting with the <a href="https://cloud.google.com/bigquery/docs/bigquery-web-ui">BigQuery SQL Workspace</a> to become familiar with with BigQuery SQL and writing queries before attempting to use the command line tools or client libraries. </p>
|
||
|
||
<p>BigQuery can be accessed through a web browser query editor:<br/>
|
||
<a href="https://console.cloud.google.com/bigquery">https://console.cloud.google.com/bigquery</a></p>
|
||
|
||
<p>BigQuery client library documentation is also available for reference if you
|
||
plan to access it through the supported programming languages:<br/>
|
||
<a href="https://cloud.google.com/bigquery/docs/reference/libraries">https://cloud.google.com/bigquery/docs/reference/libraries</a></p>
|
||
|
||
<p>BigQuery command line tools can be downloaded and set up from here <br/>
|
||
<a href="https://cloud.google.com/sdk/docs/quickstarts">https://cloud.google.com/sdk/docs/quickstarts</a><br/>
|
||
(see <a href="#commandline">Using the <code>bq</code> command-line tool</a> below for more)</p>
|
||
|
||
<h2 id="using-the-sql-workspace">Using the SQL Workspace <a href="#TOC"><img alt="MicroBIGG-E at Google Cloud Platform TOC" src="/core/assets/pathogens/images/toc_icon.png"/></a> <a href="/pathogens/pathogens_help/"><img alt="Main documentation page" src="/core/assets/pathogens/images/arrowup_blue.gif"/></a></h2>
|
||
|
||
<p>We recommend starting with the <a href="https://console.cloud.google.com/bigquery">BigQuery SQL Workspace</a> to become familiar with BigQuery SQL and the pathogen resources. </p>
|
||
|
||
<p><img alt="Find BigQuery workspace" src="/core/assets/pathogens/images/bigquery_bigquery.png" title="Search for BigQuery"/>
|
||
Click the search bar and enter <strong>BigQuery</strong> as the search term and click on the BigQuery search result.</p>
|
||
|
||
<h3 id="add-ncbipathogendetect-to-the-da">Add <code>ncbi-pathogen-detect</code> to the Data Explorer <a href="#TOC"><img alt="MicroBIGG-E at Google Cloud Platform TOC" src="/core/assets/pathogens/images/toc_icon.png"/></a> <a href="/pathogens/pathogens_help/"><img alt="Main documentation page" src="/core/assets/pathogens/images/arrowup_blue.gif"/></a></h3>
|
||
|
||
<p>Adding the project <code>ncbi-pathogen-detect</code> to the Data Explorer makes it much
|
||
more convenient to get started with the dataset. Click the <strong>ADD DATA</strong> button
|
||
on the left side of the screen, in the Explorer panel.
|
||
Next, select <strong>Star a project by name</strong> and paste <strong>ncbi-pathogen-detect</strong> into the Pin a project box and click <strong>STAR</strong>.</p>
|
||
|
||
<p><img alt="Click Add Data to add ncbi-pathogen-detect to the data explorer" src="/core/assets/pathogens/images/bigquery_data_explorer.png" title="Click ADD DATA"/><br/></p>
|
||
|
||
<p><img style="border:1px solid #000000" src="/core/assets/pathogens/images/add_data.png" border="1"/><br/></p>
|
||
|
||
<!-- Click Star a project by name](/~/images/add_data.png "Click Star a project by name")<br/> -->
|
||
|
||
<p><img alt="Type in ncbi-pathogen-detect" src="/core/assets/pathogens/images/star_a_project.png" title="Put ncbi-pathogen-detect into the dialog box and click STAR"/><br/></p>
|
||
|
||
<p>You can get to a view of the structure of a table by clicking on the tables in the Data Explorer, for example <code>ncbi-pathogen-detect.pdbrowser.microbigge</code>.
|
||
<img alt="Use the Data Explorer to get information about the BigQuery table" src="/core/assets/pathogens/images/bigquery_view_details.png" title="Click triangles to expand and select microbigge table"/><br/>
|
||
Click the Triangles (<span style="color:red">1</span>) to expand and show the collection. Click the microbigge table (<span style="color:red">2</span>) to view information about that table.</p>
|
||
|
||
<p>Within the table information panel you can click <strong>SCHEMA</strong> to list the fields and <strong>PREVIEW</strong> to show some sample data from the table. </p>
|
||
|
||
<h3 id="search-in-bigquery">Search in BigQuery <a href="#TOC"><img alt="MicroBIGG-E at Google Cloud Platform TOC" src="/core/assets/pathogens/images/toc_icon.png"/></a> <a href="/pathogens/pathogens_help/"><img alt="Main documentation page" src="/core/assets/pathogens/images/arrowup_blue.gif"/></a></h3>
|
||
|
||
<p>To search the table click <strong>QUERY</strong> or the <strong>+</strong> symbol to open a new query editor tab and enter the query in the text box. </p>
|
||
|
||
<p><img alt="Example Query to get all data: select * from ncbi-pathogen-detect.pdbrowser.microbigge" src="/core/assets/pathogens/images/bigquery_example_query1.png" title="Sample query"/><br/>
|
||
<strong>The area outlined in red shows how much data will be searched with your SQL query so that you can estimate the cost of running that query.</strong></p>
|
||
|
||
<p>Click the <strong>RUN</strong> button to execute the query. Note that there may be a small charge associated with running the query. See above and Google's <a href="https://cloud.google.com/bigquery/pricing">BigQuery pricing page</a> for more information.</p>
|
||
|
||
<h2 id="commandline">Using the <code>bq</code> command-line tool</h2>
|
||
|
||
<ol>
|
||
<li>Create your account and project through the Google web interface (see above). </li>
|
||
<li>Download install the Cloud SDK from <a href="https://cloud.google.com/sdk/docs/install-sdk">https://cloud.google.com/sdk/docs/install-sdk</a>.</li>
|
||
<li>Sign into your account by entering the command below and following the instructions.
|
||
gcloud auth login --no-launch-browser</li>
|
||
<li>
|
||
<p>Once you're logged into your account, you should set your project ID. Where <code><PROJECT_ID></code> is the ID that was set when you created your project (this is different from your project name).</p>
|
||
<p><code>gcloud config set project <PROJECT_ID></code></p>
|
||
</li>
|
||
<li>
|
||
<p>You should now be able to execute the following query to get the most common AMR genes:</p>
|
||
<p><code>bq query --nouse_legacy_sql --format=csv 'SELECT element_symbol, count(*) num_found FROM `ncbi-pathogen-detect.pdbrowser.microbigge` WHERE scope="core" GROUP BY element_symbol ORDER BY num_found DESC LIMIT 5'</code></p>
|
||
</li>
|
||
</ol>
|
||
|
||
<h2 id="exporting-large-tables">Exporting large tables</h2>
|
||
|
||
<p>Many people want to download the table data in bulk from our resources. See
|
||
<a href="https://cloud.google.com/bigquery/docs/exporting-data">Google's Export table data
|
||
documentation</a> for
|
||
details. As an example of one way, you can use a query like the following to
|
||
export all MicroBIGG-E data to a google cloud storage bucket:</p>
|
||
|
||
<pre><code>EXPORT DATA
|
||
OPTIONS (
|
||
uri = 'gs://<storage-bucket>/microbigge/*.tsv.gz',
|
||
format = 'CSV',
|
||
overwrite = true,
|
||
header = true,
|
||
field_delimiter = '\t',
|
||
compression = 'GZIP')
|
||
AS (
|
||
SELECT *
|
||
FROM `ncbi-pathogen-detect.pdbrowser.microbigge`
|
||
ORDER BY scientific_name, target_acc, contig_acc, start_on_contig
|
||
);
|
||
</code></pre>
|
||
|
||
<p>The above query will export all data from the
|
||
<code>ncbi-pathogen-detect.pdbrowser.microbigge</code> table to the storage bucket (named
|
||
<storage-bucket> above) in a series of gzipped tab-delimited files which you
|
||
can then download to your computer using
|
||
<a href="https://cloud.google.com/storage/docs/gsutil"><code>gsutil</code></a> or other <a href="https://cloud.google.com/storage/docs">cloud
|
||
storage</a> access methods.</p>
|
||
|
||
<h2 id="what-pathogen-detection-pipeline">What Pathogen Detection Pipeline data is available at BigQuery?</h2>
|
||
|
||
<p>NCBI Pathogen Detection has four tables available in GCP BigQuery:</p>
|
||
|
||
<ul>
|
||
<li><code>ncbi-pathogen-detect.pdbrowser.isolates</code> contains information and analysis results on isolate sequences in the NCBI Pathogen Detection Pipeline.<ul>
|
||
<li>See <a href="/pathogens/docs/isolates_gcp">Isolates Browser data at GCP</a> for details</li>
|
||
<li>The web interface is at <a href="https://www.ncbi.nlm.nih.gov/pathogens/isolates">https://www.ncbi.nlm.nih.gov/pathogens/isolates</a></li>
|
||
<li><a href="/pathogens/pathogens_help/#isolates-browser">Isolates Browser Documentation</a></li>
|
||
</ul>
|
||
</li>
|
||
<li><code>ncbi-pathogen-detect.pdbrowser.isolate_exceptions</code> contains information on isolate sequences or assemblies that failed Quality Control (QC) checks in the pipeline.<ul>
|
||
<li>See <a href="/pathogens/docs/isolates_gcp">Isolates Browser data at GCP</a> for details</li>
|
||
<li>The web interface is at <a href="https://www.ncbi.nlm.nih.gov/pathogens/isolates">https://www.ncbi.nlm.nih.gov/pathogens/isolates</a></li>
|
||
<li><a href="/pathogens/pathogens_help/#isolates-browser-exceptions-table">Exceptions table documentation</a></li>
|
||
</ul>
|
||
</li>
|
||
<li><code>ncbi-pathogen-detect.pdbrowser.microbigge</code> - The Microbial Browser for the
|
||
Identification of Genetic and Genomic Elements (MicroBIGG-E) contains the results of running <a href="/pathogens/antimicrobial-resistance/AMRFinder/">AMRFinderPlus</a> on assemblies in the <a href="/pathogens/isolates">Isolates Browser</a>.<ul>
|
||
<li>See <a href="/pathogens/docs/microbigge_gcp">MicroBIGG-E at GCP</a> for details </li>
|
||
<li>The web interface is at <a href="https://www.ncbi.nlm.nih.gov/pathogens/microbigge">https://www.ncbi.nlm.nih.gov/pathogens/microbigge</a></li>
|
||
<li><a href="/pathogens/pathogens_help/#microbigge">MicroBIGG-E Documentation</a></li>
|
||
</ul>
|
||
</li>
|
||
<li><code>ncbi-pathogen-detect.pdbrowser.bioproject_hierarchy</code> - Bioprojects and their parent umbrella bioprojects for all isolates in the Pathogen Detection System<ul>
|
||
<li>See <a href="/pathogens/docs/bioproject_hierarchy_gcp/">BioProject Hierarchy documentation</a> for details</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
|
||
</div>
|
||
|
||
|
||
|
||
</section>
|
||
|
||
</main>
|
||
|
||
|
||
<!-- ========== BEGIN FOOTER ========== -->
|
||
<footer>
|
||
<section class="icon-section">
|
||
<div id="icon-section-header" class="icon-section_header">Follow NCBI</div>
|
||
<div class="grid-container container">
|
||
<div class="icon-section_container">
|
||
<a class="footer-icon" id="footer_twitter" href="https://twitter.com/ncbi" aria-label="Twitter">
|
||
<svg width="40" height="40" viewBox="0 0 40 37" fill="none" xmlns="http://www.w3.org/2000/svg">
|
||
<title>Twitter</title>
|
||
<g id="twitterx1008">
|
||
<path id="path1008"
|
||
d="M6.06736 7L16.8778 20.8991L6.00001 32.2H10.2L18.6 23.1L25.668 32.2H34L22.8 17.5L31.9 7H28.4L20.7 15.4L14.401 7H6.06898H6.06736ZM9.66753 8.73423H12.9327L29.7327 30.4658H26.5697L9.66753 8.73423Z"
|
||
fill="#5B616B"/>
|
||
</g>
|
||
</svg>
|
||
</a>
|
||
<a class="footer-icon" id="footer_facebook" href="https://www.facebook.com/ncbi.nlm" aria-label="Facebook"><svg
|
||
data-name="Layer 1" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 300 300">
|
||
<title>Facebook</title>
|
||
<path class="cls-11"
|
||
d="M210.5,115.12H171.74V97.82c0-8.14,5.39-10,9.19-10h27.14V52l-39.32-.12c-35.66,0-42.42,26.68-42.42,43.77v19.48H99.09v36.32h27.24v109h45.41v-109h35Z">
|
||
</path>
|
||
</svg></a>
|
||
<a class="footer-icon" id="footer_linkedin"
|
||
href="https://www.linkedin.com/company/ncbinlm"
|
||
aria-label="LinkedIn"><svg data-name="Layer 1" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 300 300">
|
||
<title>LinkedIn</title>
|
||
<path class="cls-11"
|
||
d="M101.64,243.37H57.79v-114h43.85Zm-22-131.54h-.26c-13.25,0-21.82-10.36-21.82-21.76,0-11.65,8.84-21.15,22.33-21.15S101.7,78.72,102,90.38C102,101.77,93.4,111.83,79.63,111.83Zm100.93,52.61A17.54,17.54,0,0,0,163,182v61.39H119.18s.51-105.23,0-114H163v13a54.33,54.33,0,0,1,34.54-12.66c26,0,44.39,18.8,44.39,55.29v58.35H198.1V182A17.54,17.54,0,0,0,180.56,164.44Z">
|
||
</path>
|
||
</svg></a>
|
||
<a class="footer-icon" id="footer_github" href="https://github.com/ncbi" aria-label="GitHub"><svg
|
||
data-name="Layer 1" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 300 300">
|
||
<defs>
|
||
<style>
|
||
.cls-11,
|
||
.cls-12 {
|
||
fill: #737373;
|
||
}
|
||
|
||
.cls-11 {
|
||
fill-rule: evenodd;
|
||
}
|
||
</style>
|
||
</defs>
|
||
<title>GitHub</title>
|
||
<path class="cls-11"
|
||
d="M151.36,47.28a105.76,105.76,0,0,0-33.43,206.1c5.28,1,7.22-2.3,7.22-5.09,0-2.52-.09-10.85-.14-19.69-29.42,6.4-35.63-12.48-35.63-12.48-4.81-12.22-11.74-15.47-11.74-15.47-9.59-6.56.73-6.43.73-6.43,10.61.75,16.21,10.9,16.21,10.9,9.43,16.17,24.73,11.49,30.77,8.79,1-6.83,3.69-11.5,6.71-14.14C108.57,197.1,83.88,188,83.88,147.51a40.92,40.92,0,0,1,10.9-28.39c-1.1-2.66-4.72-13.42,1-28,0,0,8.88-2.84,29.09,10.84a100.26,100.26,0,0,1,53,0C198,88.3,206.9,91.14,206.9,91.14c5.76,14.56,2.14,25.32,1,28a40.87,40.87,0,0,1,10.89,28.39c0,40.62-24.74,49.56-48.29,52.18,3.79,3.28,7.17,9.71,7.17,19.58,0,14.15-.12,25.54-.12,29,0,2.82,1.9,6.11,7.26,5.07A105.76,105.76,0,0,0,151.36,47.28Z">
|
||
</path>
|
||
<path class="cls-12"
|
||
d="M85.66,199.12c-.23.52-1.06.68-1.81.32s-1.2-1.06-.95-1.59,1.06-.69,1.82-.33,1.21,1.07.94,1.6Zm-1.3-1">
|
||
</path>
|
||
<path class="cls-12"
|
||
d="M90,203.89c-.51.47-1.49.25-2.16-.49a1.61,1.61,0,0,1-.31-2.19c.52-.47,1.47-.25,2.17.49s.82,1.72.3,2.19Zm-1-1.08">
|
||
</path>
|
||
<path class="cls-12"
|
||
d="M94.12,210c-.65.46-1.71,0-2.37-.91s-.64-2.07,0-2.52,1.7,0,2.36.89.65,2.08,0,2.54Zm0,0"></path>
|
||
<path class="cls-12"
|
||
d="M99.83,215.87c-.58.64-1.82.47-2.72-.41s-1.18-2.06-.6-2.7,1.83-.46,2.74.41,1.2,2.07.58,2.7Zm0,0">
|
||
</path>
|
||
<path class="cls-12"
|
||
d="M107.71,219.29c-.26.82-1.45,1.2-2.64.85s-2-1.34-1.74-2.17,1.44-1.23,2.65-.85,2,1.32,1.73,2.17Zm0,0">
|
||
</path>
|
||
<path class="cls-12"
|
||
d="M116.36,219.92c0,.87-1,1.59-2.24,1.61s-2.29-.68-2.3-1.54,1-1.59,2.26-1.61,2.28.67,2.28,1.54Zm0,0">
|
||
</path>
|
||
<path class="cls-12"
|
||
d="M124.42,218.55c.15.85-.73,1.72-2,1.95s-2.37-.3-2.52-1.14.73-1.75,2-2,2.37.29,2.53,1.16Zm0,0"></path>
|
||
</svg></a>
|
||
<a class="footer-icon" id="footer_blog" href="https://ncbiinsights.ncbi.nlm.nih.gov/" aria-label="Blog">
|
||
<svg id="Layer_1" data-name="Layer 1" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 40 40"><defs><style>.cls-1{fill:#737373;}</style></defs><path class="cls-1" d="M14,30a4,4,0,1,1-4-4,4,4,0,0,1,4,4Zm11,3A19,19,0,0,0,7.05,15a1,1,0,0,0-1,1v3a1,1,0,0,0,.93,1A14,14,0,0,1,20,33.07,1,1,0,0,0,21,34h3a1,1,0,0,0,1-1Zm9,0A28,28,0,0,0,7,6,1,1,0,0,0,6,7v3a1,1,0,0,0,1,1A23,23,0,0,1,29,33a1,1,0,0,0,1,1h3A1,1,0,0,0,34,33Z"/></svg>
|
||
</a>
|
||
</div>
|
||
</div>
|
||
</section>
|
||
|
||
<section class="container-fluid bg-primary">
|
||
<div class="container pt-5">
|
||
<div class="row mt-3">
|
||
<div class="col-lg-3 col-12">
|
||
<p><a class="text-white" href="https://www.nlm.nih.gov/socialmedia/index.html">Connect with NLM</a></p>
|
||
<ul class="list-inline social_media">
|
||
<li class="list-inline-item"><a href="https://twitter.com/NLM_NIH" aria-label="Twitter"
|
||
target="_blank" rel="noopener noreferrer">
|
||
<svg width="35" height="35" viewBox="0 0 38 35" fill="none" xmlns="http://www.w3.org/2000/svg">
|
||
<title>Twitter</title>
|
||
<g id="twitterx1009" clip-path="url(#clip0_65276_3946)">
|
||
<path id="Vector" d="M17.5006 34.6565C26.9761 34.6565 34.6575 26.9751 34.6575 17.4996C34.6575 8.02416 26.9761 0.342773 17.5006 0.342773C8.02514 0.342773 0.34375 8.02416 0.34375 17.4996C0.34375 26.9751 8.02514 34.6565 17.5006 34.6565Z" fill="#205493" stroke="white" stroke-width="1.2" stroke-miterlimit="10"></path>
|
||
<path id="path1009" d="M8.54811 8.5L16.2698 18.4279L8.50001 26.5H11.5L17.5 20L22.5486 26.5H28.5L20.5 16L27 8.5H24.5L19 14.5L14.5007 8.5H8.54927H8.54811ZM11.1197 9.73873H13.4519L25.4519 25.2613H23.1926L11.1197 9.73873Z" fill="white"></path>
|
||
</g>
|
||
<defs>
|
||
<clipPath id="clip0_65276_3946">
|
||
<rect width="38" height="38" fill="white"></rect>
|
||
</clipPath>
|
||
</defs>
|
||
</svg></a>
|
||
</li>
|
||
<li class="list-inline-item"><a href="https://www.facebook.com/nationallibraryofmedicine"
|
||
aria-label="Facebook" rel="noopener noreferrer" target="_blank">
|
||
<svg version="1.1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px"
|
||
y="0px" viewBox="0 0 249 249" style="enable-background:new 0 0 249 249;" xml:space="preserve">
|
||
<style type="text/css">
|
||
.st10 {
|
||
fill: #FFFFFF;
|
||
}
|
||
|
||
.st110 {
|
||
fill: none;
|
||
stroke: #FFFFFF;
|
||
stroke-width: 8;
|
||
stroke-miterlimit: 10;
|
||
}
|
||
</style>
|
||
<title>SM-Facebook</title>
|
||
<g>
|
||
<g>
|
||
<path class="st10" d="M159,99.1h-24V88.4c0-5,3.3-6.2,5.7-6.2h16.8V60l-24.4-0.1c-22.1,0-26.2,16.5-26.2,27.1v12.1H90v22.5h16.9
|
||
v67.5H135v-67.5h21.7L159,99.1z"></path>
|
||
</g>
|
||
</g>
|
||
<circle class="st110" cx="123.6" cy="123.2" r="108.2"></circle>
|
||
</svg>
|
||
</a></li>
|
||
<li class="list-inline-item"><a href="https://www.youtube.com/user/NLMNIH" aria-label="Youtube"
|
||
target="_blank" rel="noopener noreferrer"><svg version="1.1" xmlns="http://www.w3.org/2000/svg"
|
||
xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px" viewBox="0 0 249 249"
|
||
style="enable-background:new 0 0 249 249;" xml:space="preserve">
|
||
<title>SM-Youtube</title>
|
||
<style type="text/css">
|
||
.st4 {
|
||
fill: none;
|
||
stroke: #FFFFFF;
|
||
stroke-width: 8;
|
||
stroke-miterlimit: 10;
|
||
}
|
||
|
||
.st5 {
|
||
fill: #FFFFFF;
|
||
}
|
||
</style>
|
||
<circle class="st4" cx="124.2" cy="123.4" r="108.2"></circle>
|
||
<g transform="translate(0,-952.36218)">
|
||
<path class="st5"
|
||
d="M88.4,1037.4c-10.4,0-18.7,8.3-18.7,18.7v40.1c0,10.4,8.3,18.7,18.7,18.7h72.1c10.4,0,18.7-8.3,18.7-18.7
|
||
v-40.1c0-10.4-8.3-18.7-18.7-18.7H88.4z M115.2,1058.8l29.4,17.4l-29.4,17.4V1058.8z"></path>
|
||
</g>
|
||
</svg></a></li>
|
||
</ul>
|
||
</div>
|
||
<div class="col-lg-3 col-12">
|
||
<p class="address_footer text-white">National Library of Medicine<br>
|
||
<a href="https://www.google.com/maps/place/8600+Rockville+Pike,+Bethesda,+MD+20894/@38.9959508,-77.101021,17z/data=!3m1!4b1!4m5!3m4!1s0x89b7c95e25765ddb:0x19156f88b27635b8!8m2!3d38.9959508!4d-77.0988323"
|
||
class="text-white" target="_blank" rel="noopener noreferrer">8600 Rockville Pike<br>
|
||
Bethesda, MD 20894</a></p>
|
||
</div>
|
||
<div class="col-lg-3 col-12 centered-lg">
|
||
<p><a href="https://www.nlm.nih.gov/web_policies.html" class="text-white">Web Policies</a><br>
|
||
<a href="https://www.nih.gov/institutes-nih/nih-office-director/office-communications-public-liaison/freedom-information-act-office"
|
||
class="text-white">FOIA</a><br>
|
||
<a href="https://www.hhs.gov/vulnerability-disclosure-policy/index.html" class="text-white" id="vdp">HHS Vulnerability Disclosure</a></p>
|
||
</div>
|
||
<div class="col-lg-3 col-12 centered-lg">
|
||
<p><a class="supportLink text-white" href="https://support.nlm.nih.gov/">Help</a><br>
|
||
<a href="https://www.nlm.nih.gov/accessibility.html" class="text-white">Accessibility</a><br>
|
||
<a href="https://www.nlm.nih.gov/careers/careers.html" class="text-white">Careers</a></p>
|
||
</div>
|
||
</div>
|
||
<div class="row">
|
||
<div class="col-lg-12 centered-lg">
|
||
<nav class="bottom-links">
|
||
<ul class="mt-3">
|
||
<li>
|
||
<a class="text-white" href="//www.nlm.nih.gov/">NLM</a>
|
||
</li>
|
||
<li>
|
||
<a class="text-white"
|
||
href="https://www.nih.gov/">NIH</a>
|
||
</li>
|
||
<li>
|
||
<a class="text-white" href="https://www.hhs.gov/">HHS</a>
|
||
</li>
|
||
<li>
|
||
<a
|
||
class="text-white" href="https://www.usa.gov/">USA.gov</a>
|
||
</li>
|
||
</ul>
|
||
</nav>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
</section>
|
||
</footer>
|
||
<!-- ========== END FOOTER ========== -->
|
||
<!-- javascript to inject NWDS meta tags. Note: value of nwds_version is updated by "npm version" command -->
|
||
|
||
<script type="text/javascript">
|
||
var nwds_version = "1.2.3";
|
||
|
||
var meta_nwds_ver = document.createElement('meta');
|
||
meta_nwds_ver.name = 'ncbi_nwds_ver';
|
||
meta_nwds_ver.content = nwds_version;
|
||
document.getElementsByTagName('head')[0].appendChild(meta_nwds_ver);
|
||
|
||
var meta_nwds = document.createElement('meta');
|
||
meta_nwds.name = 'ncbi_nwds';
|
||
meta_nwds.content = 'yes';
|
||
document.getElementsByTagName('head')[0].appendChild(meta_nwds);
|
||
|
||
var alertsUrl = "/core/alerts/alerts.js";
|
||
if (typeof ncbiBaseUrl !== 'undefined') {
|
||
alertsUrl = ncbiBaseUrl + alertsUrl;
|
||
}
|
||
</script>
|
||
|
||
|
||
|
||
|
||
|
||
<!-- JavaScript -->
|
||
|
||
<script src="/pathogens/static/django_uswds/uswds/js/uswds.js"></script>
|
||
|
||
|
||
|
||
<script src="https://code.jquery.com/jquery-3.5.0.min.js"
|
||
integrity="sha256-xNzN2a4ltkB44Mc/Jz3pT4iU1cmeR0FkXs4pru/JxaQ="
|
||
crossorigin="anonymous">
|
||
</script>
|
||
<script>
|
||
var fallbackJquery = "/pathogens/static/base/js/jquery-3.5.0.min.js";
|
||
window.jQuery || document.write("<script src=" + fallbackJquery + ">\x3C/script>")
|
||
</script>
|
||
|
||
|
||
|
||
<script src="/pathogens/static/nwds/js/nwds.js" type="text/javascript"> </script>
|
||
<script src="/pathogens/static/nwds/js/header.js" type="text/javascript"> </script>
|
||
<script src="/pathogens/static/nwds/js/ncbipopup.js" type="text/javascript"> </script>
|
||
<script src="/pathogens/static/nwds/js/ncbiclearbutton.js" type="text/javascript"> </script>
|
||
<script src="/pathogens/static/nwds/js/override-uswds.js" type="text/javascript"> </script>
|
||
<script src="/pathogens/static/nwds/js/ncbifeedback.js" type="text/javascript"> </script>
|
||
|
||
|
||
|
||
<script type="text/javascript" src="https://www.ncbi.nlm.nih.gov/core/pinger/pinger.js"> </script>
|
||
|
||
|
||
|
||
<script type="text/javascript" src="/pathogens/static/main/scripts/page-search.js" charset="utf-8"></script>
|
||
|
||
|
||
|
||
</body>
|
||
</html> |