92 lines
57 KiB
HTML
92 lines
57 KiB
HTML
<!DOCTYPE html>
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<html amp lang="en-US" data-amp-auto-lightbox-disable transformed="self;v=1" i-amphtml-layout="" i-amphtml-no-boilerplate="">
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/*# sourceURL=/css/ampshared.css*/</style><meta property="og:locale" content="en_US"><meta property="og:type" content="article"><meta property="og:title" content="Three outdated browsers (1000 Genomes, dbGaP Data, and Get-RM) to retire in April 2022. Data available in GDV - NCBI Insights"><meta property="og:description" content="The Genome Data Viewer (GDV) is now the comprehensive NCBI genome browser. The development of GDV led to a few different types of genome browsers along the way, each one originally delivering visual displays for particular datasets. We developed the 1000 Genomes Browser for variation data from the 1000 Genomes project, the dbGaP Data Browser … Continue reading Three outdated browsers (1000 Genomes, dbGaP Data, and Get-RM) to retire in April 2022. Data available in GDV →"><meta property="og:url" content="https://ncbiinsights.ncbi.nlm.nih.gov/2021/10/28/browser-retirement/"><meta property="og:site_name" content="NCBI Insights"><meta property="article:publisher" content="https://www.facebook.com/ncbi.nlm"><meta property="article:published_time" content="2021-10-28T20:17:18+00:00"><meta property="article:modified_time" content="2022-03-08T19:44:03+00:00"><meta property="og:image" content="https://ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2021/10/ins_region_gdv-1024x679.png"><meta name="author" content="NCBI Staff"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@NCBI"><meta name="twitter:site" content="@NCBI"><meta name="twitter:label1" content="Written by"><meta name="twitter:data1" content="NCBI Staff"><meta name="twitter:label2" content="Est. reading time"><meta name="twitter:data2" content="3 minutes"><meta name="robots" content="index, follow, max-image-preview:large, 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Data available in GDV - NCBI Insights</title></head>
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<h1 class="amp-wp-title">Three outdated browsers (1000 Genomes, dbGaP Data, and Get-RM) to retire in April 2022. Data available in GDV</h1>
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3 years ago </time>
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<p>The Genome Data Viewer (<a href="https://www.ncbi.nlm.nih.gov/genome/gdv/?utm_source=blog&utm_medium=referral&utm_campaign=3-browser-retirement&utm_content=20211028link1">GDV</a>) is now the comprehensive NCBI genome browser. The development of GDV led to a few different types of genome browsers along the way, each one originally delivering visual displays for particular datasets. We developed the 1000 Genomes Browser for variation data from the <a href="https://www.internationalgenome.org/">1000 Genomes project</a>, the <a href="https://www.ncbi.nlm.nih.gov/gap/?utm_source=blog&utm_medium=referral&utm_campaign=3-browser-retirement&utm_content=20211028link2">dbGaP</a> Data Browser for controlled-access sequence read alignment data, and the GeT-RM browser for Genome in a Bottle (<a href="https://www.nist.gov/programs-projects/genome-bottle">GIAB</a>) data.</p>
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<p>The data displayed in these three browsers is now either obsolete and/or can largely be accessed from the GDV browser or other NCBI resources. Moreover, unlike GDV, these older browsers are no longer under active development and the data has not been updated to meet changing needs of the communities they were developed to serve. For these reasons we will retire these browsers in <strong>April 2022</strong>. Please see details below for more information on the data displayed in these browsers and how to access and display these data now through GDV and other means.</p>
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<p></p>
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<h2>1000 Genomes</h2>
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<p>The <a href="https://www.internationalgenome.org/">1000 Genomes Project</a> was launched in 2007 as a global resource and survey of human variation. The 1000 Genomes browser allowed you to explore variant calls, genotype calls, supporting sequence read alignments from the 1000 Genomes Project, and corresponding variants in <a href="https://www.ncbi.nlm.nih.gov/snp/?utm_source=blog&utm_medium=referral&utm_campaign=3-browser-retirement&utm_content=20211028link3"><span data-amp-original-style="font-size: 1.125rem;" class="amp-wp-2917c00">dbSNP</span></a><span data-amp-original-style="font-size: 1.125rem;" class="amp-wp-2917c00">. The results from the final phase of the project were published in 2015 and newer population genetics data is now available through dbSNP and GDV. Currently you can access these data in the following ways.</span></p>
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<ol>
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<li>Load the 1000Genomes Variation track in GDV, accessible from the <a href="https://www.ncbi.nlm.nih.gov/tools/sviewer/configpanel/?utm_source=blog&utm_medium=referral&utm_campaign=3-browser-retirement&utm_content=20211028link4">track configuration panel</a> (Figure 1).</li>
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<li>Search for 1000G variants in dbSNP using <a href="https://www.ncbi.nlm.nih.gov/snp/?term=1000genomes%5BSubmitter+Handle%5D&utm_source=blog&utm_medium=referral&utm_campaign=3-browser-retirement&utm_content=20211028link5" data-amp-original-style="background-color: #ffffff; font-size: 1.125rem;" class="amp-wp-81eaaef">1000genomes[Submitter Handle]</a><span data-amp-original-style="font-size: 1.125rem;" class="amp-wp-2917c00"> .</span></li>
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<li>Download the data from the <a href="https://www.internationalgenome.org/data" data-amp-original-style="background-color: #ffffff; font-size: 1.125rem;" class="amp-wp-81eaaef">1000Genomes project site</a><span data-amp-original-style="font-size: 1.125rem;" class="amp-wp-2917c00"> or from the NCBI </span><a class="external-link amp-wp-81eaaef" title="Follow link" href="https://ftp-trace.ncbi.nih.gov/1000genomes/ftp/" target="_blank" rel="nofollow noopener" data-amp-original-style="background-color: #ffffff; font-size: 1.125rem;">FTP </a><span data-amp-original-style="font-size: 1.125rem;" class="amp-wp-2917c00">and <a href="https://www.ncbi.nlm.nih.gov/projects/faspftp/1000genomes/?utm_source=blog&utm_medium=referral&utm_campaign=3-browser-retirement&utm_content=20211028link6">fasp </a></span>Aspera<span data-amp-original-style="font-size: 1.125rem;" class="amp-wp-2917c00">. sites.</span></li>
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</ol>
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<p>Figure 1. GDV and the ‘Configure Tracks’ panel. The 1000 Genomes Phase 3 data are available through the ‘Variation’ tab within the dbSNP track category. Public GWAS studies with aligned data from dbGaP can be found by searching in the ‘Find Tracks’ tab with the ‘dbGaP aligned analyses’ radio button selected.</p>
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<h2>dbGaP Data Browser</h2>
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<p>The dbGaP Data Browser (DDB) displayed selected General Research Use sequence data as a read-only view on the human genome assembly. The browser has password protected interface and shows only de-identified data, thereby keeping genomic track data private in accordance with <a class="external-link" href="https://www.hhs.gov/hipaa/index.html" target="_blank" rel="nofollow noopener">HIPAA</a> requirements. The purpose of the DDB was to give controlled access read-only access (no download) to some individual level datasets. Since most people who access dbGaP data are interested in doing genome-wide analyses, maintaining the browser, which allowed inspection of specific variations across a few sequences at a time, was shown to not be cost-effective.</p>
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<h2>GeT-RM</h2>
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<p>The <a class="external-link" title="Follow link" href="http://wwwn.cdc.gov/clia/Resources/GetRM/default.aspx" target="_blank" rel="nofollow noopener">GeT-RM Coordination Program </a>is a CDC project for establishing a community process to create reference materials, quality control measures, and proficiency evaluation for genetic testing. The GeT-RM Browser provided access to the data generated by the GeT-RM project to help validate next-generation genome sequencing technologies for human samples. You can continue to access GeT-RM through the <a href="https://www.nist.gov/programs-projects/genome-bottle">Genome in a Bottle (GIAB) project</a> at the National Institute of Standards and Technology (<a href="https://www.nist.gov/">NIST</a>). The data in GeT-RM is outdated, and you can upload newer results from GIAB as <a href="https://www.ncbi.nlm.nih.gov/genome/gdv/browser/cms/gbc/user-data/?utm_source=blog&utm_medium=referral&utm_campaign=3-browser-retirement&utm_content=20211028link9">remote data</a> into GDV.</p>
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