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{"id":7063,"date":"2021-10-28T16:17:18","date_gmt":"2021-10-28T20:17:18","guid":{"rendered":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/?p=7063"},"modified":"2022-03-08T14:44:03","modified_gmt":"2022-03-08T19:44:03","slug":"browser-retirement","status":"publish","type":"post","link":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/10\/28\/browser-retirement\/","title":{"rendered":"Three outdated browsers (1000 Genomes, dbGaP Data, and Get-RM) to retire in April 2022. Data available in GDV"},"content":{"rendered":"<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\u00a0 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>\n<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.\u00a0 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>\n<p><!--more--><\/p>\n<h2>1000 Genomes<\/h2>\n<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\u00a0 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 style=\"font-size: 1.125rem;\">dbSNP<\/span><\/a><span style=\"font-size: 1.125rem;\">. 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.\u00a0 \u00a0 Currently you can access these data in the following ways.<\/span><\/p>\n<ol>\n<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>\n<li>Search for 1000G variants in dbSNP\u00a0 using <a style=\"background-color: #ffffff; font-size: 1.125rem;\" 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\">1000genomes[Submitter Handle]<\/a><span style=\"font-size: 1.125rem;\"> .<\/span><\/li>\n<li>Download the data from the <a style=\"background-color: #ffffff; font-size: 1.125rem;\" href=\"https:\/\/www.internationalgenome.org\/data\">1000Genomes project site<\/a><span style=\"font-size: 1.125rem;\">\u00a0or from the NCBI <\/span><a class=\"external-link\" style=\"background-color: #ffffff; font-size: 1.125rem;\" title=\"Follow link\" href=\"https:\/\/ftp-trace.ncbi.nih.gov\/1000genomes\/ftp\/\" target=\"_blank\" rel=\"nofollow noopener\">FTP\u00a0<\/a><span style=\"font-size: 1.125rem;\">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 style=\"font-size: 1.125rem;\">. sites.<\/span><\/li>\n<\/ol>\n<h2><img data-recalc-dims=\"1\" loading=\"lazy\" decoding=\"async\" data-attachment-id=\"7118\" data-permalink=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/10\/28\/browser-retirement\/ins_region_gdv\/\" data-orig-file=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2021\/10\/ins_region_gdv.png?fit=1638%2C1086&ssl=1\" data-orig-size=\"1638,1086\" data-comments-opened=\"1\" data-image-meta=\"{"aperture":"0","credit":"","camera":"","caption":"","created_timestamp":"0","copyright":"","focal_length":"0","iso":"0","shutter_speed":"0","title":"","orientation":"0"}\" data-image-title=\"ins_region_gdv\" data-image-description=\"\" data-image-caption=\"\" data-medium-file=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2021\/10\/ins_region_gdv.png?fit=300%2C199&ssl=1\" data-large-file=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2021\/10\/ins_region_gdv.png?fit=1024%2C679&ssl=1\" class=\"alignnone size-large wp-image-7118\" src=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2021\/10\/ins_region_gdv.png?resize=1024%2C679&ssl=1\" alt=\"\" width=\"1024\" height=\"679\" srcset=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2021\/10\/ins_region_gdv.png?resize=1024%2C679&ssl=1 1024w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2021\/10\/ins_region_gdv.png?resize=300%2C199&ssl=1 300w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2021\/10\/ins_region_gdv.png?resize=150%2C99&ssl=1 150w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2021\/10\/ins_region_gdv.png?resize=768%2C509&ssl=1 768w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2021\/10\/ins_region_gdv.png?resize=1536%2C1018&ssl=1 1536w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2021\/10\/ins_region_gdv.png?resize=1200%2C796&ssl=1 1200w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2021\/10\/ins_region_gdv.png?resize=270%2C179&ssl=1 270w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2021\/10\/ins_region_gdv.png?w=1638&ssl=1 1638w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><\/h2>\n<p>Figure 1. GDV and the ‘Configure Tracks’ panel.\u00a0 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>\n<h2>dbGaP Data Browser<\/h2>\n<p>The dbGaP Data Browser (DDB) displayed selected General Research Use sequence data as a read-only view on the human genome assembly.\u00a0 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>\n<h2>GeT-RM<\/h2>\n<p>The\u00a0<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\u00a0<\/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\u00a0 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>\n<p>Thank you for using these browsers. Please contact us with any questions or concerns at <span class=\"nobr\"><a class=\"external-link\" title=\"Follow link\" href=\"mailto:info@ncbi.nlm.nih.gov?subject=NCBI%20Insights%2020211028%20Specialized%20Browser%20Retirements\" target=\"_blank\" rel=\"nofollow noopener\">info@ncbi.nlm.nih.gov<sup><img data-recalc-dims=\"1\" loading=\"lazy\" decoding=\"async\" class=\"rendericon\" src=\"https:\/\/i0.wp.com\/jira.ncbi.nlm.nih.gov\/images\/icons\/mail_small.gif?resize=13%2C12&ssl=1\" alt=\"\" width=\"13\" height=\"12\" align=\"absmiddle\" border=\"0\" \/><\/sup><\/a><\/span>.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>The Genome Data Viewer (GDV) is now the comprehensive NCBI genome browser. The\u00a0 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 … <a href=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/10\/28\/browser-retirement\/\" class=\"more-link\">Continue reading <span class=\"screen-reader-text\">Three outdated browsers (1000 Genomes, dbGaP Data, and Get-RM) to retire in April 2022. Data available in GDV<\/span> <span class=\"meta-nav\">→<\/span><\/a><\/p>\n","protected":false},"author":42204617,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_coblocks_attr":"","_coblocks_dimensions":"","_coblocks_responsive_height":"","_coblocks_accordion_ie_support":"","jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"footnotes":"","jetpack_publicize_message":"Three outdated browsers (1000 Genomes, dbGaP Data, and Get-RM) to retire in April 2022. Data available in GDV","jetpack_publicize_feature_enabled":true,"jetpack_social_post_already_shared":true,"jetpack_social_options":{"image_generator_settings":{"template":"highway","enabled":false},"version":2}},"categories":[2248],"tags":[6611195,14750092,693060707,5381386,574293891,693060671],"table_tags":[],"class_list":["post-7063","post","type-post","status-publish","format-standard","hentry","category-whats-new","tag-1000-genomes","tag-dbgap","tag-gdh","tag-genome-browser","tag-genome-data-viewer","tag-human-variant-data"],"jetpack_publicize_connections":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v24.5 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Three outdated browsers (1000 Genomes, dbGaP Data, and Get-RM) to retire in April 2022. Data available in GDV - NCBI Insights<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/10\/28\/browser-retirement\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<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\" \/>\n<meta property=\"og:description\" content=\"The Genome Data Viewer (GDV) is now the comprehensive NCBI genome browser. The\u00a0 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. 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