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{"id":13751,"date":"2024-08-21T11:38:57","date_gmt":"2024-08-21T15:38:57","guid":{"rendered":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/?p=13751"},"modified":"2024-08-23T10:28:50","modified_gmt":"2024-08-23T14:28:50","slug":"access-mpox-data-through-ncbi-virus","status":"publish","type":"post","link":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/08\/21\/access-mpox-data-through-ncbi-virus\/","title":{"rendered":"Quick & Easy Access to Mpox Data Through NCBI Virus"},"content":{"rendered":"<p><span data-contrast=\"none\">The <\/span><a href=\"https:\/\/www.who.int\/news\/item\/14-08-2024-who-director-general-declares-mpox-outbreak-a-public-health-emergency-of-international-concern\"><span data-contrast=\"none\">World Health Organization (WHO)<\/span><\/a>\u00a0<span data-contrast=\"none\">declared the<\/span><span data-contrast=\"none\"> recent <\/span><span data-contrast=\"none\">upsurge of the mpox virus to be a public health emergency of international concern.\u202fHaving timely viral genome data freely and widely available enables researchers to explore how this virus differs from viruses isolated and sequenced in the past. <\/span><span data-contrast=\"none\">Therefore, NCBI\u2019s <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/genbank\/?utm_source=ncbi_insights&utm_medium=referral&utm_term=virus-mpox-20240821\">GenBank<\/a> is expediting the release of mpox data by annotating gene and coding region features as part of the submission process<\/span><span data-contrast=\"none\">.<\/span><span data-ccp-props=\"{}\">\u00a0<\/span><!--more--><\/p>\n<p><span data-contrast=\"none\">You can access mpox sequences <\/span><span data-contrast=\"none\">shortly after public release<\/span><span data-contrast=\"none\"> through <\/span><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/labs\/virus\/vssi\/?utm_source=ncbi_insights&utm_medium=referral&utm_term=virus-mpox-20240821#\/\"><span data-contrast=\"none\">NCBI Virus<\/span><\/a><span data-contrast=\"none\">. <\/span><span data-contrast=\"none\">Apply several filters to narrow down sequence records by collection date, release date, or the geographic region of origin and more. You can then quickly download FASTA sequences with customizable description lines or download the metadata table which includes accessions, submitter names, affiliated institutions, and the country of the institutions useful for citing the data sources.<\/span><span data-contrast=\"none\">\u00a0<\/span><span data-ccp-props=\"{}\">\u00a0<\/span><\/p>\n<p>Use NCBI Datasets command-line (CLI) tool for programmatic access to mpox data. <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/datasets\/docs\/v2\/download-and-install\/?utm_source=ncbi_insights&utm_medium=referral&utm_term=virus-mpox-20240821\">Download and install<\/a> client. See our <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/datasets\/docs\/v2\/how-tos\/virus\/virus-download\/?utm_source=ncbi_insights&utm_medium=referral&utm_term=virus-mpox-20240821\">how-to guide<\/a> to get started.<\/p>\n<h5><b><span data-contrast=\"none\">Submit your data<\/span><\/b><span data-ccp-props=\"{}\">\u00a0<\/span><\/h5>\n<p><span data-contrast=\"none\">Have you sequenced mpox virus isolates? Consider submitting your data to NCBI. Please submit raw sequence reads to <\/span><a href=\"https:\/\/submit.ncbi.nlm.nih.gov\/about\/sra\/?utm_source=ncbi_insights&utm_medium=referral&utm_term=virus-mpox-20240821\"><span data-contrast=\"none\">Sequence Read Archive (SRA)<\/span><\/a><span data-contrast=\"none\"> and assembled mpox sequences to <\/span><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/WebSub\/?utm_source=ncbi_insights&utm_medium=referral&utm_term=virus-mpox-20240821\"><span data-contrast=\"none\">GenBank<\/span><\/a><span data-contrast=\"none\">. Check out our <\/span><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/genbank\/monkeypox_submission\/?utm_source=ncbi_insights&utm_medium=referral&utm_term=virus-mpox-20240821\"><span data-contrast=\"none\">step-by step instructions<\/span><\/a><span data-contrast=\"none\"> to get started. Gene\/protein annotation is not necessary for <\/span><span data-contrast=\"none\">mpox sequence<\/span><span data-contrast=\"none\"> submission<\/span><span data-contrast=\"none\"> since it will be added by the GenBank team using <\/span><a href=\"https:\/\/github.com\/ncbi\/vadr\"><span data-contrast=\"none\">VADR<\/span><\/a>,<span data-contrast=\"none\"> which was updated for mpox.<\/span><span data-ccp-props=\"{}\">\u00a0<\/span><\/p>\n<h5><b><span data-contrast=\"none\">Stay up to date<\/span><\/b><span data-ccp-props=\"{"134233117":true,"134233118":true,"201341983":0,"335557856":16777215,"335559740":240}\">\u00a0<\/span><\/h5>\n<p><span data-contrast=\"none\">Follow us on social <\/span><a href=\"https:\/\/twitter.com\/ncbi\"><span data-contrast=\"none\">@NCBI<\/span><\/a><span data-contrast=\"none\">\u202fand\u202f<\/span><a href=\"https:\/\/public.govdelivery.com\/accounts\/USNLMOCPL\/subscriber\/new?topic_id=USNLMOCPL_52\"><span data-contrast=\"none\">join our mailing list<\/span><\/a><span data-contrast=\"none\">\u202fto keep up to date with GenBank and other NCBI news.<\/span><span data-ccp-props=\"{"134233117":true,"134233118":true,"201341983":0,"335557856":16777215,"335559740":240}\">\u00a0<\/span><\/p>\n<h5><b><span data-contrast=\"none\">Questions?<\/span><\/b><span data-ccp-props=\"{"134233117":true,"134233118":true,"201341983":0,"335557856":16777215,"335559740":240}\">\u00a0<\/span><\/h5>\n<p><span data-contrast=\"none\">Feel free to contact our help desk at\u202f<\/span><a href=\"mailto:info@ncbi.nlm.nih.gov\"><span data-contrast=\"none\">info@ncbi.nlm.nih.gov<\/span><\/a><span data-contrast=\"none\">\u202fif you have any questions or concerns.<\/span><span data-ccp-props=\"{"134233117":true,"134233118":true,"201341983":0,"335557856":16777215,"335559740":240}\">\u00a0<\/span><\/p>\n","protected":false},"excerpt":{"rendered":"<p>The World Health Organization (WHO)\u00a0declared the recent upsurge of the mpox virus to be a public health emergency of international concern.\u202fHaving timely viral genome data freely and widely available enables researchers to explore how this virus differs from viruses isolated and sequenced in the past. Therefore, NCBI\u2019s GenBank is expediting the release of mpox data … <a href=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/08\/21\/access-mpox-data-through-ncbi-virus\/\" class=\"more-link\">Continue reading <span class=\"screen-reader-text\">Quick & Easy Access to Mpox Data Through NCBI Virus<\/span> <span class=\"meta-nav\">→<\/span><\/a><\/p>\n","protected":false},"author":42204617,"featured_media":13757,"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":"Quick & Easy Access to Mpox Data Through NCBI Virus","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":[1201719,693060836,693060764,651448],"table_tags":[],"class_list":["post-13751","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-whats-new","tag-genbank","tag-ncbi-datasets","tag-ncbi-virus","tag-sra"],"jetpack_publicize_connections":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v24.6 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Quick & Easy Access to Mpox Data Through NCBI Virus - 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\/2024\/08\/21\/access-mpox-data-through-ncbi-virus\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Quick & Easy Access to Mpox Data Through NCBI Virus - NCBI Insights\" \/>\n<meta property=\"og:description\" content=\"The World Health Organization (WHO)\u00a0declared the recent upsurge of the mpox virus to be a public health emergency of international concern.\u202fHaving timely viral genome data freely and widely available enables researchers to explore how this virus differs from viruses isolated and sequenced in the past. 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