{"id":6449,"date":"2021-08-10T16:33:09","date_gmt":"2021-08-10T20:33:09","guid":{"rendered":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/?p=6449"},"modified":"2021-08-11T11:36:58","modified_gmt":"2021-08-11T15:36:58","slug":"retire-biosystems-database","status":"publish","type":"post","link":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/08\/10\/retire-biosystems-database\/","title":{"rendered":"Biosystems retiring March 2022 \u2014 use PubChem Pathways"},"content":{"rendered":"

The NCBI BioSystems Database<\/a> will be retired in March 2022. This retirement includes the representation of BioSystems records in the NCBI Entrez system and viewers of BioSystems content.<\/p>\n

NCBI now provides metabolic pathway and other biosystems data through the regularly updated PubChem Pathways<\/a> resource that offers a fresh, extended, and more modern interface. See the PubChem blog for more details<\/a> on PubChem Pathways.<\/p>\n

Table 1 presents a snapshot of the richer and more extensive data coverage in PubChem Pathways.<\/p>\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Source database<\/th>\nBioSystems<\/th>\nPubChem Pathways
\n(as of 8\/10\/21)<\/th>\n<\/tr>\n
BioCyc<\/td>\n15,259 records<\/td>\n15,037 records<\/td>\n<\/tr>\n
PlantCyc<\/td>\n<\/td>\n64,851 records<\/td>\n<\/tr>\n
Reactome<\/td>\n20,478 records<\/td>\n26,407 records<\/td>\n<\/tr>\n
Plant Reactome<\/td>\n<\/td>\n18,910 records<\/td>\n<\/tr>\n
NCI Pathway Interaction DB<\/td>\n188 records<\/td>\n745 records<\/td>\n<\/tr>\n
Wiki Pathways<\/td>\n1,478 records<\/td>\n1,823 records<\/td>\n<\/tr>\n
Lipid Maps<\/td>\n14 records<\/td>\n15 records<\/td>\n<\/tr>\n
PharmGKB<\/td>\n<\/td>\n147 records<\/td>\n<\/tr>\n
PathBank<\/td>\n<\/td>\n110,315 records<\/td>\n<\/tr>\n
COVID-19 Disease Map<\/td>\n<\/td>\n20 records<\/td>\n<\/tr>\n
INOH<\/td>\n<\/td>\n511 records<\/td>\n<\/tr>\n
GO<\/td>\n44,525 records<\/td>\n<\/td>\n<\/tr>\n
KEGG<\/td>\n902,026 records<\/td>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

Table 1: Coverage for BioSystems records in PubChem Pathways. In anticipation of retiring BioSystems, we will begin directing relevant queries to PubChem Pathways to provide users with a richer dataset and enhanced user experience.<\/em><\/p>\n

<\/p>\n

Requests to NCBI BioSystems will be directed to PubChem Pathways in order to make the transition as seamless as possible. The static content of NCBI BioSystems will remain available on the BioSystems FTP site<\/a>\u00a0but will not be updated.<\/p>\n

We thank everyone for their support of BioSystems through the years. Please contact us<\/a> with any comments, concerns, or if you need help with the use of BioSystems data.<\/p>\n","protected":false},"excerpt":{"rendered":"

The NCBI BioSystems Database will be retired in March 2022. This retirement includes the representation of BioSystems records in the NCBI Entrez system and viewers of BioSystems content. NCBI now provides metabolic pathway and other biosystems data through the regularly updated PubChem Pathways resource that offers a fresh, extended, and more modern interface. See the … Continue reading Biosystems retiring March 2022 \u2014 use PubChem Pathways<\/span> →<\/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":"NCBI to retire Biosystems database in March 2022","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":[6088049],"table_tags":[],"class_list":["post-6449","post","type-post","status-publish","format-standard","hentry","category-whats-new","tag-pubchem"],"jetpack_publicize_connections":[],"yoast_head":"\nBiosystems retiring March 2022 \u2014 use PubChem Pathways - 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\/08\/10\/retire-biosystems-database\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Biosystems retiring March 2022 \u2014 use PubChem Pathways - NCBI Insights\" \/>\n<meta property=\"og:description\" content=\"The NCBI BioSystems Database will be retired in March 2022. This retirement includes the representation of BioSystems records in the NCBI Entrez system and viewers of BioSystems content. NCBI now provides metabolic pathway and other biosystems data through the regularly updated PubChem Pathways resource that offers a fresh, extended, and more modern interface. See the … Continue reading Biosystems retiring March 2022 \u2014 use PubChem Pathways →\" \/>\n<meta property=\"og:url\" content=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/08\/10\/retire-biosystems-database\/\" \/>\n<meta property=\"og:site_name\" content=\"NCBI Insights\" \/>\n<meta property=\"article:publisher\" content=\"https:\/\/www.facebook.com\/ncbi.nlm\" \/>\n<meta property=\"article:published_time\" content=\"2021-08-10T20:33:09+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2021-08-11T15:36:58+00:00\" \/>\n<meta name=\"author\" content=\"NCBI Staff\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:creator\" content=\"@NCBI\" \/>\n<meta name=\"twitter:site\" content=\"@NCBI\" \/>\n<meta name=\"twitter:label1\" content=\"Written by\" \/>\n\t<meta name=\"twitter:data1\" content=\"NCBI Staff\" \/>\n\t<meta name=\"twitter:label2\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data2\" content=\"1 minute\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"Article\",\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/08\/10\/retire-biosystems-database\/#article\",\"isPartOf\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/08\/10\/retire-biosystems-database\/\"},\"author\":{\"name\":\"NCBI Staff\",\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#\/schema\/person\/4f41ea6a31cea38a9a1b1419c048e50b\"},\"headline\":\"Biosystems retiring March 2022 \u2014 use PubChem Pathways\",\"datePublished\":\"2021-08-10T20:33:09+00:00\",\"dateModified\":\"2021-08-11T15:36:58+00:00\",\"mainEntityOfPage\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/08\/10\/retire-biosystems-database\/\"},\"wordCount\":230,\"commentCount\":2,\"publisher\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#organization\"},\"keywords\":[\"PubChem\"],\"articleSection\":[\"What's New\"],\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"CommentAction\",\"name\":\"Comment\",\"target\":[\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/08\/10\/retire-biosystems-database\/#respond\"]}]},{\"@type\":\"WebPage\",\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/08\/10\/retire-biosystems-database\/\",\"url\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/08\/10\/retire-biosystems-database\/\",\"name\":\"Biosystems retiring March 2022 \u2014 use PubChem Pathways - NCBI Insights\",\"isPartOf\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#website\"},\"datePublished\":\"2021-08-10T20:33:09+00:00\",\"dateModified\":\"2021-08-11T15:36:58+00:00\",\"breadcrumb\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/08\/10\/retire-biosystems-database\/#breadcrumb\"},\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"ReadAction\",\"target\":[\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/08\/10\/retire-biosystems-database\/\"]}]},{\"@type\":\"BreadcrumbList\",\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/08\/10\/retire-biosystems-database\/#breadcrumb\",\"itemListElement\":[{\"@type\":\"ListItem\",\"position\":1,\"name\":\"Home\",\"item\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/\"},{\"@type\":\"ListItem\",\"position\":2,\"name\":\"Biosystems retiring March 2022 \u2014 use PubChem Pathways\"}]},{\"@type\":\"WebSite\",\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#website\",\"url\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/\",\"name\":\"National Center for Biotechnology Information\",\"description\":\"News about NCBI resources and events\",\"publisher\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#organization\"},\"potentialAction\":[{\"@type\":\"SearchAction\",\"target\":{\"@type\":\"EntryPoint\",\"urlTemplate\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/?s={search_term_string}\"},\"query-input\":{\"@type\":\"PropertyValueSpecification\",\"valueRequired\":true,\"valueName\":\"search_term_string\"}}],\"inLanguage\":\"en-US\"},{\"@type\":\"Organization\",\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#organization\",\"name\":\"National Center for Biotechnology Information\",\"alternateName\":\"NCBI\",\"url\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/\",\"logo\":{\"@type\":\"ImageObject\",\"inLanguage\":\"en-US\",\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#\/schema\/logo\/image\/\",\"url\":\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/03\/nih-nlm-ncbi-two-color.png?fit=6374%2C760&ssl=1\",\"contentUrl\":\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/03\/nih-nlm-ncbi-two-color.png?fit=6374%2C760&ssl=1\",\"width\":6374,\"height\":760,\"caption\":\"National Center for Biotechnology Information\"},\"image\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#\/schema\/logo\/image\/\"},\"sameAs\":[\"https:\/\/www.facebook.com\/ncbi.nlm\",\"https:\/\/x.com\/NCBI\",\"https:\/\/www.linkedin.com\/company\/ncbinlm\/\"]},{\"@type\":\"Person\",\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#\/schema\/person\/4f41ea6a31cea38a9a1b1419c048e50b\",\"name\":\"NCBI Staff\",\"image\":{\"@type\":\"ImageObject\",\"inLanguage\":\"en-US\",\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#\/schema\/person\/image\/\",\"url\":\"https:\/\/secure.gravatar.com\/avatar\/f706d65e16bb6bb171b72b4b26f66276?s=96&d=identicon&r=g\",\"contentUrl\":\"https:\/\/secure.gravatar.com\/avatar\/f706d65e16bb6bb171b72b4b26f66276?s=96&d=identicon&r=g\",\"caption\":\"NCBI Staff\"},\"description\":\"The National Center for Biotechnology Information (NCBI), a division of the U.S. National Library of Medicine, provides access to scientific and biomedical databases, software tools for analyzing molecular data, and performs research in computational biology.\",\"sameAs\":[\"http:\/\/ncbiinsights.wordpress.com\"],\"url\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/author\/ncbiinsights\/\"}]}<\/script>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"Biosystems retiring March 2022 \u2014 use PubChem Pathways - NCBI Insights","robots":{"index":"index","follow":"follow","max-snippet":"max-snippet:-1","max-image-preview":"max-image-preview:large","max-video-preview":"max-video-preview:-1"},"canonical":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/08\/10\/retire-biosystems-database\/","og_locale":"en_US","og_type":"article","og_title":"Biosystems retiring March 2022 \u2014 use PubChem Pathways - NCBI Insights","og_description":"The NCBI BioSystems Database will be retired in March 2022. This retirement includes the representation of BioSystems records in the NCBI Entrez system and viewers of BioSystems content. NCBI now provides metabolic pathway and other biosystems data through the regularly updated PubChem Pathways resource that offers a fresh, extended, and more modern interface. See the … Continue reading Biosystems retiring March 2022 \u2014 use PubChem Pathways →","og_url":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/08\/10\/retire-biosystems-database\/","og_site_name":"NCBI Insights","article_publisher":"https:\/\/www.facebook.com\/ncbi.nlm","article_published_time":"2021-08-10T20:33:09+00:00","article_modified_time":"2021-08-11T15:36:58+00:00","author":"NCBI Staff","twitter_card":"summary_large_image","twitter_creator":"@NCBI","twitter_site":"@NCBI","twitter_misc":{"Written by":"NCBI Staff","Est. reading time":"1 minute"},"schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"Article","@id":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/08\/10\/retire-biosystems-database\/#article","isPartOf":{"@id":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/08\/10\/retire-biosystems-database\/"},"author":{"name":"NCBI Staff","@id":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#\/schema\/person\/4f41ea6a31cea38a9a1b1419c048e50b"},"headline":"Biosystems retiring March 2022 \u2014 use PubChem Pathways","datePublished":"2021-08-10T20:33:09+00:00","dateModified":"2021-08-11T15:36:58+00:00","mainEntityOfPage":{"@id":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/08\/10\/retire-biosystems-database\/"},"wordCount":230,"commentCount":2,"publisher":{"@id":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#organization"},"keywords":["PubChem"],"articleSection":["What's New"],"inLanguage":"en-US","potentialAction":[{"@type":"CommentAction","name":"Comment","target":["https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/08\/10\/retire-biosystems-database\/#respond"]}]},{"@type":"WebPage","@id":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/08\/10\/retire-biosystems-database\/","url":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/08\/10\/retire-biosystems-database\/","name":"Biosystems retiring March 2022 \u2014 use PubChem Pathways - NCBI Insights","isPartOf":{"@id":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#website"},"datePublished":"2021-08-10T20:33:09+00:00","dateModified":"2021-08-11T15:36:58+00:00","breadcrumb":{"@id":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/08\/10\/retire-biosystems-database\/#breadcrumb"},"inLanguage":"en-US","potentialAction":[{"@type":"ReadAction","target":["https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/08\/10\/retire-biosystems-database\/"]}]},{"@type":"BreadcrumbList","@id":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/08\/10\/retire-biosystems-database\/#breadcrumb","itemListElement":[{"@type":"ListItem","position":1,"name":"Home","item":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/"},{"@type":"ListItem","position":2,"name":"Biosystems retiring March 2022 \u2014 use PubChem Pathways"}]},{"@type":"WebSite","@id":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#website","url":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/","name":"National Center for Biotechnology Information","description":"News about NCBI resources and events","publisher":{"@id":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#organization"},"potentialAction":[{"@type":"SearchAction","target":{"@type":"EntryPoint","urlTemplate":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/?s={search_term_string}"},"query-input":{"@type":"PropertyValueSpecification","valueRequired":true,"valueName":"search_term_string"}}],"inLanguage":"en-US"},{"@type":"Organization","@id":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#organization","name":"National Center for Biotechnology Information","alternateName":"NCBI","url":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/","logo":{"@type":"ImageObject","inLanguage":"en-US","@id":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#\/schema\/logo\/image\/","url":"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/03\/nih-nlm-ncbi-two-color.png?fit=6374%2C760&ssl=1","contentUrl":"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/03\/nih-nlm-ncbi-two-color.png?fit=6374%2C760&ssl=1","width":6374,"height":760,"caption":"National Center for Biotechnology Information"},"image":{"@id":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#\/schema\/logo\/image\/"},"sameAs":["https:\/\/www.facebook.com\/ncbi.nlm","https:\/\/x.com\/NCBI","https:\/\/www.linkedin.com\/company\/ncbinlm\/"]},{"@type":"Person","@id":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#\/schema\/person\/4f41ea6a31cea38a9a1b1419c048e50b","name":"NCBI Staff","image":{"@type":"ImageObject","inLanguage":"en-US","@id":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#\/schema\/person\/image\/","url":"https:\/\/secure.gravatar.com\/avatar\/f706d65e16bb6bb171b72b4b26f66276?s=96&d=identicon&r=g","contentUrl":"https:\/\/secure.gravatar.com\/avatar\/f706d65e16bb6bb171b72b4b26f66276?s=96&d=identicon&r=g","caption":"NCBI Staff"},"description":"The National Center for Biotechnology Information (NCBI), a division of the U.S. National Library of Medicine, provides access to scientific and biomedical databases, software tools for analyzing molecular data, and performs research in computational biology.","sameAs":["http:\/\/ncbiinsights.wordpress.com"],"url":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/author\/ncbiinsights\/"}]}},"jetpack_featured_media_url":"","jetpack_likes_enabled":true,"jetpack_sharing_enabled":true,"jetpack_shortlink":"https:\/\/wp.me\/p2Tuqy-1G1","amp_enabled":true,"_links":{"self":[{"href":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/wp-json\/wp\/v2\/posts\/6449","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/wp-json\/wp\/v2\/users\/42204617"}],"replies":[{"embeddable":true,"href":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/wp-json\/wp\/v2\/comments?post=6449"}],"version-history":[{"count":24,"href":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/wp-json\/wp\/v2\/posts\/6449\/revisions"}],"predecessor-version":[{"id":6481,"href":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/wp-json\/wp\/v2\/posts\/6449\/revisions\/6481"}],"wp:attachment":[{"href":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/wp-json\/wp\/v2\/media?parent=6449"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/wp-json\/wp\/v2\/categories?post=6449"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/wp-json\/wp\/v2\/tags?post=6449"},{"taxonomy":"table_tags","embeddable":true,"href":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/wp-json\/wp\/v2\/table_tags?post=6449"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}