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{"id":11747,"date":"2023-07-13T11:10:54","date_gmt":"2023-07-13T15:10:54","guid":{"rendered":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/?p=11747"},"modified":"2023-07-18T13:57:17","modified_gmt":"2023-07-18T17:57:17","slug":"dbgap-third-party-annotations","status":"publish","type":"post","link":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/07\/13\/dbgap-third-party-annotations\/","title":{"rendered":"dbGaP: Making it Easier to Find Study Data with Third-Party Annotations"},"content":{"rendered":"<p><span data-contrast=\"auto\">The <\/span><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/gap\/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=dbgap-third-party-annotations-20230713\"><span data-contrast=\"none\">database of Genotypes and Phenotypes (dbGaP)<\/span><\/a><span data-contrast=\"auto\"> is a free resource that contains human data from a variety of large-scale studies. While you can\u2019t view individual-level data without applying for controlled access, you can easily find dbGaP studies using the <\/span><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/gap\/advanced_search\/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=dbgap-third-party-annotations-20230713\"><span data-contrast=\"none\">dbGaP Advanced Search<\/span><\/a> (see screenshot below) and q<span data-contrast=\"auto\">uickly filter studies based on study variables, molecular data type, study focus, NIH Institute, study consent, and more. Third-party annotations and mapping of phenotypic and study variables to controlled vocabularies allow you to search across studies. Once you find a study of interest, you can follow the <\/span><a href=\"https:\/\/dbgap.ncbi.nlm.nih.gov\/aa\/wga.cgi?page=login&utm_source=ncbi_insights&utm_medium=referral&utm_campaign=dbgap-third-party-annotations-20230713\"><span data-contrast=\"none\">Authorized Access link<\/span><\/a><span data-contrast=\"auto\"> on records to apply for access.<\/span><span data-ccp-props=\"{"201341983":0,"335559739":0,"335559740":240}\">\u00a0<\/span><\/p>\n<h5>Phenotypic and study variables include:<\/h5>\n<ul>\n<li data-leveltext=\"\uf0b7\" data-font=\"Symbol\" data-listid=\"1\" data-list-defn-props=\"{"335552541":1,"335559684":-2,"335559685":720,"335559991":360,"469769226":"Symbol","469769242":[8226],"469777803":"left","469777804":"\uf0b7","469777815":"hybridMultilevel"}\" aria-setsize=\"-1\" data-aria-posinset=\"1\" data-aria-level=\"1\"><span data-contrast=\"auto\">Clinical measures (e.g., height, weight, blood pressure)<\/span><span data-ccp-props=\"{"201341983":0,"335559739":0,"335559740":240}\">\u00a0<\/span><\/li>\n<li data-leveltext=\"\uf0b7\" data-font=\"Symbol\" data-listid=\"1\" data-list-defn-props=\"{"335552541":1,"335559684":-2,"335559685":720,"335559991":360,"469769226":"Symbol","469769242":[8226],"469777803":"left","469777804":"\uf0b7","469777815":"hybridMultilevel"}\" aria-setsize=\"-1\" data-aria-posinset=\"2\" data-aria-level=\"1\"><span data-contrast=\"auto\">Demographic information (e.g., age, gender, ethnicity)<\/span><span data-ccp-props=\"{"201341983":0,"335559739":0,"335559740":240}\">\u00a0<\/span><\/li>\n<li data-leveltext=\"\uf0b7\" data-font=\"Symbol\" data-listid=\"1\" data-list-defn-props=\"{"335552541":1,"335559684":-2,"335559685":720,"335559991":360,"469769226":"Symbol","469769242":[8226],"469777803":"left","469777804":"\uf0b7","469777815":"hybridMultilevel"}\" aria-setsize=\"-1\" data-aria-posinset=\"3\" data-aria-level=\"1\"><span data-contrast=\"auto\">Sample information (e.g., analyte type, body site)<\/span><span data-ccp-props=\"{"201341983":0,"335559739":0,"335559740":240}\">\u00a0<\/span><\/li>\n<li data-leveltext=\"\uf0b7\" data-font=\"Symbol\" data-listid=\"1\" data-list-defn-props=\"{"335552541":1,"335559684":-2,"335559685":720,"335559991":360,"469769226":"Symbol","469769242":[8226],"469777803":"left","469777804":"\uf0b7","469777815":"hybridMultilevel"}\" aria-setsize=\"-1\" data-aria-posinset=\"3\" data-aria-level=\"1\"><span data-contrast=\"auto\">Molecular data type (e.g., DNA sequence, genotypes, gene expression)<\/span><span data-ccp-props=\"{"201341983":0,"335559739":0,"335559740":240}\">\u00a0<\/span><\/li>\n<\/ul>\n<p><!--more--><\/p>\n<p><img data-recalc-dims=\"1\" loading=\"lazy\" decoding=\"async\" data-attachment-id=\"11792\" data-permalink=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/07\/13\/dbgap-third-party-annotations\/dbgap-2\/\" data-orig-file=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/07\/dbGaP.png?fit=1238%2C844&ssl=1\" data-orig-size=\"1238,844\" 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=\"dbGaP\" data-image-description=\"\" data-image-caption=\"\" data-medium-file=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/07\/dbGaP.png?fit=300%2C205&ssl=1\" data-large-file=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/07\/dbGaP.png?fit=1024%2C698&ssl=1\" class=\"alignright size-full wp-image-11792\" src=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/07\/dbGaP.png?resize=1108%2C755&ssl=1\" alt=\"\" width=\"1108\" height=\"755\" srcset=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/07\/dbGaP.png?w=1238&ssl=1 1238w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/07\/dbGaP.png?resize=300%2C205&ssl=1 300w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/07\/dbGaP.png?resize=1024%2C698&ssl=1 1024w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/07\/dbGaP.png?resize=150%2C102&ssl=1 150w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/07\/dbGaP.png?resize=768%2C524&ssl=1 768w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/07\/dbGaP.png?resize=1200%2C818&ssl=1 1200w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/07\/dbGaP.png?resize=270%2C184&ssl=1 270w\" sizes=\"auto, (max-width: 1108px) 100vw, 1108px\" \/><\/p>\n<p><span data-contrast=\"auto\">Outside groups have also provided additional annotations to help standardize and harmonize the terms used to describe phenotypes and variables. These include mapping to controlled vocabularies in the <\/span><a href=\"https:\/\/www.nlm.nih.gov\/research\/umls\/knowledge_sources\/metathesaurus\/index.html?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=dbgap-third-party-annotations-20230713\"><span data-contrast=\"none\">Unified Medical Language System UMLS Metathesaurus<\/span><\/a><span data-contrast=\"auto\"> including the <\/span><a href=\"https:\/\/loinc.org\/\"><span data-contrast=\"none\">Logical Observation Identifiers Names and Codes (LOINC)<\/span><\/a><span data-contrast=\"auto\"> vocabulary or directly to UMLS <\/span><a href=\"https:\/\/www.nlm.nih.gov\/research\/umls\/new_users\/glossary.html#c\"><span data-contrast=\"none\">Concept Unique Identifiers (CUI)<\/span><\/a><span data-contrast=\"auto\">.\u00a0\u00a0<\/span><span data-ccp-props=\"{"201341983":0,"335559739":0,"335559740":240}\">\u00a0<\/span><\/p>\n<h5>Organizations doing the annotations include:<\/h5>\n<ul>\n<li data-leveltext=\"\uf0b7\" data-font=\"Symbol\" data-listid=\"5\" data-list-defn-props=\"{"335552541":1,"335559684":-2,"335559685":720,"335559991":360,"469769226":"Symbol","469769242":[8226],"469777803":"left","469777804":"\uf0b7","469777815":"hybridMultilevel"}\" aria-setsize=\"-1\" data-aria-posinset=\"1\" data-aria-level=\"1\"><span data-contrast=\"auto\">NLM\u2019s <\/span><a href=\"https:\/\/lhncbc.nlm.nih.gov\/\"><span data-contrast=\"none\">Lister Hill Center<\/span><\/a><span data-contrast=\"auto\"> mapping to LOINC terms<\/span><span data-ccp-props=\"{"201341983":0,"335559739":0,"335559740":240}\">\u00a0<\/span><\/li>\n<li data-leveltext=\"\uf0b7\" data-font=\"Symbol\" data-listid=\"5\" data-list-defn-props=\"{"335552541":1,"335559684":-2,"335559685":720,"335559991":360,"469769226":"Symbol","469769242":[8226],"469777803":"left","469777804":"\uf0b7","469777815":"hybridMultilevel"}\" aria-setsize=\"-1\" data-aria-posinset=\"2\" data-aria-level=\"1\"><a href=\"https:\/\/medical-data-models.org\/\"><span data-contrast=\"none\">Medical Data Models<\/span><\/a><span data-contrast=\"auto\"> mapping to UMLS CUI terms<\/span><span data-ccp-props=\"{"201341983":0,"335559739":0,"335559740":240}\">\u00a0<\/span><\/li>\n<li data-leveltext=\"\uf0b7\" data-font=\"Symbol\" data-listid=\"5\" data-list-defn-props=\"{"335552541":1,"335559684":-2,"335559685":720,"335559991":360,"469769226":"Symbol","469769242":[8226],"469777803":"left","469777804":"\uf0b7","469777815":"hybridMultilevel"}\" aria-setsize=\"-1\" data-aria-posinset=\"3\" data-aria-level=\"1\"><span data-contrast=\"auto\">NHLBI\u2019s <\/span><a href=\"https:\/\/topmed.nhlbi.nih.gov\/\"><span data-contrast=\"none\">TOPMed project<\/span><\/a><span data-contrast=\"auto\"> mapping cardiovascular disease phenotypes to UMLS terms<\/span><span data-ccp-props=\"{"201341983":0,"335559739":0,"335559740":240}\">\u00a0<\/span><\/li>\n<li data-leveltext=\"\uf0b7\" data-font=\"Symbol\" data-listid=\"5\" data-list-defn-props=\"{"335552541":1,"335559684":-2,"335559685":720,"335559991":360,"469769226":"Symbol","469769242":[8226],"469777803":"left","469777804":"\uf0b7","469777815":"hybridMultilevel"}\" aria-setsize=\"-1\" data-aria-posinset=\"3\" data-aria-level=\"1\"><span data-contrast=\"auto\">The <\/span><a href=\"https:\/\/www.phenx.org\/\"><span data-contrast=\"none\">PhenX project<\/span><\/a><span data-contrast=\"none\"> mapping to LOINC and PhenX terms<\/span><span data-ccp-props=\"{"201341983":0,"335559739":0,"335559740":240}\">\u00a0<\/span><\/li>\n<\/ul>\n<p><span data-contrast=\"auto\">The annotated vocabularies will also be included in the dbGaP FHIR schema searchable through the dbGaP <\/span><a href=\"https:\/\/github.com\/ncbi\/DbGaP-FHIR-API-Docs#readme\"><span data-contrast=\"none\">FHIR API<\/span><\/a><span data-contrast=\"auto\">.<\/span><span data-ccp-props=\"{"201341983":0,"335559739":0,"335559740":240}\">\u00a0<\/span><\/p>\n<h5>Stay up to date<\/h5>\n<p><span data-contrast=\"auto\">Follow us on Twitter<\/span><span data-contrast=\"none\">\u202f<\/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\">\u202f<\/span><span data-contrast=\"auto\">to keep up to date with dbGaP and other NCBI news.<\/span><span data-contrast=\"none\">\u202f\u00a0<\/span><span data-ccp-props=\"{"201341983":0,"335559739":160,"335559740":259}\">\u00a0<\/span><\/p>\n<h5>Questions?<\/h5>\n<p><span data-contrast=\"auto\">If you have questions or would like to provide feedback, please reach out to us at<\/span> <a href=\"mailto:info@ncbi.nlm.nih.gov\"><span data-contrast=\"none\">info@ncbi.nlm.nih.gov<\/span><\/a><span data-contrast=\"none\">.\u00a0\u00a0<\/span><span data-ccp-props=\"{"201341983":0,"335559739":160,"335559740":259}\">\u00a0<\/span><\/p>\n<p><span data-ccp-props=\"{"201341983":0,"335559739":0,"335559740":240}\">\u00a0<\/span><\/p>\n","protected":false},"excerpt":{"rendered":"<p>The database of Genotypes and Phenotypes (dbGaP) is a free resource that contains human data from a variety of large-scale studies. While you can\u2019t view individual-level data without applying for controlled access, you can easily find dbGaP studies using the dbGaP Advanced Search (see screenshot below) and quickly filter studies based on study variables, molecular … <a href=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/07\/13\/dbgap-third-party-annotations\/\" class=\"more-link\">Continue reading <span class=\"screen-reader-text\">dbGaP: Making it Easier to Find Study Data with Third-Party Annotations<\/span> <span class=\"meta-nav\">→<\/span><\/a><\/p>\n","protected":false},"author":42204617,"featured_media":11748,"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":"dbGaP: Making it Easier to Find Study Data with Third-Party Annotations","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":[14750092],"table_tags":[],"class_list":["post-11747","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-whats-new","tag-dbgap"],"jetpack_publicize_connections":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v24.6 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>dbGaP: Making it Easier to Find Study Data with Third-Party Annotations - 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\/2023\/07\/13\/dbgap-third-party-annotations\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"dbGaP: Making it Easier to Find Study Data with Third-Party Annotations - NCBI Insights\" \/>\n<meta property=\"og:description\" content=\"The database of Genotypes and Phenotypes (dbGaP) is a free resource that contains human data from a variety of large-scale studies. 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