101 lines
62 KiB
HTML
101 lines
62 KiB
HTML
<!DOCTYPE html>
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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="dbGaP: Making it Easier to Find Study Data with Third-Party Annotations - NCBI Insights"><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. While you can’t 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 … Continue reading dbGaP: Making it Easier to Find Study Data with Third-Party Annotations →"><meta property="og:url" content="https://ncbiinsights.ncbi.nlm.nih.gov/2023/07/13/dbgap-third-party-annotations/"><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="2023-07-13T15:10:54+00:00"><meta property="article:modified_time" content="2023-07-18T17:57:17+00:00"><meta property="og:image" content="https://ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/07/dbGaP_third-party-annotations-Blog-1-e1689001462497.png"><meta property="og:image:width" content="1100"><meta property="og:image:height" content="575"><meta 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<h1 class="amp-wp-title">dbGaP: Making it Easier to Find Study Data with Third-Party Annotations</h1>
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<time datetime="2023-07-13T15:10:54+00:00">
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2 years ago </time>
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<amp-img width="1024" height="535" src="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/07/dbGaP_third-party-annotations-Blog-1-e1689001462497.png?fit=1024%2C535&ssl=1" class="attachment-large size-large wp-post-image amp-wp-enforced-sizes i-amphtml-layout-intrinsic i-amphtml-layout-size-defined" alt="Background images of a human, brain, rib cage, and double helix. Text says: dbGaP, Database of Genotypes and Phenotypes. Use third party annotations to search across studies." srcset="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/07/dbGaP_third-party-annotations-Blog-1-e1689001462497.png?w=1100&ssl=1 1100w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/07/dbGaP_third-party-annotations-Blog-1-e1689001462497.png?resize=300%2C157&ssl=1 300w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/07/dbGaP_third-party-annotations-Blog-1-e1689001462497.png?resize=1024%2C535&ssl=1 1024w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/07/dbGaP_third-party-annotations-Blog-1-e1689001462497.png?resize=150%2C78&ssl=1 150w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/07/dbGaP_third-party-annotations-Blog-1-e1689001462497.png?resize=768%2C401&ssl=1 768w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/07/dbGaP_third-party-annotations-Blog-1-e1689001462497.png?resize=270%2C141&ssl=1 270w" sizes="auto, (max-width: 1024px) 100vw, 1024px" data-hero-candidate="" layout="intrinsic" disable-inline-width="" data-hero i-amphtml-ssr i-amphtml-layout="intrinsic"><i-amphtml-sizer slot="i-amphtml-svc" class="i-amphtml-sizer"><img alt="" aria-hidden="true" class="i-amphtml-intrinsic-sizer" role="presentation" src="data:image/svg+xml;base64,PHN2ZyBoZWlnaHQ9IjUzNSIgd2lkdGg9IjEwMjQiIHhtbG5zPSJodHRwOi8vd3d3LnczLm9yZy8yMDAwL3N2ZyIgdmVyc2lvbj0iMS4xIi8+"></i-amphtml-sizer><img class="i-amphtml-fill-content i-amphtml-replaced-content" decoding="async" loading="lazy" alt="Background images of a human, brain, rib cage, and double helix. Text says: dbGaP, Database of Genotypes and Phenotypes. Use third party annotations to search across studies." src="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/07/dbGaP_third-party-annotations-Blog-1-e1689001462497.png?fit=1024%2C535&ssl=1" srcset="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/07/dbGaP_third-party-annotations-Blog-1-e1689001462497.png?w=1100&ssl=1 1100w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/07/dbGaP_third-party-annotations-Blog-1-e1689001462497.png?resize=300%2C157&ssl=1 300w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/07/dbGaP_third-party-annotations-Blog-1-e1689001462497.png?resize=1024%2C535&ssl=1 1024w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/07/dbGaP_third-party-annotations-Blog-1-e1689001462497.png?resize=150%2C78&ssl=1 150w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/07/dbGaP_third-party-annotations-Blog-1-e1689001462497.png?resize=768%2C401&ssl=1 768w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/07/dbGaP_third-party-annotations-Blog-1-e1689001462497.png?resize=270%2C141&ssl=1 270w" sizes="auto, (max-width: 1024px) 100vw, 1024px"></amp-img> </figure>
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<div class="amp-wp-article-content">
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<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’t 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}'> </span></p>
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<h5>Phenotypic and study variables include:</h5>
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<ul>
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<li data-leveltext="" 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":"","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}'> </span></li>
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<li data-leveltext="" 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":"","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}'> </span></li>
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<li data-leveltext="" 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":"","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}'> </span></li>
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<li data-leveltext="" 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":"","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}'> </span></li>
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</ul>
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<p></p>
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<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">. </span><span data-ccp-props='{"201341983":0,"335559739":0,"335559740":240}'> </span></p>
|
||
<h5>Organizations doing the annotations include:</h5>
|
||
<ul>
|
||
<li data-leveltext="" 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":"","469777815":"hybridMultilevel"}' aria-setsize="-1" data-aria-posinset="1" data-aria-level="1"><span data-contrast="auto">NLM’s </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}'> </span></li>
|
||
<li data-leveltext="" 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":"","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}'> </span></li>
|
||
<li data-leveltext="" 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":"","469777815":"hybridMultilevel"}' aria-setsize="-1" data-aria-posinset="3" data-aria-level="1"><span data-contrast="auto">NHLBI’s </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}'> </span></li>
|
||
<li data-leveltext="" 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":"","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}'> </span></li>
|
||
</ul>
|
||
<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}'> </span></p>
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<h5>Stay up to date</h5>
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<p><span data-contrast="auto">Follow us on Twitter</span><span data-contrast="none"> </span><a href="https://twitter.com/ncbi"><span data-contrast="none">@NCBI</span></a><span data-contrast="none"> and </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"> </span><span data-contrast="auto">to keep up to date with dbGaP and other NCBI news.</span><span data-contrast="none"> </span><span data-ccp-props='{"201341983":0,"335559739":160,"335559740":259}'> </span></p>
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<h5>Questions?</h5>
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<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">. </span><span data-ccp-props='{"201341983":0,"335559739":160,"335559740":259}'> </span></p>
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