{"id":467,"date":"2024-02-12T17:04:34","date_gmt":"2024-02-12T17:04:34","guid":{"rendered":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/embl-ebi-programmatically\/open-targets-programmatically\/open-targets-genetics\/"},"modified":"2024-02-12T17:06:15","modified_gmt":"2024-02-12T17:06:15","slug":"open-targets-genetics","status":"publish","type":"page","link":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/embl-ebi-programmatically\/open-targets-programmatically\/open-targets-genetics\/","title":{"rendered":"Open Targets Genetics"},"content":{"rendered":"\n<p>Open Targets Genetics is a tool highlighting variant-centric statistical evidence to allow both prioritisation of candidate causal variants at trait-associated loci and identification of potential drug targets. It allows users to explore data related to genes, traits, or variants.&nbsp;<\/p>\n\n\n\n<p>This platform integrates functional and biological data, including genetic associations from the literature, UK Biobank, FinnGen, and quantitative trait loci (eQTLs, pQTLs, and sQTLs). We link variants to their proximal and distal target gene(s), to prioritise \u2018causal\u2019 genes at a trait-associated locus. Top-prioritised genes from our Locus-to-Gene scoring algorithm feed into the Open Targets Platform as evidence for target-disease associations.<\/p>\n\n\n\n<p>Open Targets Genetics is accessible via:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>A <a href=\"http:\/\/genetics.opentargets.org\/\" target=\"_blank\" rel=\"noreferrer noopener\">web interface<\/a>, in which individual data tables and visualisations can be downloaded for further analysis<\/li>\n\n\n\n<li>The <a href=\"https:\/\/genetics.opentargets.org\/api\" target=\"_blank\" rel=\"noreferrer noopener\">GraphQL API<\/a>, accessible with the programming language of your choice, or <a href=\"https:\/\/api.genetics.opentargets.org\/graphql\/browser\" target=\"_blank\" rel=\"noreferrer noopener\">API playground<\/a> with built-in documentation, which is useful for constructing and testing queries<\/li>\n<\/ul>\n\n\n\n<ul class=\"wp-block-list\">\n<li>The Google BigQuery instance \u2014 project <a href=\"https:\/\/console.cloud.google.com\/bigquery?project=open-targets-genetics&amp;p=open-targets-genetics&amp;d=genetics&amp;page=dataset\" target=\"_blank\" rel=\"noreferrer noopener\">open-targets-genetics:genetics<\/a> \u2014 which supports SQL-like queries. Open Targets Genetics data is available as a <a href=\"https:\/\/console.cloud.google.com\/marketplace\/product\/bigquery-public-data\/open-targets-genetics?project=open-targets-genetics\" target=\"_blank\" rel=\"noreferrer noopener\">Google Cloud public dataset<\/a>.<\/li>\n\n\n\n<li>The <a href=\"https:\/\/ftp.ebi.ac.uk\/pub\/databases\/opentargets\/genetics\/\" target=\"_blank\" rel=\"noreferrer noopener\">FTP data downloads<\/a>, to explore specific datasets and integrate them into your own pipelines.<\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\">For further information and help<\/h2>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Visit the documentation (<a href=\"https:\/\/platform-docs.opentargets.org\/\" target=\"_blank\" rel=\"noreferrer noopener\">Open Targets Platform<\/a>, including our <a href=\"https:\/\/platform-docs.opentargets.org\/data-access\" target=\"_blank\" rel=\"noreferrer noopener\">data access documentation<\/a> with sample scripts; <a href=\"https:\/\/genetics-docs.opentargets.org\/\" target=\"_blank\" rel=\"noreferrer noopener\">Open Targets Genetics<\/a>, including <a href=\"https:\/\/genetics-docs.opentargets.org\/data-access\/data-download\" target=\"_blank\" rel=\"noreferrer noopener\">data access documentation<\/a>)<\/li>\n\n\n\n<li>Watch the <a href=\"https:\/\/www.ebi.ac.uk\/training\/events\/exploring-target-disease-associations-open-targets-platforms-new-interface\/\" target=\"_blank\" rel=\"noreferrer noopener\">full introductory webinar<\/a> to the Open Targets Platform, or the <a href=\"https:\/\/www.ebi.ac.uk\/training\/events\/getting-started-open-targets-platform-graphql-api\/\" target=\"_blank\" rel=\"noreferrer noopener\">introduction to the GraphQL API<\/a><\/li>\n\n\n\n<li>Take a look at the <a href=\"https:\/\/github.com\/opentargets\/platform\" target=\"_blank\" rel=\"noreferrer noopener\">source code on GitHub<\/a><\/li>\n\n\n\n<li>Join the <a href=\"https:\/\/community.opentargets.org\/\" target=\"_blank\" rel=\"noreferrer noopener\">Open Targets Community<\/a> for FAQs, user questions, and example code<\/li>\n\n\n\n<li>Read the <a href=\"https:\/\/blog.opentargets.org\/\" target=\"_blank\" rel=\"noreferrer noopener\">Open Targets Blog<\/a> for in-depth dives into the software underpinning the Platform<\/li>\n<\/ul>\n\n\n\n<p>If you\u2019d like regular updates: we are on <a href=\"https:\/\/twitter.com\/opentargets\" target=\"_blank\" rel=\"noreferrer noopener\">Twitter @opentargets<\/a>, <a href=\"https:\/\/www.linkedin.com\/company\/open-targets\/\" target=\"_blank\" rel=\"noreferrer noopener\">on LinkedIn<\/a>, we post video walkthroughs and explanations on <a href=\"https:\/\/www.youtube.com\/opentargets\" target=\"_blank\" rel=\"noreferrer noopener\">YouTube<\/a> and we have a <a href=\"http:\/\/eepurl.com\/gmb5oz\" target=\"_blank\" rel=\"noreferrer noopener\">monthly newsletter<\/a>.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Open Targets Genetics is a tool highlighting variant-centric statistical evidence to allow both prioritisation of candidate causal variants at trait-associated loci and identification of potential drug targets. It allows users to explore data related to genes, traits, or variants.&nbsp; This platform integrates functional and biological data, including genetic associations from the literature, UK Biobank, FinnGen,&#8230;<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":186,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-467","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/embl-ebi-programmatically\/wp-json\/wp\/v2\/pages\/467","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/embl-ebi-programmatically\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/embl-ebi-programmatically\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/embl-ebi-programmatically\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/embl-ebi-programmatically\/wp-json\/wp\/v2\/comments?post=467"}],"version-history":[{"count":3,"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/embl-ebi-programmatically\/wp-json\/wp\/v2\/pages\/467\/revisions"}],"predecessor-version":[{"id":475,"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/embl-ebi-programmatically\/wp-json\/wp\/v2\/pages\/467\/revisions\/475"}],"up":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/embl-ebi-programmatically\/wp-json\/wp\/v2\/pages\/186"}],"wp:attachment":[{"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/embl-ebi-programmatically\/wp-json\/wp\/v2\/media?parent=467"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}