{"id":170,"date":"2020-07-31T14:44:09","date_gmt":"2020-07-31T14:44:09","guid":{"rendered":"http:\/\/www.ebi.ac.uk\/training\/online\/courses\/embl-ebi-programmatically\/ensembl-programmatically\/"},"modified":"2024-02-13T10:21:57","modified_gmt":"2024-02-13T10:21:57","slug":"ensembl-programmatically","status":"publish","type":"page","link":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/embl-ebi-programmatically\/ensembl-programmatically\/","title":{"rendered":"Ensembl, programmatically"},"content":{"rendered":"\n<p><a rel=\"noreferrer noopener\" href=\"http:\/\/www.ensembl.org\/\" target=\"_blank\">Ensembl<\/a>&nbsp;provides a genome browser that acts as a single point of access for annotated genomes. Genes, genetic variants and&nbsp;regulatory features&nbsp;are all annotated onto genomes, with comparative genomics analyses carried out on genes and genomes. The&nbsp;<a rel=\"noreferrer noopener\" href=\"http:\/\/rest.ensembl.org\/\" target=\"_blank\">Ensembl REST API<\/a>&nbsp;provides a number of endpoints for flexible programmatic access to all these data. <\/p>\n\n\n\n<p>For a practical introduction to the Ensembl API you can take the <a href=\"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/ensembl-rest-api\/\" target=\"_blank\" rel=\"noreferrer noopener\">Ensembl REST API<\/a> course. You can learn more about Ensembl in our&nbsp;<a rel=\"noreferrer noopener\" href=\"https:\/\/www.ebi.ac.uk\/training\/online\/course\/ensembl-quick-tour-0\" target=\"_blank\">Ensembl: Quick tour.<\/a><\/p>\n\n\n\n<p>This webinar took place on 6th June 2017 and was hosted by Matthew Laird. The webinar includes:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>What is Ensembl? (0:28)<\/li>\n\n\n\n<li>Methods to access Ensembl data&nbsp;(2:00)<\/li>\n\n\n\n<li>The Ensembl REST server documentation. (2:19)<\/li>\n\n\n\n<li>How to query the REST server. (3:32)<\/li>\n\n\n\n<li>Ensembl REST API endpoints (4:47)\n<ul class=\"wp-block-list\">\n<li>What does a HTTP response look like? (7:52)<\/li>\n\n\n\n<li>Content types (9:37)<\/li>\n\n\n\n<li>Chaining requests and decoding the response (10:10)<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>Live example &#8211; fetch a gene based on symbol&nbsp;(11:36)<\/li>\n\n\n\n<li>HTTP methods &#8211; POST requests (13:03)<\/li>\n\n\n\n<li>Where to go for help and documentation&nbsp;(16:47)<\/li>\n<\/ul>\n\n\n\n<figure class=\"wp-block-embed is-type-video is-provider-youtube wp-block-embed-youtube wp-embed-aspect-16-9 wp-has-aspect-ratio\"><div class=\"wp-block-embed__wrapper\">\n<iframe loading=\"lazy\" title=\"EMBL-EBI, programmatically: Ensembl\" width=\"500\" height=\"281\" src=\"https:\/\/www.youtube.com\/embed\/R2R9YOK8VQs?feature=oembed\" frameborder=\"0\" allow=\"accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share\" referrerpolicy=\"strict-origin-when-cross-origin\" allowfullscreen><\/iframe>\n<\/div><\/figure>\n\n\n\n<p><img loading=\"lazy\" decoding=\"async\" width=\"44\" height=\"41\" class=\"wp-image-487\" style=\"width: 44px;\" src=\"http:\/\/www.ebi.ac.uk\/training\/online\/courses\/embl-ebi-programmatically\/wp-content\/uploads\/sites\/128\/2024\/02\/image.png\" alt=\"\"> Please note that at the time of the recording, the\u00a0rest.ensemblgenomes.org\u00a0server was used, however\u00a0<a href=\"http:\/\/rest.ensembl.org\/\" target=\"_blank\" rel=\"noreferrer noopener\">rest.ensembl.org<\/a>\u00a0is now used for all species (vertebrates and non-vertebrates).<\/p>\n\n\n\n<p>You can find out more about&nbsp;<a rel=\"noreferrer noopener\" href=\"http:\/\/rest.ensembl.org\/\" target=\"_blank\">Ensembl REST API endpoints<\/a>&nbsp;and other Ensembl&nbsp;APIs&nbsp;on the Ensembl&nbsp;<a rel=\"noreferrer noopener\" href=\"http:\/\/www.ensembl.org\/info\/index.html\" target=\"_blank\">help pages<\/a>. You can also find a user guide and sample clients on&nbsp;<a rel=\"noreferrer noopener\" href=\"https:\/\/github.com\/Ensembl\/ensembl-rest\/wiki\" target=\"_blank\">GitHub<\/a>.<\/p>\n\n\n\n<p>For help and support with Ensembl get in touch with the&nbsp;<a href=\"http:\/\/www.ensembl.org\/Help\/Contact\" target=\"_blank\" rel=\"noreferrer noopener\">Ensembl help desk<\/a>.<\/p>\n\n\n\n<p>You can download the&nbsp;slides&nbsp;and the scripts used for the&nbsp;gene symbol&nbsp;and&nbsp;loop&nbsp;examples using these links:<\/p>\n\n\n\n<div class=\"wp-block-file\"><a id=\"wp-block-file--media-60d1bf86-2494-482d-82c2-a3b4fa28727c\" href=\"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/embl-ebi-programmatically\/wp-content\/uploads\/sites\/128\/2020\/08\/Ensembl-REST-webinar.pdf\">Ensembl REST webinar<\/a><a href=\"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/embl-ebi-programmatically\/wp-content\/uploads\/sites\/128\/2020\/08\/Ensembl-REST-webinar.pdf\" class=\"wp-block-file__button wp-element-button\" download aria-describedby=\"wp-block-file--media-60d1bf86-2494-482d-82c2-a3b4fa28727c\">Download<\/a><\/div>\n","protected":false},"excerpt":{"rendered":"<p>Ensembl&nbsp;provides a genome browser that acts as a single point of access for annotated genomes. Genes, genetic variants and&nbsp;regulatory features&nbsp;are all annotated onto genomes, with comparative genomics analyses carried out on genes and genomes. The&nbsp;Ensembl REST API&nbsp;provides a number of endpoints for flexible programmatic access to all these data. For a practical introduction to the&#8230;<\/p>\n","protected":false},"author":6,"featured_media":0,"parent":0,"menu_order":4,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-170","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\/170","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\/6"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/embl-ebi-programmatically\/wp-json\/wp\/v2\/comments?post=170"}],"version-history":[{"count":10,"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/embl-ebi-programmatically\/wp-json\/wp\/v2\/pages\/170\/revisions"}],"predecessor-version":[{"id":491,"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/embl-ebi-programmatically\/wp-json\/wp\/v2\/pages\/170\/revisions\/491"}],"wp:attachment":[{"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/embl-ebi-programmatically\/wp-json\/wp\/v2\/media?parent=170"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}