{"id":1453,"date":"2014-07-31T17:00:25","date_gmt":"2014-07-31T15:00:25","guid":{"rendered":"http:\/\/news.embl.de\/?p=1453"},"modified":"2021-07-13T12:01:18","modified_gmt":"2021-07-13T10:01:18","slug":"1408_api","status":"publish","type":"post","link":"https:\/\/www.embl.org\/news\/lab-matters\/1408_api\/","title":{"rendered":"New genomics API"},"content":{"rendered":"\n<p><a title=\"Genomics API v.0.5\" href=\"http:\/\/ga4gh.org\/#\/api\" target=\"_blank\" rel=\"noopener noreferrer\">Genomics API version 0.5<\/a>&nbsp;is a standards-compliant tool that is the first in a suite of APIs being developed by the Global Alliance for Genomics and Health&nbsp;Data Working Group. It enables the interoperable exchange of information contained in DNA sequence reads across multiple organisations and on multiple platforms. The new software is built on file formats developed over the past five years for large-scale genomic sequencing projects now managed by the Global Alliance, and features cleaner models, a modern, easy-to-use data description schema and a web-enabled interface.<\/p>\n\n\n\n<p>Genomics API is developed and distributed by the Global Alliance for Genomics and Health, which is made up of over 200 of the world\u2019s leading biomedical research institutions, healthcare providers, IT companies, research funders and patient-advocacy organisations. The API builds on the success of v. 0.1, which is already used by the European Bioinformatics Institute (EMBL-EBI), the National Center for Biotechnology Information (NCBI), Google, Genome Savant and Harvard Medical School, powering a growing community of applications.&nbsp;As analysis tools adopt the new API, researchers will be able to extend their own infrastructure to utilise cloud resources, such as those available from Amazon Web Services, Google Cloud Platform, and Microsoft Azure.<\/p>\n\n\n\n<p>Genomics API v. 0.5 uses an open development process to allow the wider bioinformatics community to participate. While the Data Working Group has a core team of active developers, interested developers from any institution are welcome to explore their sample apps, build implementations (from scratch or using existing samples) or provide feedback on the API and its documentation. The interface is managed in the <a title=\"Global Alliance for Genomics and Health developer site\" href=\"http:\/\/ga4gh.org\" target=\"_blank\" rel=\"noopener noreferrer\">Global Alliance for Genomics and Health developer site<\/a>.<\/p>\n\n\n\n<h3 class=\"wp-block-heading\">Comments from leadership<\/h3>\n\n\n\n<p>\u201cThis new Genomics API is an exciting step toward interoperability in genomic data. It advances the Global Alliance\u2019s mission of enabling the sharing of genomic and clinical data to improve human health,\u201d said David Haussler, Co-Chair of the Global Alliance\u2019s Data Working Group and Scientific Director of the UC Santa Cruz Genomics Institute. \u201cBecause this new API lets researchers work consistently with genomic data across institutions and platforms, it will help realise the benefits that come from large-scale genomic data sharing, allowing us to find the needle in the haystack for patients with rare diseases.\u201d<\/p>\n\n\n\n<p>\u201cThe Global Alliance has created a forum for technical collaboration in this important area,\u201d said <a title=\"Ewan Birney\" href=\"http:\/\/www.ebi.ac.uk\/about\/people\/ewan-birney\" target=\"_blank\" rel=\"noopener noreferrer\">EMBL-EBI Associate Director Ewan Birney<\/a>. \u201cGenomics API is one of the first fruits of this collaboration and I\u2019ve been impressed how well the different technical groups from both academia and industry have worked together.\u201d<\/p>\n\n\n\n<p>\u201cGenome sequencing is transitioning from being a powerful research tool to making an enormous impact in clinical diagnostics and care.\u201d Said Richard Durbin, Acting Head of Computational Genomics at the Wellcome Trust Sanger Institute and leader of the Genome Informatics group. \u201cThis API from the Global Alliance Data Working Group will enable genomic data processing to move beyond research file formats into modern computing and data architectures, facilitating controlled data sharing and the effective use of these new technologies for both clinical and research benefit.\u201d<\/p>\n\n\n\n<p>\u201cModern DNA sequencing, when coupled with modern data and cloud technology, can lead to breakthroughs in understanding and improving human health. This new Genomics API is a big step forward,\u201d said David Glazer, co-chair of the Reads Task Team and Engineering Director for Google Cloud Platform and Google Genomics. \u201cGoogle already supports Version 0.1 of the API, and we&#8217;ll be adding support for Version 0.5 soon, as well as continuing to contribute to the Data Working Group.\u201d<\/p>\n\n\n\n<p>\u201cThe Global Alliance is breaking new ground in combining genomic sequencing and clinical care. Amazon Web Services is proud to support these efforts, and help in defining new operating models, such as the latest Genomics API,\u201d said Matt Wood, General Manager of Data Science, Amazon Web Services, Inc. \u201cWe view these new APIs as a vital component for collaboration and development of next-generation tools that can run cost-effectively at massive scale.\u201d<\/p>\n\n\n\n<p>\u201cWe are using the Global Alliance\u2019s work to enable apps for the TBResist initiative that bridge from raw sequence data to clinically useful phenotypes,\u201d said Professor Gil Alterovitz, a faculty at the Harvard Medical School and director of the Biomedical Cybernetics Laboratory. \u201cAlso, the Substitutable Medical Applications and Reusable Technology (SMART) Genomics platform is using the Global Alliance interface to enable interoperability between electronic medical record information (HL7) and raw genetic sequence information.\u201d<\/p>\n\n\n\n<p>Other Working Groups of the Global Alliance for Genomics and Health are currently identifying best practices to integrate genomic data into clinical practice, reaching agreement on security protocols, and developing a framework to address ethics and regulatory considerations.<\/p>\n\n\n\n<h3 class=\"wp-block-heading\"><strong>About the Global Alliance for Genomics and Health<\/strong><\/h3>\n\n\n\n<p>The Global Alliance for Genomics and Health is an international, non-profit alliance formed to help accelerate the potential of genomic medicine to advance human health. Bringing together over 190 leading institutions working in healthcare, research, disease and patient advocacy, life science, and information technology, partners in the Global Alliance are working together to create a common framework of standards and harmonized approaches to enable the responsible, voluntary, and secure sharing of genomic and clinical data.<\/p>\n\n\n\n<p><em>This post was originally published on <a href=\"https:\/\/www.ebi.ac.uk\/about\/news\/press-releases\/genomics-api\" target=\"_blank\" rel=\"canonical nofollow noopener noreferrer\" data-href=\"https:\/\/www.ebi.ac.uk\/about\/news\/press-releases\/genomics-api\">EMBL-EBI News.<\/a><\/em><\/p>\n","protected":false},"excerpt":{"rendered":"<p>New genomics API allows researchers to share anonymised genetic data seamlessly across platforms.<\/p>\n","protected":false},"author":13,"featured_media":1456,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":""},"categories":[3],"tags":[368,782,36,42],"embl_taxonomy":[],"class_list":["post-1453","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-lab-matters","tag-birney","tag-database","tag-embl-ebi","tag-genomics"],"acf":{"article_intro":"<p>The Global Alliance for Genomics and Health has released a new, open-source Application Programming Interface (API) that will allow DNA data providers and consumers to better share information and work together on a global scale.<\/p>\n","related_links":[{"link_description":"Get new Genomics API from the Global Alliance ","link_url":"http:\/\/ga4gh.org\/#\/api"},{"link_description":"Global Alliance for Genomics and Health","link_url":"http:\/\/genomicsandhealth.org\/"},{"link_description":"Read this news item on the EMBL-EBI website","link_url":"http:\/\/www.ebi.ac.uk\/about\/news\/press-releases\/genomics-api"},{"link_description":"This consortium press release originally appeared on Global Alliance member websites on 31 July 2014","link_url":"http:\/\/genomicsandhealth.org\/files\/public\/Global%20Alliance_DWG%20API%20release%20distribution_forAlliance_1.pdf"}],"article_sources":false,"vf_locked":false,"featured":false,"color":"#007B53"},"embl_taxonomy_terms":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v26.2 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>New Genomics API<\/title>\n<meta name=\"description\" content=\"New genomics API allows researchers to share anonymised genetic data seamlessly across platforms.\" \/>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.embl.org\/news\/lab-matters\/1408_api\/\" \/>\n<meta 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