{"id":44382,"date":"2021-11-10T17:41:41","date_gmt":"2021-11-10T16:41:41","guid":{"rendered":"https:\/\/www.embl.org\/news\/?p=44382"},"modified":"2024-03-22T15:15:26","modified_gmt":"2024-03-22T14:15:26","slug":"duo-streamlining-access-to-biomedical-datasets","status":"publish","type":"post","link":"https:\/\/www.embl.org\/news\/science\/duo-streamlining-access-to-biomedical-datasets\/","title":{"rendered":"DUO: streamlining access to biomedical datasets"},"content":{"rendered":"\n

A large group of international experts within the Global Alliance for Genomics and Health (GA4GH)<\/a>, including users at EMBL\u2019s European Bioinformatics Institute (EMBL-EBI)<\/a> and the Broad Institute of MIT and Harvard<\/a>, have developed the Data Use Ontology (DUO) standard. DUO annotations allow terms and definitions in data consent forms and data sharing policies to be standardised and machine readable. This helps in streamlining consent to use controlled-access biomedical datasets.<\/p>\n\n\n\n

Human biomedical datasets often contain sensitive information about individuals. Consequently, the owner of the data must take great care when these data are being made available for secondary use by other researchers. Access and sharing of such data need to comply with legal, ethical, and informed consent rules and regulations. Navigating this complex landscape can slow research down as researchers require permission to access sensitive datasets. <\/p>\n\n\n\n

\"Infographic
Infographic showing how DUO is used for depositing and requesting data. Credit: Stephanie Li\/GA4GH<\/figcaption><\/figure>\n\n\n\n

Using the Data Use Ontology (DUO) standard will streamline these processes by supporting a data authorisation and access framework for granting researchers permission to reuse biomedical datasets based on their credentials and research purposes. As described in a recent publication<\/a> in a special issue of Cell Genomics<\/em><\/a>, DUO, together with the GA4GH Passport standard<\/a>, accelerates responsible sharing of biomedical datasets worldwide.<\/p>\n\n\n\n

Moving away from manual workflows<\/h2>\n\n\n\n

To retrieve and reuse biomedical datasets, researchers must submit a data access request to Data Access Committees. This can be a long process as a typical workflow involves manual review of applications against the data use letter that specifies how the dataset can be used, to determine whether access should be granted.<\/p>\n\n\n\n

\u201cResearch consent forms often do not provide clear information about biomedical dataset sharing. Not having a standard way of representing data use conditions can really slow research down when trying to re-use those datasets,\u201d said Melanie Courtot, Metadata Standards Coordinator at EMBL-EBI<\/a> and co-lead of the DUO development team. \u201cUsing the GA4GH DUO standard is a first step to help researchers around the globe access the biomedical data they need quickly and easily.\u201d<\/p>\n\n\n\n

\u201cI\u2019m incredibly thankful to the many contributors to DUO,\u201d added Melanie. \u201cThis was a huge collaborative effort that received input from many international experts and users.\u201d<\/p>\n\n\n\n

A machine-readable vocabulary<\/h2>\n\n\n\n

DUO is a machine-readable standard vocabulary of data use terms, aiming at describing data use conditions and automating the matching of specific datasets against the data access requests. Pairing DUO with the GA4GH Passport<\/a> further automates this step by providing a researcher’s authentication and authorisation levels.<\/p>\n\n\n\n

\u201cOver 200,000 datasets worldwide have already been annotated with DUO terms and it has been successfully implemented in various institutions such as the Broad Institute and the Wellcome Sanger Institute,\u201d said Tommi Nyr\u00f6nen, Head of Node at ELIXIR Finland<\/a>, and co-lead of the GA4GH Data Use and Researcher Identities Work Stream that developed the DUO. \u201cThere\u2019s still more to be done; we want to include different data types and the Resource Entitlement Management System<\/a> tool we are developing and deploying with EGA will leverage both DUO and Passport implementation.\u201d<\/p>\n\n\n\n

Further reading<\/strong><\/h2>\n\n\n\n

This work was published as part of a Cell Genomics<\/em> special issue<\/a> focusing on the work of GA4GH. To find out more, see the list of articles below.<\/p>\n\n\n\n

This post was originally published on EMBL-EBI News<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"

The GA4GH Data Use Ontology (DUO) supports a data authorisation and access framework to streamline consent to use biomedical data<\/p>\n","protected":false},"author":77,"featured_media":44388,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":""},"categories":[2,17591],"tags":[297,918,1345,782,179,36],"embl_taxonomy":[2906],"class_list":["post-44382","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-science","category-science-technology","tag-biomedical","tag-data","tag-data-sharing","tag-database","tag-elixir","tag-embl-ebi","embl_taxonomy-embl-ebi"],"acf":{"featured":true,"show_featured_image":false,"field_target_display":"","article_intro":"

The GA4GH Data Use Ontology (DUO) supports a data authorisation and access framework to streamline consent to use biomedical data<\/p>\n","related_links":[{"link_description":"Global Alliance for Genomics & Health","link_url":"https:\/\/www.ga4gh.org\/"}],"source_article":[{"publication_title":"The Data Use Ontology to streamline responsible access to human biomedical datasets","publication_link":{"title":"","url":"https:\/\/www.cell.com\/cell-genomics\/fulltext\/S2666-979X(21)00035-5","target":""},"publication_authors":"Lawson J., et al.","publication_source":"Cell Genomics","publication_date":"10 November 2021","publication_doi":"10.1016\/j.xgen.2021.100028"},{"publication_title":"GA4GH: international policies and standards for data sharing across genomic research and healthcare","publication_link":{"title":"","url":"https:\/\/www.cell.com\/cell-genomics\/fulltext\/S2666-979X(21)00036-7","target":""},"publication_authors":"Rehm H.L., et al","publication_source":"Cell Genomics","publication_date":"10 November 2021","publication_doi":"10.1016\/j.xgen.2021.100029"},{"publication_title":"International Federation of Genomic Medicine Databases Using GA4GH Standards","publication_link":{"title":"","url":"https:\/\/www.cell.com\/cell-genomics\/fulltext\/S2666-979X(21)00039-2","target":""},"publication_authors":"Thorogood A., et al.","publication_source":"Cell Genomics","publication_date":"10 November 2021","publication_doi":"10.1016\/j.xgen.2021.100032"},{"publication_title":"GA4GH Passport standard for digital identity and access permissions","publication_link":{"title":"","url":"https:\/\/www.cell.com\/cell-genomics\/fulltext\/S2666-979X(21)00037-9","target":""},"publication_authors":"Voisin C., et al.","publication_source":"Cell Genomics","publication_date":"10 November 2021","publication_doi":"10.1016\/j.xgen.2021.100030"},{"publication_title":"Empirical validation of an automated approach to data use oversight","publication_link":{"title":"","url":"https:\/\/www.cell.com\/cell-genomics\/fulltext\/S2666-979X(21)00038-0","target":""},"publication_authors":"Cabili M.N., et al.","publication_source":"Cell Genomics","publication_date":"10 November 2021","publication_doi":"10.1016\/j.xgen.2021.100031"},{"publication_title":"The GA4GH Variation Representation Specification (VRS): a Computational Framework for the Precise Representation and Federated Identification of Molecular Variation","publication_link":{"title":"","url":"https:\/\/www.cell.com\/cell-genomics\/fulltext\/S2666-979X(21)00034-3","target":""},"publication_authors":"Wagner A., et al.","publication_source":"Cell Genomics","publication_date":"10 November 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