Open AccessDOI
GA4GH: International policies and standards for data sharing across genomic research and healthcare
Heidi L. Rehm,Heidi L. Rehm,Angela Page,Lindsay Smith,Jeremy Adams,Gil Alterovitz,Gil Alterovitz,Lawrence J. Babb,Maxmillian P. Barkley,Michael Baudis,Michael Baudis,Michael J.S. Beauvais,Tim Beck,Jacques S. Beckmann,Sergi Beltran,Sergi Beltran,David Bernick,Alexander Bernier,James K. Bonfield,Tiffany Boughtwood,Guillaume Bourque,Sarion R. Bowers,Anthony J. Brookes,Michael Brudno,Matthew H. Brush,David Bujold,Tony Burdett,Orion J. Buske,Moran N. Cabili,Daniel L Cameron,Daniel L Cameron,Robert J. Carroll,Esmeralda Casas-Silva,Debyani Chakravarty,Bimal Chaudhari,Bimal Chaudhari,Shu Hui Chen,J. Michael Cherry,Justina Chung,Melissa S. Cline,Hayley L. Clissold,Robert Cook-Deegan,Mélanie Courtot,Fiona Cunningham,Miro Cupak,Robert L. Davies,Danielle Denisko,Megan Doerr,Lena I. Dolman,Edward S. Dove,L. Jonathan Dursi,Stephanie O.M. Dyke,James A. Eddy,Karen Eilbeck,Kyle Ellrott,Susan Fairley,Khalid A. Fakhro,Khalid A. Fakhro,Helen V. Firth,Michael S. Fitzsimons,Marc Fiume,Paul Flicek,Ian Fore,Mallory A. Freeberg,Robert R. Freimuth,Lauren A. Fromont,Jonathan Fuerth,Clara L. Gaff,Weiniu Gan,Elena M. Ghanaim,David Glazer,Robert C. Green,Robert C. Green,Malachi Griffith,Obi L. Griffith,Robert L. Grossman,Tudor Groza,Jaime M. Guidry Auvil,Roderic Guigó,Dipayan Gupta,Melissa Haendel,Ada Hamosh,David Hansen,Reece K. Hart,Dean Hartley,David Haussler,Rachele M. Hendricks-Sturrup,Calvin W. L. Ho,Ashley E. Hobb,Michael M. Hoffman,Michael M. Hoffman,Oliver Hofmann,Oliver Hofmann,Petr Holub,Jacob Shujui Hsu,Jean-Pierre Hubaux,Sarah E. Hunt,Ammar Husami,Julius O.B. Jacobsen,Saumya Shekhar Jamuar,Elizabeth L. Janes,Francis Jeanson,Aina Jene,Amber L. Johns,Yann Joly,Steven J.M. Jones,Alexander Kanitz,Alexander Kanitz,Kazuto Kato,Thomas M. Keane,Thomas M. Keane,Kristina Kekesi-Lafrance,Jerome Kelleher,Giselle Kerry,Seik-Soon Khor,Bartha Maria Knoppers,Melissa A. Konopko,Kenjiro Kosaki,Martin Kuba,Jonathan Lawson,Rasko Leinonen,Stephanie Li,Michael F. Lin,Mikael Linden,Xianglin Liu,Isuru Udara Liyanage,Javier Lopez,Anneke M. Lucassen,Michael Lukowski,Alice L. Mann,John F. Marshall,Michele Mattioni,Alejandro Metke-Jimenez,Anna Middleton,Richard Milne,Fruzsina Molnár-Gábor,Nicola Mulder,Monica C. Munoz-Torres,Rishi Nag,Hidewaki Nakagawa,Jamal Nasir,Arcadi Navarro,Tristan H. Nelson,Ania Niewielska,Amy Nisselle,Jeffrey Niu,Tommi Nyrönen,Brian O'Connor,Sabine Oesterle,Soichi Ogishima,Vivian Ota Wang,Laura A.D. Paglione,Emilio Palumbo,Helen Parkinson,Anthony A. Philippakis,Angel Pizarro,Andreas Prlic,Jordi Rambla,Augusto Rendon,Renee A. Rider,Peter N. Robinson,Kurt W. Rodarmer,Laura Lyman Rodriguez,Alan F. Rubin,Alan F. Rubin,Manuel Rueda,Gregory A. Rushton,Rosalyn S. Ryan,Gary I. Saunders,Helen Schuilenburg,Torsten Schwede,Torsten Schwede,Serena Scollen,Alexander Senf,Nathan C. Sheffield,Neerjah Skantharajah,Albert V. Smith,Heidi J. Sofia,Dylan Spalding,Amanda B. Spurdle,Zornitza Stark,Lincoln Stein,Lincoln Stein,Makoto Suematsu,Patrick Tan,Patrick Tan,Jonathan A. Tedds,Alastair A. Thomson,Adrian Thorogood,Adrian Thorogood,Timothy L. Tickle,Katsushi Tokunaga,Juha Törnroos,David Torrents,David Torrents,Sean Upchurch,Alfonso Valencia,Alfonso Valencia,Roman Valls Guimera,Jessica Vamathevan,Susheel Varma,Danya F. Vears,Coby Viner,Coby Viner,Craig Voisin,Alex H. Wagner,Alex H. Wagner,Susan E. Wallace,Brian Walsh,Marc S. Williams,Eva C. Winkler,Barbara J. Wold,Grant M. Wood,J. Patrick Woolley,Chisato Yamasaki,Andrew D. Yates,Christina K. Yung,Lyndon J. Zass,Ksenia Zaytseva,Junjun Zhang,Peter Goodhand,Kathryn North,Kathryn North,Ewan Birney +223 more
- Vol. 1, Iss: 2, pp 100029
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TLDR
The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical and genomic data through both harmonized data aggregation and federated approaches.Abstract:
Summary The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical and genomic data through both harmonized data aggregation and federated approaches. The decreasing cost of genomic sequencing (along with other genome-wide molecular assays) and increasing evidence of its clinical utility will soon drive the generation of sequence data from tens of millions of humans, with increasing levels of diversity. In this perspective, we present the GA4GH strategies for addressing the major challenges of this data revolution. We describe the GA4GH organization, which is fueled by the development efforts of eight Work Streams and informed by the needs of 24 Driver Projects and other key stakeholders. We present the GA4GH suite of secure, interoperable technical standards and policy frameworks and review the current status of standards, their relevance to key domains of research and clinical care, and future plans of GA4GH. Broad international participation in building, adopting, and deploying GA4GH standards and frameworks will catalyze an unprecedented effort in data sharing that will be critical to advancing genomic medicine and ensuring that all populations can access its benefits.read more
Citations
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Journal ArticleDOI
The GA4GH Phenopacket schema defines a computable representation of clinical data
Julius O.B. Jacobsen,Michael Baudis,Gareth Baynam,Jacques S. Beckmann,Sergi Beltran,Orion J. Buske,Tiffany J. Callahan,Christopher G. Chute,Mélanie Courtot,Daniel Danis,Olivier Elemento,Andrea Essenwanger,Robert R. Freimuth,Michael A. Gargano,Tudor Groza,Ada Hamosh,Nomi L. Harris,Rajaram Kaliyaperumal,Kevin C K Lloyd,Alyazia Khalifa,Peter Krawitz,Sebastian Köhler,Bryan Laraway,Heikki Lehväslaiho,Leslie Matalonga,Julie A. McMurry,Alejandro Metke-Jimenez,Christopher J. Mungall,Monica Munoz-Torres,Soichi Ogishima,Anastasios Papakonstantinou,D. Piscia,Nikolas Pontikos,Núria Queralt-Rosinach,Marco Roos,Julian Sass,Paul N. Schofield,Dominik Seelow,Anastasios Siapos,Damian Smedley,Lindsay Smith,Robin Steinhaus,Jagadish Chandrabose Sundaramurthi,Emilia M. Swietlik,Sylvia Thun,Nicole Vasilevsky,Alex H. Wagner,Jeremy L. Warner,Claus Weiland,Melissa A. Haendel,Peter N. Robinson +50 more
Journal ArticleDOI
Packaging research artefacts with RO-Crate
TL;DR: RO-Crate as mentioned in this paper is an open, community-driven, and lightweight approach to packaging research artefacts along with their metadata in a machine readable manner, aiming to establish best practices to formally describe metadata in an accessible and practical way for their use in a wide variety of situations.
The Data Use Ontology to streamline responsible access to human biomedical datasets.
Jonathan Lawson,Moran N. Cabili,Giselle Kerry,Tiffany Boughtwood,Adrian Thorogood,Adrian Thorogood,Pinar Alper,Sarion R. Bowers,Rebecca R. Boyles,Anthony J. Brookes,Matthew Brush,Tony Burdett,Hayley L. Clissold,Stacey Donnelly,Stephanie O. M. Dyke,Mallory A. Freeberg,Melissa Haendel,Chihiro Hata,Petr Holub,Francis Jeanson,Aina Jene,Minae Kawashima,Shuichi Kawashima,Melissa A. Konopko,Irene Kyomugisha,Haoyuan Li,Mikael Linden,Laura Lyman Rodriguez,Mizuki Morita,Nicola Mulder,Jean Muller,Satoshi Nagaie,Jamal Nasir,Soichi Ogishima,Vivian Ota Wang,Laura A.D. Paglione,Ravi N. Pandya,Helen Parkinson,Anthony A. Philippakis,Fabian Prasser,Jordi Rambla,Kathy Reinold,Gregory A. Rushton,Andrea Saltzman,Gary I. Saunders,Heidi J. Sofia,John Dylan Spalding,Morris A. Swertz,Ilia Tulchinsky,Esther van Enckevort,Susheel Varma,Craig Voisin,Natsuko Yamamoto,Chisato Yamasaki,Lyndon Zass,Jaime M. Guidry Auvil,Tommi Nyrönen,Mélanie Courtot +57 more
TL;DR: The Data Use Ontology (DUO) as mentioned in this paper is a hierarchical vocabulary of human and machine-readable data use terms that consistently and unambiguously represents a dataset's allowable data uses.
International federation of genomic medicine databases using GA4GH standards
Adrian Thorogood,Adrian Thorogood,Heidi L. Rehm,Heidi L. Rehm,Peter Goodhand,Angela Page,Yann Joly,Michael Baudis,Jordi Rambla,Arcadi Navarro,Tommi Nyrönen,Mikael Linden,Edward S. Dove,Marc Fiume,Michael Brudno,Melissa S. Cline,Ewan Birney +16 more
TL;DR: The GA4GH as mentioned in this paper encourages a federated approach to connect national genomics initiatives into a global network and precision medicine resource, enabling connections and insights across independent, secure databases.
GA4GH Passport standard for digital identity and access permissions.
Craig Voisin,Mikael Linden,Stephanie O.M. Dyke,Sarion R. Bowers,Pinar Alper,Maxmillian P. Barkley,David Bernick,Jianpeng Chao,Mélanie Courtot,Francis Jeanson,Melissa A. Konopko,Martin Kuba,Jonathan Lawson,Jaakko Leinonen,Stephanie Li,Vivian Ota Wang,Anthony A. Philippakis,Kathy Reinold,Gregory A. Rushton,J. Dylan Spalding,Juha Törnroos,Ilya Tulchinsky,Jaime M. Guidry Auvil,Tommi Nyrönen +23 more
TL;DR: The Global Alliance for Genomics and Health (GA4GH) Passport standard as mentioned in this paper defines a machine-readable digital identity that conveys roles and data access permissions (called "visas") for individual users.
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