Cell Genomics (Nov 2021)
The Data Use Ontology to streamline responsible access to human biomedical datasets
- Jonathan Lawson,
- Moran N. Cabili,
- Giselle Kerry,
- Tiffany Boughtwood,
- Adrian Thorogood,
- Pinar Alper,
- Sarion R. Bowers,
- Rebecca R. Boyles,
- Anthony J. Brookes,
- Matthew Brush,
- Tony Burdett,
- Hayley Clissold,
- Stacey Donnelly,
- Stephanie O.M. Dyke,
- Mallory A. Freeberg,
- Melissa A. Haendel,
- Chihiro Hata,
- Petr Holub,
- Francis Jeanson,
- Aina Jene,
- Minae Kawashima,
- Shuichi Kawashima,
- Melissa 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 D. Paglione,
- Ravi N. Pandya,
- Helen Parkinson,
- Anthony A. Philippakis,
- Fabian Prasser,
- Jordi Rambla,
- Kathy Reinold,
- Gregory A. Rushton,
- Andrea Saltzman,
- Gary Saunders,
- Heidi J. Sofia,
- John D. Spalding,
- Morris A. Swertz,
- Ilia Tulchinsky,
- Esther J. van Enckevort,
- Susheel Varma,
- Craig Voisin,
- Natsuko Yamamoto,
- Chisato Yamasaki,
- Lyndon Zass,
- Jaime M. Guidry Auvil,
- Tommi H. Nyrönen,
- Mélanie Courtot
Affiliations
- Jonathan Lawson
- Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, MA, USA
- Moran N. Cabili
- Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, MA, USA
- Giselle Kerry
- European Molecular Biology Laboratory—European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- Tiffany Boughtwood
- Australian Genomics, Murdoch Children’s Research Institute, Parkville, VIC, Australia
- Adrian Thorogood
- Centre of Genomics and Policy, Department of Human Genetics, McGill University, Montreal, QC, Canada; ELIXIR-Luxembourg, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
- Pinar Alper
- ELIXIR-Luxembourg, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
- Sarion R. Bowers
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Rebecca R. Boyles
- RTI International, Research Triangle Park, NC, USA
- Anthony J. Brookes
- University of Leicester, Leicester, UK
- Matthew Brush
- University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Tony Burdett
- European Molecular Biology Laboratory—European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- Hayley Clissold
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Stacey Donnelly
- Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, MA, USA
- Stephanie O.M. Dyke
- McGill Centre for Integrative Neuroscience, Montreal Neurological Institute, Department of Neurology & Neurosurgery, Faculty of Medicine, McGill University, Montreal, QC, Canada
- Mallory A. Freeberg
- European Molecular Biology Laboratory—European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- Melissa A. Haendel
- University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Chihiro Hata
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Japan
- Petr Holub
- BBMRI-ERIC, AT and Masaryk University, Brno, Czech Republic
- Francis Jeanson
- University Health Network, Toronto, ON, Canada
- Aina Jene
- Centre de Regulació Genòmica (CRG), Barcelona, Spain
- Minae Kawashima
- National Bioscience Database Center, Japan Science and Technology Agency, Tokyo, Japan
- Shuichi Kawashima
- Database Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Kashiwa, Japan
- Melissa Konopko
- ELIXIR Hub, Wellcome Genome Campus, Hinxton, UK
- Irene Kyomugisha
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Haoyuan Li
- Canada’s Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
- Mikael Linden
- ELIXIR-Finland, CSC - IT Center for Science Ltd, Espoo, Finland
- Laura Lyman Rodriguez
- Patient-Centered Outcomes Research Institute, Washington, DC, USA
- Mizuki Morita
- Okayama University, Okayama, Japan
- Nicola Mulder
- Computational Biology Division, IDM, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Jean Muller
- Laboratoire de Génétique Médicale, Institut de Génétique Médicale d’Alsace, INSERM U1112, Université; de Strasbourg, Strasbourg, France; Laboratoire de Diagnostic Génétique, Institut de Génétique Médicale d’Alsace, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
- Satoshi Nagaie
- Tohoku Medical Megabank Organization (ToMMo), Tohoku University, Sendai, Japan
- Jamal Nasir
- Department of Life Sciences, University of Northampton, Northampton, UK
- Soichi Ogishima
- Tohoku Medical Megabank Organization (ToMMo), Tohoku University, Sendai, Japan
- Vivian Ota Wang
- Office of Data Sharing, National Cancer Institute, NIH, Rockville, MD, USA
- Laura D. Paglione
- Spherical Cow Group, Rego Park, NY 11374, USA
- Ravi N. Pandya
- Microsoft Research, Redmond, WA 98052, USA
- Helen Parkinson
- European Molecular Biology Laboratory—European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- Anthony A. Philippakis
- Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, MA, USA
- Fabian Prasser
- Berlin Institute of Health at Charité—Universitätsmedizin Berlin, Berlin, Germany
- Jordi Rambla
- Centre de Regulació Genòmica (CRG), Barcelona, Spain
- Kathy Reinold
- Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, MA, USA
- Gregory A. Rushton
- Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, MA, USA
- Andrea Saltzman
- Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, MA, USA
- Gary Saunders
- ELIXIR Hub, Wellcome Genome Campus, Hinxton, UK
- Heidi J. Sofia
- National Human Genome Research Institute, NIH, Bethesda, MD, USA
- John D. Spalding
- European Molecular Biology Laboratory—European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- Morris A. Swertz
- Genomics Coordination Center, Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Ilia Tulchinsky
- Google Cloud, Kitchener, ON N2H 5G5, Canada
- Esther J. van Enckevort
- Genomics Coordination Center, Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Susheel Varma
- Health Data Research UK, Gibbs Building, 215 Euston Road, London NW1 2BE, UK
- Craig Voisin
- Google Cloud, Kitchener, ON N2H 5G5, Canada
- Natsuko Yamamoto
- Osaka University, Osaka, Japan
- Chisato Yamasaki
- Osaka University, Osaka, Japan
- Lyndon Zass
- Computational Biology Division, IDM, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Jaime M. Guidry Auvil
- Office of Data Sharing, National Cancer Institute, NIH, Rockville, MD, USA
- Tommi H. Nyrönen
- ELIXIR-Finland, CSC - IT Center for Science Ltd, Espoo, Finland
- Mélanie Courtot
- European Molecular Biology Laboratory—European Bioinformatics Institute (EMBL-EBI), Hinxton, UK; Corresponding author
- Journal volume & issue
-
Vol. 1,
no. 2
p. 100028
Abstract
Summary: Human biomedical datasets that are critical for research and clinical studies to benefit human health also often contain sensitive or potentially identifying information of individual participants. Thus, care must be taken when they are processed and made available to comply with ethical and regulatory frameworks and informed consent data conditions. To enable and streamline data access for these biomedical datasets, the Global Alliance for Genomics and Health (GA4GH) Data Use and Researcher Identities (DURI) work stream developed and approved the Data Use Ontology (DUO) standard. DUO is a hierarchical vocabulary of human and machine-readable data use terms that consistently and unambiguously represents a dataset’s allowable data uses. DUO has been implemented by major international stakeholders such as the Broad and Sanger Institutes and is currently used in annotation of over 200,000 datasets worldwide. Using DUO in data management and access facilitates researchers’ discovery and access of relevant datasets. DUO annotations increase the FAIRness of datasets and support data linkages using common data use profiles when integrating the data for secondary analyses. DUO is implemented in the Web Ontology Language (OWL) and, to increase community awareness and engagement, hosted in an open, centralized GitHub repository. DUO, together with the GA4GH Passport standard, offers a new, efficient, and streamlined data authorization and access framework that has enabled increased sharing of biomedical datasets worldwide.
