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Voisin C, Linden M, Dyke SO, Bowers SR, Alper P, Barkley MP, Bernick D, Chao J, Courtot M, Jeanson F, Konopko MA, Kuba M, Lawson J, Leinonen J, Li S, Ota Wang V, Philippakis AA, Reinold K, Rushton GA, Spalding JD, Törnroos J, Tulchinsky I, Guidry Auvil JM, Nyrönen TH. GA4GH Passport standard for digital identity and access permissions. CELL GENOMICS 2021; 1:None. [PMID: 34820660 PMCID: PMC8591913 DOI: 10.1016/j.xgen.2021.100030] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 07/08/2021] [Accepted: 09/02/2021] [Indexed: 12/21/2022]
Abstract
The Global Alliance for Genomics and Health (GA4GH) supports international standards that enable a federated data sharing model for the research community while respecting data security, ethical and regulatory frameworks, and data authorization and access processes for sensitive data. The GA4GH Passport standard (Passport) defines a machine-readable digital identity that conveys roles and data access permissions (called "visas") for individual users. Visas are issued by data stewards, including data access committees (DACs) working with public databases, the entities responsible for the quality, integrity, and access arrangements for the datasets in the management of human biomedical data. Passports streamline management of data access rights across data systems by using visas that present a data user's digital identity and permissions across organizations, tools, environments, and services. We describe real-world implementations of the GA4GH Passport standard in use cases from ELIXIR Europe, National Institutes of Health, and the Autism Sharing Initiative. These implementations demonstrate that the Passport standard has provided transparent mechanisms for establishing permissions and authorizing data access across platforms.
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Affiliation(s)
- Craig Voisin
- Google LLC, Kitchener, ON N2H 5G5, Canada,Corresponding author
| | - Mikael Linden
- CSC–IT Center for Science, Espoo 02101, Finland,ELIXIR Finland, Espoo 02101, Finland
| | - Stephanie O.M. Dyke
- McGill Centre for Integrative Neuroscience, McGill University, Montreal, QC H3A 2B4, Canada
| | | | - Pinar Alper
- ELIXIR Luxembourg, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4367 Belvaux, Luxembourg
| | | | - David Bernick
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Mélanie Courtot
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire CB10 1SD, UK
| | | | - Melissa A. Konopko
- Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK,Global Alliance for Genomics and Health, Toronto, ON M5G 0A3, Canada
| | - Martin Kuba
- Masaryk University, Brno 602 00, Czech Republic
| | - Jonathan Lawson
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Stephanie Li
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Global Alliance for Genomics and Health, Toronto, ON M5G 0A3, Canada
| | - Vivian Ota Wang
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Kathy Reinold
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - J. Dylan Spalding
- CSC–IT Center for Science, Espoo 02101, Finland,ELIXIR Finland, Espoo 02101, Finland
| | - Juha Törnroos
- CSC–IT Center for Science, Espoo 02101, Finland,ELIXIR Finland, Espoo 02101, Finland
| | | | | | - Tommi H. Nyrönen
- CSC–IT Center for Science, Espoo 02101, Finland,ELIXIR Finland, Espoo 02101, Finland,Corresponding author
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Jalili V, Afgan E, Gu Q, Clements D, Blankenberg D, Goecks J, Taylor J, Nekrutenko A. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update. Nucleic Acids Res 2020; 48:W395-W402. [PMID: 32479607 PMCID: PMC7319590 DOI: 10.1093/nar/gkaa434] [Citation(s) in RCA: 254] [Impact Index Per Article: 63.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/24/2020] [Accepted: 05/11/2020] [Indexed: 12/18/2022] Open
Abstract
Galaxy (https://galaxyproject.org) is a web-based computational workbench used by tens of thousands of scientists across the world to analyze large biomedical datasets. Since 2005, the Galaxy project has fostered a global community focused on achieving accessible, reproducible, and collaborative research. Together, this community develops the Galaxy software framework, integrates analysis tools and visualizations into the framework, runs public servers that make Galaxy available via a web browser, performs and publishes analyses using Galaxy, leads bioinformatics workshops that introduce and use Galaxy, and develops interactive training materials for Galaxy. Over the last two years, all aspects of the Galaxy project have grown: code contributions, tools integrated, users, and training materials. Key advances in Galaxy's user interface include enhancements for analyzing large dataset collections as well as interactive tools for exploratory data analysis. Extensions to Galaxy's framework include support for federated identity and access management and increased ability to distribute analysis jobs to remote resources. New community resources include large public servers in Europe and Australia, an increasing number of regional and local Galaxy communities, and substantial growth in the Galaxy Training Network.
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Affiliation(s)
- Vahid Jalili
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA
| | - Enis Afgan
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Qiang Gu
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA
| | - Dave Clements
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Daniel Blankenberg
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Jeremy Goecks
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA
| | - James Taylor
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Anton Nekrutenko
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA, USA
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