Humans; Access to Information; Computer Security; Software; Information Dissemination; Statistics and Probability; Information Systems; Education; Computer Science Applications; Statistics, Probability and Uncertainty; Library and Information Sciences
Résumé :
[en] The EU General Data Protection Regulation (GDPR) requirements have prompted a shift from centralised controlled access genome-phenome archives to federated models for sharing sensitive human data. In a data-sharing federation, a central node facilitates data discovery; meanwhile, distributed nodes are responsible for handling data access requests, concluding agreements with data users and providing secure access to the data. Research institutions that want to become part of such federations often lack the resources to set up the required controlled access processes. The DS-PACK tool assembly is a reusable, open-source middleware solution that semi-automates controlled access processes end-to-end, from data submission to access. Data protection principles are engraved into all components of the DS-PACK assembly. DS-PACK centralises access control management and distributes access control enforcement with support for data access via cloud-based applications. DS-PACK is in production use at the ELIXIR Luxembourg data hosting platform, combined with an operational model including legal facilitation and data stewardship.
Précision sur le type de document :
Compte rendu
Disciplines :
Sciences informatiques
Auteur, co-auteur :
ALPER, Pinar ; University of Luxembourg ; Luxembourg National Data Service, PNED GIE, Esch-sur-Alzette, L-4362, Luxembourg. pinar.alper@elixir-luxembourg.org ; ELIXIR Luxembourg, Belvaux, Luxembourg. pinar.alper@elixir-luxembourg.org
DED, Vilem ; University of Luxembourg ; ELIXIR Luxembourg, Belvaux, Luxembourg
HERZINGER, Sascha ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Bioinformatics Core ; ELIXIR Luxembourg, Belvaux, Luxembourg
GROUES, Valentin ; University of Luxembourg ; ELIXIR Luxembourg, Belvaux, Luxembourg
PETER, Sarah ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Bioinformatics Core ; ELIXIR Luxembourg, Belvaux, Luxembourg
LEBIODA, Jacek ; University of Luxembourg ; Luxembourg National Data Service, PNED GIE, Esch-sur-Alzette, L-4362, Luxembourg ; ELIXIR Luxembourg, Belvaux, Luxembourg
EBERMANN, Linda ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > LCSB Operations > Grants and Finance ; Luxembourg National Data Service, PNED GIE, Esch-sur-Alzette, L-4362, Luxembourg ; ELIXIR Luxembourg, Belvaux, Luxembourg
POPLETEEVA, Marina ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Bioinformatics Core ; ELIXIR Luxembourg, Belvaux, Luxembourg
BARRY, Nene Djenaba ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine > Bioinformatics Core > R3/Stewards ; Luxembourg National Data Service, PNED GIE, Esch-sur-Alzette, L-4362, Luxembourg ; ELIXIR Luxembourg, Belvaux, Luxembourg
WELTER, Danielle ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine > Bioinformatics Core > Translational Informatics ; Luxembourg National Data Service, PNED GIE, Esch-sur-Alzette, L-4362, Luxembourg ; ELIXIR Luxembourg, Belvaux, Luxembourg
GHOSH, Soumyabrata ; University of Luxembourg ; ELIXIR Luxembourg, Belvaux, Luxembourg
BECKER, Regina ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine > Bioinformatics Core > Research BioCore ; Luxembourg National Data Service, PNED GIE, Esch-sur-Alzette, L-4362, Luxembourg ; ELIXIR Luxembourg, Belvaux, Luxembourg
SCHNEIDER, Reinhard ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Bioinformatics Core ; ELIXIR Luxembourg, Belvaux, Luxembourg
GU, Wei ; University of Luxembourg ; Luxembourg National Data Service, PNED GIE, Esch-sur-Alzette, L-4362, Luxembourg ; ELIXIR Luxembourg, Belvaux, Luxembourg
TREFOIS, Christophe ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine > Bioinformatics Core > R3 and IT infrastructure ; Luxembourg National Data Service, PNED GIE, Esch-sur-Alzette, L-4362, Luxembourg ; ELIXIR Luxembourg, Belvaux, Luxembourg
SATAGOPAM, Venkata ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Bioinformatics Core ; ELIXIR Luxembourg, Belvaux, Luxembourg. venkata.satagopam@uni.lu
D.B. Resnik Genomic research data: open vs. restricted access IRB: Ethics & Human Research 2010 32 1 https://link.gale.com/apps/doc/A239462724/AONE?u=googlescholar&sid=bookmark-AONE&xid=5d539e1d1
C. Voisin et al. GA4GH Passport standard for digital identity and access permissions Cell Genomics 2021 1 1:CAS:528:DC%2BB38Xht1SrsLfL 10.1016/j.xgen.2021.100030 34820660 8591913
M.A. Freeberg et al. The European Genome-phenome Archive in 2021 Nucleic Acids Research 2022 50 D980 D987 1:CAS:528:DC%2BB38Xis1ChtbY%3D 10.1093/nar/gkab1059 34791407
K.A. Tryka et al. NCBI’s Database of Genotypes and Phenotypes: dbGaP Nucleic Acids Research 2014 42 D975 D979 1:CAS:528:DC%2BC2cXoslSn 10.1093/nar/gkt1211 24297256
European Parliament & Council of the European Union. Regulation (EU) 2016/679 of the European Parliament and of the Council. https://data.europa.eu/eli/reg/2016/679/oj (2016).
R. Becker A. Thorogood J. Bovenberg C. Mitchell A. Hall Applying GDPR roles and responsibilities to scientific data sharing International Data Privacy Law 2022 12 207 219 10.1093/idpl/ipac011
R.T. Lawlor The impact of GDPR on data sharing for European cancer research The Lancet Oncology 2023 24 6 8 10.1016/S1470-2045(22)00653-2 36400103
Freeberg, M. & Curwin, A. Federated EGA Updates in 2022. F1000 Research https://doi.org/10.7490/F1000RESEARCH.1118988.1. Publisher: F1000 Research Limited (2022).
B.D. Athey M. Braxenthaler M. Haas Y. Guo tranSMART: An Open Source and Community-Driven Informatics and Data Sharing Platform for Clinical and Translational Research AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science 2013 2013 6 8 24303286 3814495
M. Boeckhout G.A. Zielhuis A.L. Bredenoord The FAIR guiding principles for data stewardship: fair enough? European Journal of Human Genetics 2018 26 931 936 10.1038/s41431-018-0160-0 29777206 6018669
R. Becker et al. DAISY: A Data Information System for accountability under the General Data Protection Regulation GigaScience 2019 8 10.1093/gigascience/giz140 31800037 6892452
J. Harrow et al. ELIXIR: providing a sustainable infrastructure for life science data at European scale Bioinformatics 2021 37 2506 2511 1:CAS:528:DC%2BB3MXisFantbnO 10.1093/bioinformatics/btab481 34175941 8388016
D. Welter et al. The Translational Data Catalog - discoverable biomedical datasets Scientific Data 2023 10 10.1038/s41597-023-02258-0 37474618 10359386
Sakimura, N., Bradley, J., Jones, M., de Medeiros, B. & Mortimore, C. Openid connect core 1.0 incorporating errata set 1. https://openid.net/specs/openid-connect-core-1_0.html (2014).
Jones, M. B., Bradley, J. Sakimura, N. JSON Web Token (JWT). RFC 7519 https://www.rfc-editor.org/info/rfc7519, 10.17487/RFC7519 (2015).
S.O.M. Dyke et al. Registered access: authorizing data access European Journal of Human Genetics 2018 26 1721 1731 1:CAS:528:DC%2BC1cXhsVartL7P 10.1038/s41431-018-0219-y 30069064 6244209
S.-A. Sansone et al. DATS, the data tag suite to enable discoverability of datasets Scientific Data 2017 4 10.1038/sdata.2017.59 28585923 5460592
Albertoni, R. et al. The W3C Data Catalog Vocabulary, Version 2: Rationale, Design Principles, and Uptake (2023).
J. Lawson et al. The Data Use Ontology to streamline responsible access to human biomedical datasets Cell Genomics 2021 1 1:CAS:528:DC%2BB38Xht1SrsLfE 10.1016/j.xgen.2021.100028 34820659 8591903
M. Dumontier et al. The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery Journal of Biomedical Semantics 2014 5 10.1186/2041-1480-5-14 24602174 4015691
J. Golbeck et al. The National Cancer Institute’s Thesaurus and Ontology SSRN Electronic Journal 2003 10.2139/ssrn.3199007
Vasilevsky, N. A. et al. Mondo: Unifying diseases for the world, by the world. preprint, Health Informatics. https://doi.org/10.1101/2022.04.13.22273750 (2022).
J. Ison et al. EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats Bioinformatics 2013 29 1325 1332 1:CAS:528:DC%2BC3sXnvV2msbk%3D 10.1093/bioinformatics/btt113 23479348 3654706
G.V. Gkoutos P.N. Schofield R. Hoehndorf The Units Ontology: a tool for integrating units of measurement in science Database 2012 2012 bas033 bas033 1:CAS:528:DC%2BC3sXhtlyitbnJ 10.1093/database/bas033 23060432 3468815
De Matos, P. et al. ChEBI: a chemistry ontology and database. Journal of Cheminformatics 2, P6, 1758–2946–2–S1–P6, https://doi.org/10.1186/1758-2946-2-S1-P6 (2010).
M. Brandizi et al. Orchestrating differential data access for translational research: a pilot implementation BMC Medical Informatics and Decision Making 2017 17 10.1186/s12911-017-0424-6 28330491 5363029
P.A. Harris et al. Research electronic data capture (REDCap)–A metadata-driven methodology and workflow process for providing translational research informatics support Journal of Biomedical Informatics 2009 42 377 381 10.1016/j.jbi.2008.08.010 18929686
R. Becker P. Alper V. Ded L. Ebermann ELIXIR Luxembourg Data Information Sheet - DISH 2021 10.5281/ZENODO.7371006 Zenodo
Patrick Woolley, J. How Data Are Transforming the Landscape of Biomedical Ethics: The Need for ELSI Metadata on Consent. In Mittelstadt, B. D. & Floridi, L. (eds.) The Ethics of Biomedical Big Data, vol. 29, 171–197, https://doi.org/10.1007/978-3-319-33525-4_8 (Springer International Publishing, Cham, 2016).
L. Ebermann R. Becker ELIXIR Luxembourg Data Hosting Agreement 2023 10.5281/ZENODO.8278663 Zenodo
L. Ebermann R. Becker ELIXIR Luxembourg Data Use Agreement 2023 10.5281/ZENODO.8279599 Zenodo
L. Ebermann R. Becker ELIXIR Luxembourg Data Use Responsibilities Agreement 2023 10.5281/ZENODO.8279642 Zenodo
A. Vlahou et al. Data sharing under the general data protection regulation Hypertension 2021 77 1029 1035 1:CAS:528:DC%2BB3MXhsF2jurjL 10.1161/HYPERTENSIONAHA.120.16340 33583200
National institutes of health (NIH). Final NIH policy for data management and sharing and supplemental information. https://www.federalregister.gov/d/2020-23674 (2020).
Y. Joly E.S. Dove B.M. Knoppers M. Bobrow D. Chalmers Data Sharing in the Post-Genomic World: The Experience of the International Cancer Genome Consortium (ICGC) Data Access Compliance Office (DACO) PLoS Computational Biology 2012 8 e1002549 2012PLSCB..8E2549J 1:CAS:528:DC%2BC38XhtVOnsLjJ 10.1371/journal.pcbi.1002549 22807659 3395593
Abboud, L. et al. TEHDAS - WP5 - D5.1 - Report on secondary use of health data through European case studies (2022).
Foster, E. D. & Deardorff, A. Open Science Framework (OSF). Journal of the Medical Library Association 105, https://doi.org/10.5195/jmla.2017.88 (2017).
J.B. Byrd A.C. Greene D.V. Prasad X. Jiang C.S. Greene Responsible, practical genomic data sharing that accelerates research Nature Reviews Genetics 2020 21 615 629 1:CAS:528:DC%2BB3cXhsVCju7nL 10.1038/s41576-020-0257-5 32694666 7974070
European Commission. Proposal for a regulation of the european parliament and of the council on the european health data space.https://eur-lex.europa.eu/legal-content/EN/TXT/?uri=celex:52022PC0197 (2022).
Carletti, L., Scollen, S., Arenas, J. & Hurst, H. European Genomic Data Infrastructure (GDI): Advancing data-driven biomedical research and personalised medicine solutions to benefit citizens of Europe. F1000 Research https://doi.org/10.7490/F1000RESEARCH.1119428.1 (2023).
Jeanson, F. et al. Getting Your DUCs in a Row - Standardising the Representation of Digital Use Conditions. Scientific Data 11, 464 https://doi.org/10.1038/s41597-024-03280-6 (2024).
Precisesads326 imi-ju ga 115565 sustainability studies. ELIXIR Luxembourg. https://datacatalog.elixir-luxembourg.org/e/dataset/ELU-2-E592B0-1 (2017).
S. Courbier R. Dimond V. Bros-Facer Share and protect our health data: an evidence based approach to rare disease patients’ perspectives on data sharing and data protection - quantitative survey and recommendations Orphanet Journal of Rare Diseases 2019 14 10.1186/s13023-019-1123-4 31300010 6625078
S.O.M. Dyke et al. Consent Codes: Upholding Standard Data Use Conditions PLOS Genetics 2016 12 e1005772 1:CAS:528:DC%2BC28XhtFCgs77J 10.1371/journal.pgen.1005772 26796797 4721915
R.B. Mikkelsen M. Gjerris G. Waldemar P. Sandøe Broad consent for biobanks is best – provided it is also deep BMC Medical Ethics 2019 20 10.1186/s12910-019-0414-6 31615491 6794864