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Alper P, Dĕd V, Herzinger S, Grouès V, Peter S, Lebioda J, Ebermann L, Popleteeva M, Barry ND, Welter D, Ghosh S, Becker R, Schneider R, Gu W, Trefois C, Satagopam V. DS-PACK: Tool assembly for the end-to-end support of controlled access human data sharing. Sci Data 2024; 11:501. [PMID: 38750048 PMCID: PMC11096168 DOI: 10.1038/s41597-024-03326-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 04/29/2024] [Indexed: 05/18/2024] Open
Abstract
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.
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Affiliation(s)
- Pinar Alper
- Luxembourg National Data Service, PNED GIE, Esch-sur-Alzette, L-4362, Luxembourg.
- ELIXIR Luxembourg, Belvaux, Luxembourg.
| | - Vilém Dĕd
- ELIXIR Luxembourg, Belvaux, Luxembourg
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, L-4367, Luxembourg
| | - Sascha Herzinger
- ELIXIR Luxembourg, Belvaux, Luxembourg
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, L-4367, Luxembourg
| | - Valentin Grouès
- ELIXIR Luxembourg, Belvaux, Luxembourg
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, L-4367, Luxembourg
| | - Sarah Peter
- ELIXIR Luxembourg, Belvaux, Luxembourg
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, L-4367, Luxembourg
| | - Jacek Lebioda
- Luxembourg National Data Service, PNED GIE, Esch-sur-Alzette, L-4362, Luxembourg
- ELIXIR Luxembourg, Belvaux, Luxembourg
| | - Linda Ebermann
- Luxembourg National Data Service, PNED GIE, Esch-sur-Alzette, L-4362, Luxembourg
- ELIXIR Luxembourg, Belvaux, Luxembourg
| | - Marina Popleteeva
- ELIXIR Luxembourg, Belvaux, Luxembourg
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, L-4367, Luxembourg
| | - Nene Djenaba Barry
- Luxembourg National Data Service, PNED GIE, Esch-sur-Alzette, L-4362, Luxembourg
- ELIXIR Luxembourg, Belvaux, Luxembourg
| | - Danielle Welter
- Luxembourg National Data Service, PNED GIE, Esch-sur-Alzette, L-4362, Luxembourg
- ELIXIR Luxembourg, Belvaux, Luxembourg
| | - Soumyabrata Ghosh
- ELIXIR Luxembourg, Belvaux, Luxembourg
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, L-4367, Luxembourg
| | - Regina Becker
- Luxembourg National Data Service, PNED GIE, Esch-sur-Alzette, L-4362, Luxembourg
- ELIXIR Luxembourg, Belvaux, Luxembourg
| | - Reinhard Schneider
- ELIXIR Luxembourg, Belvaux, Luxembourg
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, L-4367, Luxembourg
| | - Wei Gu
- Luxembourg National Data Service, PNED GIE, Esch-sur-Alzette, L-4362, Luxembourg
- ELIXIR Luxembourg, Belvaux, Luxembourg
| | - Christophe Trefois
- Luxembourg National Data Service, PNED GIE, Esch-sur-Alzette, L-4362, Luxembourg
- ELIXIR Luxembourg, Belvaux, Luxembourg
| | - Venkata Satagopam
- ELIXIR Luxembourg, Belvaux, Luxembourg.
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, L-4367, Luxembourg.
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TASKA: A modular task management system to support health research studies. BMC Med Inform Decis Mak 2019; 19:121. [PMID: 31266480 PMCID: PMC6604289 DOI: 10.1186/s12911-019-0844-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 06/20/2019] [Indexed: 11/25/2022] Open
Abstract
Background Many healthcare databases have been routinely collected over the past decades, to support clinical practice and administrative services. However, their secondary use for research is often hindered by restricted governance rules. Furthermore, health research studies typically involve many participants with complementary roles and responsibilities which require proper process management. Results From a wide set of requirements collected from European clinical studies, we developed TASKA, a task/workflow management system that helps to cope with the socio-technical issues arising when dealing with multidisciplinary and multi-setting clinical studies. The system is based on a two-layered architecture: 1) the backend engine, which follows a micro-kernel pattern, for extensibility, and RESTful web services, for decoupling from the web clients; 2) and the client, entirely developed in ReactJS, allowing the construction and management of studies through a graphical interface. TASKA is a GNU GPL open source project, accessible at https://github.com/bioinformatics-ua/taska. A demo version is also available at https://bioinformatics.ua.pt/taska. Conclusions The system is currently used to support feasibility studies across several institutions and countries, in the context of the European Medical Information Framework (EMIF) project. The tool was shown to simplify the set-up of health studies, the management of participants and their roles, as well as the overall governance process.
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Abstract
OBJECTIVE To summarize notable research contributions published in 2017 on data sharing and privacy issues in medical informatics. METHODS An extensive search of PubMed/Medline, Web of Science, ACM Digital Library, IEEE Xplore, and AAAI Digital Library was conducted to uncover the scientific contributions published in 2017 that addressed issues of biomedical data sharing, with a focus on data access and privacy. The selection process was based on three steps: (i) a selection of candidate best papers, (ii) the review of the candidate best papers by a team of international experts with respect to six predefined criteria, and (iii) the selection of the best papers by the editorial board of the Yearbook Results: Five best papers were selected. They cover the lifecycle of biomedical data collection, use, and sharing. The papers introduce 1) consenting strategies for emerging environments, 2) software for searching and retrieving datasets in organizationally distributed environments, 3) approaches to measure the privacy risks of sharing new data increasingly utilized in research and the clinical setting (e.g., genomic), 4) new cryptographic techniques for querying clinical data for cohort discovery, and 5) novel game theoretic strategies for publishing summary information about genome-phenome studies that balance the utility of the data with potential privacy risks to the participants of such studies. CONCLUSION The papers illustrated that there is no one-size-fitsall solution to privacy while working with biomedical data. At the same time, the papers show that there are opportunities for leveraging newly emerging technologies to enable data use while minimizing privacy risks.
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Affiliation(s)
- Bradley Malin
- Department of Biomedical Informatics, Vanderbilt University, Nashville, Tennessee, USA.,Department of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, Tennessee, USA
| | - Kenneth Goodman
- Institute for Bioethics and Health Policy, University of Miami, Miami, Florida, USA
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Abstract
INTRODUCTION This article is part of the Focus Theme of Methods of Information in Medicine on the German Medical Informatics Initiative. Future medicine will be predictive, preventive, personalized, participatory and digital. Data and knowledge at comprehensive depth and breadth need to be available for research and at the point of care as a basis for targeted diagnosis and therapy. Data integration and data sharing will be essential to achieve these goals. For this purpose, the consortium Data Integration for Future Medicine (DIFUTURE) will establish Data Integration Centers (DICs) at university medical centers. OBJECTIVES The infrastructure envisioned by DIFUTURE will provide researchers with cross-site access to data and support physicians by innovative views on integrated data as well as by decision support components for personalized treatments. The aim of our use cases is to show that this accelerates innovation, improves health care processes and results in tangible benefits for our patients. To realize our vision, numerous challenges have to be addressed. The objective of this article is to describe our concepts and solutions on the technical and the organizational level with a specific focus on data integration and sharing. GOVERNANCE AND POLICIES Data sharing implies significant security and privacy challenges. Therefore, state-of-the-art data protection, modern IT security concepts and patient trust play a central role in our approach. We have established governance structures and policies safeguarding data use and sharing by technical and organizational measures providing highest levels of data protection. One of our central policies is that adequate methods of data sharing for each use case and project will be selected based on rigorous risk and threat analyses. Interdisciplinary groups have been installed in order to manage change. ARCHITECTURAL FRAMEWORK AND METHODOLOGY The DIFUTURE Data Integration Centers will implement a three-step approach to integrating, harmonizing and sharing structured, unstructured and omics data as well as images from clinical and research environments. First, data is imported and technically harmonized using common data and interface standards (including various IHE profiles, DICOM and HL7 FHIR). Second, data is preprocessed, transformed, harmonized and enriched within a staging and working environment. Third, data is imported into common analytics platforms and data models (including i2b2 and tranSMART) and made accessible in a form compliant with the interoperability requirements defined on the national level. Secure data access and sharing will be implemented with innovative combinations of privacy-enhancing technologies (safe data, safe settings, safe outputs) and methods of distributed computing. USE CASES From the perspective of health care and medical research, our approach is disease-oriented and use-case driven, i.e. following the needs of physicians and researchers and aiming at measurable benefits for our patients. We will work on early diagnosis, tailored therapies and therapy decision tools with focuses on neurology, oncology and further disease entities. Our early uses cases will serve as blueprints for the following ones, verifying that the infrastructure developed by DIFUTURE is able to support a variety of application scenarios. DISCUSSION Own previous work, the use of internationally successful open source systems and a state-of-the-art software architecture are cornerstones of our approach. In the conceptual phase of the initiative, we have already prototypically implemented and tested the most important components of our architecture.
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Affiliation(s)
- Fabian Prasser
- Institute of Medical Informatics, Statistics and Epidemiology, University Hospital rechts der Isar, Technical University of Munich, Munich, Germany
- Correspondence to: Dr. Fabian Prasser Institute of Medical InformaticsStatistics and EpidemiologyUniversity Hospital rechts der IsarTechnical University of MunichIsmaninger Straße 2281675 MunichGermany
| | - Oliver Kohlbacher
- Department of Computer Science, Center for Bioinformatics and Quantitative Biology Center, Eberhard-Karls-Universität Tübingen, Tübingen, Germany
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Ulrich Mansmann
- Institute for Medical Information Processing, Biometry, and Epidemiology, Faculty of Medicine, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Bernhard Bauer
- Department of Computer Science, University of Augsburg, Augsburg, Germany
| | - Klaus A. Kuhn
- Institute of Medical Informatics, Statistics and Epidemiology, University Hospital rechts der Isar, Technical University of Munich, Munich, Germany
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