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Gainotti S, Torreri P, Wang CM, Reihs R, Mueller H, Heslop E, Roos M, Badowska DM, de Paulis F, Kodra Y, Carta C, Martìn EL, Miller VR, Filocamo M, Mora M, Thompson M, Rubinstein Y, Posada de la Paz M, Monaco L, Lochmüller H, Taruscio D. The RD-Connect Registry & Biobank Finder: a tool for sharing aggregated data and metadata among rare disease researchers. Eur J Hum Genet 2018; 26:631-643. [PMID: 29396563 PMCID: PMC5945774 DOI: 10.1038/s41431-017-0085-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 11/20/2017] [Accepted: 11/23/2017] [Indexed: 12/20/2022] Open
Abstract
In rare disease (RD) research, there is a huge need to systematically collect biomaterials, phenotypic, and genomic data in a standardized way and to make them findable, accessible, interoperable and reusable (FAIR). RD-Connect is a 6 years global infrastructure project initiated in November 2012 that links genomic data with patient registries, biobanks, and clinical bioinformatics tools to create a central research resource for RDs. Here, we present RD-Connect Registry & Biobank Finder, a tool that helps RD researchers to find RD biobanks and registries and provide information on the availability and accessibility of content in each database. The finder concentrates information that is currently sparse on different repositories (inventories, websites, scientific journals, technical reports, etc.), including aggregated data and metadata from participating databases. Aggregated data provided by the finder, if appropriately checked, can be used by researchers who are trying to estimate the prevalence of a RD, to organize a clinical trial on a RD, or to estimate the volume of patients seen by different clinical centers. The finder is also a portal to other RD-Connect tools, providing a link to the RD-Connect Sample Catalogue, a large inventory of RD biological samples available in participating biobanks for RD research. There are several kinds of users and potential uses for the RD-Connect Registry & Biobank Finder, including researchers collaborating with academia and the industry, dealing with the questions of basic, translational, and/or clinical research. As of November 2017, the finder is populated with aggregated data for 222 registries and 21 biobanks.
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Affiliation(s)
- Sabina Gainotti
- Bioethics Unit, Office of the President, Istituto Superiore di Sanità, Rome, Italy.
- National Center for Rare Diseases, Istituto Superiore di Sanità, Rome, Italy.
| | - Paola Torreri
- National Center for Rare Diseases, Istituto Superiore di Sanità, Rome, Italy
| | | | - Robert Reihs
- Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Heimo Mueller
- Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Emma Heslop
- John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University, Newcastle, UK
| | - Marco Roos
- Human Genetics Department, Leiden University Medical Center, Leiden, The Netherlands
| | - Dorota Mazena Badowska
- John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University, Newcastle, UK
| | - Federico de Paulis
- National Center for Rare Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Yllka Kodra
- National Center for Rare Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Claudio Carta
- National Center for Rare Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Estrella Lopez Martìn
- Institute of Rare Diseases Research (IIER) & Centre for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Madrid, Spain
| | | | - Mirella Filocamo
- Centro di diagnostica genetica e biochimica delle malattie metaboliche, Istituto Giannina Gaslini, Genoa, Italy
| | - Marina Mora
- Neuromuscular Diseases and Neuroimmunology Unit, Fondazione Istituto Neurologico C. Besta, Milan, Italy
| | - Mark Thompson
- Human Genetics Department, Leiden University Medical Center, Leiden, The Netherlands
| | - Yaffa Rubinstein
- Office of Health Information Programs Development, National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Manuel Posada de la Paz
- Institute of Rare Diseases Research (IIER) & Centre for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Madrid, Spain
| | | | - Hanns Lochmüller
- John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University, Newcastle, UK
| | - Domenica Taruscio
- National Center for Rare Diseases, Istituto Superiore di Sanità, Rome, Italy
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Pang C, Kelpin F, van Enckevort D, Eklund N, Silander K, Hendriksen D, de Haan M, Jetten J, de Boer T, Charbon B, Holub P, Hillege H, Swertz MA. BiobankUniverse: automatic matchmaking between datasets for biobank data discovery and integration. Bioinformatics 2017; 33:3627-3634. [PMID: 29036577 PMCID: PMC5870622 DOI: 10.1093/bioinformatics/btx478] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 07/22/2017] [Indexed: 11/24/2022] Open
Abstract
Motivation Biobanks are indispensable for large-scale genetic/epidemiological studies, yet it remains difficult for researchers to determine which biobanks contain data matching their research questions. Results To overcome this, we developed a new matching algorithm that identifies pairs of related data elements between biobanks and research variables with high precision and recall. It integrates lexical comparison, Unified Medical Language System ontology tagging and semantic query expansion. The result is BiobankUniverse, a fast matchmaking service for biobanks and researchers. Biobankers upload their data elements and researchers their desired study variables, BiobankUniverse automatically shortlists matching attributes between them. Users can quickly explore matching potential and search for biobanks/data elements matching their research. They can also curate matches and define personalized data-universes. Availability and implementation BiobankUniverse is available at http://biobankuniverse.com or can be downloaded as part of the open source MOLGENIS suite at http://github.com/molgenis/molgenis. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Chao Pang
- Department of Genetics, Genomics Coordination Center, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Fleur Kelpin
- Department of Genetics, Genomics Coordination Center, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - David van Enckevort
- Department of Genetics, Genomics Coordination Center, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Niina Eklund
- Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
| | - Kaisa Silander
- Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
| | - Dennis Hendriksen
- Department of Genetics, Genomics Coordination Center, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Mark de Haan
- Department of Genetics, Genomics Coordination Center, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Jonathan Jetten
- Department of Genetics, Genomics Coordination Center, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Tommy de Boer
- Department of Genetics, Genomics Coordination Center, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Bart Charbon
- Department of Genetics, Genomics Coordination Center, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Petr Holub
- Biobanking and BioMolecular Resources Research Infrastructure (BBMRI-ERIC), Graz, Austria
| | - Hans Hillege
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Morris A Swertz
- Department of Genetics, Genomics Coordination Center, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
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Wichmann HE. Epidemiology in Germany-general development and personal experience. Eur J Epidemiol 2017; 32:635-656. [PMID: 28815360 DOI: 10.1007/s10654-017-0290-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Accepted: 07/27/2017] [Indexed: 12/19/2022]
Abstract
Did you ever hear about epidemiology in Germany? Starting from an epidemiological desert the discipline has grown remarkably, especially during the last 10-15 years: research institutes have been established, research funding has improved, multiple curriculae in Epidemiology and Public Health are offered. This increase has been quite steep, and now the epidemiological infrastructure is much better. Several medium-sized and even big population cohorts are ongoing, and the number and quality of publications from German epidemiologists has reached a respectable level. My own career in epidemiology started in the field of environmental health. After German reunification I concentrated for many years on environmental problems in East Germany and observed the health benefits after improvement of the situation. Later, I concentrated on population-based cohorts in newborns (GINI/LISA) and adults (KORA, German National Cohort), and on biobanking. This Essay describes the development in Germany after worldwar 2, illustrated by examples of research results and build-up of epidemiological infractructures worth mentioning.
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Affiliation(s)
- Heinz-Erich Wichmann
- Institute of Epidemiology, 2, Helmholtz Center Munich, Munich, Germany. .,Chair of Epidemiology, University of Munich, Munich, Germany.
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Ellis H, Joshi MB, Lynn AJ, Walden A. Consensus-Driven Development of a Terminology for Biobanking, the Duke Experience. Biopreserv Biobank 2017; 15:126-133. [PMID: 28338350 PMCID: PMC5397220 DOI: 10.1089/bio.2016.0092] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Biobanking at Duke University has existed for decades and has grown over time in silos and based on specialized needs, as is true with most biomedical research centers. These silos developed informatics systems to support their own individual requirements, with no regard for semantic or syntactic interoperability. Duke undertook an initiative to implement an enterprise-wide biobanking information system to serve its many diverse biobanking entities. A significant part of this initiative was the development of a common terminology for use in the commercial software platform. Common terminology provides the foundation for interoperability across biobanks for data and information sharing. We engaged experts in research, informatics, and biobanking through a consensus-driven process to agree on 361 terms and their definitions that encompass the lifecycle of a biospecimen. Existing standards, common terms, and data elements from published articles provided a foundation on which to build the biobanking terminology; a broader set of stakeholders then provided additional input and feedback in a secondary vetting process. The resulting standardized biobanking terminology is now available for sharing with the biobanking community to serve as a foundation for other institutions who are considering a similar initiative.
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Affiliation(s)
- Helena Ellis
- Biobanking Without Borders, LLC, Durham, North Carolina
| | - Mary-Beth Joshi
- Department of Surgery, Duke University, Durham, North Carolina
| | - Aenoch J. Lynn
- Buck Institute for Research on Aging, Novato, California
| | - Anita Walden
- University of Arkansas for Medical Sciences, Little Rock, Arkansas
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