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Nikolski M, Hovig E, Al-Shahrour F, Blomberg N, Scollen S, Valencia A, Saunders G. Roadmap for a European cancer data management and precision medicine infrastructure. Nat Cancer 2024; 5:367-372. [PMID: 38321342 DOI: 10.1038/s43018-023-00717-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Affiliation(s)
- Macha Nikolski
- University of Bordeaux, CNRS-IBGC, UMR 5095, Bordeaux, France.
- University of Bordeaux, Bordeaux Bioinformatics Center CBiB, Bordeaux, France.
| | - Eivind Hovig
- Centre for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Fatima Al-Shahrour
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | | | - Serena Scollen
- ELIXIR Hub, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Alfonso Valencia
- Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain
- ICREA, Barcelona, Spain
| | - Gary Saunders
- ELIXIR Hub, Wellcome Genome Campus, Hinxton, Cambridge, UK
- EATRIS-ERIC, Amsterdam, the Netherlands
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David R, Rybina A, Burel J, Heriche J, Audergon P, Boiten J, Coppens F, Crockett S, Exter K, Fahrner S, Fratelli M, Goble C, Gormanns P, Grantner T, Grüning B, Gurwitz KT, Hancock JM, Harmse H, Holub P, Juty N, Karnbach G, Karoune E, Keppler A, Klemeier J, Lancelotti C, Legras J, Lister AL, Longo DL, Ludwig R, Madon B, Massimi M, Matser V, Matteoni R, Mayrhofer MT, Ohmann C, Panagiotopoulou M, Parkinson H, Perseil I, Pfander C, Pieruschka R, Raess M, Rauber A, Richard AS, Romano P, Rosato A, Sánchez‐Pla A, Sansone S, Sarkans U, Serrano‐Solano B, Tang J, Tanoli Z, Tedds J, Wagener H, Weise M, Westerhoff HV, Wittner R, Ewbank J, Blomberg N, Gribbon P. "Be sustainable": EOSC-Life recommendations for implementation of FAIR principles in life science data handling. EMBO J 2023; 42:e115008. [PMID: 37964598 PMCID: PMC10690449 DOI: 10.15252/embj.2023115008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/12/2023] [Accepted: 09/18/2023] [Indexed: 11/16/2023] Open
Abstract
The main goals and challenges for the life science communities in the Open Science framework are to increase reuse and sustainability of data resources, software tools, and workflows, especially in large-scale data-driven research and computational analyses. Here, we present key findings, procedures, effective measures and recommendations for generating and establishing sustainable life science resources based on the collaborative, cross-disciplinary work done within the EOSC-Life (European Open Science Cloud for Life Sciences) consortium. Bringing together 13 European life science research infrastructures, it has laid the foundation for an open, digital space to support biological and medical research. Using lessons learned from 27 selected projects, we describe the organisational, technical, financial and legal/ethical challenges that represent the main barriers to sustainability in the life sciences. We show how EOSC-Life provides a model for sustainable data management according to FAIR (findability, accessibility, interoperability, and reusability) principles, including solutions for sensitive- and industry-related resources, by means of cross-disciplinary training and best practices sharing. Finally, we illustrate how data harmonisation and collaborative work facilitate interoperability of tools, data, solutions and lead to a better understanding of concepts, semantics and functionalities in the life sciences.
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Neves A, Cuesta I, Hjerde E, Klemetsen T, Salgado D, van Helden J, Rahman N, Fatima N, Karathanasis N, Zmora P, Åkerström WN, Grellscheid SN, Waheed Z, Blomberg N. FAIR+E pathogen data for surveillance and research: lessons from COVID-19. Front Public Health 2023; 11:1289945. [PMID: 38074768 PMCID: PMC10703184 DOI: 10.3389/fpubh.2023.1289945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 10/30/2023] [Indexed: 12/18/2023] Open
Abstract
The COVID-19 pandemic has exemplified the importance of interoperable and equitable data sharing for global surveillance and to support research. While many challenges could be overcome, at least in some countries, many hurdles within the organizational, scientific, technical and cultural realms still remain to be tackled to be prepared for future threats. We propose to (i) continue supporting global efforts that have proven to be efficient and trustworthy toward addressing challenges in pathogen molecular data sharing; (ii) establish a distributed network of Pathogen Data Platforms to (a) ensure high quality data, metadata standardization and data analysis, (b) perform data brokering on behalf of data providers both for research and surveillance, (c) foster capacity building and continuous improvements, also for pandemic preparedness; (iii) establish an International One Health Pathogens Portal, connecting pathogen data isolated from various sources (human, animal, food, environment), in a truly One Health approach and following FAIR principles. To address these challenging endeavors, we have started an ELIXIR Focus Group where we invite all interested experts to join in a concerted, expert-driven effort toward sustaining and ensuring high-quality data for global surveillance and research.
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Affiliation(s)
- Aitana Neves
- SIB Swiss Institute of Bioinformatics, Clinical Bioinformatics, Geneva, Switzerland
| | - Isabel Cuesta
- Bioinformatics Unit, Institute of Health Carlos III, Madrid, Spain
| | - Erik Hjerde
- Institute of Chemistry, The Arctic University of Norway, Tromsø, Norway
| | - Terje Klemetsen
- Institute of Chemistry, The Arctic University of Norway, Tromsø, Norway
| | - David Salgado
- CNRS, Institut Français de Bioinformatique, IFB-core, UMS 3601, Evry, France
| | - Jacques van Helden
- CNRS, Institut Français de Bioinformatique, IFB-core, UMS 3601, Evry, France
- Aix-Marseille Univ, INSERM, Lab. Theory and Approaches of Genome Complexity (TAGC), Marseille, France
| | - Nadim Rahman
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Nazeefa Fatima
- ELIXIR Norway, Centre for Bioinformatics, University of Oslo, Oslo, Norway
| | - Nestoras Karathanasis
- Bioinformatics Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Pawel Zmora
- Department of Molecular Virology, Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland
| | - Wolmar Nyberg Åkerström
- NBIS National Bioinformatics Infrastructure Sweden, SciLifeLab, Uppsala University, Uppsala, Sweden
| | | | - Zahra Waheed
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Niklas Blomberg
- ELIXIR Hub, Wellcome Genome Campus, Cambridge, United Kingdom
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Sanz F, Pognan F, Steger-Hartmann T, Díaz C, Asakura S, Amberg A, Bécourt-Lhote N, Blomberg N, Bosc N, Briggs K, Bringezu F, Brulle-Wohlhueter C, Brunak S, Bueters R, Callegaro G, Capella-Gutierrez S, Centeno E, Corvi J, Cronin MTD, Drew P, Duchateau-Nguyen G, Ecker GF, Escher S, Felix E, Ferreiro M, Frericks M, Furlong LI, Geiger R, George C, Grandits M, Ivanov-Draganov D, Kilgour-Christie J, Kiziloren T, Kors JA, Koyama N, Kreuchwig A, Leach AR, Mayer MA, Monecke P, Muster W, Nakazawa CM, Nicholson G, Parry R, Pastor M, Piñero J, Oberhauser N, Ramírez-Anguita JM, Rodrigo A, Smajic A, Schaefer M, Schieferdecker S, Soininen I, Terricabras E, Trairatphisan P, Turner SC, Valencia A, van de Water B, van der Lei JL, van Mulligen EM, Vock E, Wilkinson D. eTRANSAFE: data science to empower translational safety assessment. Nat Rev Drug Discov 2023; 22:605-606. [PMID: 37316648 DOI: 10.1038/d41573-023-00099-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
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Blomberg N, Kristyanto H, Verstappen M, Neppelenbroek S, Kampstra ASB, Van der Helm-van Mil A, Toes R, Scherer HU. POS0403 DYNAMIC CHANGES IN AUTOREACTIVE MEMORY B CELLS IN RHEUMATOID ARTHRITIS: KEY TO UNDERSTANDING IMMUNOLOGICAL DISEASE ACTIVITY. Ann Rheum Dis 2022. [DOI: 10.1136/annrheumdis-2022-eular.4504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BackgroundRheumatoid arthritis (RA) patients with autoantibodies against citrullinated antigens (ACPA) are characterized by poor chances to achieve sustained DMARD free remission. We have previously observed that autoreactive ACPA-expressing memory B cells (MBC) display an activated phenotype and frequently maintain this state of activation even in patients in clinical remission in whom joint inflammation is absent through treatment. Conceptually, these observations could reflect ongoing immunological activity. In fact, they indicate that most current therapeutic interventions do not induce immunological remission and could explain why disease frequently flares when treatment is stopped. ACPA-expressing MBC display the phenotype of recent germinal centre emigrants, actively proliferating (Ki-67 positive), expressing CD95 and co-stimulatory markers CD80 and CD86, and the signature cytokine IL-8.[1] Notably, in autoantibody-positive individuals with arthralgia that did not progress to inflammatory arthritis within 2 years, the autoreactive B cells were readily detectable in the circulation and proliferated but lacked, in most cases, the upregulation of CD80 seen at the onset of disease. Now, we studied these autoreactive B cells longitudinally in the ‘at-risk’ phase of clinically suspect arthralgia (CSA) and in a population of patients in sustained (>1 year) drug-free remission (SDFR).ObjectivesTo define dynamic changes of the ACPA-expressing B cell compartment throughout clinical disease stages with the aim to evaluate this response as a possibly predictive biomarker of immunological disease activity.MethodsACPA-expressing MBC were identified by flow cytometry in peripheral blood of RA patients with chronic disease or at disease-onset (treatment-naïve), in ACPA-positive CSA patients ‘at-risk’ for RA, and in patients in SDFR. B cells were characterized by a combination of markers to classify B cell subpopulations and activation- and germinal centre related markers. Tetanus-toxoid-specific B cells were analysed in the same individuals as antigen-specific comparators.ResultsIn patients in SDFR, significantly less autoreactive B cells expressed CD80 compared to active disease, while they persistently showed signs of proliferation, similar to the phenotype observed in CSA patients that did not progress to RA. ACPA-specific plasmablasts (defined as CD20-CD27hi) were practically absent in SDFR and CSA non-progressors, while they were readily detectable in patients with RA at disease onset, during treatment, and in CSA-individuals that later progressed to RA. Notably, two arthralgia patients that developed RA within one year showed high CD80 expression in the autoreactive MBC compartment already in the ‘at-risk’ phase, whereas patients that so far did not progress to RA during the time of follow-up, showed less CD80-positive autoreactive MBC.ConclusionThe phenotype of autoreactive B cells is dynamic in different disease phases of RA. By studying extremes of clinical phenotypes (‘at-risk’ phase, disease onset, SDFR), we found evidence for dynamic expression of CD80 by ACPA-expressing MBC in relation to clinical disease stage. Intriguingly, CD80-positive B cells, but not CD80-negative B cells, have been shown to be able to differentiate into antibody secreting cells in mice.[2] Our finding that plasmablasts were practically absent in ACPA-positive arthralgia patients that did not progress to RA and in SDFR would fit with this notion and suggests that in SDFR autoreactive MBC lack, although actively proliferating, triggers that induce CD80 upregulation, differentiation to plasmablasts and, possibly, their active participation in processes causing joint inflammation. Based on this observation, it is possible that induction of this CD80lo phenotype in autoreactive MBC may be an important step towards achieving immunological remission, a conceptual proxy for cure.References[1]H. Kristyanto et al., Sci Transl Med12, (2020).[2]G. V. Zuccarino-Catania et al., Nat Immunol15, 631-637 (2014).Disclosure of InterestsNone declared.
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Sarntivijai S, Blomberg N, Lauer KB, Briggs K, Steger-Hartmann T, van der Lei J, Sauer JM, Liwski R, Mourby M, Camprubi M. eTRANSAFE: Building a sustainable framework to share reproducible drug safety knowledge with the public domain. F1000Res 2022; 11. [PMID: 35602243 PMCID: PMC9096149 DOI: 10.12688/f1000research.74024.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/18/2022] [Indexed: 11/20/2022] Open
Abstract
Integrative drug safety research in translational health informatics has rapidly evolved and included data that are drawn in from many resources, combining diverse data that are either reused from (curated) repositories, or newly generated at source. Each resource is mandated by different sets of metadata rules that are imposed on the incoming data. Combination of the data cannot be readily achieved without interference of data stewardship and the top-down policy guidelines that supervise and inform the process for data combination to aid meaningful interpretation and analysis of such data. The eTRANSAFE Consortium's effort to drive integrative drug safety research at a large scale hereby present the lessons learnt and the proposal of solution at the guidelines in practice at this Innovative Medicines Initiative (IMI) project. Recommendations in these guidelines were compiled from feedback received from key stakeholders in regulatory agencies, EFPIA companies, and academic partners. The research reproducibility guidelines presented in this study lay the foundation for a comprehensive data sharing and knowledge management plans accounting for research data management in the drug safety space - FAIR data sharing guidelines, and the model verification guidelines as generic deliverables that best practices that can be reused by other scientific community members at large. FAIR data sharing is a dynamic landscape that rapidly evolves with fast-paced technology advancements. The research reproducibility in drug safety guidelines introduced in this study provides a reusable framework that can be adopted by other research communities that aim to integrate public and private data in biomedical research space.
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Affiliation(s)
| | - Niklas Blomberg
- ELIXIR Hub, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | | | - Katharine Briggs
- Lhasa Limited, Granary Wharf House, 2 Canal Wharf, Leeds, LS11 5PS, UK
| | - Thomas Steger-Hartmann
- Bayer AG, Research & Development, Pharmaceuticals, Investigational Toxicology, 13342 Berlin, Germany
| | - Johan van der Lei
- Department of Medical Informatics, Erasmus University Rotterdam, EUR - Erasmus Medical Center (MC), Rotterdam, The Netherlands
| | - John-Michael Sauer
- Predictive Safety Testing Consortium, Critical Path Institute, Tucson, Arizona, 85718, USA
| | - Richard Liwski
- Predictive Safety Testing Consortium, Critical Path Institute, Tucson, Arizona, 85718, USA
| | - Miranda Mourby
- Centre for Health, Law and Emerging Technologies (HeLEX), Faculty of Law, University of Oxford, Oxford, OX2 7DD, UK
| | - Montse Camprubi
- Synapse Research Management Partners S.L., C. Diputació 237, Àtic 3a, 08007, Barcelona, Spain
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Harrison PW, Lopez R, Rahman N, Allen SG, Aslam R, Buso N, Cummins C, Fathy Y, Felix E, Glont M, Jayathilaka S, Kadam S, Kumar M, Lauer KB, Malhotra G, Mosaku A, Edbali O, Park YM, Parton A, Pearce M, Estrada Pena JF, Rossetto J, Russell C, Selvakumar S, Sitjà XP, Sokolov A, Thorne R, Ventouratou M, Walter P, Yordanova G, Zadissa A, Cochrane G, Blomberg N, Apweiler R. The COVID-19 Data Portal: accelerating SARS-CoV-2 and COVID-19 research through rapid open access data sharing. Nucleic Acids Res 2021; 49:W619-W623. [PMID: 34048576 PMCID: PMC8218199 DOI: 10.1093/nar/gkab417] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/20/2021] [Accepted: 05/01/2021] [Indexed: 01/07/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic will be remembered as one of the defining events of the 21st century. The rapid global outbreak has had significant impacts on human society and is already responsible for millions of deaths. Understanding and tackling the impact of the virus has required a worldwide mobilisation and coordination of scientific research. The COVID-19 Data Portal (https://www.covid19dataportal.org/) was first released as part of the European COVID-19 Data Platform, on April 20th 2020 to facilitate rapid and open data sharing and analysis, to accelerate global SARS-CoV-2 and COVID-19 research. The COVID-19 Data Portal has fortnightly feature releases to continue to add new data types, search options, visualisations and improvements based on user feedback and research. The open datasets and intuitive suite of search, identification and download services, represent a truly FAIR (Findable, Accessible, Interoperable and Reusable) resource that enables researchers to easily identify and quickly obtain the key datasets needed for their COVID-19 research.
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Affiliation(s)
- Peter W Harrison
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Rodrigo Lopez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nadim Rahman
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Stefan Gutnick Allen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Raheela Aslam
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nicola Buso
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Carla Cummins
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Yasmin Fathy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Eloy Felix
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Mihai Glont
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Suran Jayathilaka
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sandeep Kadam
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Manish Kumar
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | | | - Geetika Malhotra
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Abayomi Mosaku
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ossama Edbali
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Young Mi Park
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Andrew Parton
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Matt Pearce
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jose Francisco Estrada Pena
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Joseph Rossetto
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Craig Russell
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sandeep Selvakumar
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | | | - Alexey Sokolov
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ross Thorne
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Marianna Ventouratou
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Peter Walter
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Galabina Yordanova
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Amonida Zadissa
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Guy Cochrane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Niklas Blomberg
- ELIXIR, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Rolf Apweiler
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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Harrow J, Drysdale R, Smith A, Repo S, Lanfear J, Blomberg N. ELIXIR: Providing a Sustainable Infrastructure for Life Science Data at European Scale. Bioinformatics 2021; 37:2506-2511. [PMID: 34175941 PMCID: PMC8388016 DOI: 10.1093/bioinformatics/btab481] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/19/2021] [Accepted: 06/25/2021] [Indexed: 11/12/2022] Open
Affiliation(s)
- Jennifer Harrow
- ELIXIR Hub, South Building, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Rachel Drysdale
- ELIXIR Hub, South Building, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Andrew Smith
- ELIXIR Hub, South Building, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Susanna Repo
- ELIXIR Hub, South Building, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Jerry Lanfear
- ELIXIR Hub, South Building, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Niklas Blomberg
- ELIXIR Hub, South Building, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
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Blomberg N, Kristyanto H, Huizinga T, Toes R, Scherer HU. AB0022 AUTOREACTIVE B CELLS IN RHEUMATOID ARTHRITIS DISPLAY AN ACTIVATED PHENOTYPE OF RECENT ANTIGEN EXPOSURE. Ann Rheum Dis 2021. [DOI: 10.1136/annrheumdis-2021-eular.2050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Background:Rheumatoid arthritis, in particular ACPA+ RA, is characterized by frequent disease flares and poor chances to achieve DMARD-free sustained remission. Recently, we have shown that ACPA-expressing memory B cells (MBC) remain in a persistently activated state throughout disease, even in patients in DMARD-induced clinical remission.(1) The reasons why the ACPA B cell response is continuously activated are unknown, as well as why the response does not revert to a resting, ‘quiescent’ state. We hypothesized that continuous antigen exposure in germinal centres drives ACPA B cell activation, leading to a ‘recent germinal centre emigrant’ phenotype of these cells in the circulation.Objectives:To understand whether the activated phenotype of ACPA-expressing B cells could be induced by recent antigen exposure, to thereby discern the processes of immune activation that remain active in patients even in clinical remission and to argue whether these processes could be targets for therapeutic intervention.Methods:ACPA-expressing B cells were identified in peripheral blood of RA patients by flow cytometry during different stages of disease and characterized by a panel of activation- and germinal centre related markers (CD80, CD86, CD32, CD95, Ki-67). In addition, three healthy donors received a TT booster vaccination. TT-specific MBC were identified in blood at different timepoints (before vaccination and up to 22 weeks after vaccination) and analysed phenotypically over time.Results:The majority of ACPA-expressing B cells strongly expressed CD95 and the co-stimulatory marker CD80. A part was also positive for the proliferation marker Ki-67 (on average 30%), and most cells downregulated the inhibitory marker CD32. TT-specific MBC adopted a comparable phenotype after booster vaccination, but most markers returned to the pre-vaccination expression level gradually over time. These effects were antigen-dependent because the phenotype of TT-negative B cells remained unchanged. The phenotypic composition of the proliferating ACPA-positive B cell pool most closely corresponded to a stimulation history of 1-2 weeks after antigen exposure. Notably, none of the Ki-67 negative ACPA-specific MBC showed phenotypic quiescence, indicating either a short life-time (in circulation) after antigen encounter or persistent additional factors of activation.Figure 1.Ki-67 expression on ACPA-specific MBC in RA (A) and on TT-specific MBC in 3 healthy donors before and after booster vaccination (B).Conclusion:ACPA-expressing MBC phenotypically resemble TT-specific MBC after recent (1-2 weeks) booster vaccination, reflecting the phenotype of recent germinal centre emigrants, and remain activated, whereas TT-specific MBC lose this marker profile over time. These observations suggest that ACPA-expressing MBC either home to tissue or survive shortly in the circulation, or that additional factors drive or program these cells to persistent activation. Transcriptomic profiling and analysis of the homing marker profile may help to answer these questions. Furthermore, it will be important to understand the association of persistent activation of ACPA-expressing B cells in clinical remission and the risk for disease flares upon treatment discontinuation.References:[1]Kristyanto H, Blomberg NJ, Slot LM, van der Voort EIH, Kerkman PF, Bakker A, et al. Persistently activated, proliferative memory autoreactive B cells promote inflammation in rheumatoid arthritis. Sci Transl Med. 2020;12(570).Disclosure of Interests:Nienke Blomberg: None declared, Hendy Kristyanto: None declared, Thomas Huizinga Grant/research support from: Gilead, Rene Toes: None declared, Hans Ulrich Scherer Grant/research support from: Pfizer, Lilly, Sanofi, BMS
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Pognan F, Steger-Hartmann T, Díaz C, Blomberg N, Bringezu F, Briggs K, Callegaro G, Capella-Gutierrez S, Centeno E, Corvi J, Drew P, Drewe WC, Fernández JM, Furlong LI, Guney E, Kors JA, Mayer MA, Pastor M, Piñero J, Ramírez-Anguita JM, Ronzano F, Rowell P, Saüch-Pitarch J, Valencia A, van de Water B, van der Lei J, van Mulligen E, Sanz F. The eTRANSAFE Project on Translational Safety Assessment through Integrative Knowledge Management: Achievements and Perspectives. Pharmaceuticals (Basel) 2021; 14:ph14030237. [PMID: 33800393 PMCID: PMC7999019 DOI: 10.3390/ph14030237] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/25/2021] [Accepted: 02/27/2021] [Indexed: 12/19/2022] Open
Abstract
eTRANSAFE is a research project funded within the Innovative Medicines Initiative (IMI), which aims at developing integrated databases and computational tools (the eTRANSAFE ToxHub) that support the translational safety assessment of new drugs by using legacy data provided by the pharmaceutical companies that participate in the project. The project objectives include the development of databases containing preclinical and clinical data, computational systems for translational analysis including tools for data query, analysis and visualization, as well as computational models to explain and predict drug safety events.
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Affiliation(s)
- François Pognan
- Preclinical Safety/Translational Medicine, Novartis, 4057 Basel, Switzerland;
| | | | - Carlos Díaz
- Synapse Research Managers SL, 28006 Madrid, Spain;
| | | | - Frank Bringezu
- Chemical & Preclinical Safety, Merck Healthcare KGaA, 64293 Darmstadt, Germany;
| | | | - Giulia Callegaro
- Leiden Academic Centre for Drug Research (LACDR), Leiden University, 2300 RA Leiden, The Netherlands; (G.C.); (B.v.d.W.)
| | | | - Emilio Centeno
- GRIB, Hospital del Mar Institute of Medical Research (IMIM), DCEXS, Pompeu Fabra University (UPF), 08003 Barcelona, Spain; (E.C.); (L.I.F.); (E.G.); (M.A.M.); (M.P.); (J.P.); (J.M.R.-A.); (F.R.); (J.S.-P.)
| | - Javier Corvi
- Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain; (S.C.-G.); (J.C.); (J.M.F.); (A.V.)
| | | | | | - José M. Fernández
- Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain; (S.C.-G.); (J.C.); (J.M.F.); (A.V.)
| | - Laura I. Furlong
- GRIB, Hospital del Mar Institute of Medical Research (IMIM), DCEXS, Pompeu Fabra University (UPF), 08003 Barcelona, Spain; (E.C.); (L.I.F.); (E.G.); (M.A.M.); (M.P.); (J.P.); (J.M.R.-A.); (F.R.); (J.S.-P.)
- MedBioinformatics Solutions SL, 08018 Barcelona, Spain
| | - Emre Guney
- GRIB, Hospital del Mar Institute of Medical Research (IMIM), DCEXS, Pompeu Fabra University (UPF), 08003 Barcelona, Spain; (E.C.); (L.I.F.); (E.G.); (M.A.M.); (M.P.); (J.P.); (J.M.R.-A.); (F.R.); (J.S.-P.)
| | - Jan A. Kors
- Department of Medical Informatics, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (J.A.K.); (J.v.d.L.); (E.v.M.)
| | - Miguel Angel Mayer
- GRIB, Hospital del Mar Institute of Medical Research (IMIM), DCEXS, Pompeu Fabra University (UPF), 08003 Barcelona, Spain; (E.C.); (L.I.F.); (E.G.); (M.A.M.); (M.P.); (J.P.); (J.M.R.-A.); (F.R.); (J.S.-P.)
| | - Manuel Pastor
- GRIB, Hospital del Mar Institute of Medical Research (IMIM), DCEXS, Pompeu Fabra University (UPF), 08003 Barcelona, Spain; (E.C.); (L.I.F.); (E.G.); (M.A.M.); (M.P.); (J.P.); (J.M.R.-A.); (F.R.); (J.S.-P.)
| | - Janet Piñero
- GRIB, Hospital del Mar Institute of Medical Research (IMIM), DCEXS, Pompeu Fabra University (UPF), 08003 Barcelona, Spain; (E.C.); (L.I.F.); (E.G.); (M.A.M.); (M.P.); (J.P.); (J.M.R.-A.); (F.R.); (J.S.-P.)
| | - Juan Manuel Ramírez-Anguita
- GRIB, Hospital del Mar Institute of Medical Research (IMIM), DCEXS, Pompeu Fabra University (UPF), 08003 Barcelona, Spain; (E.C.); (L.I.F.); (E.G.); (M.A.M.); (M.P.); (J.P.); (J.M.R.-A.); (F.R.); (J.S.-P.)
| | - Francesco Ronzano
- GRIB, Hospital del Mar Institute of Medical Research (IMIM), DCEXS, Pompeu Fabra University (UPF), 08003 Barcelona, Spain; (E.C.); (L.I.F.); (E.G.); (M.A.M.); (M.P.); (J.P.); (J.M.R.-A.); (F.R.); (J.S.-P.)
| | - Philip Rowell
- Lhasa Limited, Leeds LS11 5PS, UK; (K.B.); (W.C.D.); (P.R.)
| | - Josep Saüch-Pitarch
- GRIB, Hospital del Mar Institute of Medical Research (IMIM), DCEXS, Pompeu Fabra University (UPF), 08003 Barcelona, Spain; (E.C.); (L.I.F.); (E.G.); (M.A.M.); (M.P.); (J.P.); (J.M.R.-A.); (F.R.); (J.S.-P.)
| | - Alfonso Valencia
- Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain; (S.C.-G.); (J.C.); (J.M.F.); (A.V.)
- Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
| | - Bob van de Water
- Leiden Academic Centre for Drug Research (LACDR), Leiden University, 2300 RA Leiden, The Netherlands; (G.C.); (B.v.d.W.)
| | - Johan van der Lei
- Department of Medical Informatics, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (J.A.K.); (J.v.d.L.); (E.v.M.)
| | - Erik van Mulligen
- Department of Medical Informatics, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (J.A.K.); (J.v.d.L.); (E.v.M.)
| | - Ferran Sanz
- GRIB, Hospital del Mar Institute of Medical Research (IMIM), DCEXS, Pompeu Fabra University (UPF), 08003 Barcelona, Spain; (E.C.); (L.I.F.); (E.G.); (M.A.M.); (M.P.); (J.P.); (J.M.R.-A.); (F.R.); (J.S.-P.)
- Correspondence:
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11
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Harrow J, Hancock J, Blomberg N. ELIXIR-EXCELERATE: establishing Europe's data infrastructure for the life science research of the future. EMBO J 2021; 40:e107409. [PMID: 33565128 PMCID: PMC7957415 DOI: 10.15252/embj.2020107409] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 12/14/2020] [Accepted: 12/16/2020] [Indexed: 02/06/2023] Open
Abstract
A new inter-governmental research infrastructure, ELIXIR, aims to unify bioinformatics resources and life science data across Europe, thereby facilitating their mining and (re-)use.
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Affiliation(s)
| | - John Hancock
- ELIXIR Hub, Wellcome Genome Campus, Hinxton, Cambridge, UK
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12
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Drysdale R, Cook CE, Petryszak R, Baillie-Gerritsen V, Barlow M, Gasteiger E, Gruhl F, Haas J, Lanfear J, Lopez R, Redaschi N, Stockinger H, Teixeira D, Venkatesan A, Blomberg N, Durinx C, McEntyre J. The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences. Bioinformatics 2020; 36:2636-2642. [PMID: 31950984 PMCID: PMC7446027 DOI: 10.1093/bioinformatics/btz959] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 10/08/2019] [Accepted: 01/07/2020] [Indexed: 01/07/2023] Open
Abstract
Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Rachel Drysdale
- ELIXIR Hub, South Building, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Charles E Cook
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Robert Petryszak
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | | | - Mary Barlow
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | | | - Franziska Gruhl
- SIB Swiss Institute of Bioinformatics Quartier Sorge-Bâtiment Amphipôle, 1015 Lausanne, Switzerland
| | - Jürgen Haas
- SIB Swiss Institute of Bioinformatics & Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Jerry Lanfear
- ELIXIR Hub, South Building, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Rodrigo Lopez
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nicole Redaschi
- SIB Swiss Institute of Bioinformatics, CMU, 1211 Geneva, Switzerland
| | - Heinz Stockinger
- SIB Swiss Institute of Bioinformatics Quartier Sorge-Bâtiment Amphipôle, 1015 Lausanne, Switzerland
| | - Daniel Teixeira
- SIB Swiss Institute of Bioinformatics Quartier Sorge-Bâtiment Amphipôle, 1015 Lausanne, Switzerland.,Hôpitaux Universitaires de Genève, Rue Gabrielle-Perret-Gentil 4, 1205 Geneva, Switzerland
| | - Aravind Venkatesan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | | | - Niklas Blomberg
- ELIXIR Hub, South Building, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Christine Durinx
- SIB Swiss Institute of Bioinformatics Quartier Sorge-Bâtiment Amphipôle, 1015 Lausanne, Switzerland
| | - Johanna McEntyre
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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13
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Abstract
ELIXIR, the European research infrastructure for life science data, provides open access to data, tools and workflows in the response to the COVID-19 pandemic. ELIXIR's 23 nodes have reacted swiftly to support researchers in their combined efforts against the pandemic setting out three joint priorities: 1. Connecting national COVID-19 data platforms to create federated European COVID-19 Data Spaces; 2. Fostering good data management to make COVID-19 data open, FAIR and reusable over the long term; 3. Providing open tools, workflows and computational resources to drive reproducible and collaborative science. ELIXIR's strategy is based on the support given by our national nodes - collectively spanning over 200 institutes - to research projects and on partnering with community initiatives to drive development and adoption of good data practice and community driven standards. ELIXIR Nodes provide support activities locally and internationally, from provisioning compute capabilities to helping collect viral sequence data from hospitals. Some Nodes have prioritised access to their national cloud and compute facilities for all COVID-19 research projects, while others have developed tools to search, access and share all data related to the pandemic in a national healthcare setting.
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Affiliation(s)
- Niklas Blomberg
- ELIXIR Wellcome Genome Campus Hinxton, Cambridge, CB10 1SD, UK.
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14
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Aarestrup FM, Albeyatti A, Armitage WJ, Auffray C, Augello L, Balling R, Benhabiles N, Bertolini G, Bjaalie JG, Black M, Blomberg N, Bogaert P, Bubak M, Claerhout B, Clarke L, De Meulder B, D'Errico G, Di Meglio A, Forgo N, Gans-Combe C, Gray AE, Gut I, Gyllenberg A, Hemmrich-Stanisak G, Hjorth L, Ioannidis Y, Jarmalaite S, Kel A, Kherif F, Korbel JO, Larue C, Laszlo M, Maas A, Magalhaes L, Manneh-Vangramberen I, Morley-Fletcher E, Ohmann C, Oksvold P, Oxtoby NP, Perseil I, Pezoulas V, Riess O, Riper H, Roca J, Rosenstiel P, Sabatier P, Sanz F, Tayeb M, Thomassen G, Van Bussel J, Van den Bulcke M, Van Oyen H. Towards a European health research and innovation cloud (HRIC). Genome Med 2020; 12:18. [PMID: 32075696 PMCID: PMC7029532 DOI: 10.1186/s13073-020-0713-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 01/29/2020] [Indexed: 12/21/2022] Open
Abstract
The European Union (EU) initiative on the Digital Transformation of Health and Care (Digicare) aims to provide the conditions necessary for building a secure, flexible, and decentralized digital health infrastructure. Creating a European Health Research and Innovation Cloud (HRIC) within this environment should enable data sharing and analysis for health research across the EU, in compliance with data protection legislation while preserving the full trust of the participants. Such a HRIC should learn from and build on existing data infrastructures, integrate best practices, and focus on the concrete needs of the community in terms of technologies, governance, management, regulation, and ethics requirements. Here, we describe the vision and expected benefits of digital data sharing in health research activities and present a roadmap that fosters the opportunities while answering the challenges of implementing a HRIC. For this, we put forward five specific recommendations and action points to ensure that a European HRIC: i) is built on established standards and guidelines, providing cloud technologies through an open and decentralized infrastructure; ii) is developed and certified to the highest standards of interoperability and data security that can be trusted by all stakeholders; iii) is supported by a robust ethical and legal framework that is compliant with the EU General Data Protection Regulation (GDPR); iv) establishes a proper environment for the training of new generations of data and medical scientists; and v) stimulates research and innovation in transnational collaborations through public and private initiatives and partnerships funded by the EU through Horizon 2020 and Horizon Europe.
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Affiliation(s)
- F M Aarestrup
- Technical University of Denmark, Kongens Lyngby, Denmark
| | - A Albeyatti
- Medicalchain, York Road, London, SQ1 7NQ, UK.,National Health Service, London, UK
| | - W J Armitage
- Translation Health Sciences, Bristol Medical School, Bristol, BS81UD, UK
| | - C Auffray
- European Institute for Systems Biology and Medicine (EISBM), Vourles, France.
| | - L Augello
- Regional Agency for Innovation & Procurement (ARIA), Welfare Services Division, Lombardy, Milan, Italy
| | - R Balling
- Luxembourg Centre for Systems Biomedicine, Campus Belval, University of Luxembourg, Luxembourg City, Luxembourg
| | - N Benhabiles
- CEA, French Atomic Energy and Alternative Energy Commission, Direction de la Recherche Fondamentale, Université Paris-Saclay, F-91191, Gif-sur-Yvette, France.
| | - G Bertolini
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Bergamo, Italy
| | - J G Bjaalie
- Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - M Black
- Ulster University, Belfast, BT15 1ED, UK
| | - N Blomberg
- ELIXIR, Welcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
| | - P Bogaert
- Sciensano, Brussels, Belgium and Tilburg University, Tilburg, The Netherlands
| | - M Bubak
- Department of Computer Science and Academic Computing Center Cyfronet, Akademia Gornizco Hutnizca University of Science and Technology, Krakow, Poland
| | | | - L Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - B De Meulder
- European Institute for Systems Biology and Medicine (EISBM), Vourles, France
| | - G D'Errico
- Fondazione Toscana Life Sciences, 53100, Siena, Italy
| | - A Di Meglio
- CERN, European Organization for Nuclear Research, Meyrin, Switzerland
| | - N Forgo
- University of Vienna, Vienna, Austria
| | - C Gans-Combe
- INSEEC School of Business & Economics, Paris, France
| | - A E Gray
- PwC, Dronning Eufemiasgate, N-0191, Oslo, Norway
| | - I Gut
- Center for Genomic Regulations, Barcelona, Spain
| | - A Gyllenberg
- Neuroimmunology Unit, The Karolinska Neuroimmunology & Multiple Sclerosis Centre, Department of Clinical Neuroscience, Karolinska Institute, Stockholm, Sweden
| | - G Hemmrich-Stanisak
- Institute of Clinical Molecular Biology, Kiel University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - L Hjorth
- Department of Clinical Sciences, Pediatrics, Lund University, Skåne University Hospital, Lund, Sweden
| | - Y Ioannidis
- Athena Research & Innovation Center and University of Athens, Athens, Greece
| | | | - A Kel
- geneXplain GmbH, Wolfenbüttel, Germany
| | - F Kherif
- Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - J O Korbel
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany.
| | - C Larue
- Integrated Biobank of Luxembourg, Rue Louis Rech, L-3555, Dudelange, Luxembourg
| | | | - A Maas
- Antwerp University Hospital and University of Antwerp, Edegem, Belgium
| | - L Magalhaes
- Clinerion Ltd, Elisabethenanlage, 4051, Basel, Switzerland
| | - I Manneh-Vangramberen
- European Cancer Patient Coalition, Rue de Montoyer/Montoyerstraat, B-1000, Brussels, Belgium
| | - E Morley-Fletcher
- Lynkeus, Via Livenza, 00198, Rome, Italy.,Public Policy Consultant, Rome, Italy
| | - C Ohmann
- European Clinical Research Infrastructure Network, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - P Oksvold
- Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - N P Oxtoby
- Centre for Medical Image Computing, Department of Computer Science, University College London, London, UK
| | - I Perseil
- Information Technology Department, Institut National de la Santé et de la Recherche Médicale, Paris, France
| | - V Pezoulas
- Unit of Medical Technology and Intelligent Information Systems, Department of Materials Science and Engineering, University of Ioannina, Ioannina, Greece
| | - O Riess
- Institute of Medical Genetics and Applied Genomics, Rare Disease Center, Tübingen, Germany
| | - H Riper
- Section Clinical, Neuro and Developmental Psychology, Department of Behavioural and Movement Sciences, Vrije Universiteit, Amsterdam, The Netherlands
| | - J Roca
- Hospital Clínic de Barcelona, IDIBAPS, University of Barcelona, Barcelona, Spain
| | - P Rosenstiel
- Institute of Clinical Molecular Biology, Kiel University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - P Sabatier
- French National Centre for Scientific Research, Grenoble, France
| | - F Sanz
- Hospital del Mar Medical Research Institute (IMIM), Universitat Pompeu Fabra, Barcelona, Spain
| | - M Tayeb
- Medicalchain, York Road, London, SQ1 7NQ, UK.,National Health Service, London, UK
| | | | - J Van Bussel
- Scientific Institute of Public Health, Brussels, Belgium
| | | | - H Van Oyen
- Department of Computer Science and Academic Computing Center Cyfronet, Akademia Gornizco Hutnizca University of Science and Technology, Krakow, Poland.,Sciensano, Juliette Wystmanstraat, 1050, Brussels, Belgium
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15
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Saunders G, Baudis M, Becker R, Beltran S, Béroud C, Birney E, Brooksbank C, Brunak S, Van den Bulcke M, Drysdale R, Capella-Gutierrez S, Flicek P, Florindi F, Goodhand P, Gut I, Heringa J, Holub P, Hooyberghs J, Juty N, Keane TM, Korbel JO, Lappalainen I, Leskosek B, Matthijs G, Mayrhofer MT, Metspalu A, Navarro A, Newhouse S, Nyrönen T, Page A, Persson B, Palotie A, Parkinson H, Rambla J, Salgado D, Steinfelder E, Swertz MA, Valencia A, Varma S, Blomberg N, Scollen S. Leveraging European infrastructures to access 1 million human genomes by 2022. Nat Rev Genet 2019; 20:693-701. [PMID: 31455890 PMCID: PMC7115898 DOI: 10.1038/s41576-019-0156-9] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/03/2019] [Indexed: 01/22/2023]
Abstract
Human genomics is undergoing a step change from being a predominantly research-driven activity to one driven through health care as many countries in Europe now have nascent precision medicine programmes. To maximize the value of the genomic data generated, these data will need to be shared between institutions and across countries. In recognition of this challenge, 21 European countries recently signed a declaration to transnationally share data on at least 1 million human genomes by 2022. In this Roadmap, we identify the challenges of data sharing across borders and demonstrate that European research infrastructures are well-positioned to support the rapid implementation of widespread genomic data access.
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Affiliation(s)
- Gary Saunders
- ELIXIR Hub, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Regina Becker
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Luxembourg, Luxembourg
| | - Sergi Beltran
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Christophe Béroud
- Aix Marseille Univ, INSERM, MMG, Marseille, France
- Département de Génétique Médicale et de Biologie Cellulaire, APHM, Hôpital d'Enfants de la Timone, Marseille, France
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Cath Brooksbank
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Søren Brunak
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Peter Goodhand
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Global Alliance for Genomics and Health, Toronto, Ontario, Canada
| | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Jaap Heringa
- Department of Computer Science, Vrije Universiteit, Amsterdam, Netherlands
| | | | - Jef Hooyberghs
- Flemish Institute for Technological Research, VITO, Mol, Belgium
| | - Nick Juty
- School of Computer Science, The University of Manchester, Manchester, UK
| | - Thomas M Keane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Jan O Korbel
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | | | - Brane Leskosek
- IBMI, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | | | | | | | - Arcadi Navarro
- Institute of Evolutionary Biology (UPF-CSIC), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Steven Newhouse
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Angela Page
- Global Alliance for Genomics and Health, Toronto, Ontario, Canada
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Bengt Persson
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala, Sweden
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Helen Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Jordi Rambla
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | | | | | - Morris A Swertz
- BBMRI-NL/University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Alfonso Valencia
- Barcelona Supercomputing Centre (BSC), Barcelona, Spain
- ICREA, Pg., Barcelona, Spain
| | - Susheel Varma
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Serena Scollen
- ELIXIR Hub, Wellcome Genome Campus, Hinxton, Cambridge, UK.
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16
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Dyke SOM, Linden M, Lappalainen I, De Argila JR, Carey K, Lloyd D, Spalding JD, Cabili MN, Kerry G, Foreman J, Cutts T, Shabani M, Rodriguez LL, Haeussler M, Walsh B, Jiang X, Wang S, Perrett D, Boughtwood T, Matern A, Brookes AJ, Cupak M, Fiume M, Pandya R, Tulchinsky I, Scollen S, Törnroos J, Das S, Evans AC, Malin BA, Beck S, Brenner SE, Nyrönen T, Blomberg N, Firth HV, Hurles M, Philippakis AA, Rätsch G, Brudno M, Boycott KM, Rehm HL, Baudis M, Sherry ST, Kato K, Knoppers BM, Baker D, Flicek P. Registered access: authorizing data access. Eur J Hum Genet 2018; 26:1721-1731. [PMID: 30069064 PMCID: PMC6244209 DOI: 10.1038/s41431-018-0219-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 05/08/2018] [Accepted: 06/20/2018] [Indexed: 12/14/2022] Open
Abstract
The Global Alliance for Genomics and Health (GA4GH) proposes a data access policy model-"registered access"-to increase and improve access to data requiring an agreement to basic terms and conditions, such as the use of DNA sequence and health data in research. A registered access policy would enable a range of categories of users to gain access, starting with researchers and clinical care professionals. It would also facilitate general use and reuse of data but within the bounds of consent restrictions and other ethical obligations. In piloting registered access with the Scientific Demonstration data sharing projects of GA4GH, we provide additional ethics, policy and technical guidance to facilitate the implementation of this access model in an international setting.
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Affiliation(s)
- Stephanie O M Dyke
- Centre of Genomics and Policy, Faculty of Medicine, McGill University, Montreal, QC, Canada.
- Montreal Neurological Institute, Faculty of Medicine, McGill University, Montreal, QC, Canada.
| | - Mikael Linden
- CSC - IT Center for Science, Espoo, Finland
- ELIXIR Hub, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ilkka Lappalainen
- CSC - IT Center for Science, Espoo, Finland
- ELIXIR Hub, Wellcome Genome Campus, Hinxton, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Jordi Rambla De Argila
- Centre for Genomic Regulation, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | | | - David Lloyd
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
- The Global Alliance for Genomics and Health, MaRS Centre, West Tower, 661 University Avenue, Suite 510, Toronto, M5G 0A3, ON, Canada
| | - J Dylan Spalding
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | | | - Giselle Kerry
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Julia Foreman
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Tim Cutts
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Mahsa Shabani
- Center for Biomedical Ethics and Law, Department of Public Health and Primary Care, University of Leuven, Leuven, Belgium
| | | | | | | | - Xiaoqian Jiang
- Department of Biomedical Informatics, UC San Diego, La Jolla, CA, USA
| | - Shuang Wang
- Department of Biomedical Informatics, UC San Diego, La Jolla, CA, USA
| | - Daniel Perrett
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Tiffany Boughtwood
- Australian Genomics Health Alliance, 50 Flemington Road, Parkville, VIC, 3052, Australia
| | | | - Anthony J Brookes
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | | | | | | | | | - Serena Scollen
- ELIXIR Hub, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Samir Das
- McGill Centre for Integrative Neurosciences, Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | - Alan C Evans
- McGill Centre for Integrative Neurosciences, Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | | | - Stephan Beck
- UCL Cancer Institute, University College London, London, UK
| | - Steven E Brenner
- Department of Plant & Microbial Biology, University of California, Berkeley, CA, USA
| | - Tommi Nyrönen
- CSC - IT Center for Science, Espoo, Finland
- ELIXIR Compute Platform, ELIXIR, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Helen V Firth
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Matthew Hurles
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Gunnar Rätsch
- Department of Computer Science, Biomedical Informatics, ETH Zurich, Zurich, Switzerland
| | - Michael Brudno
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
- Centre for Computational Medicine, Hospital for Sick Children, Toronto, ON, Canada
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Heidi L Rehm
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pathology, Brigham & Women's Hospital & Harvard Medical School, Boston, MA, USA
| | - Michael Baudis
- University of Zurich & Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Stephen T Sherry
- National Centre for Biotechnology Information, US National Library of Medicine, Bethesda, MD, USA
| | - Kazuto Kato
- Department of Biomedical Ethics and Public Policy, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Bartha M Knoppers
- Centre of Genomics and Policy, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Dixie Baker
- Martin, Blanck & Associates, Alexandria, VA, USA
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
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17
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McMurry JA, Juty N, Blomberg N, Burdett T, Conlin T, Conte N, Courtot M, Deck J, Dumontier M, Fellows DK, Gonzalez-Beltran A, Gormanns P, Grethe J, Hastings J, Hériché JK, Hermjakob H, Ison JC, Jimenez RC, Jupp S, Kunze J, Laibe C, Le Novère N, Malone J, Martin MJ, McEntyre JR, Morris C, Muilu J, Müller W, Rocca-Serra P, Sansone SA, Sariyar M, Snoep JL, Soiland-Reyes S, Stanford NJ, Swainston N, Washington N, Williams AR, Wimalaratne SM, Winfree LM, Wolstencroft K, Goble C, Mungall CJ, Haendel MA, Parkinson H. Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data. PLoS Biol 2017; 15:e2001414. [PMID: 28662064 PMCID: PMC5490878 DOI: 10.1371/journal.pbio.2001414] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In many disciplines, data are highly decentralized across thousands of online databases (repositories, registries, and knowledgebases). Wringing value from such databases depends on the discipline of data science and on the humble bricks and mortar that make integration possible; identifiers are a core component of this integration infrastructure. Drawing on our experience and on work by other groups, we outline 10 lessons we have learned about the identifier qualities and best practices that facilitate large-scale data integration. Specifically, we propose actions that identifier practitioners (database providers) should take in the design, provision and reuse of identifiers. We also outline the important considerations for those referencing identifiers in various circumstances, including by authors and data generators. While the importance and relevance of each lesson will vary by context, there is a need for increased awareness about how to avoid and manage common identifier problems, especially those related to persistence and web-accessibility/resolvability. We focus strongly on web-based identifiers in the life sciences; however, the principles are broadly relevant to other disciplines.
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Affiliation(s)
- Julie A. McMurry
- Department of Medical Informatics and Epidemiology and OHSU Library, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Nick Juty
- European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Niklas Blomberg
- ELIXIR Hub, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Tony Burdett
- European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Tom Conlin
- Department of Medical Informatics and Epidemiology and OHSU Library, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Nathalie Conte
- European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Mélanie Courtot
- European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - John Deck
- Berkeley Natural History Museums, University of California at Berkeley, Berkely, California, United States of America
| | - Michel Dumontier
- Institute of Data Science, Maastricht University, Maastricht, the Netherlands
| | - Donal K. Fellows
- School of Computer Science, The University of Manchester, Manchester, United Kingdom
| | | | - Philipp Gormanns
- Institute of Experimental Genetics, Helmholtz Centre Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Jeffrey Grethe
- Center for Research in Biological Systems, University of California San Diego, La Jolla, California, United States of America
| | | | | | - Henning Hermjakob
- European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Jon C. Ison
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Rafael C. Jimenez
- European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Simon Jupp
- European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - John Kunze
- California Digital Library, Oakland, California, United States of America
| | - Camille Laibe
- European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | | | - James Malone
- European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Maria Jesus Martin
- European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Johanna R. McEntyre
- European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Chris Morris
- Science and Technology Facilities Council, Daresbury Laboratory, Warrington, United Kingdom
| | - Juha Muilu
- Genomics Coordination Center, Department of Genetics, University Medical Center Groningen and Groningen Bioinformatics Center, University of Groningen, Groningen, the Netherlands
| | - Wolfgang Müller
- Scientific Databases and Visualization at Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | | | | | - Murat Sariyar
- Institute for Medical Informatics, Bern University of Applied Sciences, Engineering and Information Technology, Bern, Switzerland
| | - Jacky L. Snoep
- Manchester Institute of Biology, University of Manchester, Manchester, United Kingdom
- Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa
| | - Stian Soiland-Reyes
- School of Computer Science, The University of Manchester, Manchester, United Kingdom
| | - Natalie J. Stanford
- School of Computer Science, The University of Manchester, Manchester, United Kingdom
| | - Neil Swainston
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals, University of Manchester, Manchester, United Kingdom
| | - Nicole Washington
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Alan R. Williams
- School of Computer Science, The University of Manchester, Manchester, United Kingdom
| | - Sarala M. Wimalaratne
- European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Lilly M. Winfree
- Department of Medical Informatics and Epidemiology and OHSU Library, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Katherine Wolstencroft
- Leiden Institute of Advanced Computer Science, Leiden University, Leiden, the Netherlands
| | - Carole Goble
- School of Computer Science, The University of Manchester, Manchester, United Kingdom
| | - Christopher J. Mungall
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Melissa A. Haendel
- Department of Medical Informatics and Epidemiology and OHSU Library, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Helen Parkinson
- European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
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18
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van Gool AJ, Bietrix F, Caldenhoven E, Zatloukal K, Scherer A, Litton JE, Meijer G, Blomberg N, Smith A, Mons B, Heringa J, Koot WJ, Smit MJ, Hajduch M, Rijnders T, Ussi A. Bridging the translational innovation gap through good biomarker practice. Nat Rev Drug Discov 2017; 16:587-588. [DOI: 10.1038/nrd.2017.72] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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19
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Abstract
Most bioinformatics tools available today were not written by professional software developers, but by people that wanted to solve their own problems, using computational solutions and spending the minimum time and effort possible, since these were just the means to an end. Consequently, a vast number of software applications are currently available, hindering the task of identifying the utility and quality of each. At the same time, this situation has hindered regular adoption of these tools in clinical practice. Typically, they are not sufficiently developed to be used by most clinical researchers and practitioners. To address these issues, it is necessary to re-think how biomedical applications are built and adopt new strategies that ensure quality, efficiency, robustness, correctness and reusability of software components. We also need to engage end-users during the development process to ensure that applications fit their needs. In this review, we present a set of guidelines to support biomedical software development, with an explanation of how they can be implemented and what kind of open-source tools can be used for each specific topic.
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Affiliation(s)
| | | | | | - José Luis Oliveira
- Institute of Electronics and Informatics Engineering of Aveiro, University of Aveiro, Aveiro, Portugal
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20
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Abstract
Most bioinformatics tools available today were not written by professional software developers, but by people that wanted to solve their own problems, using computational solutions and spending the minimum time and effort possible, since these were just the means to an end. Consequently, a vast number of software applications are currently available, hindering the task of identifying the utility and quality of each. At the same time, this situation has hindered regular adoption of these tools in clinical practice. Typically, they are not sufficiently developed to be used by most clinical researchers and practitioners. To address these issues, it is necessary to re-think how biomedical applications are built and adopt new strategies that ensure quality, efficiency, robustness, correctness and reusability of software components. We also need to engage end-users during the development process to ensure that applications fit their needs. In this review, we present a set of guidelines to support biomedical software development, with an explanation of how they can be implemented and what kind of open-source tools can be used for each specific topic.
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Affiliation(s)
| | | | | | - José Luis Oliveira
- Institute of Electronics and Informatics Engineering of Aveiro, University of Aveiro, Aveiro, Portugal
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21
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Auffray C, Balling R, Barroso I, Bencze L, Benson M, Bergeron J, Bernal-Delgado E, Blomberg N, Bock C, Conesa A, Del Signore S, Delogne C, Devilee P, Di Meglio A, Eijkemans M, Flicek P, Graf N, Grimm V, Guchelaar HJ, Guo YK, Gut IG, Hanbury A, Hanif S, Hilgers RD, Honrado Á, Hose DR, Houwing-Duistermaat J, Hubbard T, Janacek SH, Karanikas H, Kievits T, Kohler M, Kremer A, Lanfear J, Lengauer T, Maes E, Meert T, Müller W, Nickel D, Oledzki P, Pedersen B, Petkovic M, Pliakos K, Rattray M, I Màs JR, Schneider R, Sengstag T, Serra-Picamal X, Spek W, Vaas LAI, van Batenburg O, Vandelaer M, Varnai P, Villoslada P, Vizcaíno JA, Wubbe JPM, Zanetti G. Erratum to: Making sense of big data in health research: towards an EU action plan. Genome Med 2016; 8:118. [PMID: 27821178 PMCID: PMC5100330 DOI: 10.1186/s13073-016-0376-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 10/26/2016] [Indexed: 11/10/2022] Open
Affiliation(s)
- Charles Auffray
- European Institute for Systems Biology and Medicine, 1 avenue Claude Vellefaux, 75010, Paris, France. .,CIRI-UMR5308, CNRS-ENS-INSERM-UCBL, Université de Lyon, 50 avenue Tony Garnier, 69007, Lyon, France.
| | - Rudi Balling
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts Fourneaux, 4362, Esch-sur-Alzette, Luxembourg.
| | - Inês Barroso
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - László Bencze
- Health Services Management Training Centre, Faculty of Health and Public Services, Semmelweis University, Kútvölgyi út 2, 1125, Budapest, Hungary
| | - Mikael Benson
- Centre for Personalised Medicine, Linköping University, 581 85, Linköping, Sweden
| | - Jay Bergeron
- Translational & Bioinformatics, Pfizer Inc., 300 Technology Square, Cambridge, MA, 02139, USA
| | - Enrique Bernal-Delgado
- Institute for Health Sciences, IACS - IIS Aragon, San Juan Bosco 13, 50009, Zaragoza, Spain
| | - Niklas Blomberg
- ELIXIR, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT25.2, 1090, Vienna, Austria.,Department of Laboratory Medicine, Medical University of Vienna, Lazarettgasse 14, AKH BT25.2, 1090, Vienna, Austria.,Max Planck Institute for Informatics, Campus E1 4, 66123, Saarbrücken, Germany
| | - Ana Conesa
- Príncipe Felipe Research Center, C/Eduardo Primo Yúfera 3, 46012, Valencia, Spain.,University of Florida, Institute of Food and Agricultural Sciences (IFAS), 2033 Mowry Road, Gainesville, FL, 32610, USA
| | | | - Christophe Delogne
- Technology, Data & Analytics, KPMG Luxembourg, Société Coopérative, 39 Avenue John F. Kennedy, 1855, Luxembourg, Luxembourg
| | - Peter Devilee
- Department of Human Genetics, Department of Pathology, Leiden University Medical Centre, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Alberto Di Meglio
- Information Technology Department, European Organization for Nuclear Research (CERN), 385 Route de Meyrin, 1211, Geneva 23, Switzerland
| | - Marinus Eijkemans
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Heidelberglaan 100, 3508 GA, Utrecht, The Netherlands
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Norbert Graf
- Department of Pediatric Oncology/Hematology, Saarland University, Campus Homburg, Building 9, 66421, Homburg, Germany
| | - Vera Grimm
- Project Management Jülich, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52428, Jülich, Germany
| | - Henk-Jan Guchelaar
- Department of Clinical Pharmacy & Toxicology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Yi-Ke Guo
- Data Science Institute, Imperial College London, South Kensington, London, SW7 2AZ, UK
| | - Ivo Glynne Gut
- CNAG-CRG, Center for Genomic Regulation, Barcelona Institute for Science and Technology (BIST), C/Baldiri Reixac 4, 08029, Barcelona, Spain
| | - Allan Hanbury
- Institute of Software Technology and Interactive Systems, TU Wien, Favoritenstrasse 9-11/188, 1040, Vienna, Austria
| | - Shahid Hanif
- The Association of the British Pharmaceutical Industry, 7th Floor, Southside, 105 Victoria Street, London, SW1E 6QT, UK
| | - Ralf-Dieter Hilgers
- Department of Medical Statistics, RWTH-Aachen University, Universitätsklinikum Aachen, Pauwelsstraße 30, 52074, Aachen, Germany
| | - Ángel Honrado
- SYNAPSE Research Management Partners, Diputació 237, Àtic 3ª, 08007, Barcelona, Spain
| | - D Rod Hose
- Department of Infection, Immunity and Cardiovascular Disease and Insigneo Institute for In-Silico Medicine, Medical School, University of Sheffield, Beech Hill Road, Sheffield, S10 2RX, UK
| | | | - Tim Hubbard
- Department of Medical & Molecular Genetics, King's College London, London, SE1 9RT, UK.,Genomics England, London, EC1M 6BQ, UK
| | - Sophie Helen Janacek
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Haralampos Karanikas
- National and Kapodistrian University of Athens, Medical School, Xristou Lada 6, 10561, Athens, Greece
| | - Tim Kievits
- Vitromics Healthcare Holding B.V., Onderwijsboulevard 225, 5223 DE, 's-Hertogenbosch, The Netherlands
| | - Manfred Kohler
- Fraunhofer Institute for Molecular Biology and Applied Ecology ScreeningPort, Schnackenburgallee 114, 22525, Hamburg, Germany
| | - Andreas Kremer
- ITTM S.A., 9 avenue des Hauts Fourneaux, 4362, Esch-sur-Alzette, Luxembourg
| | - Jerry Lanfear
- Research Business Technology, Pfizer Ltd, GP4 Building, Granta Park, Cambridge, CB21 6GP, UK
| | - Thomas Lengauer
- Max Planck Institute for Informatics, Campus E1 4, 66123, Saarbrücken, Germany
| | - Edith Maes
- Health Economics & Outcomes Research, Deloitte Belgium, Berkenlaan 8A, 1831, Diegem, Belgium
| | - Theo Meert
- Janssen Pharmaceutica N.V., R&D G3O, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Werner Müller
- Faculty of Life Sciences, University of Manchester, AV Hill Building, Oxford Road, Manchester, M13 9PT, UK
| | - Dörthe Nickel
- UMR3664 IC/CNRS, Institut Curie, Section Recherche, Pavillon Pasteur, 26 rue d'Ulm, 75248, Paris cedex 05, France
| | - Peter Oledzki
- Linguamatics Ltd, 324 Cambridge Science Park Milton Rd, Cambridge, CB4 0WG, UK
| | - Bertrand Pedersen
- PwC Luxembourg, 2 rue Gerhard Mercator, 2182, Luxembourg, Luxembourg
| | - Milan Petkovic
- Philips, HighTechCampus 36, 5656AE, Eindhoven, The Netherlands
| | - Konstantinos Pliakos
- Department of Public Health and Primary Care, KU Leuven Kulak, Etienne Sabbelaan 53, 8500, Kortrijk, Belgium
| | - Magnus Rattray
- Faculty of Life Sciences, University of Manchester, AV Hill Building, Oxford Road, Manchester, M13 9PT, UK
| | - Josep Redón I Màs
- INCLIVA Health Research Institute, University of Valencia, CIBERobn ISCIII, Avenida Menéndez Pelayo 4 accesorio, 46010, Valencia, Spain
| | - Reinhard Schneider
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts Fourneaux, 4362, Esch-sur-Alzette, Luxembourg
| | - Thierry Sengstag
- Swiss Institute of Bioinformatics (SIB) and University of Basel, Klingelbergstrasse 50/ 70, 4056, Basel, Switzerland
| | - Xavier Serra-Picamal
- Agency for Health Quality and Assessment of Catalonia (AQuAS), Carrer de Roc Boronat 81-95, 08005, Barcelona, Spain
| | - Wouter Spek
- EuroBioForum Foundation, Chrysantstraat 10, 3135 HG, Vlaardingen, The Netherlands
| | - Lea A I Vaas
- Fraunhofer Institute for Molecular Biology and Applied Ecology ScreeningPort, Schnackenburgallee 114, 22525, Hamburg, Germany
| | - Okker van Batenburg
- EuroBioForum Foundation, Chrysantstraat 10, 3135 HG, Vlaardingen, The Netherlands
| | - Marc Vandelaer
- Integrated BioBank of Luxembourg, 6 rue Nicolas-Ernest Barblé, 1210, Luxembourg, Luxembourg
| | - Peter Varnai
- Technopolis Group, 3 Pavilion Buildings, Brighton, BN1 1EE, UK
| | - Pablo Villoslada
- Hospital Clinic of Barcelona, Institute d'Investigacions Biomediques August Pi Sunyer (IDIBAPS), Rosello 149, 08036, Barcelona, Spain
| | - Juan Antonio Vizcaíno
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - John Peter Mary Wubbe
- European Platform for Patients' Organisations, Science and Industry (Epposi), De Meeûs Square 38-40, 1000, Brussels, Belgium
| | - Gianluigi Zanetti
- CRS4, Ed.1 POLARIS, 09129, Pula, Italy.,BBMRI-ERIC, Neue Stiftingtalstrasse 2/B/6, 8010, Graz, Austria
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22
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Durinx C, McEntyre J, Appel R, Apweiler R, Barlow M, Blomberg N, Cook C, Gasteiger E, Kim JH, Lopez R, Redaschi N, Stockinger H, Teixeira D, Valencia A. Identifying ELIXIR Core Data Resources. F1000Res 2016; 5. [PMID: 27803796 PMCID: PMC5070591 DOI: 10.12688/f1000research.9656.2] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/03/2017] [Indexed: 12/01/2022] Open
Abstract
The core mission of ELIXIR is to build a stable and sustainable infrastructure for biological information across Europe. At the heart of this are the data resources, tools and services that ELIXIR offers to the life-sciences community, providing stable and sustainable access to biological data. ELIXIR aims to ensure that these resources are available long-term and that the life-cycles of these resources are managed such that they support the scientific needs of the life-sciences, including biological research. ELIXIR Core Data Resources are defined as a set of European data resources that are of fundamental importance to the wider life-science community and the long-term preservation of biological data. They are complete collections of generic value to life-science, are considered an authority in their field with respect to one or more characteristics, and show high levels of scientific quality and service. Thus, ELIXIR Core Data Resources are of wide applicability and usage. This paper describes the structures, governance and processes that support the identification and evaluation of ELIXIR Core Data Resources. It identifies key indicators which reflect the essence of the definition of an ELIXIR Core Data Resource and support the promotion of excellence in resource development and operation. It describes the specific indicators in more detail and explains their application within ELIXIR’s sustainability strategy and science policy actions, and in capacity building, life-cycle management and technical actions. The identification process is currently being implemented and tested for the first time. The findings and outcome will be evaluated by the ELIXIR Scientific Advisory Board in March 2017. Establishing the portfolio of ELIXIR Core Data Resources and ELIXIR Services is a key priority for ELIXIR and publicly marks the transition towards a cohesive infrastructure.
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Affiliation(s)
| | - Jo McEntyre
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Ron Appel
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Rolf Apweiler
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Mary Barlow
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | | | - Chuck Cook
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | | | - Jee-Hyub Kim
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Rodrigo Lopez
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | | | | | - Daniel Teixeira
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
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23
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Durinx C, McEntyre J, Appel R, Apweiler R, Barlow M, Blomberg N, Cook C, Gasteiger E, Kim JH, Lopez R, Redaschi N, Stockinger H, Teixeira D, Valencia A. Identifying ELIXIR Core Data Resources. F1000Res 2016; 5:ELIXIR-2422. [PMID: 27803796 PMCID: PMC5070591 DOI: 10.12688/f1000research.9656.1] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/03/2017] [Indexed: 11/10/2023] Open
Abstract
The core mission of ELIXIR is to build a stable and sustainable infrastructure for biological information across Europe. At the heart of this are the data resources, tools and services that ELIXIR offers to the life-sciences community, providing stable and sustainable access to biological data. ELIXIR aims to ensure that these resources are available long-term and that the life-cycles of these resources are managed such that they support the scientific needs of the life-sciences, including biological research. ELIXIR Core Data Resources are defined as a set of European data resources that are of fundamental importance to the wider life-science community and the long-term preservation of biological data. They are complete collections of generic value to life-science, are considered an authority in their field with respect to one or more characteristics, and show high levels of scientific quality and service. Thus, ELIXIR Core Data Resources are of wide applicability and usage. This paper describes the structures, governance and processes that support the identification and evaluation of ELIXIR Core Data Resources. It identifies key indicators which reflect the essence of the definition of an ELIXIR Core Data Resource and support the promotion of excellence in resource development and operation. It describes the specific indicators in more detail and explains their application within ELIXIR's sustainability strategy and science policy actions, and in capacity building, life-cycle management and technical actions. The identification process is currently being implemented and tested for the first time. The findings and outcome will be evaluated by the ELIXIR Scientific Advisory Board in March 2017. Establishing the portfolio of ELIXIR Core Data Resources and ELIXIR Services is a key priority for ELIXIR and publicly marks the transition towards a cohesive infrastructure.
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Affiliation(s)
| | - Jo McEntyre
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Ron Appel
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Rolf Apweiler
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Mary Barlow
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | | | - Chuck Cook
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | | | - Jee-Hyub Kim
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Rodrigo Lopez
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | | | | | - Daniel Teixeira
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
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24
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Auffray C, Balling R, Barroso I, Bencze L, Benson M, Bergeron J, Bernal-Delgado E, Blomberg N, Bock C, Conesa A, Del Signore S, Delogne C, Devilee P, Di Meglio A, Eijkemans M, Flicek P, Graf N, Grimm V, Guchelaar HJ, Guo YK, Gut IG, Hanbury A, Hanif S, Hilgers RD, Honrado Á, Hose DR, Houwing-Duistermaat J, Hubbard T, Janacek SH, Karanikas H, Kievits T, Kohler M, Kremer A, Lanfear J, Lengauer T, Maes E, Meert T, Müller W, Nickel D, Oledzki P, Pedersen B, Petkovic M, Pliakos K, Rattray M, I Màs JR, Schneider R, Sengstag T, Serra-Picamal X, Spek W, Vaas LAI, van Batenburg O, Vandelaer M, Varnai P, Villoslada P, Vizcaíno JA, Wubbe JPM, Zanetti G. Making sense of big data in health research: Towards an EU action plan. Genome Med 2016; 8:71. [PMID: 27338147 PMCID: PMC4919856 DOI: 10.1186/s13073-016-0323-y] [Citation(s) in RCA: 124] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Medicine and healthcare are undergoing profound changes. Whole-genome sequencing and high-resolution imaging technologies are key drivers of this rapid and crucial transformation. Technological innovation combined with automation and miniaturization has triggered an explosion in data production that will soon reach exabyte proportions. How are we going to deal with this exponential increase in data production? The potential of "big data" for improving health is enormous but, at the same time, we face a wide range of challenges to overcome urgently. Europe is very proud of its cultural diversity; however, exploitation of the data made available through advances in genomic medicine, imaging, and a wide range of mobile health applications or connected devices is hampered by numerous historical, technical, legal, and political barriers. European health systems and databases are diverse and fragmented. There is a lack of harmonization of data formats, processing, analysis, and data transfer, which leads to incompatibilities and lost opportunities. Legal frameworks for data sharing are evolving. Clinicians, researchers, and citizens need improved methods, tools, and training to generate, analyze, and query data effectively. Addressing these barriers will contribute to creating the European Single Market for health, which will improve health and healthcare for all Europeans.
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Affiliation(s)
- Charles Auffray
- European Institute for Systems Biology and Medicine, 1 avenue Claude Vellefaux, 75010, Paris, France.
- CIRI-UMR5308, CNRS-ENS-INSERM-UCBL, Université de Lyon, 50 avenue Tony Garnier, 69007, Lyon, France.
| | - Rudi Balling
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts Fourneaux, 4362, Esch-sur-Alzette, Luxembourg.
| | - Inês Barroso
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - László Bencze
- Health Services Management Training Centre, Faculty of Health and Public Services, Semmelweis University, Kútvölgyi út 2, 1125, Budapest, Hungary
| | - Mikael Benson
- Centre for Personalised Medicine, Linköping University, 581 85, Linköping, Sweden
| | - Jay Bergeron
- Translational & Bioinformatics, Pfizer Inc., 300 Technology Square, Cambridge, MA, 02139, USA
| | - Enrique Bernal-Delgado
- Institute for Health Sciences, IACS - IIS Aragon, San Juan Bosco 13, 50009, Zaragoza, Spain
| | - Niklas Blomberg
- ELIXIR, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT25.2, 1090, Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, Lazarettgasse 14, AKH BT25.2, 1090, Vienna, Austria
- Max Planck Institute for Informatics, Campus E1 4, 66123, Saarbrücken, Germany
| | - Ana Conesa
- Príncipe Felipe Research Center, C/ Eduardo Primo Yúfera 3, 46012, Valencia, Spain
- University of Florida, Institute of Food and Agricultural Sciences (IFAS), 2033 Mowry Road, Gainesville, FL, 32610, USA
| | | | - Christophe Delogne
- Technology, Data & Analytics, KPMG Luxembourg, Société Coopérative, 39 Avenue John F. Kennedy, 1855, Luxembourg, Luxembourg
| | - Peter Devilee
- Department of Human Genetics, Department of Pathology, Leiden University Medical Centre, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Alberto Di Meglio
- Information Technology Department, European Organization for Nuclear Research (CERN), 385 Route de Meyrin, 1211, Geneva 23, Switzerland
| | - Marinus Eijkemans
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Heidelberglaan 100, 3508 GA, Utrecht, The Netherlands
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Norbert Graf
- Department of Pediatric Oncology/Hematology, Saarland University, Campus Homburg, Building 9, 66421, Homburg, Germany
| | - Vera Grimm
- Project Management Jülich, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52428, Jülich, Germany
| | - Henk-Jan Guchelaar
- Department of Clinical Pharmacy & Toxicology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Yi-Ke Guo
- Data Science Institute, Imperial College London, South Kensington, London, SW7 2AZ, UK
| | - Ivo Glynne Gut
- CNAG-CRG, Center for Genomic Regulation, Barcelona Institute for Science and Technology (BIST), C/Baldiri Reixac 4, 08029, Barcelona, Spain
| | - Allan Hanbury
- Institute of Software Technology and Interactive Systems, TU Wien, Favoritenstrasse 9-11/188, 1040, Vienna, Austria
| | - Shahid Hanif
- The Association of the British Pharmaceutical Industry, 7th Floor, Southside, 105 Victoria Street, London, SW1E 6QT, UK
| | - Ralf-Dieter Hilgers
- Department of Medical Statistics, RWTH-Aachen University, Universitätsklinikum Aachen, Pauwelsstraße 30, 52074, Aachen, Germany
| | - Ángel Honrado
- SYNAPSE Research Management Partners, Diputació 237, Àtic 3ª, 08007, Barcelona, Spain
| | - D Rod Hose
- Department of Infection, Immunity and Cardiovascular Disease and Insigneo Institute for In-Silico Medicine, Medical School, University of Sheffield, Beech Hill Road, Sheffield, S10 2RX, UK
| | | | - Tim Hubbard
- Department of Medical & Molecular Genetics, King's College London, London, SE1 9RT, UK
- Genomics England, London, EC1M 6BQ, UK
| | - Sophie Helen Janacek
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Haralampos Karanikas
- National and Kapodistrian University of Athens, Medical School, Xristou Lada 6, 10561, Athens, Greece
| | - Tim Kievits
- Vitromics Healthcare Holding B.V., Onderwijsboulevard 225, 5223 DE, 's-Hertogenbosch, The Netherlands
| | - Manfred Kohler
- Fraunhofer Institute for Molecular Biology and Applied Ecology ScreeningPort, Schnackenburgallee 114, 22525, Hamburg, Germany
| | - Andreas Kremer
- ITTM S.A., 9 avenue des Hauts Fourneaux, 4362, Esch-sur-Alzette, Luxembourg
| | - Jerry Lanfear
- Research Business Technology, Pfizer Ltd, GP4 Building, Granta Park, Cambridge, CB21 6GP, UK
| | - Thomas Lengauer
- Max Planck Institute for Informatics, Campus E1 4, 66123, Saarbrücken, Germany
| | - Edith Maes
- Health Economics & Outcomes Research, Deloitte Belgium, Berkenlaan 8A, 1831, Diegem, Belgium
| | - Theo Meert
- Janssen Pharmaceutica N.V., R&D G3O, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Werner Müller
- Faculty of Life Sciences, University of Manchester, AV Hill Building, Oxford Road, Manchester, M13 9PT, UK
| | - Dörthe Nickel
- UMR3664 IC/CNRS, Institut Curie, Section Recherche, Pavillon Pasteur, 26 rue d'Ulm, 75248, Paris cedex 05, France
| | - Peter Oledzki
- Linguamatics Ltd, 324 Cambridge Science Park Milton Rd, Cambridge, CB4 0WG, UK
| | - Bertrand Pedersen
- PwC Luxembourg, 2 rue Gerhard Mercator, 2182, Luxembourg, Luxembourg
| | - Milan Petkovic
- Philips, HighTechCampus 36, 5656AE, Eindhoven, The Netherlands
| | - Konstantinos Pliakos
- Department of Public Health and Primary Care, KU Leuven Kulak, Etienne Sabbelaan 53, 8500, Kortrijk, Belgium
| | - Magnus Rattray
- Faculty of Life Sciences, University of Manchester, AV Hill Building, Oxford Road, Manchester, M13 9PT, UK
| | - Josep Redón I Màs
- INCLIVA Health Research Institute, University of Valencia, CIBERobn ISCIII, Avenida Menéndez Pelayo 4 accesorio, 46010, Valencia, Spain
| | - Reinhard Schneider
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts Fourneaux, 4362, Esch-sur-Alzette, Luxembourg
| | - Thierry Sengstag
- Swiss Institute of Bioinformatics (SIB) and University of Basel, Klingelbergstrasse 50/70, 4056, Basel, Switzerland
| | - Xavier Serra-Picamal
- Agency for Health Quality and Assessment of Catalonia (AQuAS), Carrer de Roc Boronat 81-95, 08005, Barcelona, Spain
| | - Wouter Spek
- EuroBioForum Foundation, Chrysantstraat 10, 3135 HG, Vlaardingen, The Netherlands
| | - Lea A I Vaas
- Fraunhofer Institute for Molecular Biology and Applied Ecology ScreeningPort, Schnackenburgallee 114, 22525, Hamburg, Germany
| | - Okker van Batenburg
- EuroBioForum Foundation, Chrysantstraat 10, 3135 HG, Vlaardingen, The Netherlands
| | - Marc Vandelaer
- Integrated BioBank of Luxembourg, 6 rue Nicolas-Ernest Barblé, 1210, Luxembourg, Luxembourg
| | - Peter Varnai
- Technopolis Group, 3 Pavilion Buildings, Brighton, BN1 1EE, UK
| | - Pablo Villoslada
- Hospital Clinic of Barcelona, Institute d'Investigacions Biomediques August Pi Sunyer (IDIBAPS), Rosello 149, 08036, Barcelona, Spain
| | - Juan Antonio Vizcaíno
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - John Peter Mary Wubbe
- European Platform for Patients' Organisations, Science and Industry (Epposi), De Meeûs Square 38-40, 1000, Brussels, Belgium
| | - Gianluigi Zanetti
- CRS4, Ed.1 POLARIS, 09129, Pula, Italy
- BBMRI-ERIC, Neue Stiftingtalstrasse 2/B/6, 8010, Graz, Austria
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Bousfield D, McEntyre J, Velankar S, Papadatos G, Bateman A, Cochrane G, Kim JH, Graef F, Vartak V, Alako B, Blomberg N. Patterns of database citation in articles and patents indicate long-term scientific and industry value of biological data resources. F1000Res 2016; 5:ELIXIR-160. [PMID: 27092246 PMCID: PMC4821287 DOI: 10.12688/f1000research.7911.1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/05/2016] [Indexed: 01/26/2023] Open
Abstract
Data from open access biomolecular data resources, such as the European Nucleotide Archive and the Protein Data Bank are extensively reused within life science research for comparative studies, method development and to derive new scientific insights. Indicators that estimate the extent and utility of such secondary use of research data need to reflect this complex and highly variable data usage. By linking open access scientific literature, via Europe PubMedCentral, to the metadata in biological data resources we separate data citations associated with a deposition statement from citations that capture the subsequent, long-term, reuse of data in academia and industry. We extend this analysis to begin to investigate citations of biomolecular resources in patent documents. We find citations in more than 8,000 patents from 2014, demonstrating substantial use and an important role for data resources in defining biological concepts in granted patents to both academic and industrial innovators. Combined together our results indicate that the citation patterns in biomedical literature and patents vary, not only due to citation practice but also according to the data resource cited. The results guard against the use of simple metrics such as citation counts and show that indicators of data use must not only take into account citations within the biomedical literature but also include reuse of data in industry and other parts of society by including patents and other scientific and technical documents such as guidelines, reports and grant applications.
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Affiliation(s)
- David Bousfield
- ELIXIR, Wellcome Genome Campus, Cambridge, UK
- Ganesha Associates, Cambridge, UK
| | - Johanna McEntyre
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK
| | - Sameer Velankar
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK
| | - George Papadatos
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK
| | - Alex Bateman
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK
| | - Guy Cochrane
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK
| | - Jee-Hyub Kim
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK
| | - Florian Graef
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK
| | - Vid Vartak
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK
| | - Blaise Alako
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK
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Abstract
ELIXIR, the European life science infrastructure for biological information, is a unique initiative to consolidate Europe's national centres, services, and core bioinformatics resources into a single, coordinated infrastructure. ELIXIR brings together Europe's major life-science data archives and connects these with national bioinformatics infrastructures - the ELIXIR Nodes. This editorial introduces the ELIXIR channel in F1000Research; the aim of the channel is to collect and present ELIXIR's scientific and operational output, engage with the broad life science community and encourage discussion on proposed infrastructure solutions. Submissions will be assessed by the ELIXIR channel Advisory Board to ensure they are relevant to ELIXIR community, and subjected to F1000Research open peer review process.
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Affiliation(s)
- Niklas Blomberg
- ELIXIR Hub, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | | | - Barend Mons
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Bengt Persson
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Inge Jonassen
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
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27
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Bott TS, Urschitz MS, Poets C, Blomberg N, Poets A. [A Randomized Controlled Trial on the Effect of Earmuffs on Intermittent Hypoxia and Bradycardia in Preterm Infants]. Klin Padiatr 2015; 227:269-73. [PMID: 26070052 DOI: 10.1055/s-0035-1547308] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
BACKGROUND Irregular breathing causing hypoxia and bradycardia is a common problem of preterm infants but its pathophysiology is incompletely understood. Agitation provoked by environmental noise may play a role. We wanted to know if earmuffs can at least halve the rate of intermittent hypoxia in premies. PATIENTS AND METHODS In this randomized controlled trial 31 infants (14 male; median [min.-max.] birth weight and gestational age: 1 323 g [560-1 990] and 30(1/7) weeks [25(5/7)-33(0/7)]) had the effect of earmuffs on the frequency of pulse oximeter desaturations (SpO(2) <80%) and bradycardia events (<80 beats per minute) tested, documented via a standard home monitor. Infants were measured 2 h each with or without earmuffs; the sequence of intervention was randomised. Measurement conditions were kept constant while a noise meter recorded sound pressure levels at a 1 Hz sampling rate. RESULTS Median sound pressure level was 46.8 dB(A). In a pre-study, ear muffs yielded a sound reduction by 7.2 dB. 19 infants had a total of 474 desaturations. The median (25.-75. percentile) number of desaturations was 1 (1-10.5) without, and 1 (1-10) with earmuffs. The amount of infants with at least one desaturation was equal in both treatment protocols. Only 7 bradycardias occurred. CONCLUSION The earmuffs had, in a rather quiet environment, no effect on intermittent hypoxia in these infants.
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Affiliation(s)
- T S Bott
- Universitätsklinikum Tübingen, Abteilung für Neonatologie
| | - M S Urschitz
- Institut für Medizinische Biometrie, Epidemiologie und Informatik der Universitätsmedizin der Johannes Gutenberg-Universität Mainz
| | - C Poets
- Universitätsklinikum Tübingen, Abteilung für Neonatologie
| | - N Blomberg
- Universität Tübingen, Institut für Arbeitsmedizin, Sozialmedizin und Versorgungsforschung
| | - A Poets
- Universitätsklinikum Tübingen, Abteilung für Neonatologie
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28
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Budd A, Corpas M, Brazas MD, Fuller JC, Goecks J, Mulder NJ, Michaut M, Ouellette BFF, Pawlik A, Blomberg N. A quick guide for building a successful bioinformatics community. PLoS Comput Biol 2015; 11:e1003972. [PMID: 25654371 PMCID: PMC4318577 DOI: 10.1371/journal.pcbi.1003972] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
"Scientific community" refers to a group of people collaborating together on scientific-research-related activities who also share common goals, interests, and values. Such communities play a key role in many bioinformatics activities. Communities may be linked to a specific location or institute, or involve people working at many different institutions and locations. Education and training is typically an important component of these communities, providing a valuable context in which to develop skills and expertise, while also strengthening links and relationships within the community. Scientific communities facilitate: (i) the exchange and development of ideas and expertise; (ii) career development; (iii) coordinated funding activities; (iv) interactions and engagement with professionals from other fields; and (v) other activities beneficial to individual participants, communities, and the scientific field as a whole. It is thus beneficial at many different levels to understand the general features of successful, high-impact bioinformatics communities; how individual participants can contribute to the success of these communities; and the role of education and training within these communities. We present here a quick guide to building and maintaining a successful, high-impact bioinformatics community, along with an overview of the general benefits of participating in such communities. This article grew out of contributions made by organizers, presenters, panelists, and other participants of the ISMB/ECCB 2013 workshop "The 'How To Guide' for Establishing a Successful Bioinformatics Network" at the 21st Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and the 12th European Conference on Computational Biology (ECCB).
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Affiliation(s)
- Aidan Budd
- Structural and Computational Biology (SCB) Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Manuel Corpas
- The Genome Analysis Centre (TGAC), Norwich Research Park, Norwich, United Kingdom
| | - Michelle D. Brazas
- Ontario Institute for Cancer Research, MaRS Centre, West Tower, Toronto, Ontario, Canada
| | - Jonathan C. Fuller
- Heidelberg Institute for Theoretical Studies (HITS) gGmbH, Heidelberg, Germany
| | - Jeremy Goecks
- The Computational Biology Institute, George Washington University, Innovation Hall, Virginia, United States of America
| | - Nicola J. Mulder
- Computational Biology Group, Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town Faculty of Health Sciences, Cape Town, South Africa
| | - Magali Michaut
- Computational Cancer Biology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - B. F. Francis Ouellette
- Ontario Institute for Cancer Research, MaRS Centre, West Tower, Toronto, Ontario, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada
| | - Aleksandra Pawlik
- The Software Sustainability Institute, School of Computer Science, University of Manchester, Manchester, United Kingdom
| | - Niklas Blomberg
- ELIXIR Hub, Wellcome Trust Genome Campus, Cambridge, United Kingdom
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29
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Dura E, Muresan S, Engkvist O, Blomberg N, Chen H. Mining Molecular Pharmacological Effects from Biomedical Text: a Case Study for Eliciting Anti-Obesity/Diabetes Effects of Chemical Compounds. Mol Inform 2014; 33:332-42. [DOI: 10.1002/minf.201300144] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 02/28/2014] [Indexed: 11/07/2022]
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30
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Azzaoui K, Jacoby E, Senger S, Rodríguez EC, Loza M, Zdrazil B, Pinto M, Williams AJ, de la Torre V, Mestres J, Pastor M, Taboureau O, Rarey M, Chichester C, Pettifer S, Blomberg N, Harland L, Williams-Jones B, Ecker GF. Scientific competency questions as the basis for semantically enriched open pharmacological space development. Drug Discov Today 2013; 18:843-52. [DOI: 10.1016/j.drudis.2013.05.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Revised: 04/17/2013] [Accepted: 05/14/2013] [Indexed: 10/26/2022]
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31
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Kogej T, Blomberg N, Greasley PJ, Mundt S, Vainio MJ, Schamberger J, Schmidt G, Hüser J. Big pharma screening collections: more of the same or unique libraries? The AstraZeneca-Bayer Pharma AG case. Drug Discov Today 2012; 18:1014-24. [PMID: 23127858 DOI: 10.1016/j.drudis.2012.10.011] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 09/24/2012] [Accepted: 10/26/2012] [Indexed: 11/18/2022]
Abstract
In this study, the screening collections of two major pharmaceutical companies (AstraZeneca and Bayer Pharma AG) have been compared using a 2D molecular fingerprint by a nearest neighborhood approach. Results revealed a low overlap between both collections in terms of compound identity and similarity. This emphasizes the value of screening multiple compound collections to expand the chemical space that can be accessed by high-throughput screening (HTS).
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Affiliation(s)
- Thierry Kogej
- Chemistry Innovation Centre/Discovery Sciences, AstraZeneca R&D Mölndal, SE-43183 Mölndal, Sweden.
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Shamovsky I, Ripa L, Blomberg N, Eriksson LA, Hansen P, Mee C, Tyrchan C, O'Donovan M, Sjö P. Theoretical Studies of Chemical Reactivity of Metabolically Activated Forms of Aromatic Amines toward DNA. Chem Res Toxicol 2012; 25:2236-52. [DOI: 10.1021/tx300313b] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Igor Shamovsky
- Department of Medicinal Chemistry, R&I iMed, AstraZeneca R&D, Pepparedsleden 1, S-431 83 Mölndal, Sweden
| | - Lena Ripa
- Department of Medicinal Chemistry, R&I iMed, AstraZeneca R&D, Pepparedsleden 1, S-431 83 Mölndal, Sweden
| | - Niklas Blomberg
- Department of Medicinal Chemistry, R&I iMed, AstraZeneca R&D, Pepparedsleden 1, S-431 83 Mölndal, Sweden
| | - Leif A. Eriksson
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-412 96 Göteborg, Sweden
| | - Peter Hansen
- Department of Medicinal Chemistry, R&I iMed, AstraZeneca R&D, Pepparedsleden 1, S-431 83 Mölndal, Sweden
| | - Christine Mee
- Genetic Toxicology, AstraZeneca R&D, Alderley Park, Macclesfield, Cheshire, SK10 4TG, United Kingdom
| | - Christian Tyrchan
- Department of Medicinal Chemistry, CVGI iMed, AstraZeneca R&D, Pepparedsleden 1, S-431 83 Mölndal, Sweden
| | - Mike O'Donovan
- Genetic Toxicology, AstraZeneca R&D, Alderley Park, Macclesfield, Cheshire, SK10 4TG, United Kingdom
| | - Peter Sjö
- Department of Medicinal Chemistry, R&I iMed, AstraZeneca R&D, Pepparedsleden 1, S-431 83 Mölndal, Sweden
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Eriksson M, Nilsson I, Kogej T, Southan C, Johansson M, Tyrchan C, Muresan S, Blomberg N, Bjäreland M. SARConnect: A Tool to Interrogate the Connectivity Between Proteins, Chemical Structures and Activity Data. Mol Inform 2012; 31:555-568. [PMID: 23308082 PMCID: PMC3535785 DOI: 10.1002/minf.201200030] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Accepted: 04/14/2012] [Indexed: 11/21/2022]
Abstract
The access and use of large-scale structure-activity relationships (SAR) is increasing as the range of targets and availability of bioactive compound-to-protein mappings expands. However, effective exploitation requires merging and normalisation of activity data, mappings to target classifications as well as visual display of chemical structure relationships. This work describes the development of the application "SARConnect" to address these issues. We discuss options for delivery and analysis of large-scale SAR data together with a set of use-cases to illustrate the design choices and utility. The main activity sources of ChEMBL,1 GOSTAR2 and AstraZeneca's internal system IBIS, had already been integrated in Chemistry Connect.3 For target relationships we selected human UniProtKB/Swiss-Prot4 as our primary source of a heuristic target classification. Similarly, to explore chemical relationships we combined several methods for framework and scaffold analysis into a unified, hierarchical classification where ease of navigation was the primary goal. An application was built on TIBCO Spotfire to retrieve data for visual display. Consequently, users can explore relationships between target, activity and structure across internal, external and commercial sources that encompass approximately 3 million compounds, 2000 human proteins and 10 million activity values. Examples showing the utility of the application are given.
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Affiliation(s)
- Mats Eriksson
- Discovery Sciences, Computational
Sciences, AstraZeneca R&D Mölndal,
S-431 83 Mölndal, Sweden
| | | | - Thierry Kogej
- Discovery Sciences, Computational
Sciences, AstraZeneca R&D Mölndal,
S-431 83 Mölndal, Sweden
| | | | | | | | - Sorel Muresan
- Discovery Sciences, Computational
Sciences, AstraZeneca R&D Mölndal,
S-431 83 Mölndal, Sweden
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34
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Abstract
The ever-growing availability of large-scale open data and its maturation is having a significant impact on industrial drug-discovery, as well as on academic and non-profit research. As industry is changing to an 'open innovation' business concept, precompetitive initiatives and strong public-private partnerships including academic research cooperation partners are gaining more and more importance. Now, the bioinformatics and cheminformatics communities are seeking for web tools which allow the integration of this large volume of life science datasets available in the public domain. Such a data exploitation tool would ideally be able to answer complex biological questions by formulating only one search query. In this short review/perspective, we outline the use of semantic web approaches for data and knowledge integration. Further, we discuss strengths and current limitations of public available data retrieval tools and integrated platforms.
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Affiliation(s)
- Barbara Zdrazil
- University of Vienna, Department of Medicinal Chemistry, Pharmacoinformatics Research GroupAlthanstrasse 14, 1090 Vienna, Austria
| | - Niklas Blomberg
- Medicinal Chemistry, Respiratory and Inflammation iMEDAstraZeneca R&D Mölndal, S-43183 Mölndal, Sweden
| | - Gerhard F Ecker
- University of Vienna, Department of Medicinal Chemistry, Pharmacoinformatics Research GroupAlthanstrasse 14, 1090 Vienna, Austria
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35
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Williams AJ, Harland L, Groth P, Pettifer S, Chichester C, Willighagen EL, Evelo CT, Blomberg N, Ecker G, Goble C, Mons B. Open PHACTS: semantic interoperability for drug discovery. Drug Discov Today 2012; 17:1188-98. [PMID: 22683805 DOI: 10.1016/j.drudis.2012.05.016] [Citation(s) in RCA: 172] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Revised: 05/18/2012] [Accepted: 05/31/2012] [Indexed: 01/22/2023]
Abstract
Open PHACTS is a public-private partnership between academia, publishers, small and medium sized enterprises and pharmaceutical companies. The goal of the project is to deliver and sustain an 'open pharmacological space' using and enhancing state-of-the-art semantic web standards and technologies. It is focused on practical and robust applications to solve specific questions in drug discovery research. OPS is intended to facilitate improvements in drug discovery in academia and industry and to support open innovation and in-house non-public drug discovery research. This paper lays out the challenges and how the Open PHACTS project is hoping to address these challenges technically and socially.
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Affiliation(s)
- Antony J Williams
- Royal Society of Chemistry, ChemSpider, US Office, Wake Forest, NC 27587, USA.
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36
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Chen H, Engkvist O, Blomberg N, Li J. A comparative analysis of the molecular topologies for drugs, clinical candidates, natural products, human metabolites and general bioactive compounds. Med Chem Commun 2012. [DOI: 10.1039/c2md00238h] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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37
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Luker T, Alcaraz L, Chohan KK, Blomberg N, Brown DS, Butlin RJ, Elebring T, Griffin AM, Guile S, St-Gallay S, Swahn BM, Swallow S, Waring MJ, Wenlock MC, Leeson PD. Strategies to improve in vivo toxicology outcomes for basic candidate drug molecules. Bioorg Med Chem Lett 2011; 21:5673-9. [DOI: 10.1016/j.bmcl.2011.07.074] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2011] [Accepted: 07/18/2011] [Indexed: 11/25/2022]
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38
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Abstract
Combinatorial and parallel chemical synthesis technologies are powerful tools in early drug discovery projects. Over the past couple of years an increased emphasis on targeted lead generation libraries and focussed screening libraries in the pharmaceutical industry has driven a surge in computational methods to explore molecular frameworks to establish new chemical equity. In this chapter we describe a complementary technique in the library design process, termed ProSAR, to effectively cover the accessible pharmacophore space around a given scaffold. With this method reagents are selected such that each R-group on the scaffold has an optimal coverage of pharmacophoric features. This is achieved by optimising the Shannon entropy, i.e. the information content, of the topological pharmacophore distribution for the reagents. As this method enumerates compounds with a systematic variation of user-defined pharmacophores to the attachment point on the scaffold, the enumerated compounds may serve as a good starting point for deriving a structure-activity relationship (SAR).
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Affiliation(s)
- Hongming Chen
- DECS GCS Computational Chemistry, AstraZeneca R&D Mölndal, Mölndal, Sweden.
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39
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Hanessian S, Larsson A, Fex T, Knecht W, Blomberg N. Design and synthesis of macrocyclic indoles targeting blood coagulation cascade Factor XIa. Bioorg Med Chem Lett 2010; 20:6925-8. [DOI: 10.1016/j.bmcl.2010.09.141] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Revised: 09/27/2010] [Accepted: 09/28/2010] [Indexed: 11/27/2022]
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40
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Tyrchan C, Blomberg N, Engkvist O, Kogej T, Muresan S. Physicochemical property profiles of marketed drugs, clinical candidates and bioactive compounds. Bioorg Med Chem Lett 2009; 19:6943-7. [PMID: 19879759 DOI: 10.1016/j.bmcl.2009.10.068] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2009] [Revised: 10/13/2009] [Accepted: 10/14/2009] [Indexed: 11/29/2022]
Abstract
We performed a comparison of several simple physicochemical properties between marketed drugs, clinical candidates and bioactive compounds using commercially available databases (GVKBIO, Hyderabad, India). In contrast to previous studies this comparison was performed at the individual target level. Confirming earlier studies this shows that marketed drugs have, on average and taken as a single set, lower physicochemical property values than the corresponding clinical candidates and bioactive compounds but that there is considerable variation between drug targets. This work complements earlier studies by using a much larger annotated dataset and confirms that there is a shift in physicochemical properties for targets with launched drugs and clinical candidates compared to bioactive compounds.
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Affiliation(s)
- Christian Tyrchan
- DECS Global Compound Sciences, AstraZeneca R&D Mölndal, SE-431 83 Mölndal, Sweden
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41
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Henrich S, Feierberg I, Wang T, Blomberg N, Wade RC. Comparative binding energy analysis for binding affinity and target selectivity prediction. Proteins 2009; 78:135-53. [DOI: 10.1002/prot.22579] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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42
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Blomberg N, Cosgrove DA, Kenny PW, Kolmodin K. Design of compound libraries for fragment screening. J Comput Aided Mol Des 2009; 23:513-25. [DOI: 10.1007/s10822-009-9264-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2008] [Accepted: 02/16/2009] [Indexed: 01/15/2023]
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43
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Chen H, Börjesson U, Engkvist O, Kogej T, Svensson MA, Blomberg N, Weigelt D, Burrows JN, Lange T. ProSAR: A New Methodology for Combinatorial Library Design. J Chem Inf Model 2009; 49:603-14. [DOI: 10.1021/ci800231d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hongming Chen
- DECS GCS Computational Chemistry, AstraZeneca R&D Mölndal, Pepparedsleden 1, SE-43183 Mölndal, Sweden, and Medicinal Chemistry, AstraZeneca R&D Södertälje, SE-151 85 Södertälje, Sweden
| | - Ulf Börjesson
- DECS GCS Computational Chemistry, AstraZeneca R&D Mölndal, Pepparedsleden 1, SE-43183 Mölndal, Sweden, and Medicinal Chemistry, AstraZeneca R&D Södertälje, SE-151 85 Södertälje, Sweden
| | - Ola Engkvist
- DECS GCS Computational Chemistry, AstraZeneca R&D Mölndal, Pepparedsleden 1, SE-43183 Mölndal, Sweden, and Medicinal Chemistry, AstraZeneca R&D Södertälje, SE-151 85 Södertälje, Sweden
| | - Thierry Kogej
- DECS GCS Computational Chemistry, AstraZeneca R&D Mölndal, Pepparedsleden 1, SE-43183 Mölndal, Sweden, and Medicinal Chemistry, AstraZeneca R&D Södertälje, SE-151 85 Södertälje, Sweden
| | - Mats A. Svensson
- DECS GCS Computational Chemistry, AstraZeneca R&D Mölndal, Pepparedsleden 1, SE-43183 Mölndal, Sweden, and Medicinal Chemistry, AstraZeneca R&D Södertälje, SE-151 85 Södertälje, Sweden
| | - Niklas Blomberg
- DECS GCS Computational Chemistry, AstraZeneca R&D Mölndal, Pepparedsleden 1, SE-43183 Mölndal, Sweden, and Medicinal Chemistry, AstraZeneca R&D Södertälje, SE-151 85 Södertälje, Sweden
| | - Dirk Weigelt
- DECS GCS Computational Chemistry, AstraZeneca R&D Mölndal, Pepparedsleden 1, SE-43183 Mölndal, Sweden, and Medicinal Chemistry, AstraZeneca R&D Södertälje, SE-151 85 Södertälje, Sweden
| | - Jeremy N. Burrows
- DECS GCS Computational Chemistry, AstraZeneca R&D Mölndal, Pepparedsleden 1, SE-43183 Mölndal, Sweden, and Medicinal Chemistry, AstraZeneca R&D Södertälje, SE-151 85 Södertälje, Sweden
| | - Tim Lange
- DECS GCS Computational Chemistry, AstraZeneca R&D Mölndal, Pepparedsleden 1, SE-43183 Mölndal, Sweden, and Medicinal Chemistry, AstraZeneca R&D Södertälje, SE-151 85 Södertälje, Sweden
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44
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Albert J, Blomberg N, Breeze A, Brown A, Burrows J, Edwards P, Folmer R, Geschwindner S, Griffen E, Kenny P, Nowak T, Olsson LL, Sanganee H, Shapiro A. An Integrated Approach to Fragment-Based Lead Generation:Philosophy, Strategy and Case Studies from AstraZenecas Drug Discovery Programmes. Curr Top Med Chem 2007; 7:1600-29. [DOI: 10.2174/156802607782341091] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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45
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Hanessian S, Ersmark K, Wang X, Del Valle JR, Blomberg N, Xue Y, Fjellström O. Structure-based organic synthesis of unnatural aeruginosin hybrids as potent inhibitors of thrombin. Bioorg Med Chem Lett 2007; 17:3480-5. [PMID: 17428662 DOI: 10.1016/j.bmcl.2007.03.075] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2007] [Revised: 03/21/2007] [Accepted: 03/23/2007] [Indexed: 11/21/2022]
Abstract
Based on X-ray crystallographic data of complexes of chlorodysinosin A with the enzyme thrombin, a series of analogs were synthesized varying the nature of the P(1), P(2), and P(3) pharmacophoric sites and the central octahydroindole carboxyamide core. In general, introduction of a hydrophobic substituent on the d-leucine amide residue dramatically improved the inhibition of the enzyme. This is rationalized based on a better fit of the P(3) subunit in the hydrophobic S(3) enzyme site. Single digit nanomolar inhibition expressed as IC(50) was observed for several analogs.
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Affiliation(s)
- Stephen Hanessian
- Department of Chemistry, Université de Montréal, PO Box 6128, Station, Centre-Ville, Montréal, QC, Canada H3C 3J7.
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46
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Gavaghan CL, Arnby CH, Blomberg N, Strandlund G, Boyer S. Development, interpretation and temporal evaluation of a global QSAR of hERG electrophysiology screening data. J Comput Aided Mol Des 2007; 21:189-206. [PMID: 17384921 DOI: 10.1007/s10822-006-9095-6] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2006] [Accepted: 12/02/2006] [Indexed: 10/23/2022]
Abstract
A 'global' model of hERG K(+) channel was built to satisfy three basic criteria for QSAR models in drug discovery: (1) assessment of the applicability domain, (2) assuring that model decisions can be interpreted by medicinal chemists and (3) assessment of model performance after the model was built. A combination of D-optimal onion design and hierarchical partial least squares modelling was applied to construct a global model of hERG blockade in order to maximize the applicability domain of the model and to enhance its interpretability. Additionally, easily interpretable hERG specific fragment-based descriptors were developed. Model performance was monitored, throughout a time period of 15 months, after model implementation. It was found that after this time duration a greater proportion of molecules were outside the model's applicability domain and that these compounds had a markedly higher average prediction error than those from molecules within the model's applicability domain. The model's predictive performance deteriorated within 4 months after building, illustrating the necessity of regular updating of global models within a drug discovery environment.
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Affiliation(s)
- Claire L Gavaghan
- Computational Toxicology, Safety Assessment, AstraZeneca R&D, Molndal, Sweden.
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47
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Hanessian S, Del Valle JR, Xue Y, Blomberg N. Total Synthesis and Structural Confirmation of Chlorodysinosin A [J. Am. Chem. Soc. 2006, 128, 10491−10495]. J Am Chem Soc 2006. [DOI: 10.1021/ja069971q] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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48
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Abstract
The first enantiocontrolled total synthesis of the marine sponge metabolite chlorodysinosin A is described. The structure and absolute configuration are identical to those of dysinosin A except for the presence of a novel 2S,3R-3-chloroleucine residue in the former. A concise stereocontrolled synthesis of the new chlorine-containing amino acid fragment was developed. An X-ray cocrystal structure of synthetic chlorodysinosin A with the enzyme thrombin confirms the structure and configuration assignment achieved through total synthesis. Within the aeruginosin family of natural products, chlorodysinosin A is the most potent inhibitor of the serine proteases thrombin, factor VIIa, and factor Xa, which are critical enzymes in the process leading to platelet aggregation and fibrin mesh formation in humans.
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Affiliation(s)
- Stephen Hanessian
- Department of Chemistry, Université de Montréal, C.P. 6128, Station Centre-ville, Montréal, P.Q., H3C 3J7 Canada
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49
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Abstract
Molecular fingerprints are widely used for similarity-based virtual screening in drug discovery projects. In this paper we discuss the performance and the complementarity of nine two-dimensional fingerprints (Daylight, Unity, AlFi, Hologram, CATS, TRUST, Molprint 2D, ChemGPS, and ALOGP) in retrieving active molecules by similarity searching against a set of query compounds. For this purpose, we used biological data from HTS screening campaigns of four protein families (GPCRs, kinases, ion channels, and proteases). We have established threshold values for the similarity index (Tanimoto index) to be used as starting points for similarity searches. Based on the complementarities between the selections made by using different fingerprints we propose a multifingerprint approach as an efficient tool to balance the strengths and weaknesses of various fingerprints.
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Affiliation(s)
- Thierry Kogej
- AstraZeneca R&D Mölndal, GDECS Computational Chemistry, Pepparedsleden 1, 431 83 Mölndal, Sweden
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50
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Cronet P, Petersen JF, Folmer R, Blomberg N, Sjöblom K, Karlsson U, Lindstedt EL, Bamberg K. Structure of the PPARalpha and -gamma ligand binding domain in complex with AZ 242; ligand selectivity and agonist activation in the PPAR family. Structure 2001; 9:699-706. [PMID: 11587644 DOI: 10.1016/s0969-2126(01)00634-7] [Citation(s) in RCA: 269] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BACKGROUND The peroxisome proliferator-activated receptors (PPAR) are ligand-activated transcription factors belonging to the nuclear receptor family. The roles of PPARalpha in fatty acid oxidation and PPARgamma in adipocyte differentiation and lipid storage have been characterized extensively. PPARs are activated by fatty acids and eicosanoids and are also targets for antidyslipidemic drugs, but the molecular interactions governing ligand selectivity for specific subtypes are unclear due to the lack of a PPARalpha ligand binding domain structure. RESULTS We have solved the crystal structure of the PPARalpha ligand binding domain (LBD) in complex with the combined PPARalpha and -gamma agonist AZ 242, a novel dihydro cinnamate derivative that is structurally different from thiazolidinediones. In addition, we present the crystal structure of the PPARgamma_LBD/AZ 242 complex and provide a rationale for ligand selectivity toward the PPARalpha and -gamma subtypes. Heteronuclear NMR data on PPARalpha in both the apo form and in complex with AZ 242 shows an overall stabilization of the LBD upon agonist binding. A comparison of the novel PPARalpha/AZ 242 complex with the PPARgamma/AZ 242 complex and previously solved PPARgamma structures reveals a conserved hydrogen bonding network between agonists and the AF2 helix. CONCLUSIONS The complex of PPARalpha and PPARgamma with the dual specificity agonist AZ 242 highlights the conserved interactions required for receptor activation. Together with the NMR data, this suggests a general model for ligand activation in the PPAR family. A comparison of the ligand binding sites reveals a molecular explanation for subtype selectivity and provides a basis for rational drug design.
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Affiliation(s)
- P Cronet
- Department of Molecular Biology, AstraZeneca R&D Mölndal, S-431 83, Mölndal, Sweden
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