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Large-Scale Data Sharing in the Life Sciences: Data Standards, Incentives, Barriers and Funding Models (The “Joint Data Standards Study”)

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Large-Scale Data Sharing in the Life Sciences: Data Standards, Incentives, Barriers and Funding Models (The “Joint Data Standards Study”) Large-scale data sharing in the life sciences: Data standards, incentives, barriers and funding models (The “Joint Data Standards Study”) Prepared for The Biotechnology and Biological Sciences Research Council The Department of Trade and Industry The Joint Information Systems Committee for Support for Research The Medical Research Council The Natural Environment Research Council The Wellcome Trust Prepared by The Digital Archiving Consultancy (DAC) The Bioinformatics Research Centre, University of Glasgow (BRC) The National e-Science Centre (NeSC) August 2005 Large-scale data sharing in the life sciences 2 Table of contents VOLUME 1 - Report Page Abbreviations 4 Acknowledgements 5 Executive summary 8 PART 1 1. Background to report 13 2. Method 14 3. Key concepts 17 PART 2 Findings: general introduction 20 4. Technical issues 21 5. Tools 27 6. Standards 33 7. Planning and management over the data life cycle 37 8. Nature of content 45 9. Organisational and management issues 50 10. Culture and careers 55 11. Support, training and awareness 59 12. Legal, regulatory, and rights management issues 61 13. Corporate sector 64 14. International issues 68 PART 3 15. Core models for data sharing 71 Large-scale data sharing in the life sciences 3 VOLUME 2 – Appendices Page Appendix 1: Bibliography A-2 Appendix 2: Glossary A-10 Appendix 3: Case studies A-19 Case study 1: Arts & Humanities Data Service A-23 Case study 2: BADC / NERC DataGrid A-29 Case study 3: BRIDGES A-38 Case study 4: CLEF A-47 Case study 5: Common Data Access A-54 Case study 6: Ensembl A-61 Case study 7: Genome Information Management System A-67 Case study 8: Malaria (Plasmodium falciparum) A-72 Case study 9: Nottingham Arabidopsis Stock Centre A-76 Case study 10: Proteomics Standards Initiative A-83 Appendix 4: Further sharing models A-97 Appendix 5: Supplementary materials A-104 5.1 The data provenance issue A-104 5.2 Standards and data sharing A-109 5.3 Databases A-113 Large-scale data sharing in the life sciences 4 Abbreviations commonly used in the text The following abbreviations are used commonly throughout the text. Less frequently used abbreviations are listed in Appendix 2. AHDS Arts and Humanities Data Service AHRC Arts and Humanities Research Council BADC British Atmospheric Data Centre BBSRC Biotechnology and Biological Sciences Research Council BGS British Geological Survey BODC British Oceanographic Data Centre BRIDGES Biomedical Research Informatics Delivered by Grid Enabled Services CDA Common Data Access CLEF Clinical eScience Framework DCC Digital Curation Centre DTI Department of Trade and Industry EBI European Bioinformatics Institute EMBL European Molecular Biology Laboratory GIMS Genome Information Management System ICT Information and Communications Technology IP Intellectual property IT Information technology JCSR JISC Committee for the Support of Research JISC Joint Information Systems committee MIPS Munich Information Centre for Protein Sequences MRC Medical Research Council NASC Nottingham Arabidopsis Stock Centre NCRI National Cancer Research Institute NDG NERC DataGrid NERC Natural Environment Research Council NHS National Health Service NIH National Institutes of Health NTRAC National Translational Cancer Research Network OECD Organisation for Economic Cooperation and Development PDB Protein Data Bank PI Principal investigator PSI Proteomics Standards Initiative W3C World-Wide Web Consortium XML eXtensible Mark-up Language Large-scale data sharing in the life sciences 5 Acknowledgements We would like to thank the following for their generous and substantial contribution to the preparation of this report, as interviewees for case studies or as key informants. (In brackets we indicate the name of a case study, where a meeting was specifically related to a case study or a specific project.) Dr. Sheila Anderson Arts & Humanities Data Service (AHDS) Dr. Rolf Apweiler European Bioinformatics Institute Professor Geoff Barton University of Dundee Dr. Andrew Berry Wellcome Trust Sanger Institute (Malaria) Dr. Ewan Birney European Bioinformatics Institute (Ensembl) Ian Bishop Foster Wheeler Energy UK Professor Andy Brass University of Manchester Professor Graham Cameron European Bioinformatics Institute Tara Camm The Wellcome Trust Professor Rory Collins University of Oxford Dr. Michael Cornell University of Manchester (GIMS) Damian Counsell Rosalind Franklin Centre for Genomic Research David Craigon NASC University of Nottingham (NASC) Dr. Richard Durbin Wellcome Trust Sanger Institute (Ensembl) Dr. Dawn Field NERC Environmental Genomics Programme Dr. Andrew Finney University of Hertfordshire Malcolm Fleming CDA Limited (CDA) Professor Jeremy Frey University of Southampton (eBank) Kevin Garwood University of Manchester Dr. Peter Ghazal University of Edinburgh Dr. Neil Hanlon University of Glasgow BRC (BRIDGES) Dr. Rachel Heery UKOLN (eBank) Dr. Kim Henrick European Bioinformatics Institute Professor Pawel Herzyk University of Glasgow (BRIDGES) Derek Houghton University of Glasgow, BRC (BRIDGES) Dr. Tim Hubbard Sanger Institute (Ensembl) Professor Michael Hursthouse University of Southampton (eBank) Professor David Ingram University College, London (CLEF and OpenEHR) Dr. Hamish James Arts & Humanities Data Service (AHDS) Dr. Nick James NASC University of Nottingham (NASC) Dr. Dipak Kalra University College London (CLEF) Dr. Arek Kasprzyk European Bioinformatics Institute (Ensembl) Professor Douglas Kell University of Manchester Dr. Peter Kerr National Cancer Research Institute Dr. Bryan Lawrence Rutherford Appleton Laboratory (BADC/NDG) Professor Ottoline Leyser University of York Dr. Liz Lyon UKOLN/DCC (eBank) Large-scale data sharing in the life sciences 6 Gary Magill Foster Wheeler Energy UK Dr. Bob Mann Institute for Astronomy, University of Edinburgh & DCC Dr. Paul Matthews European Bioinformatics Institute Dr. Sean May NASC University of Nottingham (NASC) John McInnes British Geological Survey (CDA) Dr. Muriel Mewissen University of Edinburgh Helen Munn Academy of Medical Sciences Professor Christopher Newbold University of Oxford (Malaria) Professor Steve Oliver University of Manchester (GIMS) Professor Ken Peach The Council for the Central Laboratory of the Research Councils Dr. Chris Peacock Wellcome Trust Sanger Institute Dr. Robert Proctor University of Edinburgh (NTRAC) Professor Alan Rector University of Manchester (CLEF) Dr. Fiona Reddington National Cancer Research Institute Dr. Peter Rice European Bioinformatics Institute Beatrice Schildknecht NASC University of Nottingham (NASC) Steven Searle Wellcome Trust Sanger Institute (Ensembl) Peter Singleton Cambridge Health Informatics (CLEF) Dr. Barbara Skene The Wellcome Trust Dr. Arne Stabenau European Bioinformatics Institute (Ensembl) Dr. James Stalker Wellcome Trust Sanger Institute (Ensembl) Professor Alex Szalay Dept. Physics, John Hopkins University, USA, and project director of US National Virtual Observatory Dr. Chris Taylor European Bioinformatics Institute (PSI) Dr. Bela Tiwari NERC Environmental Genomics Programme Dr. Alexander Voss University of Edinburgh (NTRAC) Professor Michael Wadsworth University College, London Martin Wadsworth CDA Limited (CDA) Dr. Matthew West Shell UK Dr. Anne Westcott AstraZeneca Dr. Max Wilkinson National Cancer Research Institute Dr. Emma Wigmore NASC University of Nottingham (NASC) Dr. Michael Williamson University of Manchester Professor Keith Wilson University of York Dr. Matthew Woollard Arts & Humanities Data Service (AHDS) In addition to these interviews, several events and other projects provided the authors with opportunities to talk with many experts and practitioners in the life sciences, environmental and geophysical sciences, and IT. The 2004 e-Science All Hands Meeting was an opportunity to hear presentations about many areas and projects of relevance to this report, and to talk to many key informants. Our thanks in particular to Professors Carole Goble and Norman Paton of the University of Manchester. Large-scale data sharing in the life sciences 7 The 2004 International Systems Biology Conference presented an extended opportunity to talk with key informants from all around the world: from the UK, Professor Andy Brass of the University of Manchester, Dr. Albert Burger, Heriot-Watt University, and many from further afield, from America, France, Germany, South Africa. Of the many relevant presentations and posters, there was a very interesting debate centred around a discussion of strengths, weaknesses, opportunities and threats, at the Ontologies Special Interest Group chaired by Helen Parkinson (EBI), with Dr. Jeremy Rogers (University of Manchester, CLEF), Dr. Crispin Miller (University of Manchester), Professor Barry Smith (University of Buffalo), and Professor Michael Ashburner, and a helpful day on modelling in systems biology, chaired by Professor Igor Goryanin and Dr. Ian Humphery-Smith. The JISC runs many projects and studies relevant to this study; the JISC July 2004 Conference included presentations by Alan Robiette (JISC), Jane Barton on a JISC study on metadata, Brian Kelly on quality assurance for libraries, and Jon Duke and Andy Jordan on their study on Developing Technical Standards and Specifications for JISC Development Activity and Service Interoperability. The clinical domain presents particular problems in data sharing. Our work has been enormously helped by involvement in the Consent and Confidentiality project conducted by the MRC. Several events helped inform this study, including a one-day symposium was
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