Open data and open access: sharing our research with the world


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A presentation I gave in the Department of Pathology, University of Cambridge on the importance of data sharing, and publishing in open access journals. The presentation was based heavily on Jelena Aleksic's talk at Open Research Cambridge (

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Open data and open access: sharing our research with the world

  1. 1. Ben Skinner Open data & open access Sharing our research with the world
  2. 2. Why it matters Open Access models Tools for open access & data sharing
  3. 3. Traditional publishing model - Journals are commercial entities - Scientists submit articles for free and publish for free - Scientists perform peer review for free - Journals make money selling subscriptions
  4. 4. What is the problem? Ideas and data are the building blocks of science
  5. 5. Obvious problems of the traditional model Prohibitively expensive for: - Scientists (and students) from less well off institutions - Startups, small businesses - Interested members of the public - Implications for policy decisions! - MPs (or their science advisers) can’t read the research
  6. 6. Other less obvious problems - 1 million papers per year just in biosciences – a valuable resource for text mining - only available for open access papers - Not just text mining – figure-mining - Testing the reproducibility of prior research is easier when data and results are shared - Duplication of effort and waste of time and money
  7. 7. The problem is large scale Some journals cost up to $40,000
  8. 8. Open access idea: All public scientific efforts should be freely available globally
  9. 9. Adapted from Gargouri et al 2012 How much open access is there now? Estimated percent open access publication by discipline 0% 10% 20% 30% 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 Biology Biomedical research Clinical medicine Health
  10. 10. Why it matters Open Access models Tools for open access & data sharing
  11. 11. Current Open Access models Gold Access Green Access
  12. 12. Gold model - An open access take on traditional publishing - Instead of relying on subscriptions for profit, the journals instead charge the authors a submission fee (~£1000+ per paper) - For universities, this means that subscription fees can instead be used as submission fees.
  13. 13. Successful example - Spin-off from a publishing company - Publishes 258 open access journals - Currently owned by Springer
  14. 14. Problems - Prohibitively expensive; opens up who can read the research, but restricts who can publish - Works for well-funded universities and disciplines, but not necessarily widely applicable - However: not all OA journals charge fees, and some do waive them - ‘Predatory publishers’ – fake journals charging authors - Beall’s List: - Publishers that misbehave (Elsevier…)
  15. 15. Green model - Publishers allow authors to publish some version of their manuscript on their own website (or equivalent) - preprint = manuscript before peer-review - postprint = accepted manuscript after review - Usually does not include the publisher formatted pdf - Green access model relies on authors depositing their work online to be accessed freely - Currently around 900,000 papers in arXiv
  16. 16. Green model pros - Free access without submission fees - Potential to subvert tradtional publishing - Well off universities can still pay subscription fees, but more individual papers are available to people who could not otherwise afford them
  17. 17. Why isn’t everyone doing it? - Popularity varies by field; almost all papers in physics and maths are self-archived, but less popular in others (like biosciences) - Not all journals allow it (~65% permit it) - Requires effort, and navigating different policies between journals can be off-putting - Reluctance to deposit preprints
  18. 18. Spectrum of Open Access PLoS information sheet
  19. 19. Why it matters Open Access models Tools for open access & data sharing
  20. 20. - RCUK require all publicly funded research to be made open access 6 months after publication - HEFCE recommendation for post-2014 REF: - paper must be placed in an institutional repository immediately upon acceptance to be eligible for consideration - Such schemes have measurable impacts: Top-down initiatives Gargouri et al 2012
  21. 21. Finding open access policies
  22. 22. bioRxiv pre-print server - Free online archive for unpublished preprints in the life sciences - Operated by Cold Spring Harbor Laboratory - Immediately available to the scientific community - feedback on draft manuscripts before submission - Modelled after the arXiv pre-print server widely used in physics and mathematics
  23. 23. - University of Cambridge institutional repository - Provides access to content created by University members - Managed by the University Library - Keeps electronic copies of open access papers and theses
  24. 24. Costs vary … Sharing data - Well known repositories for some data types - e.g. microarray (GEO, ArrayExpress) - Other types of data useful to share but no dedicated repository - How to avoid the ‘disappearing supplementary material’ syndrome? - Generic repositories:
  25. 25. Other publishing models - Faculty of 1000 ( - Inverts traditional model - Check methodological completeness, then publish and use open peer-review - all comments public - PeerJ ( - Lifetime subscription per author - Cambridge experimenting with pre-purchased subscriptions – publishing may be free for faculty - PLoS (Public Library of Science) - Gold model, but fee based on country - PLoS One will publish anything with appropriate methods, irrespective of ‘impact’ - >20,000 papers per year
  26. 26. Openness is about more than papers - Where we publish - What we share - machine readable formats? - How we share it - Opening peer-review - Can we discourage ‘reviewer number 3’?
  27. 27. Dr Jelena Aleksic Dr Keren Limor-Waisberg Open Research Cambridge Acknowledgements
  28. 28. References: Gargouri, Yassine, Lariviere, Vincent, Gingras, Yves, Carr, Les and Harnad, Stevan (2012) Green and Gold Open Access percentages and growth, by discipline. In, 17th International Conference on Science and Technology Indicators (STI), Montreal, CA, 05 - 08 Sep 2012. 11pp. Higher Education Funding Council for England (HEFCE) consultation on open access: Research Councils UK (RCUK) policies on open access: Attributions: Gold ingots: Copyright devilZ, Elbaite: Copyright Rob Lavinsky, Bricks: Beaker: Copyright Theresa knott ( Chemical structures: Copright Linnea Herzog ( Globe: Copyright Azcolvin429 Original slides: