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 (http://www.slideshare.net/jelena121)

1. Ben Skinner
Open data & open access
Sharing our research with the world

2. Why it matters
Open Access models
Tools for open access & data sharing

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. What is the problem?
Ideas and data are the
building blocks of science

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. 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. The problem is large scale
Some journals cost up to $40,000

8. Open access idea:
All public scientific efforts
should be freely available
globally

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. Why it matters
Open Access models
Tools for open access & data sharing

11. Current Open Access models
Gold Access Green Access

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. Successful example
- Spin-off from a publishing company
- Publishes 258 open access journals
- Currently owned by Springer
http://www.biomedcentral.com/

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: scholarlyoa.com/publishers/
- Publishers that misbehave (Elsevier…)

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. 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. 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. Spectrum of Open Access
PLoS information sheet
http://www.plos.org/open-access/howopenisit/

19. Why it matters
Open Access models
Tools for open access & data sharing

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. Finding open access policies
http://www.sherpa.ac.uk/romeo/search.php

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
http://biorxiv.org

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
https://www.repository.cam.ac.uk/

24. http://figshare.com http://datadryad.org/
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. Other publishing models
- Faculty of 1000 (http://f1000.com/)
- Inverts traditional model
- Check methodological completeness, then publish and use
open peer-review - all comments public
- PeerJ (https://peerj.com)
- 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. 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. Dr Jelena Aleksic
Dr Keren Limor-Waisberg
Open Research Cambridge
Acknowledgements
http://www.slideshare.net/bmskinner

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. http://eprints.soton.ac.uk/340294/
Higher Education Funding Council for England (HEFCE) consultation on open access:
http://www.hefce.ac.uk/pubs/year/2013/201316/#d.en.82765
Research Councils UK (RCUK) policies on open access:
http://www.rcuk.ac.uk/research/outputs/
Attributions:
Gold ingots: Copyright devilZ, http://www.officialpsds.com/Gold-Ingots-PSD68741.html
Elbaite: Copyright Rob Lavinsky, iRocks.com
Bricks: http://www.texturemate.com
Beaker: Copyright Theresa knott (https://commons.wikimedia.org/wiki/File:Beakerred.png)
Chemical structures: Copright Linnea Herzog (https://commons.wikimedia.org/wiki/File:Chemical_Structures.png)
Globe: Copyright Azcolvin429
Original slides: http://www.slideshare.net/jelena121