Talk by Jonathan Eisen for the UC Davis CTSC Brown Bag Series. Kind of a rehashing of a talk I gave two years ago at U. Washington.

1. What is Open Access
Publishing in Scientific Research?
Jonathan A. Eisen
August 11, 2010
CTSC Brown Bag Seminar

2. Full Disclosure

3. Outline
• I: Open Access and Me
• II: What is Open Access?
• III: Benefits of Open Access
• IV: The future of Open Access

4. Part I: Me and Open Access

5. Public Library of Science (PLoS)
• Started in 2000 by
– Harold Varmus
– Pat Brown
– Michael Eisen
• First action was to circulate an
open letter on publishing

6. The Letter
We support the establishment of an online public library that would
provide the full contents of the published record of research and
scholarly discourse in medicine and the life sciences in a freely accessible,
fully searchable, interlinked form. Establishment of this public library would
vastly increase the accessibility and utility of the scientific literature,
enhance scientific productivity, and catalyze integration of the disparate
communities of knowledge and ideas in biomedical sciences.We recognize
that the publishers of our scientific journals have a legitimate right to a fair
financial return for their role in scientific communication. We believe,
however, that the permanent, archival record of scientific research and
ideas should neither be owned nor controlled by publishers, but should
belong to the public and should be freely available through an international
online public library.To encourage the publishers of our journals to support
this endeavor, we pledge that, beginning in September 2001, we will
publish in, edit or review for, and personally subscribe to only those
scholarly and scientific journals that have agreed to grant
unrestricted free distribution rights to any and all original research
reports that they have published, through PubMed Central and similar
online public resources, within 6 months of their initial publication date.

7. The Letter
We support the establishment of an online public library that would
provide the full contents of the published record of research and
scholarly discourse in medicine and the life sciences in a freely accessible,
fully searchable, interlinked form. Establishment of this public library would
vastly increase the accessibility and utility of the scientific literature,
enhance scientific productivity, and catalyze integration of the disparate
communities of knowledge and ideas in biomedical sciences.We recognize
that the publishers of our scientific journals have a legitimate right to a fair
financial return for their role in scientific communication. We believe,
however, that the permanent, archival record of scientific research and
ideas should neither be owned nor controlled by publishers, but should
belong to the public and should be freely available through an international
online public library.To encourage the publishers of our journals to support
this endeavor, we pledge that, beginning in September 2001, we will
publish in, edit or review for, and personally subscribe to only those
scholarly and scientific journals that have agreed to grant
unrestricted free distribution rights to any and all original research
reports that they have published, through PubMed Central and similar
online public resources, within 6 months of their initial publication date.

10. PLoS After the Letter (2003)
• > 25,000 people signed the letter
• Small increase in open access support
• But not enough
• So PLoS announced the launch of their
own journals
– PLoS Biology
– PLoS Medicine

11. Me and PLoS
• Joined founding
Editorial Board of
PLoS Biology
• Still not fully
convinced about need
for OA
• Worried more about
User agrees to
not publish push for full “Open
genome level Science”
analyses

12. Ft. Lauderdale Agreement
• Feb 2003 meeting in Ft. Lauderdale on “Genome
Sequencing Data Release Policies”
• Follow up to the “Bermuda Accord”
• Debate about how open to be with data
• NHGRI had supported a similar policy to TIGRs (see
http://www.genome.gov/10506537)
• Sean Eddy gave a talk that convinced me that these
restrictions we in direct conflict with the whole point of
giving money to places to generate the data
• So I did what any scientist should do - some experiments

13. Open Data Experiment
• Unrestricted data access
policy on Tetrahymena
thermophila
• First time done at TIGR
• Many people published
papers before we did
• But many more helped
with our paper
Thanks for the message about
1 The Institute for Genomic Research, Rockville, Maryland, United States of America, 2
Department of Biology, York University, Toronto, Ontario, Canada, 3 Centre for Research in Mass
the genome, that is a nice
Spectrometry, York University, Toronto, Ontario, Canada, 4 Department of Biological Sciences,
Marquette University, Milwaukee, Wisconsin, United States of America, 5 Razavi-Newman Center
for Bioinformatics, The Salk Institute for Biological Studies, San Diego, California, United States of
America, 6 Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago,
surprise. Lots of Bacillus DNA in
Illinois, United States of America, 7 Department of Biology, Harvey Mudd College, Claremont,
California, United States of America, 8 Department of Biology, University of Texas at San Antonio,
San Antonio, Texas, United States of America, 9 Department of Electrical Engineering, University
there unfortunately but we are
of Texas at San Antonio, San Antonio, Texas, United States of America, 10 Department of
Molecular and Cellular Biology, University of California Berkeley, Berkeley, California, United States
of America, 11 Department of Computer Science and Engineering, University of Washington,
Seattle, Washington, United States of America, 12 Department of Cellular Biology, University of
going to go wild looking in it.
Georgia, Athens, Georgia, United States of America, 13 Department of Biological Sciences,
University of Iowa, Iowa City, Iowa, United States of America, 14 Department of Biology,
University of Rochester, Rochester, New York, United States of America, 15 Canadian Institute for
Advanced Research, Department of Botany, University of British Columbia, Vancouver, British
Columbia, Canada, 16 Department of Genetics, Stanford University, Stanford, California, United
States of America, 17 Department of Molecular, Cellular, and Developmental Biology, University of
Patrick
California Santa Barbara, Santa Barbara, California, United States of America

14. Open Access Experiment
• Had published one paper in an Open
Access journal (Genome Biology)
• We were working on a paper on the
WMD - the first Wolbachia genome
Wolbachia of • Wolbachia are maternally transmitted
Male Destruction parasites that target males in many
species
• In filarial nematodes appear to be
mutualistic symbionts
• Our paper was being recruited by
Nature and Science

16. Wolbachia in PLoS Biology

17. Experiments in Progress …
• But still unclear to me whether this Open
Access thing was a good idea or not
• Then real life intervened

19. RhoGam
• Supplier
– RhoGAM should be administered within 72 hours of
known or suspected exposure to Rh-positive red blood
cells.
• Wikipedia
– It is given by intramuscular injection as part of modern
routine antenatal care at about 28 weeks of pregnancy,
and within 72 hours after childbirth.[5] It is also given
after antenatal pathological events that are likely to
cause a feto-maternal hemorrhage.[6]
• Question
– What happens if you do it even later?

22. You can purchase online access to
this article (and all its versions) for a
24-hour period. Articles are US $
29.95, with some exceptions where
prices may vary. Click "Buy Now" to
display the price

25. Access Blocked - What Next?
• Bought lots of articles
• Tried to contact experts
• Got friends to get some articles from libraries
• Got more and more pissed off

26. Medical Guesswork
• Wife got Rhogam 11 days after blood exposure
• Other treatments became in part guesswork as
well
• Note, doctors at this time were spectacular
• They even asked for assistance in finding out
answers to some treatment questions
• In theory, the scientific / medical literature could
help ....

27. Baby Lost
• Benjamin Augustin Eisen stillborn August
29, 2003

28. Lack of Access
• Scientist without access
• Would access have helped?
• Is limiting access useful or needed?
• Goal of much of scientific and medical
research is to spread knowledge

29. Full Disclosure

30. Part II: Open Access Details

31. Many Flavors of
Accessibility and Openness
• Free in University repositories
• Free on journal web site after six months
(e.g., Genome Research)
• Free on journal web site with registration
(e.g., Science)
• Free in PubMed Central after 6 months (e.g.,
ASM journals)
• Free and unrestricted everywhere
immediately (e.g., PLoS and BMC)

32. Many Flavors of
Accessibility and Openness
Cost Free $, $$, or $$$
Timing of free Immediate Later
Location Archives Journal site
Reuse Unrestricted Restricted
Copyright Author Journal
Who archives Journal Individual

33. Green Access
Cost Free $, $$, or $$$
Timing of free Immediate Later
Location Archives Journal site
Reuse Unrestricted Restricted
Copyright Author Journal
Who archives Journal Individual

34. Gold /Open Access
Cost Free $, $$, or $$$
Timing of free Immediate Later
Location Archives Journal site
Reuse Unrestricted Restricted
Copyright Author Journal
Who archives Journal Individual
Based on the Bethesda Principles, April 2003

35. Open Access
• Free, immediate access online
Unrestricted distribution and re-use
Author retains rights to attribution
Papers are immediately deposited in a
public online archive, such as PubMed Central
Bethesda Principles, April 2003

36. Biomed Central
• Commercial open access publisher
• Launched first open access journals in 2000
• Now publish >160 OA titles
• Purchased by Springer-Verlag in October 2008
• CEO: “This acquisition reinforces the fact that we
see open access publishing as a sustainable part of
STM publishing, and not an ideological crusade. “

38. PLoS Biology
October, 2003
PLoS Medicine
October, 2004
PLoS Community Journals
June-September, 2005 October, 2007

39. Web2.0
Interaction changes everything
14.1

40. Gold Open Access
Cost Free $, $$, or $$$
Timing of free Immediate Later
Location Archives Journal site
Reuse Unrestricted Restricted
Copyright Author Journal
Who archives Journal Individual
Based on the Bethesda Principles, April 2003

41. Component #1:
Free Access

42. “Ten million American
adults look online for
health information on a
From the Pew Research Center
Seeking Health On-line 2006 study
http://pewresearch.org/reports/?ReportID=65

43. Everyone should have access to
research findings
• “It is not for either publishers or academics to
decide who should, and who should not, be
allowed to read scientific journal articles. We are
encouraged by the growing interest in research
findings shown by the public. It is in society’s
interest that public understanding of science
should increase. Increased public access to
research findings should be encouraged by
publishers, academics and Government alike”
• HoC S&T Committee Report, July 2004

44. The inspiration for Free Access is
not a new idea
“I want a poor student to have the same means
of indulging his learned curiosity,
of following his rational pursuits,
of consulting the same authorities,
of fathoming the most intricate inquiry
as the richest man in the kingdom…”
Antonio Panizzi, 1836
Principle Librarian of the British Museum

45. Component #2:
Immediate Access

46. Timing of Access
• NIH and other guidelines now require
access after six months
• Delay supposedly improves ability of
journals to maintain subscriptions
• Immediate OA is the way science should
work
– Public and others can get engaged when press
coverage occurs
– Science happens rapidly
– Articles there whenever you look

47. Component #3:
Archives

49. Self-archiving sluggishness
• “Of the authors who have not yet self-
archived any articles, 71% remain unaware
of the option.”
– Alma Swan and Sheridan Brown, Open access self-
archiving: An author study
– http://cogprints.org/4385/
Slide based on one by Peter Suber

50. Component #4:
License

51. Creative Commons
Attribution License
Copyright: © Eisen et al. 2006. This is an open-access article distributed
under the terms of the Creative Commons Attribution License, which
permits unrestricted use, distribution, and reproduction in any medium,
provided the original work is properly cited.
Goal: overcome access barriers and encourage creative uses.
www.creativecommons.org

52. No permission

53. Translation Coursepacks
Photocopying Deposit in
databases
No permission
Downloading
Reproduction
data
Text mining of figures
Redistribution

54. Component #5:
Copyright

55. Copyright Issues
1. Authors are the copyright holders until they transfer
away their rights.
2. Transferring full copyright to a publisher gives the OA
decision to the publisher.
3. Many journals will alter the standard contract when
asked.
Slide based on one by Peter Suber

56. Part III: Benefits of Open Access

57. OA is about Freeing The Literature

58. OA is about Freeing The Literature

59. OA is about Freeing The Literature

60. OA is about Freeing The Literature

64. You can purchase online access to
this article (and all its versions) for a
24-hour period. Articles are US $
29.95, with some exceptions where
prices may vary. Click "Buy Now" to
display the price

69. You can purchase online access to
this article (and all its versions) for a
24-hour period. Articles are US $
29.95, with some exceptions where
prices may vary. Click "Buy Now" to
display the price

70. Benefit #1:
New mining

71. Document
A network of literature

72. Document
Database A network of literature and data

73. Jensen, Saric and Bork Nature Reviews Genetics
Feb 2006

74. Text mining and open access
“So far, more that 90% of all biomedical literature
mining has been based on Medline, mainly because it is
freely available in a convenient format.”
“…future methods should be able to extract
information from the full text of papers…”
“However, it is restricted access to the full text of
papers…that is currently the greatest limitation…”
Jensen, Saric and Bork Nature Reviews Genetics
Feb 2006

75. Benefit #2:
Education

76. Educational Benefits of OA
• No debate about “fair use”
• No need for password’s or logins for course
web sites
• No lawyers have to be involved
• Material from OA publications can be
repackaged for any purpose

77. Part IV: Future of Open Access

78. Issues in Publishing
• Canceling subscriptions?
• End of surrogate metrics?
– Journal impact factor vs. article impact factor
– Need to change tenure, promotion, etc systems
to assess quality of work
• Funding for publishing
– OA is sustainable
– But still not free
• Peer review
– Pre vs. post-publication?

79. Open Access and Open Science
• Related but not the same things
• Open science examples
– OA publishing
– Open source software
– Open data release
– Open notebooks
– Open materials and methods
• All can be good things, but even if against
one you can support the others

80. What can you do so support OA?
• Publishing
– Try it and/or shift to more and more OA
– Quit non OA cold turkey
• Service
– Do not review for non OA journals
– If involved in journal, work to change OA policies
• Lobby
– Push for OA at your Institution and with government
• Hiring
– Give credit for OA publishing
– Same as you would do for data, software release
• Education
– Use CC material freely