The document discusses open science and open access. It provides examples of open science like open access publishing, open notebooks, prepublication data release, and open source software. It discusses three aspects of open science: cost, restrictions, and timing. It discusses the costs of publishing, creative commons licenses, and examples of organizations that promote open access like the Public Library of Science (PLoS) and how they circulated an open letter to encourage open access. Overall, the document discusses the history and concepts of open science and open access.

1. Open Science

2. Why do governments fund
scientific research?

3. NIH Mission
• foster fundamental creative discoveries, innovative research
strategies, and their applications as a basis to advance
significantly the Nation's capacity to protect and improve health;
• develop, maintain, and renew scientific human and physical
resources that will assure the Nation's capability to prevent
disease;
• expand the knowledge base in medical and associated sciences
in order to enhance the Nation's economic well-being and
ensure a continued high return on the public investment in
research; and
• exemplify and promote the highest level of scientific integrity,
public accountability, and social responsibility in the conduct of
science.

4. Examples of Open Science
• Open Access publishing
• Open Notebooks
• Prepublication Data Release
• Open Source software

5. Three aspects of open
science
• Cost
• Restrictions
• Timing

6. Costs of publishing
• Peer review
• Formatting and editing
• Dissemination

7. 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

8. Translation Coursepacks
Photocopying Deposit in
databases
No permission
required
for any reuse
Downloading
data Reproduction
Text mining of figures
Redistribution

9. Public Library of Science
(PLoS) NIH)
• Started in 2000 by
– Harold Varmus (ex-head of
– Pat Brown (HHMI, Stanford)
– Michael Eisen (my brother)
• PLoS's first action was to circulate an open
letter
• Letter “encouraged” scientific publishers to
make the research literature available for
distribution through free online public archives
such as the US National Library of Medicine's
PubMed Central.

10. 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.

11. 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.

14. After the Letter (2003)
• > 25,000 people signed the letter
• Letter had some impact in moving some publishers to
freer access
• Led to some increase in support for existing OA
journals like those from Biomed Central
• Unfortunately, not enough impact
• So announced the launch of their own journals
– PLoS Biology
– PLoS Medicine

15. Data Release
• Represented TIGR at 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
• Surprised to learn that 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

16. Open Data Experiment data
• Unrestricted
access policy on
Tetrahymena
thermophila
• First time done at
TIGR
• Many people published
papers before we did
• But many more helped
with our paper
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 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, 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 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 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 California Santa Barbara, Santa Barbara, California, United
States of America

17. Open Publishing Experiment
• Had published one paper in a BMC Open Access
journal (Genome Biology)
• But not a high profile one
• We were working on a paper on the first Wolbachia
genome
• Wolbachia are intracellular bacteria that target males
for detrimental effects in some invertebrates
• Wolbachia also are mutualistic symbionts of filiarial
nematodes
• Our paper was being recruited by Nature and
Science
• We agreed to submit the paper to PLoS Biology

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.
– Few were helpful.
– Note - can’t read before buying
• Tried to contact experts
– Wrote to authors if I could find email addresses.
– Got back some papers but many came weeks or months
later.
– Called authors and others
– Time was of the essence
• Got friends to get some articles from libraries
– Hard to do at 3 AM sitting bedside at hospital
• Got more and more pissed off

26. Medical Guesswork
• Wife got Rhogam 9 days after blood exposure
• Other treatments (for clots, bleeding, infection, loss of
amniotic fluid, etc,) became in part guesswork as well
• Common theme
– If you have a somewhat unusual situation
– Your doctors may not know all they need to know
– They are busy
– Need to take medical care into your own hands
– But frequently you can’t

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

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

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

30. Component #1:
Free Access

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

32. 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

33. The inspiration for Open
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

34. Component #2:
Immediate Access

35. 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

36. Component #3:
Archives

38. Component #4:
License

39. 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

40. Translation Coursepacks
Photocopying Deposit in
databases
No permission
required
for any reuse
Downloading
data Reproduction
Text mining of figures
Redistribution

41. Component #5:
Copyright

42. 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.
4. There’s no harm in asking.
5. Experts can help (e.g. author addenda).
Slide based on one by Peter Suber

43. Component #6:
Journal Handles Archiving

44. 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

45. Part III: Benefits of Open
Access

46. OA is about Freeing The
Literature

50. 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

55. 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

56. Benefit #1:
New mining

57. Document
A network of literature

58. Document
Database
A network of literature and
data

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

60. 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

61. Benefit #2:
Education

62. 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