A personal perspective on open access publishing

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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.

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.

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  • One of leaders of open access movement.








  • Giving everyone access to information is not a new idea - the quote is from an influential librarian in the 19th century.




  • May 2005

  • A word about copyright – this is the license we use.
    It’s very important that authors do pay attention to this issue – the signing of a more restrictive license limits the uses to which the literature can be put.
  • A word about copyright – this is the license we use.
    It’s very important that authors do pay attention to this issue – the signing of a more restrictive license limits the uses to which the literature can be put.
  • A word about copyright – this is the license we use.
    It’s very important that authors do pay attention to this issue – the signing of a more restrictive license limits the uses to which the literature can be put.
  • A word about copyright – this is the license we use.
    It’s very important that authors do pay attention to this issue – the signing of a more restrictive license limits the uses to which the literature can be put.
  • A word about copyright – this is the license we use.
    It’s very important that authors do pay attention to this issue – the signing of a more restrictive license limits the uses to which the literature can be put.
  • A word about copyright – this is the license we use.
    It’s very important that authors do pay attention to this issue – the signing of a more restrictive license limits the uses to which the literature can be put.
  • A word about copyright – this is the license we use.
    It’s very important that authors do pay attention to this issue – the signing of a more restrictive license limits the uses to which the literature can be put.
  • A word about copyright – this is the license we use.
    It’s very important that authors do pay attention to this issue – the signing of a more restrictive license limits the uses to which the literature can be put.
  • A word about copyright – this is the license we use.
    It’s very important that authors do pay attention to this issue – the signing of a more restrictive license limits the uses to which the literature can be put.

  • One more: publishers don’t need full copyright

  • A word about copyright – this is the license we use.
    It’s very important that authors do pay attention to this issue – the signing of a more restrictive license limits the uses to which the literature can be put.
  • A word about copyright – this is the license we use.
    It’s very important that authors do pay attention to this issue – the signing of a more restrictive license limits the uses to which the literature can be put.
  • A word about copyright – this is the license we use.
    It’s very important that authors do pay attention to this issue – the signing of a more restrictive license limits the uses to which the literature can be put.





















  • So how does it work? Publishing costs money, so how are we going to fund it.
    Subscription based publishing works like this – there is a financial barrier to reading literature, and that money is paid by funding agencies, institutions, and ultimately by the government.
  • With OA, that payment step is moved up the chain – the sources of funding stay the same, the cost stays the same (or probably comes down). But by having the payment made earlier, no money needs to be paid to access the literature.

    Central to this idea – publishing is an integral part of the research process

    So the challenge is to alter the way publishing is funded – not how much money is needed.



Transcript

  • 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.
  • 8. 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
  • 9. 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
  • 10. 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
  • 11. 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
  • 12. 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
  • 13. Wolbachia in PLoS Biology
  • 14. Experiments in Progress … • But still unclear to me whether this Open Access thing was a good idea or not • Then real life intervened
  • 15. 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?
  • 16. 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
  • 17. 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
  • 18. 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 ....
  • 19. Baby Lost • Benjamin Augustin Eisen stillborn August 29, 2003
  • 20. 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
  • 21. Full Disclosure
  • 22. Part II: Open Access Details
  • 23. 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)
  • 24. 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
  • 25. Green Access Cost Free $, $$, or $$$ Timing of free Immediate Later Location Archives Journal site Reuse Unrestricted Restricted Copyright Author Journal Who archives Journal Individual
  • 26. 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
  • 27. 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
  • 28. 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. “
  • 29. PLoS Biology October, 2003 PLoS Medicine October, 2004 PLoS Community Journals June-September, 2005 October, 2007
  • 30. Web2.0 Interaction changes everything 14.1
  • 31. 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
  • 32. Component #1: Free Access
  • 33. “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
  • 34. 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
  • 35. 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
  • 36. Component #2: Immediate Access
  • 37. 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
  • 38. Component #3: Archives
  • 39. 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
  • 40. Component #4: License
  • 41. 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
  • 42. No permission
  • 43. Translation Coursepacks Photocopying Deposit in databases No permission Downloading Reproduction data Text mining of figures Redistribution
  • 44. Component #5: Copyright
  • 45. 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
  • 46. Part III: Benefits of Open Access
  • 47. OA is about Freeing The Literature
  • 48. OA is about Freeing The Literature
  • 49. OA is about Freeing The Literature
  • 50. OA is about Freeing The Literature
  • 51. 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
  • 52. 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
  • 53. Benefit #1: New mining
  • 54. Document A network of literature
  • 55. Document Database A network of literature and data
  • 56. Jensen, Saric and Bork Nature Reviews Genetics Feb 2006
  • 57. 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
  • 58. Benefit #2: Education
  • 59. 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
  • 60. Part IV: Future of Open Access
  • 61. 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?
  • 62. 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
  • 63. 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