PLoS - Why It is a Model to be Emulated


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Joint ICTP-IAEA-UNESCO Workshop on New Trends for Science Dissemination, Trieste Italy Sept 26, 2011

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  • Specifically, our aim is to achieve open access to the literature, whereby journal articles are freely available immediately upon publication their use is unrestricted, so that readers can download, print off, reanalyse, extract data and so on authors retain the copyright, and specifically the right to be appropriately cited papers are also deposited separately from the publisher in a public online archive (PMC)
  • This illustrates one aspect of the frustration with the existing system From 1986- 2002 journals increased in price over 200%, and library purchasing has been struggling just to maintain the status quo. Commercially STM pubishing is a huge success story. But many commentators have now asserted that this commercial success has been achieved at the expense of the scientific community, and only those in rich institutions can afford access. And that this position is unsustainable - we are heading for a meltdown.
  • In my penulimate slide I ’d just like to emphasize that the RCUK proposal resonates with many other related initiatives that are supporting open access internationally. In Europe there is the Berlin Declaration, which has been signed by major funders such as the DFG in Germany, INSERM, CNRS in France. Amongst other things the signatories support the kind of licensing that I mentioned in the previous slide. Redistribution for any purpose subject only to the condition of proper attribution The NIH has a proposal to increase access to the literature, and has invested a great deal in the establishment of PubMed Central, which provides powerful full text searching across published literature, and is committed to long term archiving, interoperability with other repositories, and public access. We strongly encourage the initiative to develop a similar full text archive in collaboration with the BL. Finally, more broadly still the UN ’s World Summit on the Information Society strongly endorses open access publishing.
  • As you know, the way in which OA journals are financed is by a publication fee, paid for by the same organizations that currently fund subscription journals. As stated in the RCUK draft policy, the costs of communication and dissemination are an integral part of the costs of research itself the challenge is to reroute the funds that currently support publishing towards researchers, so that they are able to pay publication fees.
  • Harold Varmus, Pat Brown and Mike Eisen established the Public Library of Science, initially as a sort of pressure group whose aim was to force publishers to change their ways.
  • Initially, they circulated an open letter urging publishers to deposit research literature in freely accessible databases, 6 months after publication. In many people ’s eyes this was seen as a naïve proposal, but it generated massive support in the community. The upshot was that some publishers did alter their policies - notably the society and non profit publishers - but the vast bulk of the literature remained accessible only to subscribers. The reason was simply that researchers had nowhere else to go with their papers - but the level of support indicated that it was the right time to launch journals based on a new business model - open access. And in December last year, Harold, Pat and Mike secured funding from the Moore foundation to the tune of 9 million dollars.
  • PLoS - Why It is a Model to be Emulated

    1. 1. The Public Library of Science (PLoS) Why it is a Model to be Emulated Philip E. Bourne University of California San Diego [email_address]
    2. 2. My Two Lectures <ul><li>The promise - Open Access, Open Science with particular reference to PLoS </li></ul><ul><li>The fulfillment - What Open Access facilitates and examples of how it benefits science </li></ul>
    3. 3. The promise - Open Access, Open Science with particular reference to PLoS <ul><li>What you might get from this lecture: </li></ul><ul><ul><li>Further insights into open repositories </li></ul></ul><ul><ul><li>Further insights into open access </li></ul></ul><ul><ul><li>What is happening with open journals </li></ul></ul><ul><ul><li>Some ideas for how you might proceed … </li></ul></ul>
    4. 4. My Perspective <ul><li>I am a domain scientist (computational biology) </li></ul><ul><li>I got involved with the Public Library of Science (PLoS) and subsequently the promise of open access </li></ul><ul><li>I co-founded a company, SciVee Inc., that is attempting to leverage the perceived changes in scholarly communication </li></ul><ul><li>I support a small academic scholarly communication group </li></ul>
    5. 5. Scholarly Communication Group <ul><li>Can we improve the way science is disseminated and comprehended? </li></ul><ul><li>Through openness can we increase the number of people interested in science? </li></ul>
    6. 6. What is Open Access? <ul><li>A spectrum of things! </li></ul><ul><li>Free, relatively fast online access </li></ul><ul><li>Usage with less restrictions </li></ul><ul><li>Author retains copyright </li></ul><ul><li>Attribution must be given </li></ul><ul><li>Green – Authors make papers publically available </li></ul><ul><li>Gold – Publishers make papers publically available </li></ul>
    7. 7. Why is Open Access Important? <ul><li>Authors </li></ul><ul><li>access to the largest possible audience </li></ul><ul><li>Readers </li></ul><ul><li>access to the entire literature </li></ul><ul><li>Reuse of articles </li></ul><ul><li>download, copy, print, archive </li></ul><ul><li>Full-text searching and mining </li></ul><ul><li>beyond Boolean text searches </li></ul>
    8. 8. The journals crisis Journal prices CPI/inflation Journals purchased Source: Association of Research Libraries
    9. 9. Examples of International Support for Open Access <ul><li>Berlin Declaration on Open Access </li></ul><ul><ul><li>Dozens of major European Funders </li></ul></ul><ul><ul><li>Stipulates that articles ’ copyrights should permit virtually unrestricted redistribution </li></ul></ul><ul><li>NIH proposal to increase access, investment in PubMed Central </li></ul><ul><li>UN ’s World Summit on the Information Society endorses open-access publishing </li></ul>
    10. 10. Sources of Funding Publishing is the final step in a research project Researcher Publisher Reader £ Public Digital Library Gov Funders Charity Business Institutions £
    11. 11. The Human Face of Open Access
    12. 12. Josh Sommer – A Remarkable Young Man Co-founder & Executive Director the Chordoma Foundation
    13. 13. Chordoma <ul><li>A rare form of brain cancer </li></ul><ul><li>No known drugs </li></ul><ul><li>Treatment – surgical resection followed by intense radiation therapy </li></ul>
    14. 14.
    15. 15.
    16. 16.
    17. 17. Adapted: Isaac If I have seen further it is only by standing on the shoulders of giants Isaac Newton From Josh’s point of view the climb up just takes too long > 15 years and > $850M to be more precise
    18. 18.
    19. 19.
    20. 20.
    21. 21. Committed to making the world ’ s scientific and medical literature a public resource
    22. 22. PLoS Represents the Purest Form of Open Science – CC-BY
    23. 23. Some PLoS History…
    24. 24. PLoS Founding Board of Directors Harold Varmus PLoS Co-founder Nobel Laureate, Director NCI Patrick O. Brown PLoS Co-founder Howard Hughes Medical Institute & Stanford University School of Medicine Michael B. Eisen PLoS Co-founder Lawrence Berkeley National Laboratory & University of California at Berkeley
    25. 25. What is the Public Library of Science? <ul><li>By driving a change in the publishing model to open access publishing </li></ul><ul><li>By generating tools for mining the scientific literature </li></ul><ul><li>By making it comprehensible to the non-specialist </li></ul>A nonprofit organization of scientists committed to making the world ’ s scientific and medical literature a public resource
    26. 26. PLoS – A Brief History <ul><li>Founded in October, 2000 </li></ul><ul><li>Circulated an open letter urging publishers to increase access to research literature </li></ul><ul><li>>30,000 signatories </li></ul><ul><li>Some positive effects, but overall response from publishers fell short of demands </li></ul><ul><li>In December, 2002, $9 million grant from Moore Foundation to launch open access journals. </li></ul>
    27. 27. PLoS Biology October, 2003 PLoS Medicine October, 2004 PLoS Community Journals June-September, 2005 & October, 2007 (NTDs) PLoS ONE December, 2006 “ a very large compendium of papers that have been vetted for scientific quality, but which will not be confined in terms of their likely importance.&quot; Harold Varmus, Oct 2005 on PLoS ONE IF ~12 $$$ IF 5-10 $$ IF ~4 $
    28. 28. PLoS ONE is the first so-called “ mega journal ”
    29. 29. <ul><li>Covering all of Science (but mostly bio and health sciences) </li></ul><ul><li>Rapid editorial decisions </li></ul><ul><li>Publishing daily (currently ~70 per day) </li></ul><ul><li>Full colour throughout (no extra charge) </li></ul><ul><li>Papers of unlimited extent (no extra charge) </li></ul><ul><li>Unlimited supplementary materials (no extra charge) </li></ul><ul><li>Utilizes many ‘Web 2.0’ features (Comments, Notes, Star Ratings) </li></ul><ul><li>Utilizes many web 2.0 tools (Editorial Board discussion forum; everyONE blog; Twitter; FriendFeed; Facebook) </li></ul><ul><li>Encouraging of debate and commenting </li></ul><ul><li>Uses the most liberal ‘CC BY’ copyright license </li></ul><ul><li>Open source platform & 2 ‘open’ APIs (Search and ALM) </li></ul>Some of the Features of PLoS ONE
    30. 30. <ul><li>Objective Editorial criteria </li></ul><ul><ul><li>Scientifically rigorous ; Ethical ; Properly reported ; Conclusions supported by the data </li></ul></ul><ul><ul><li>Accepts negative results </li></ul></ul><ul><li>Editors and reviewers do not ask subjective questions such as: </li></ul><ul><ul><li>How important is the work? </li></ul></ul><ul><ul><li>Which is the relevant audience? </li></ul></ul><ul><li>Everything that deserves to be published, will be published </li></ul><ul><ul><li>Therefore the journal is not artificially limited in size </li></ul></ul><ul><li>Online tools are used to evaluate, sort & filter the content after publication, not before </li></ul>The ‘ full ’ PLoS ONE Model
    31. 31. <ul><li>Looking at all PLoS ONE articles one year or older: </li></ul><ul><ul><li>76% already have at least one citation </li></ul></ul><ul><ul><li>20% have 9 or more citations </li></ul></ul><ul><ul><li>10% have 15 or more citations </li></ul></ul><ul><ul><li>Some articles already have more than 200 citations </li></ul></ul><ul><ul><li>(n=16,976 articles. Citation data from Scopus.) </li></ul></ul><ul><li>250 articles have more than 10,000 downloads </li></ul><ul><li>Many Nobel Laureates have published (and one Ignobel!) </li></ul><ul><li>Several articles have won ‘best of’ awards from their societies </li></ul>Quality Output
    32. 33. What is PLoS Doing With Its Open Access Content? <ul><ul><li>Collections </li></ul></ul><ul><ul><ul><li>A journal within a journal </li></ul></ul></ul><ul><ul><li>Hubs </li></ul></ul><ul><ul><ul><li>Virtual aggregations </li></ul></ul></ul><ul><ul><ul><li>Using expert selection </li></ul></ul></ul><ul><ul><li>‘ Alt Metrics ’ (aka Article Level Metrics) </li></ul></ul><ul><ul><ul><li>Automated quality indicators </li></ul></ul></ul><ul><ul><ul><li>Integrated into search / browse </li></ul></ul></ul>
    33. 35. Article Level Metrics
    34. 36. The PLoS/PMC Corpus – Under the Hood <ul><li>Conforms well/partially to the NLM DTD – little markup of content </li></ul><ul><li>PMC – some PDFs ! </li></ul><ul><li>The lack of conformance will come back to haunt us! </li></ul>
    35. 37. What is PLoS Computational Biology Doing Specifically? <ul><li>Mission: </li></ul><ul><li>To serve the community of computational biologists by providing a means for communicating their best research </li></ul><ul><li>To serve the community of life scientists by making them aware of the power of computation in advancing their science </li></ul><ul><li>Introduce innovation in education, software, and data to these communities </li></ul>
    36. 38. The Wikipedia Experiment – Topic Pages <ul><li>Identify areas of Wikipedia that relate to the journal that are missing of stubs </li></ul><ul><li>Develop a Wikipedia page in the sandbox </li></ul><ul><li>Have a Topic Page Editor Review the page </li></ul><ul><li>Publish the copy of record with associated rewards </li></ul><ul><li>Release the living version into Wikipedia </li></ul>
    37. 39. PLoS Comp Biol Software <ul><li>Requires source be deposited in an open source public repository </li></ul><ul><li>Encourages a copy of record be deposited with the article </li></ul><ul><li>Requires that the reviewer be able to test the software if they wish (implies data, documentation, test parameters and output be provided for checking </li></ul>Motivation: S.Veretnik, J.L.Fink, and P.E. Bourne 2008 Computational Biology Resources Lack Persistence and Usability. PLoS Comp. Biol. . 4(7): e1000136
    38. 40. PLoS Comp Biol Software Guess What We Don’ t Have Many Papers So Far!
    39. 41. PLoS Comp Biol – Lessons Learned <ul><li>It takes a lot of time </li></ul><ul><li>You have to believe (publish) in it </li></ul><ul><li>The community has to believe in it </li></ul><ul><li>Dedicated editors are a must e.g. Fran Lewitter (Education) </li></ul>
    40. 42. What About the Future?
    41. 43. <ul><li>A paper when complete is thrown over a high wall to a publisher and essentially forgotten – Perhaps it is time to climb the wall? </li></ul> The Future – Requires a different kind of publisher than we have today
    42. 44. My Wish… <ul><li>As a scientist I want an interaction with a “publisher” that does not begin when the scientific process ends, but begins at the beginning of the scientific process itself </li></ul>What I want from a Publisher of the Future PLoS Comp Biol 2010 6(5): e1000787 UKSG 2011
    43. 45. What Does That Mean? The “Publisher” becomes Part of the Scientific Workflow Scientist Idea Experiment Data Conclusions Publish Laboratory Publisher Maybe The Line is Somewhere Else? UKSG 2011
    44. 46. Maybe The Line is Somewhere Else? Scientist Idea Experiment Data Conclusions Publish Laboratory Publisher Institution? Lab Notebook UKSG 2011 ?
    45. 47. Maybe The Line is Somewhere Else? Scientist Idea Experiment Data Conclusions Publish Laboratory Publisher Institution? Lab Notebook UKSG 2011 ?
    46. 48. If All This is Realized What Could the Future Hold? <ul><li>The worlds scientific literature delivered to all at a minimal cost </li></ul><ul><li>The ability to make the most of that knowledge by all concerned </li></ul>
    47. 49. Questions? [email_address]