Open Access NBIC Workshop April 19, 2011


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Part of a workshop on open access given with Jan Velterop at the Netherlands Bioinformatics Center annual meeting on April 19, 2011

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Open Access NBIC Workshop April 19, 2011

  1. 1. What Open Access Potentially Means to a Scientist <br />Philip E. Bourne<br />University of California San Diego<br /><br /><br />NBIC April 19, 2011<br />
  2. 2. My Bias Towards Open Access (OA)<br />Co-founder and EIC of an open OA journal<br />Co-director of the RCSB PDB which has always been open – see parallels between databases and the literature<br />Always been a supporter of open source software<br />Have a small company trying to leverage OA content<br />Believe OA must have a successful business model<br />
  3. 3. What OA Means to a Scientist<br />$$ to publish<br />A broader readership – more citations?<br />Retention of copyright<br />Misconceptions by fellow scientists<br />Potentially a change in the way scholarship is disseminated and comprehended<br />
  4. 4. Open Access – The Driver(Creative Commons License) <br />All published materials available on-line free to all (author pays model)<br />Unrestricted access to all published material in various formats eg XML provided attribution is given to the original author(s)<br />Copyright remains with the author <br />Open Access<br />
  5. 5. Open Access – The Driver(Creative Commons License) <br />All published materials available on-line free to all (reader pays model)<br />Unrestricted access to all published material in various formats eg XML provided attribution is given to the original author(s)<br />Copyright remains with the author <br />Open Access: Taking Full Advantage of the Content<br />PLoS Comp. Biol. 2008 4(3) e1000037<br />Open Access<br />
  6. 6. Why is OA Important?It enables scientists to take matters into their own hands –We have done so for a long time with biological databases, why not with the biological literature?<br />
  7. 7. Why is OA Important?<br />In the time I have been talking ~20 papers have been indexed by PubMed<br />
  8. 8. We Cannot Possibly Read a Fraction of the Papers We Should<br />Renear & Palmer 2009 Science 325:828-832<br />
  9. 9. We Are Scanning More Reading Less<br />Renear & Palmer 2009 Science 325:828-832<br />
  10. 10. We Need Tools Beyond the Aggregation Provided by PubMed, ISI etc. to Digest the Literature .. The Development of Such Tools Require Open Access to the Literature<br />But Wait There is More….<br />
  11. 11. More Drivers of Change<br />Scientific publication has not changed since the invention of the printing press – the Internet changed the mode of delivery is all. Hence even in an eScience environment:<br />The publication is divorced from the experiments that produced it<br />Data and the publication are not integrated<br />A printed format may be the worst way to comprehend the science<br />
  12. 12. Data and Knowledge are Disparate Which Makes no Sense in the Digital Age<br />1078 databases reported in NAR 2008<br />MetaBase reports 2,651 entries edited 12,587 times<br />PubMed contains 18,792,257 entries<br />~100,000 papers indexed per month<br />In Feb 2009:<br />67,406,898 interactive searches were done<br />92,216,786 entries were viewed<br />Data as of April 14, 2009<br />We need data and knowledge about that data to interoperate<br />PLoS Comp. Biol. 2005 1(3) e34<br />
  13. 13. Journals are Becoming More Like Databases and Databases are Becoming More like Journals<br />Electronic <br />Supplements<br />Biocuration<br />Unstructured data are <br />submitted as supplements<br />A great deal of money<br />is spent extracting from the <br />literature to structure in databases<br />Databases vs Journals<br />
  14. 14. Lets Do A Mashup!<br />PLoS Comp. Biol. 2008. 4(7): e1000136<br />Databases vs Journals<br />
  15. 15. We Are Making Progress But it is Incremental<br />UKSG 2011<br />
  16. 16. The Database View<br /><br />
  17. 17. The Literature View – Web 3.0?<br />PLoS Comp Biol2010 6(2) e1000673<br />Databases vs Journals<br /><br />
  18. 18. The New Reader Workflow<br />The Knowledge and Data Cycle<br />0. Full text of PLoS papers stored <br />in a database<br />4. The composite view has<br />links to pertinent blocks <br />of literature text and back to the PDB<br />User clicks on thumbnail<br />Metadata and a webservices call provide a renderable image that can be annotated<br />Selecting a features provides a database/literature mashup<br />That leads to new papers<br />4.<br />1.<br />3. A composite view of<br />journal and database<br />content results<br />1. A link brings up figures <br />from the paper<br />3.<br />2.<br />2. Clicking the paper figure retrieves<br />data from the PDB which is<br />analyzed<br />Databases vs Journals<br />
  19. 19. Cardiac Disease<br />Literature<br />Immunology Literature<br />Take This Notion to its Logical ConclusionData Clustering via the Literature & Databases<br />Shared Function<br />Databases vs Journals<br />
  20. 20. Lets Do Another Mashup!<br />PLoS Comp. Biol. 2008. 4(7): e1000136<br />
  21. 21. More Drivers of Change<br />Drivers of Change<br />
  22. 22. So What Will Happen? – Integrated Multimedia<br />Present -<br />
  23. 23. Why Do I Want This?Integrated Rich Media Can Improve Comprehension<br />Already happening but post publication not Prepublication<br />Lab discussions, presentations of the work etc. are part of the new discourse<br />23<br />UKSG 2011<br />
  24. 24. So Lets Take This to Its Logical Conclusion …<br />
  25. 25. The Research Article of the Future …<br />.. will be the select parts of <br />of a container that holds the<br />complete academic work flow <br />PLoS Comp Biol 2010 6(5): e1000787<br />
  26. 26. Open source cohesive tools<br />New standards<br />Business rights and IP<br />Attribution/evaluation/archiving<br />A “publisher” to take the plunge<br />Beyond the PDF<br />26<br />What Will It Take to Get There?<br /><br />
  27. 27. What Will It Take to Get There?You as advocates of OA and of change<br />
  28. 28.<br />Questions?<br />
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