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Open Access NBIC Workshop April 19, 2011
Open Access NBIC Workshop April 19, 2011
Open Access NBIC Workshop April 19, 2011
Open Access NBIC Workshop April 19, 2011
Open Access NBIC Workshop April 19, 2011
Open Access NBIC Workshop April 19, 2011
Open Access NBIC Workshop April 19, 2011
Open Access NBIC Workshop April 19, 2011
Open Access NBIC Workshop April 19, 2011
Open Access NBIC Workshop April 19, 2011
Open Access NBIC Workshop April 19, 2011
Open Access NBIC Workshop April 19, 2011
Open Access NBIC Workshop April 19, 2011
Open Access NBIC Workshop April 19, 2011
Open Access NBIC Workshop April 19, 2011
Open Access NBIC Workshop April 19, 2011
Open Access NBIC Workshop April 19, 2011
Open Access NBIC Workshop April 19, 2011
Open Access NBIC Workshop April 19, 2011
Open Access NBIC Workshop April 19, 2011
Open Access NBIC Workshop April 19, 2011
Open Access NBIC Workshop April 19, 2011
Open Access NBIC Workshop April 19, 2011
Open Access NBIC Workshop April 19, 2011
Open Access NBIC Workshop April 19, 2011
Open Access NBIC Workshop April 19, 2011
Open Access NBIC Workshop April 19, 2011
Open Access NBIC Workshop April 19, 2011
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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

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

Published in: Education, Technology
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  • 1. What Open Access Potentially Means to a Scientist <br />Philip E. Bourne<br />University of California San Diego<br />pbourne@ucsd.edu<br />www.sdsc.edu/pb<br />NBIC April 19, 2011<br />
  • 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. 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. 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. 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. 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. Why is OA Important?<br />In the time I have been talking ~20 papers have been indexed by PubMed<br />
  • 8. We Cannot Possibly Read a Fraction of the Papers We Should<br />Renear & Palmer 2009 Science 325:828-832<br />
  • 9. We Are Scanning More Reading Less<br />Renear & Palmer 2009 Science 325:828-832<br />
  • 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. 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. Data and Knowledge are Disparate Which Makes no Sense in the Digital Age<br />1078 databases reported in NAR 2008<br />MetaBase http://biodatabase.org 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. 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. Lets Do A Mashup!<br />PLoS Comp. Biol. 2008. 4(7): e1000136<br />Databases vs Journals<br />
  • 15. We Are Making Progress But it is Incremental<br />UKSG 2011<br />
  • 16. The Database View<br />www.rcsb.org/pdb/explore/literature.do?structureId=1TIM<br />
  • 17. The Literature View – Web 3.0?<br />PLoS Comp Biol2010 6(2) e1000673<br />Databases vs Journals<br />http://www.rcsb.org/pdb/static.do?p=widgets/widgetShowcase.jsp<br />
  • 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. 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. Lets Do Another Mashup!<br />PLoS Comp. Biol. 2008. 4(7): e1000136<br />
  • 21. More Drivers of Change<br />Drivers of Change<br />
  • 22. So What Will Happen? – Integrated Multimedia<br />Present - www.scivee.tv<br />
  • 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. So Lets Take This to Its Logical Conclusion …<br />
  • 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. 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 />https://sites.google.com/site/beyondthepdf/<br />
  • 27. What Will It Take to Get There?You as advocates of OA and of change<br />
  • 28. pbourne@ucsd.edu<br />Questions?<br />

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