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

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Open Access NBIC Workshop April 19, 2011 Presentation Transcript

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