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Open Access NBIC Workshop April 19, 2011
 

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 Open Access NBIC Workshop April 19, 2011 Presentation Transcript

    • 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
    • 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
    • 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
    • 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
    • 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
    • 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?
    • Why is OA Important?
      In the time I have been talking ~20 papers have been indexed by PubMed
    • We Cannot Possibly Read a Fraction of the Papers We Should
      Renear & Palmer 2009 Science 325:828-832
    • We Are Scanning More Reading Less
      Renear & Palmer 2009 Science 325:828-832
    • 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….
    • 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
    • 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
    • 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
    • Lets Do A Mashup!
      PLoS Comp. Biol. 2008. 4(7): e1000136
      Databases vs Journals
    • We Are Making Progress But it is Incremental
      UKSG 2011
    • The Database View
      www.rcsb.org/pdb/explore/literature.do?structureId=1TIM
    • 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
    • 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
    • Cardiac Disease
      Literature
      Immunology Literature
      Take This Notion to its Logical ConclusionData Clustering via the Literature & Databases
      Shared Function
      Databases vs Journals
    • Lets Do Another Mashup!
      PLoS Comp. Biol. 2008. 4(7): e1000136
    • More Drivers of Change
      Drivers of Change
    • So What Will Happen? – Integrated Multimedia
      Present - www.scivee.tv
    • 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
    • So Lets Take This to Its Logical Conclusion …
    • 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
    • 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/
    • What Will It Take to Get There?You as advocates of OA and of change
    • pbourne@ucsd.edu
      Questions?