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UKSG Meeting April 4, 2011
UKSG Meeting April 4, 2011
UKSG Meeting April 4, 2011
UKSG Meeting April 4, 2011
UKSG Meeting April 4, 2011
UKSG Meeting April 4, 2011
UKSG Meeting April 4, 2011
UKSG Meeting April 4, 2011
UKSG Meeting April 4, 2011
UKSG Meeting April 4, 2011
UKSG Meeting April 4, 2011
UKSG Meeting April 4, 2011
UKSG Meeting April 4, 2011
UKSG Meeting April 4, 2011
UKSG Meeting April 4, 2011
UKSG Meeting April 4, 2011
UKSG Meeting April 4, 2011
UKSG Meeting April 4, 2011
UKSG Meeting April 4, 2011
UKSG Meeting April 4, 2011
UKSG Meeting April 4, 2011
UKSG Meeting April 4, 2011
UKSG Meeting April 4, 2011
UKSG Meeting April 4, 2011
UKSG Meeting April 4, 2011
UKSG Meeting April 4, 2011
UKSG Meeting April 4, 2011
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UKSG Meeting April 4, 2011

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A talk of what one scientist wants of publishers delivered to UK and European publishers at the UKSG meeting.

A talk of what one scientist wants of publishers delivered to UK and European publishers at the UKSG meeting.

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  • 1. Digital Research Analog Publishing – One Scientist’s View<br />Philip E. Bourne<br />University of California San Diego<br />pbourne@ucsd.edu<br />http://www.sdsc.edu/pb<br />1<br />UKSG 2011<br />
  • 2. My Bias..<br />Computational biologist (only one of many domains)<br />Open access advocate<br />Maintainer of an important biological data resource (PDB)<br />UKSG 2011<br />2<br />
  • 3. My Wish…<br />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 <br />What I want from a Publisher of the Future<br />PLoS Comp Biol 2010 6(5): e1000787<br />UKSG 2011<br />
  • 4. What Does That Mean? The “Publisher” becomes Part of the Scientific Workflow<br />Scientist<br />Laboratory<br />Idea<br />Experiment<br />Data<br />Conclusions<br />Publisher<br />uzar.wordpress.com<br />Maybe The Line is Somewhere Else?<br />Publish<br />4<br />UKSG 2011<br />
  • 5. Maybe The Line is Somewhere Else?<br />Laboratory<br />Scientist<br />?<br />Idea<br />Experiment<br />Institution?<br />Data<br />Lab Notebook<br />Conclusions<br />Publisher<br />Publish<br />5<br />UKSG 2011<br />
  • 6. ?<br />Laboratory<br />Scientist<br />Idea<br />Experiment<br />Institution?<br />Data<br />Lab Notebook<br />Conclusions<br />Publisher<br />Publish<br />Maybe The Line is Somewhere Else?<br />UKSG 2011<br />6<br />
  • 7. Why Do I Want This?<br />UKSG 2011<br />7<br />
  • 8. I Want Interoperability with the Data and Applications that Understand That Data<br />What is needed?<br />Standard set of apps for data exploration<br />Standard calling interfaces<br />Who manages the data?<br />Publisher<br />Author<br />Database<br />3rd party<br />User annotates <br />view<br />Metadata stored with the article<br />Fetches the data and provides a <br />Staring point for interactive enquiry<br />UKSG 2011<br />
  • 9. We Are Making Progress But it is Incremental<br />UKSG 2011<br />
  • 10. Already Being Done by Databases and on Mobile<br />Tight Integration with MyPDB<br /><ul><li>Access to saved queries
  • 11. Add/delete queries
  • 12. Flag interesting entries
  • 13. Add personal structure annotations</li></ul>UKSG 2011<br />
  • 14. 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 />11<br />UKSG 2011<br />
  • 15. Mashup with Content from Other Articles / Data<br />Sure its happening already, but…<br />It remains too difficult<br />It must be at the point of capture not post anything<br />UKSG 2011<br />
  • 16. Proposal - The TeachU Workflow<br />Step 1<br />presenter starts <br />PowerPoint<br />Mac<br />PC<br />Step 4<br />slides are<br />uploaded<br />Slides<br />Website<br />Step 3<br />presenter stops <br />recording and<br />initiates upload<br />Step 5<br />slides and podcast<br />are automatically<br />synchronized<br />Step 2<br />presenter starts <br />recording on<br />smart phone<br />Step 6<br />listener<br />plays back <br />synchronized <br />presentation<br />Sync File<br />Podcast<br />Android<br />iPhone<br />Windows Phone 7<br />
  • 17. Why Do I Want This?Semantic Linking of Data Can Lead to New Knowledge Discovery<br />www.rcsb.org/pdb/explore/literature.do?structureId=1TIM<br />BMC Bioinformatics 2010 11:220<br />14<br />UKSG 2011<br />
  • 18. Cardiac Disease<br />Literature<br />Immunology Literature<br />Why Do I Want This?Semantic Linking of Data Can Lead to New Knowledge Discovery<br />Shared Function<br />15<br />UKSG 2011<br />
  • 19. Why Do I Want This?<br />?<br />Laboratory<br />Scientist<br />Idea<br />Experiment<br />Institution?<br />Data<br />Lab Notebook<br />Conclusions<br />Publisher<br />Publish<br />UKSG 2011<br />16<br />
  • 20. Why I Want This?The Truth About the Scientific eLaboratory<br />I have ?? mail folders!<br />The intellectual memory of my laboratory is in those folders<br />This is an unhealthy hub and spoke mentality<br />17<br />UKSG 2011<br />
  • 21. Why I Want This?The Truth About the Scientific eLaboratory<br />I generate way more negative that positive data, but where is it? <br />Content management is a mess<br />Slides, posters…..<br />Data, lab notebooks ….<br />Collaborations, Journal clubs …<br />Software is open but where is it?<br />Farewell is for the data too<br />Computational Biology Resources Lack Persistence and Usability. PLoS Comp. Biol. 4(7): e1000136<br />18<br />UKSG 2011<br />
  • 22. Why I Want ThisThe Truth About the Published Record<br />Preservation of the digital record?<br />Reproducibility?<br />The need for the library to reinvent itself/ institutional repositories to invent themselves?<br />Digital chaos in the long tail?<br />19<br />UKSG 2011<br />
  • 23. What Will It Take to Get There?<br />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 <br />What I want from a Publisher of the Future<br />PLoS Comp Biol 2010 6(5): e1000787<br />UKSG 2011<br />
  • 24. 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 />21<br />UKSG 2011<br />What Will It Take to Get There?<br />https://sites.google.com/site/beyondthepdf/<br />
  • 25. Sounds Insurmountable?<br />UKSG 2011<br />22<br />
  • 26. But Wait..There Are Many Great Tools Out There<br />Taverna<br />We Need Scientist Management Tools<br />23<br />UKSG 2011<br />
  • 27. But Wait..There Are Many Great Ideas Out There<br />Nano publications<br />Semantic tagging of PDFs and beyond<br />Citation ontologies<br />Scholarly HTML<br />Authoring tools<br />UKSG 2011<br />24<br />
  • 28. A Test BedSpinal Muscular Atrophy (SMA)<br />Coalesce a set of disparate tools<br />Engage the publishers<br />Make some progress on a treatable disease<br />25<br />UKSG 2011<br />
  • 29. Acknowledgements<br />Beyond the PDF Workshop<br />Funded by DDCF, Microsoft, NCI, Science Commons<br />The SciVee Team including:<br />Marc Friedmann, J. Lynn Fink, Alex Gramos, Willy Suwanto<br />The PDB Team including:<br />Andreas Prlic, DimitrisDimitanopolos<br />26<br />UKSG 2011<br />
  • 30. pbourne@ucsd.edu<br />Discussion<br />27<br />UKSG 2011<br />

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