UKSG Meeting April 4, 2011

2,626 views
2,509 views

Published on

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

Published in: Education
0 Comments
0 Likes
Statistics
Notes
  • Be the first to comment

  • Be the first to like this

No Downloads
Views
Total views
2,626
On SlideShare
0
From Embeds
0
Number of Embeds
3
Actions
Shares
0
Downloads
14
Comments
0
Likes
0
Embeds 0
No embeds

No notes for slide

UKSG Meeting April 4, 2011

  1. 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. 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. 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. 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. 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. 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. 7. Why Do I Want This?<br />UKSG 2011<br />7<br />
  8. 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. 9. We Are Making Progress But it is Incremental<br />UKSG 2011<br />
  10. 10. Already Being Done by Databases and on Mobile<br />Tight Integration with MyPDB<br /><ul><li>Access to saved queries
  11. 11. Add/delete queries
  12. 12. Flag interesting entries
  13. 13. Add personal structure annotations</li></ul>UKSG 2011<br />
  14. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 25. Sounds Insurmountable?<br />UKSG 2011<br />22<br />
  26. 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. 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. 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. 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. 30. pbourne@ucsd.edu<br />Discussion<br />27<br />UKSG 2011<br />

×