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Future of Data Sharing

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Philip Bourne, Ph.D.
University of California, San Diego
The Future of Data Sharing Platforms in Academic Medicine: A Basic Science Perspective
Meeting: Physician-Scientist Career Development Meeting, New York Academy of Sciences, November 3-5, 2010
View this online, complete with audio, at http://community.sciencecareers.org/ctscinet/groups/sessions/2010/12/the-future-of-data-sharing-platforms-in-academic-medicine-a-basic-science-perspective.php

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Future of Data Sharing

  1. 1. The Future of Data Sharing Platforms in Academic MedicineA Basic Science Perspective<br />Philip E. Bourne<br />University of California San Diego<br />pbourne@ucsd.edu<br />Nov. 4, 2010<br />Physician Scientist Careeer Development<br />http://www.slideshare.net/pebourne/jim-gray-award-lecture<br />
  2. 2. Why Am I Here?<br />I am a practicing basic life scientist who is concerned about the speedof dissemination and level of comprehension in an eScience world<br />I am fortunate enough to have a major biological resource (the Protein Data Bank) and a major biological journal (PLoS Computational Biology) as my playground for experimenting how we might do better<br />It is your engagement that will facilitate change<br />I believe your ability to embrace these changes will impact your career <br />Nov. 4, 2010<br />Physician Scientist Careeer Development<br />
  3. 3. The Scientific Process is Too Slow to Respond to a Crisis – Either Global or Personal<br />Nov. 4, 2010<br />Physician Scientist Careeer Development<br />By the time the paper is published<br /> we could all be dead<br />http://knol.google.com/k/plos-currents-influenza#<br />Motivation<br />
  4. 4. In a time of crisis the need for fast access <br />to accurate data and any knowledge of<br />that data are paramount<br />Structure Summary page activity for<br />H1N1 Influenza related structures<br />Jan. 2008<br />Jan. 2009<br />Jan. 2010<br />Jul. 2009<br />Jul. 2008<br />Jul. 2010<br />3B7E: Neuraminidase of A/Brevig Mission/1/1918 <br />H1N1 strain in complex with zanamivir<br />1RUZ: 1918 H1 Hemagglutinin<br />* http://www.cdc.gov/h1n1flu/estimates/April_March_13.htm<br />Motivation<br />Nov. 4, 2010<br />
  5. 5. If that is not enough…For some people the scientific process may be too slow to save their life<br />Nov. 4, 2010<br />Physician Scientist Careeer Development<br />Motivation<br />
  6. 6. Josh Sommer – A Remarkable Young ManCo-founder & Executive Director the Chordoma Foundation<br />Nov. 4, 2010<br />Physician Scientist Careeer Development<br />http://sagecongress.org/Presentations/Sommer.pdf<br />Motivation<br />
  7. 7. Chordoma<br />A rare form of brain cancer<br />No known drugs<br />Treatment – surgical resection followed by intense radiation therapy<br />Nov. 4, 2010<br />Physician Scientist Careeer Development<br />http://upload.wikimedia.org/wikipedia/commons/2/2b/Chordoma.JPG<br />Motivation<br />
  8. 8. Nov. 4, 2010<br />Physician Scientist Careeer Development<br />http://sagecongress.org/Presentations/Sommer.pdf<br />Motivation<br />
  9. 9. Nov. 4, 2010<br />Physician Scientist Careeer Development<br />http://sagecongress.org/Presentations/Sommer.pdf<br />Motivation<br />
  10. 10. Nov. 4, 2010<br />Physician Scientist Careeer Development<br />http://sagecongress.org/Presentations/Sommer.pdf<br />Motivation<br />
  11. 11. Nov. 4, 2010<br />Physician Scientist Careeer Development<br />If I have seen further it is only by<br />standing on the shoulders of giants<br />Isaac<br />Isaac Newton<br />From Josh’s point of view the climb <br />up just takes too long<br />> 15 years and > $850M to be <br />more precise<br />Adapted: http://sagecongress.org/Presentations/Sommer.pdf<br />Motivation<br />
  12. 12. Nov. 4, 2010<br />Physician Scientist Careeer Development<br />http://sagecongress.org/Presentations/Sommer.pdf<br />Motivation<br />
  13. 13. Nov. 4, 2010<br />Physician Scientist Careeer Development<br />http://sagecongress.org/Presentations/Sommer.pdf<br />Motivation<br />
  14. 14. Nov. 4, 2010<br />Physician Scientist Careeer Development<br />http://fora.tv/2010/04/23/Sage_Commons_Josh_Sommer_Chordoma_Foundation<br />Motivation<br />
  15. 15. Now we are all hopefully motivated let us break this down to what actually needs to be done in my opinion Here are a few big things …<br />Nov. 4, 2010<br />Physician Scientist Careeer Development<br />
  16. 16. A Few Things to Accelerate the Rate of Scientific Discovery<br />A commitment to greater openness <br />Improved characterization (i.e. metadata including provenance) and persistence of data<br />A change in the reward system<br />Seamless integration between the data and the knowledge derived from that data<br />Better management of the digital scientific workflow<br />Unleash the full power of the Internet <br />Nov. 4, 2010<br />Physician Scientist Careeer Development<br />
  17. 17. We Need Data and Knowledge About That Data to Interoperate<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 content<br />Metadata and webservices to data provide an interactiveview that can be annotated<br />Selecting features provides a data/knowledge mashup<br />Analysis leads to new content I can share<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 />PLoS Comp. Biol. 2005 1(3) e34<br />Nov. 4, 2010<br />
  18. 18. Seamless Integration Between the Data and the Knowledge Derived from that Data – What is Stopping US?<br />Technology - NO<br />STM publishers - Yes<br />Funding agencies - Yes<br />You - ???<br />Nov. 4, 2010<br />Physician Scientist Careeer Development<br />
  19. 19. The Publishers are Starting to Do It<br />Nov. 4, 2010<br />Physician Scientist Careeer Development<br />From Anita de Waard, Elsevier <br />
  20. 20. A Few Things to Accelerate the Rate of Scientific Discovery<br />A commitment to greater openness <br />Improved characterization (i.e. metadata including provenance) and persistence of data<br />A change in the reward system<br />Seamless integration between the data and the knowledge derived from that data<br />Better management of the digital scientific workflow<br />Unleash the full power of the Internet <br />Nov. 4, 2010<br />Physician Scientist Careeer Development<br />
  21. 21. Reward Systems Need to ChangeWhat is Needed?<br />Author disambiguation<br />Auditing (identification and metrics) of all scholarship - means new tools<br />Seniors need to promote alternative forms of scholarship<br />Juniors need to respond to it<br />Nov. 4, 2010<br />Physician Scientist Careeer Development<br />Ten Simple Rules for Getting Promoted as a Computational Biologist in Academia <br />PLoS Comp Biol to appear Nov. 2010<br />Reward Systems Need to Change<br />
  22. 22. Example Tools<br />Nov. 4, 2010<br />Physician Scientist Careeer Development<br />http://www.researcherid.com/<br />http://pubnet.gersteinlab.org/<br />http://www.biomedexperts.com<br />
  23. 23. What Are these Alternative Forms of Scholarship?<br />Reviews<br />Curation<br />Research<br />[Grants]<br />Journal<br />Article<br />Poster<br />Session<br />Conference<br />Paper<br />Blogs<br />Community Service/Data<br />Reward Systems Need to Change<br />Nov. 4, 2010<br />Physician Scientist Careeer Development<br />
  24. 24. Reward Systems Need to Change<br />Nov. 4, 2010<br />Physician Scientist Careeer Development<br />
  25. 25. A Unique Identifier is Going to Happen <br />It is DOIs for people<br />Some scientists will resist<br />The winner is ORCHID?<br />Reward Systems Need to Change<br />Nov. 4, 2010<br />Physician Scientist Careeer Development<br />I an Not a Scientist I am a Number<br />PLoS Comp. Biol. 2008 4(12) e1000247<br />
  26. 26. Ideally the ID will be Tagged to Every Piece of Scholarly Communication<br />I an Not a Scientist I am a Number<br />PLoS Comp. Biol. 2008 4(12) e1000247<br />Reward Systems Need to Change<br />Nov. 4, 2010<br />Physician Scientist Careeer Development<br />
  27. 27. A Few Things to Accelerate the Rate of Scientific Discovery<br />A commitment to greater openness <br />Improved characterization (i.e. metadata including provenance) and persistence of data<br />A change in the reward system<br />Seamless integration between the data and the knowledge derived from that data<br />Better management of the digital scientific workflow<br />Unleash the full power of the Internet <br />Nov. 4, 2010<br />Physician Scientist Careeer Development<br />
  28. 28. Yes YouTube Can Increase the Rate of Discovery<br />Unleash the full power of the Internet<br />Nov. 4, 2010<br />
  29. 29. The Lab ExperimentPaper+Rich Media<br />My students enjoyed the experience<br />The shyest student was actually the most bold in front of the camera<br />“We will become a generation of “science castors”<br />They liked the exposure for the most part – rather than the PI it puts them out in front<br />Unleash the full power of the Internet<br />Nov. 4, 2010<br />Physician Scientist Careeer Development<br />
  30. 30. What Emerged: SciveeCasts<br />Products<br />ApplicationProductPrimary Customers<br />Journals PubCastJournals, publishers, societies<br />Meetings PosterCast Societies, conference orgs.<br />SlideCast<br />Comm. PaperCast Societies, journals<br />Podcast<br />SlideCast<br />Education PosterCast Societies, universities<br />SlideCast<br />BooksBookCast Publishers, book sellers<br />Unleash the full power of the Internet<br />Nov. 4, 2010<br />Physician Scientist Careeer Development<br />
  31. 31. The Promise – A Hypothetical Example<br />Cardiac Disease<br />Literature<br />Immunology Literature<br />Shared Function<br />Nov. 4, 2010<br />Physician Scientist Careeer Development<br />
  32. 32. Acknowledgements<br />BioLit Team<br />Lynn Fink<br />Parker Williams<br />Marco Martinez<br />RahulChandran<br />Greg Quinn<br />MBT<br />John Moreland<br />John Beaver<br />Microsoft Scholarly Communications<br />Pablo Fernicola<br />Lee Dirks<br />SavasParastitidas<br />Alex Wade<br />Tony Hey<br />wwPDB team<br />Andreas Prilc<br />DimitrisDimitropoulos<br />SciVee Team<br />Apryl Bailey<br />Leo Chalupa<br />Lynn Fink<br />Marc Friedman (CEO)<br />Ken Liu<br />Alex Ramos<br />Willy Suwanto<br />Ben Yukich<br />http://www.scivee.tv<br />http://biolit.ucsd.edu<br />http//www.pdb.org<br />http://www.codeplex.com/ucsdbiolit<br />Nov. 4, 2010<br />
  33. 33. pbourne@ucsd.edu<br />Questions?<br />Nov. 4, 2010<br />Physician Scientist Careeer Development<br />http://www.slideshare.net/pebourne/jim-gray-award-lecture<br />

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