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

1. The Future of Data Sharing Platforms in Academic MedicineA Basic Science Perspective Philip E. Bourne University of California San Diego pbourne@ucsd.edu Nov. 4, 2010 Physician Scientist Careeer Development http://www.slideshare.net/pebourne/jim-gray-award-lecture

2. Why Am I Here? I am a practicing basic life scientist who is concerned about the speedof dissemination and level of comprehension in an eScience world 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 It is your engagement that will facilitate change I believe your ability to embrace these changes will impact your career Nov. 4, 2010 Physician Scientist Careeer Development

3. The Scientific Process is Too Slow to Respond to a Crisis – Either Global or Personal Nov. 4, 2010 Physician Scientist Careeer Development By the time the paper is published we could all be dead http://knol.google.com/k/plos-currents-influenza# Motivation

4. In a time of crisis the need for fast access to accurate data and any knowledge of that data are paramount Structure Summary page activity for H1N1 Influenza related structures Jan. 2008 Jan. 2009 Jan. 2010 Jul. 2009 Jul. 2008 Jul. 2010 3B7E: Neuraminidase of A/Brevig Mission/1/1918 H1N1 strain in complex with zanamivir 1RUZ: 1918 H1 Hemagglutinin * http://www.cdc.gov/h1n1flu/estimates/April_March_13.htm Motivation Nov. 4, 2010

5. If that is not enough…For some people the scientific process may be too slow to save their life Nov. 4, 2010 Physician Scientist Careeer Development Motivation

6. Josh Sommer – A Remarkable Young ManCo-founder & Executive Director the Chordoma Foundation Nov. 4, 2010 Physician Scientist Careeer Development http://sagecongress.org/Presentations/Sommer.pdf Motivation

7. Chordoma A rare form of brain cancer No known drugs Treatment – surgical resection followed by intense radiation therapy Nov. 4, 2010 Physician Scientist Careeer Development http://upload.wikimedia.org/wikipedia/commons/2/2b/Chordoma.JPG Motivation

8. Nov. 4, 2010 Physician Scientist Careeer Development http://sagecongress.org/Presentations/Sommer.pdf Motivation

9. Nov. 4, 2010 Physician Scientist Careeer Development http://sagecongress.org/Presentations/Sommer.pdf Motivation

10. Nov. 4, 2010 Physician Scientist Careeer Development http://sagecongress.org/Presentations/Sommer.pdf Motivation

11. Nov. 4, 2010 Physician Scientist Careeer Development If I have seen further it is only by standing on the shoulders of giants Isaac Isaac Newton From Josh’s point of view the climb up just takes too long > 15 years and > $850M to be more precise Adapted: http://sagecongress.org/Presentations/Sommer.pdf Motivation

12. Nov. 4, 2010 Physician Scientist Careeer Development http://sagecongress.org/Presentations/Sommer.pdf Motivation

13. Nov. 4, 2010 Physician Scientist Careeer Development http://sagecongress.org/Presentations/Sommer.pdf Motivation

14. Nov. 4, 2010 Physician Scientist Careeer Development http://fora.tv/2010/04/23/Sage_Commons_Josh_Sommer_Chordoma_Foundation Motivation

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 … Nov. 4, 2010 Physician Scientist Careeer Development

16. A Few Things to Accelerate the Rate of Scientific Discovery A commitment to greater openness Improved characterization (i.e. metadata including provenance) and persistence of data A change in the reward system Seamless integration between the data and the knowledge derived from that data Better management of the digital scientific workflow Unleash the full power of the Internet Nov. 4, 2010 Physician Scientist Careeer Development

17. We Need Data and Knowledge About That Data to Interoperate 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 content Metadata and webservices to data provide an interactiveview that can be annotated Selecting features provides a data/knowledge mashup Analysis leads to new content I can share 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 PLoS Comp. Biol. 2005 1(3) e34 Nov. 4, 2010

18. Seamless Integration Between the Data and the Knowledge Derived from that Data – What is Stopping US? Technology - NO STM publishers - Yes Funding agencies - Yes You - ??? Nov. 4, 2010 Physician Scientist Careeer Development

19. The Publishers are Starting to Do It Nov. 4, 2010 Physician Scientist Careeer Development From Anita de Waard, Elsevier

20. A Few Things to Accelerate the Rate of Scientific Discovery A commitment to greater openness Improved characterization (i.e. metadata including provenance) and persistence of data A change in the reward system Seamless integration between the data and the knowledge derived from that data Better management of the digital scientific workflow Unleash the full power of the Internet Nov. 4, 2010 Physician Scientist Careeer Development

21. Reward Systems Need to ChangeWhat is Needed? Author disambiguation Auditing (identification and metrics) of all scholarship - means new tools Seniors need to promote alternative forms of scholarship Juniors need to respond to it Nov. 4, 2010 Physician Scientist Careeer Development Ten Simple Rules for Getting Promoted as a Computational Biologist in Academia PLoS Comp Biol to appear Nov. 2010 Reward Systems Need to Change

22. Example Tools Nov. 4, 2010 Physician Scientist Careeer Development http://www.researcherid.com/ http://pubnet.gersteinlab.org/ http://www.biomedexperts.com

23. What Are these Alternative Forms of Scholarship? Reviews Curation Research [Grants] Journal Article Poster Session Conference Paper Blogs Community Service/Data Reward Systems Need to Change Nov. 4, 2010 Physician Scientist Careeer Development

24. Reward Systems Need to Change Nov. 4, 2010 Physician Scientist Careeer Development

25. A Unique Identifier is Going to Happen It is DOIs for people Some scientists will resist The winner is ORCHID? Reward Systems Need to Change Nov. 4, 2010 Physician Scientist Careeer Development I an Not a Scientist I am a Number PLoS Comp. Biol. 2008 4(12) e1000247

26. Ideally the ID will be Tagged to Every Piece of Scholarly Communication I an Not a Scientist I am a Number PLoS Comp. Biol. 2008 4(12) e1000247 Reward Systems Need to Change Nov. 4, 2010 Physician Scientist Careeer Development

27. A Few Things to Accelerate the Rate of Scientific Discovery A commitment to greater openness Improved characterization (i.e. metadata including provenance) and persistence of data A change in the reward system Seamless integration between the data and the knowledge derived from that data Better management of the digital scientific workflow Unleash the full power of the Internet Nov. 4, 2010 Physician Scientist Careeer Development

28. Yes YouTube Can Increase the Rate of Discovery Unleash the full power of the Internet Nov. 4, 2010

29. The Lab ExperimentPaper+Rich Media My students enjoyed the experience The shyest student was actually the most bold in front of the camera “We will become a generation of “science castors” They liked the exposure for the most part – rather than the PI it puts them out in front Unleash the full power of the Internet Nov. 4, 2010 Physician Scientist Careeer Development

30. What Emerged: SciveeCasts Products ApplicationProductPrimary Customers Journals PubCastJournals, publishers, societies Meetings PosterCast Societies, conference orgs. SlideCast Comm. PaperCast Societies, journals Podcast SlideCast Education PosterCast Societies, universities SlideCast BooksBookCast Publishers, book sellers Unleash the full power of the Internet Nov. 4, 2010 Physician Scientist Careeer Development

31. The Promise – A Hypothetical Example Cardiac Disease Literature Immunology Literature Shared Function Nov. 4, 2010 Physician Scientist Careeer Development

32. Acknowledgements BioLit Team Lynn Fink Parker Williams Marco Martinez RahulChandran Greg Quinn MBT John Moreland John Beaver Microsoft Scholarly Communications Pablo Fernicola Lee Dirks SavasParastitidas Alex Wade Tony Hey wwPDB team Andreas Prilc DimitrisDimitropoulos SciVee Team Apryl Bailey Leo Chalupa Lynn Fink Marc Friedman (CEO) Ken Liu Alex Ramos Willy Suwanto Ben Yukich http://www.scivee.tv http://biolit.ucsd.edu http//www.pdb.org http://www.codeplex.com/ucsdbiolit Nov. 4, 2010

33. pbourne@ucsd.edu Questions? Nov. 4, 2010 Physician Scientist Careeer Development http://www.slideshare.net/pebourne/jim-gray-award-lecture