1. Open Science One Person’s View and What We Are Doing About It Philip E. Bourne University of California San Diego pbourne@ucsd.edu 1PSB Open Science Workshop 2009

2. So Why am I Here? 1. Jonathon Eisen could not make it 2.Open science seems to offer many opportunities which are yet to be realized 3.We have some developments which illustrate the promise which I would like to share with you PSB Open Science Workshop 2009 2

3. Agenda The research contract is changing That change can be embodied in a vision Components of that vision are already under development PSB Open Science Workshop 2009 3

4. Agenda The research contract is changing That change can be embodied in a vision Components of that vision are already under development PSB Open Science Workshop 2009 4

5. Today’s Research Contract Research [Grants] Journal Article Conference Paper Poster Session Feds Societies Publishers Reviews Blogs Community Service/Data 5

6. Tomorrows Research Contract The research product will be different The relationship between scientist and publisher will be different The publisher will be a warehouse for the workflow of scientific endeavor not just a repository for the end product 66PSB Open Science Workshop 2009

7. Tomorrows Research Contract: Evidence Publishers hubs: –Elsevier portals –PLoS collections Data hubs Open Access/open review e.g. Biology Direct NIH Roadmap requires data be accessible New Resources: –www.researchgate.netwww.researchgate.net –MetaLab (Borya Shakhnovich) 7

8. Agenda The research contract is changing That change can be embodied in a vision Components of that vision are already under development PSB Open Science Workshop 2009 8

9. The Vision… Prior to leaving home a UCSD graduate student syncs her IPOL with the latest papers delivered overnight by the journal via RSS feed. On the bus she reviews the stream, selecting a paper close to her interest in HIV-1 proteases. The data shows apparent anomalies with her own work. Being on-line she notices that a colleague has also discovered the same paper and they IM annotating the results. By the time the bus stops she has recomputed the results, proven the anomaly and made a rebuttal in the form of a “pubcast” to the Editor and sent it to the journal. 9PSB Open Science Workshop 2009

10. What is Missing to Make the Vision a Reality? 1.Seamless integration between the data and the publication upon which that data are based 2.Seamless integration of the authoring and publishing process 3.Notion of traditional publications being associated with podcasts and video 4.Professional networking akin to social networking 10PSB Open Science Workshop 2009

11. What are the Catalysts for Change? New publishing paradigms, most importantly open access publishing The emerging generation of digital scientists The increased ease of working with digital media, notably sound and video 11PSB Open Science Workshop 2009

12. 12 Where are we Today? NIH and other government and private funders have mandated open access Full text increasingly on-line and potentially usable Traditional publishers have used the internet as a distribution medium, but the power of the medium, notably rich media, has yet to be realized Data increasingly on-line but not integrated with the publication derived from it PSB Open Science Workshop 2009

13. Catalyst for Change: Open Access (Creative Commons License) 1.All published materials available on-line free to all (author pays model) 2.Unrestricted access to all published material in various formats eg XML provided attribution is given to the original author(s) 3.Copyright remains with the author 13 PSB Open Science Workshop 2009

14. Catalyst for Change: Open Access (Creative Commons License) 1.All published materials available on-line free to all (author pays model) 2.Unrestricted access to all published material in various formats eg XML provided attribution is given to the original author(s) 3.Copyright remains with the author The catalyst PLoS Comp Biol 2008 4(3) e1000037 14PSB Open Science Workshop 2009

15. Community Reaction? Most scientists have no idea that this implies that anyone can take their material and enhance it e.g., via mashup and effectively republish it 15PSB Open Science Workshop 2009

16. Agenda The research contract will change in years to come That change can be embodied in a vision Components of that vision are already under development PSB Open Science Workshop 2009 16

17. Database and Journal Integration- The Test Bed http://www.pdb.org/ Journals Database 17 http://www.pubmedcentral.nih.gov PSB Open Science Workshop 2009

18. 1. A link brings up figures from the paper 0. Full text of PLoS papers stored in a database 2. Clicking the paper figure retrieves data from the PDB which is analyzed 3. A composite view of journal and database content results BioLit: Tools for New Modes of Scientific Dissemination Biolit integrates biological literature and biological databases and includes: –A database of journal text –Authoring tools to facilitate database storage of journal text –Tools to make static tables and figures interactive 4. The composite view has links to pertinent blocks of literature text and back to the PDB 1. 2. 3. 4. The Knowledge and Data Cycle http://biolit.ucsd.edu 18

19. http://biolit.ucsd.edu http://biolit.ucsd.edu Nucleic Acids Research 2008 36(S2) W385-389 PSP Washington DC Feb. 2008 19

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23. ICTP Trieste, December 10, 2007 23

24. Data Clustering via the Literature PSB Open Science Workshop 2009 24 Immunology Literature Cardiac Disease Literature

25. Author Paper Word File in Docx format Publisher Semantic Richness Should be at the Point of Authoring - BioLit Plugin Project 25

26. Plugin Architecture 26

27. Notion of traditional publications being associated with podcasts and video www.scivee.tv 27

28. Pubcast – Video Integrated with the Full Text of the Paper 28

29. Professional Profile ICTP Trieste, December 2007 29

30. SciVee – Viral Projects Sweetwater School District “Postercasts” Science video competitions “CVcasts” 30

31. Postercasts 31PSB Open Science Workshop 2009

32. Summary The contract by which research is undertaken is changing, hence Numerous opportunities exist to further the dissemination and comprehension of science A couple of examples (Biolit & SciVee) of what is possible have been shown PSB Open Science Workshop 2009 32

33. Acknowledgements SciVee Team –Apryl Bailey –Tim Beck –Leo Chalupa –Marc Friedman –Alex Ramos –Willy Suwanto BioLit Team J. Lynn Fink Sergey Kushch Marco Martinez Greg Quinn Parker Williams CT Watch 2007, 3(3) 26-31 33PSB Open Science Workshop 2009

34. Questions? pbourne@ucsd.edu 34PSB Open Science Workshop 2009