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The Promise of Open Access Philip E. Bourne PhD University of California San Diego Open Access Day October 14, 2008

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Presentation on theme: "The Promise of Open Access Philip E. Bourne PhD University of California San Diego Open Access Day October 14, 2008"— Presentation transcript:

1 The Promise of Open Access Philip E. Bourne PhD University of California San Diego pbourne@ucsd.edu www.sdsc.edu/pb Open Access Day October 14, 2008 http://openaccessday.org/

2 Open Access Day October 14, 2008 2 Some Background & Prejudices Editor in Chief of PLoS Computational Biology Associate Director Protein Data Bank Strong supporter of OA but.. –Not religious about it –Recognize there must be an associated business model to achieve longevity –See it existing with closed access for some time to come Driven by the promise of new opportunities for scientific dissemination and comprehension….

3 It is My Excitement about the Promise of Open Access that I am Going to Try and Impart Here

4 Open Access Day October 14, 2008 4 Openness is About More than Just Journal Articles Through communication and integration comes comprehension and dissemination catalyzed by the Internet

5 JournalsDOIsKnowledge The Open Matrix Providers Cyberspace ID Content

6 PeopleOpenID/ ResearcherID Profile/ Personality SoftwareNot Well Identified SorceForge etc.. DatabasesDatabase Identifier Raw Data/ Metadata/Ontologies WebNot Well Identified Wiki, blog, video.. postings JournalsDOIsKnowledge The Open Matrix Providers Cyberspace ID Content

7 PeopleOpenID/ ResearcherID Profile/ Personality SoftwareNot Well Identified SourceForge etc.. DatabasesDatabase Identifier Raw Data/ Metadata/Ontologies WebNot Well Identified Wiki, blog, video.. postings JournalsDOIsKnowledge The Open Matrix Providers Cyberspace ID Content

8 PeopleOpenID/ ResearcherID Profile/ Personality SoftwareNot Well Identified SourceForge etc.. DatabasesDatabase Identifier Raw Data/ Metadata/Ontologies WebNot Well Identified Wiki, blog, video.. postings JournalsDOIsKnowledge The Open Matrix Providers Cyberspace ID Content

9 PeopleOpenID/ ResearcherID Profile/ Personality SoftwareNot Well Identified SourceForge etc.. DatabasesDatabase Identifier Raw Data/ Metadata/Ontologies WebNot Well Identified Wiki, blog, video.. postings JournalsDOIsKnowledge The Open Matrix Providers Cyberspace ID Content

10 PeopleOpenID/ ResearcherID Profile/ Personality SoftwareNot Well Identified SourceForge etc.. DatabasesDatabase Identifier Raw Data/ Metadata/Ontologies WebNot Well Identified Wiki, blog, video.. postings JournalsDOIsKnowledge The Open Matrix Providers Cyberspace ID Content

11 Open Access Day October 14, 2008 11 Pubcast – Video Integrated with the Full Text of the Paper

12 Open Access Day October 14, 2008 12 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 Open Access Day October 14, 2008 13 Professional Profile ICTP Trieste, December 2007

14 Note: Profiles Are a First Step to Virtual Research Environments Social Professional Networking Expert finding [Thanks to Carole Goble]

15 Open Access Day October 14, 2008 15 Create & Join Communities and Discussion Groups ICTP Trieste, December 2007

16 PeopleOpenID/ ResearcherID Profile/ Personality SoftwareNot Well Identified SourceForge etc.. DatabasesDatabase Identifier Raw Data/ Metadata/Ontologies WebNot Well Identified Wiki, blog, video.. postings JournalsDOIsKnowledge The Open Matrix Providers Cyberspace ID Content biolit.ucsd.edu

17 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 Semantic Enrichment http://imageweb.zoo.ox.ac.uk/pub/2008/plospaper/latest/ Courtesy David Shotton http://biolit.ucsd.edu

19 Open Access Day October 14, 2008 19 Semantic Enrichment at the Point of Authoring

20 Open Access Day October 14, 2008 20 A Knowledge Workflow of the Future ExperimentResults Publish Science 2.0 Nature Procedings

21 Open Access Day October 14, 2008 21 Motivation

22 Open Access Day October 14, 2008 22 Acknowledgements SciVee Team –Apryl Bailey –Tim Beck –Leo Chalupa –Marc Friedman –Alex Ramos –Willy Suwanto BioLit Team J. Lynn Fink Marco Martinez Sergey Kushch Greg Quinn Vianca Ramirez Parker Williams CT Watch 2007, 3(3) 26-31

23 Open Access Day October 14, 2008 23 Questions? pbourne@ucsd.edu

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