The Promise of Open Access Philip E. Bourne PhD University of California San Diego [email protected] ...

The Promise of Open Access

Philip E. Bourne PhDUniversity of California San Diego

[email protected]/pb

Open Access DayOctober 14, 2008

http://openaccessday.org/

mailto:[email protected]

http://www.sdsc.edu/pb

Open Access Day October 14, 2008

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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….

It is My Excitement about the Promise of Open Access that I

am Going to Try and Impart Here


4

Openness is About More than Just Journal Articles

Through communication and integration comes comprehension and

dissemination catalyzed by the

Internet

Journals DOIs Knowledge

The Open MatrixProviders Cyberspace ID Content

People OpenID/

ResearcherID

Profile/

Personality

Software Not Well Identified

SorceForge etc..

Databases Database Identifier

Raw Data/ Metadata/Ontologies

Web Not Well Identified

Wiki, blog, video.. postings



People OpenID/

ResearcherID

Profile/

Personality


SourceForge etc..







People OpenID/

ResearcherID

Profile/

Personality


SourceForge etc..







People OpenID/

ResearcherID

Profile/

Personality


SourceForge etc..







People OpenID/

ResearcherID

Profile/

Personality


SourceForge etc..








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Pubcast – Video Integrated with the Full Text of the Paper

http://www.scivee.tv/pubcast/16244704


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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


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Professional Profile

ICTP Trieste, December 2007

Note: Profiles Are a First Step to Virtual Research Environments

Social Professional NetworkingExpert finding

[Thanks to Carole Goble]


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Create & Join Communities and Discussion Groups

ICTP Trieste, December 2007

People OpenID/

ResearcherID

Profile/

Personality


SourceForge etc..







biolit.ucsd.edu

1. A link brings up figures from the paper

0. Full text of PLoS papers stored in a database

2. Clicking the paper figure retrievesdata from the PDB which is

analyzed

3. A composite view ofjournal 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 haslinks to pertinent blocks

of literature text and back to the PDB

1.

2.

3.

4.

The Knowledge and Data Cycle

http://biolit.ucsd.edu

Semantic Enrichment

http://imageweb.zoo.ox.ac.uk/pub/2008/plospaper/latest/Courtesy David Shottonhttp://biolit.ucsd.edu

http://imageweb.zoo.ox.ac.uk/pub/2008/plospaper/latest/


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Semantic Enrichment at the Point of Authoring


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A Knowledge Workflow of the Future

Experiment Results Publish

Science 2.0

Nature Procedings


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Motivation


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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 WilliamsCT Watch 2007, 3(3) 26-31


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Questions? [email protected]

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The Promise of Open Access Philip E. Bourne PhD University of California San Diego [email protected] ...

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