the promise of open access philip e. bourne phd university of california san diego [email protected] ...
TRANSCRIPT
The Promise of Open Access
Philip E. Bourne PhDUniversity of California San Diego
Open Access DayOctober 14, 2008
http://openaccessday.org/
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….
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
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
Journals DOIs Knowledge
The Open MatrixProviders Cyberspace ID Content
People OpenID/
ResearcherID
Profile/
Personality
Software Not Well Identified
SourceForge etc..
Databases Database Identifier
Raw Data/ Metadata/Ontologies
Web Not Well Identified
Wiki, blog, video.. postings
Journals DOIs Knowledge
The Open MatrixProviders Cyberspace ID Content
People OpenID/
ResearcherID
Profile/
Personality
Software Not Well Identified
SourceForge etc..
Databases Database Identifier
Raw Data/ Metadata/Ontologies
Web Not Well Identified
Wiki, blog, video.. postings
Journals DOIs Knowledge
The Open MatrixProviders Cyberspace ID Content
People OpenID/
ResearcherID
Profile/
Personality
Software Not Well Identified
SourceForge etc..
Databases Database Identifier
Raw Data/ Metadata/Ontologies
Web Not Well Identified
Wiki, blog, video.. postings
Journals DOIs Knowledge
The Open MatrixProviders Cyberspace ID Content
People OpenID/
ResearcherID
Profile/
Personality
Software Not Well Identified
SourceForge etc..
Databases Database Identifier
Raw Data/ Metadata/Ontologies
Web Not Well Identified
Wiki, blog, video.. postings
Journals DOIs Knowledge
The Open MatrixProviders Cyberspace ID Content
Open Access Day October 14, 2008
11
Pubcast – Video Integrated with the Full Text of the Paper
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
Note: Profiles Are a First Step to Virtual Research Environments
Social Professional NetworkingExpert finding
[Thanks to Carole Goble]
Open Access Day October 14, 2008
15
Create & Join Communities and Discussion Groups
ICTP Trieste, December 2007
People OpenID/
ResearcherID
Profile/
Personality
Software Not Well Identified
SourceForge etc..
Databases Database Identifier
Raw Data/ Metadata/Ontologies
Web Not Well Identified
Wiki, blog, video.. postings
Journals DOIs Knowledge
The Open MatrixProviders Cyberspace ID Content
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
Open Access Day October 14, 2008
20
A Knowledge Workflow of the Future
Experiment Results Publish
Science 2.0
Nature Procedings
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 WilliamsCT Watch 2007, 3(3) 26-31