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/
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
2
It is My Excitement about the
Promise of Open Access that I
am Going to Try and Impart Here
Openness is About More than Just
Journal Articles
Through communication
and integration comes
comprehension and
dissemination
catalyzed by the
Internet
Open Access Day October 14,
2008
4
The Open Matrix
Providers
Journals
Cyberspace ID
DOIs
Content
Knowledge
The Open Matrix
Providers
People
Software
Databases
Web
Journals
Cyberspace ID
Content
OpenID/
Profile/
ResearcherID
Personality
SorceForge etc..
Not Well
Identified
Raw Data/
Database
Metadata/Ontologies
Identifier
Wiki, blog, video..
Not Well
postings
Identified
DOIs
Knowledge
The Open Matrix
Providers
People
Software
Databases
Web
Journals
Cyberspace ID
Content
OpenID/
Profile/
ResearcherID
Personality
Not Well
SourceForge
Identified
etc..
Raw Data/
Database
Metadata/Ontologies
Identifier
Wiki, blog, video..
Not Well
postings
Identified
DOIs
Knowledge
The Open Matrix
Providers
People
Software
Databases
Web
Journals
Cyberspace ID
Content
OpenID/
Profile/
ResearcherID
Personality
Not Well
SourceForge
Identified
etc..
Raw Data/
Database
Metadata/Ontologies
Identifier
Wiki, blog, video..
Not Well
postings
Identified
DOIs
Knowledge
The Open Matrix
Providers
People
Software
Databases
Web
Journals
Cyberspace ID
Content
OpenID/
Profile/
ResearcherID
Personality
Not Well
SourceForge
Identified
etc..
Raw Data/
Database
Metadata/Ontologies
Identifier
Wiki, blog, video..
Not Well
postings
Identified
DOIs
Knowledge
The Open Matrix
Providers
People
Software
Databases
Web
Journals
Cyberspace ID
Content
OpenID/
Profile/
ResearcherID
Personality
Not Well
SourceForge
Identified
etc..
Raw Data/
Database
Metadata/Ontologies
Identifier
Wiki, blog, video..
Not Well
postings
Identified
DOIs
Knowledge
Pubcast – Video Integrated
with the Full Text of the Paper
Open Access Day October 14,
2008
11
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
Open Access Day October 14,
2008
12
Professional Profile
Open
Access Day
October
14,
ICTP Trieste,
December
2007
2008
13
Note: Profiles Are a First Step to Virtual
Research Environments
Social Professional Networking
Expert finding
[Thanks to Carole Goble]
Create & Join Communities
and Discussion Groups
Open
Access Day
October
14,
ICTP Trieste,
December
2007
2008
15
The Open Matrix
Providers
People
Software
Databases
Web
Journals
Cyberspace ID
Content
OpenID/
Profile/
ResearcherID
Personality
Not Well biolit.ucsd.edu
SourceForge
Identified
etc..
Raw Data/
Database
Metadata/Ontologies
Identifier
Wiki, blog, video..
Not Well
postings
Identified
DOIs
Knowledge
BioLit: Tools for New Modes of Scientific Dissemination
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
4.
1.
1. A link brings up figures
from the paper
3. A composite view of
journal and database
content results
3.
2.
2. Clicking the paper figure retrieves
data from the PDB which is
analyzed
• 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
http://biolit.ucsd.edu
Semantic Enrichment
http://biolit.ucsd.edu
http://imageweb.zoo.ox.ac.uk/pub/2008/plospaper/latest/
Courtesy David Shotton
Semantic Enrichment at the Point of Authoring
Open Access Day October 14,
2008
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A Knowledge Workflow of the
Future
Experiment
Results
Publish
Science 2.0
Nature Procedings
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2008
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Motivation
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2008
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Acknowledgements
• SciVee Team
– Apryl Bailey
– Tim Beck
– Leo Chalupa
– Marc Friedman
– Alex Ramos
– Willy Suwanto
CT Watch 2007, 3(3) 26-31
• BioLit Team
• J. Lynn Fink
• Marco Martinez
• Sergey Kushch
• Greg Quinn
• Vianca Ramirez
• Parker Williams
Open Access Day October 14,
2008
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Questions?
pbourne@ucsd.edu
Open Access Day October 14,
2008
23