Transcript Open Science One Person’s View and What We Are Doing About It Philip E.

Open Science
One Person’s View and What We
Are Doing About It
Philip E. Bourne
University of California San Diego
[email protected]
PSB Open Science Workshop
2009
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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
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Agenda
• The research contract is changing
• That change can be embodied in a vision
• Components of that vision are already
under development
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Agenda
• The research contract is changing
• That change can be embodied in a vision
• Components of that vision are already
under development
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Today’s Research Contract
Reviews
Feds
Research
[Grants]
Journal
Article
Publishers
Poster
Session
Conference
Paper
Societies
Community Service/Data
Blogs
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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
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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.net
– MetaLab (Borya Shakhnovich)
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Agenda
• The research contract is changing
• That change can be embodied in a vision
• Components of that vision are already
under development
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2009
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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.
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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
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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
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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
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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
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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
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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
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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
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Database and Journal IntegrationThe Test Bed
Journals
http://www.pubmedcentral.nih.gov
Database
http://www.pdb.org/
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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
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http://biolit.ucsd.edu
Nucleic Acids Research 2008 36(S2) W385-389
PSP Washington DC Feb. 2008
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ICTP Trieste, December 10, 2007
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Data Clustering via the Literature
Cardiac Disease
Literature
Immunology Literature
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Semantic Richness Should be at the Point of Authoring BioLit Plugin Project
Author
Publisher
Paper
Word File in Docx format
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Plugin Architecture
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Notion of traditional publications being
associated with podcasts and video
www.scivee.tv
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Pubcast – Video Integrated
with the Full Text of the Paper
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Professional Profile
ICTP Trieste, December 2007
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SciVee – Viral Projects
•
•
•
•
Sweetwater School District
“Postercasts”
Science video competitions
“CVcasts”
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Postercasts
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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
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Acknowledgements
• SciVee Team
– Apryl Bailey
– Tim Beck
–
–
–
–
• BioLit Team
• J. Lynn Fink
• Sergey Kushch
• Marco Martinez
• Greg Quinn
• Parker Williams
Leo Chalupa
Marc Friedman
Alex Ramos
Willy Suwanto
CT Watch 2007, 3(3) 26-31
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[email protected]
Questions?
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