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Open ScienceOne Person’s View and What We
Are Doing About It
Philip E. BourneUniversity of California San Diego
1PSB Open Science Workshop 2009
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
PSB Open Science Workshop 2009
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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
PSB Open Science Workshop 2009
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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
Research[Grants]
JournalArticle
ConferencePaper
PosterSession
Feds
Societies
Publishers
Reviews
BlogsCommunity Service/Data 5
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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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.
9PSB Open Science Workshop 2009
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
13PSB Open Science Workshop
2009
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) e100003714PSB Open Science Workshop
2009
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 Integration- The Test Bed
http://www.pdb.org/
Journals
Database
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http://www.pubmedcentral.nih.gov
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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.edu18
http://biolit.ucsd.eduNucleic Acids Research 2008 36(S2) W385-389
PSP Washington DC Feb. 2008 19
20PSB Open Science Workshop 2009
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22PSB Open Science Workshop 2009
ICTP Trieste, December 10, 2007 23
Data Clustering via the Literature
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Immunology Literature
Cardiac DiseaseLiterature
Author Paper
Word File in Docx formatPublisher
Semantic Richness Should be at the Point of Authoring - BioLit Plugin Project
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Plugin Architecture
26
Notion of traditional publications being associated with podcasts and video
www.scivee.tv
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Professional Profile
ICTP Trieste, December 2007 29
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
– Leo Chalupa
– Marc Friedman– Alex Ramos– Willy Suwanto
• BioLit Team• J. Lynn Fink• Sergey Kushch• Marco Martinez• Greg Quinn• Parker Williams
CT Watch 2007, 3(3) 26-31
33PSB Open Science Workshop 2009