Transcript Slide 1

New Modes of Scholarly
Communication and Learning
Philip E. Bourne
University of California San Diego
[email protected]
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Disclaimer
I am not an expert, but through my
involvement with Open Access
(OA) I have seen the possibilities
for improved scholarly
communication and learning
It is this vision I would like to
share with you today
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Let me cast that vision into a
scenario that we can dissect and
study
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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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Science Fiction – Yes or No?
I would argue that the only part of
this vision that is science fiction is
finding a bus in San Diego
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Science Fiction?
• Five years ago Yes… Today No…
• Five years ago the idea of downloading data
on a bus would have been absurd – not today
• Five years ago an IPOL would be absurd not today (consider the smart phone)
• Journals and databases are providing RSS
feeds today
• IM is prevalent but not for scientific discourse
• Video and podcasting are prevalent but not
for scientific discourse
• Full text journal articles and data are on-line
but not integrated
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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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NIH Public Access Policy
“The research supported by the
National Institutes of Health
(NIH) is essential to improving
human health. Public access to
this research is vital – today
and for generations to come.”
From a letter from NIH Director Zerhouni
to grantees, February 3rd, 2005
SSPPS 205
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More and more authors care
about improving access to their
papers…
“Faced with the option of submitting to an
open-access or closed-access journal, we
now wonder whether it is ethical for us to
opt for closed access on the grounds of
impact factor or preferred specialist
audience.”
-- Costello and Osrin in The Lancet
SSPPS 205
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Where are we Today?
• NIH and other government 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 has yet to be realized
• Data increasingly on-line but not integrated with
the publication derived from it
SSPPS 205
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The Growth of Open Access Literature
PubMed Central Article Holdings (Research Articles only)
50000
40000
PLoS and PubMed Central founded
BioMed Central begins deposition
35000
Number of Articles
30000
25000
20000
15000
10000
PLoS publishes first journal issue
45000
5000
Back issue
deposition,
digitization
0
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Publication Year
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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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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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Okay so much for the 1%
inspiration, where is the 99%
perspiration?
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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
PLoS Comp. Biol. 2005 1(3), e34
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Database and Journal IntegrationThe Test Bed
Journals
http://www.wwpdb.org/
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Database
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The Protein Data Bank
http://www.pdb.org
• Paper not published
unless data are
deposited – strong
data to literature
correspondence
• Highly structured data
conforming to an
extensive ontology
• DOI’s assigned to
every structure –
http://www.doi.org
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Seamless Integration between
Data and the Literature – What
Does That Imply?
• Improving semantic consistency in the
literature – best done at the point of
authoring
• Post processing to establish semantic
content
• New forms of visualization and
interaction at the presentation layer
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Seamless Integration between
Data and the Literature – What
Does That Imply?
• Improving semantic consistency in the
literature – best done at the point of
authoring
• Post processing to establish semantic
content
• New forms of visualization and
interaction at the presentation layer
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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
PSP Washington DC Feb. 2008
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December
2, 2008
ICTPWSU
Trieste,
December
10, 2007
27
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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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BioLit Plugin Project
Author
Publisher
Paper
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Word File in Docx format
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Sidebar: Imagine a Future Where…
• The relationship between author and
publisher is quite different
• The publisher is a warehouse for the
workflow of scientific endeavor not just a
repository for the end product
• Evidence:
– www.researchgate.net
– MetaLab (Borya Shakhnovich)
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BioLit Plugin Project
Automated Ontology & ID Tagging within Microsoft Word Documents
• Leverages Office Open XML used in Microsoft Office
2007
• Custom schema attached to document and used to
automatically XML tag ontology terms and database
identifiers within a research paper
• Ontology tagging assists publication of scientific
research by aiding efficient and accurate automated
categorization and promotion of information
dissemination
• Conversion of manuscript to NLM DTD for direct
submission to publisher
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BioLit Plugin Project
Rather than Post-processing the Document the
Author Controls the Semantic Tagging
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Plugin Architecture
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Context-Sensitive Data Access
• Display of information of
database entries when
the user clicks on the ID
in the document
• Display of ontology
terms related to terms in
the document text, using
local database search
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Ontologies are Stored in a Local Database
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User Configurable Selection
• Fully user configuration
ontology and database
identifier selection
• All searches occur within
the user’s desktop
computer
• Desired ontologies are
downloaded and
installed automatically,
and update periodically
• BioLit installer XML file
provides the application
with the information
needed to download and
install ontologies.
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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
December
2008
PSPWSU
Washington
DC2,Feb.
2008
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YouTube for Scientists
www.scivee.tv
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Motivation
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Pubcast – Video Integrated
with the Full Text of the Paper
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Pubcast - Making
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Channels – Just Like TV
ICTP Trieste, December 2007
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Professional Profile
ICTP Trieste, December 2007
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Create & Join Communities
and Discussion Groups
ICTP Trieste, December 2007
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The Role of Ontologies
• Tag clouds generated
automatically from
MESH headings
• Semantic enrichment
can be included with
a pubcast
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SciVee – Viral Projects
•
•
•
•
Sweetwater School District
“Postercasts”
Science video competitions
“CVcasts”
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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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