Open Access NBIC Workshop April 19, 2011

What Open Access Potentially Means to a Scientist
Philip E. Bourne
University of California San Diego
pbourne@ucsd.edu
www.sdsc.edu/pb
NBIC April 19, 2011

My Bias Towards Open Access (OA)
Co-founder and EIC of an open OA journal
Co-director of the RCSB PDB which has always been open – see parallels between databases and the literature
Always been a supporter of open source software
Have a small company trying to leverage OA content
Believe OA must have a successful business model

What OA Means to a Scientist
$$ to publish
A broader readership – more citations?
Retention of copyright
Misconceptions by fellow scientists
Potentially a change in the way scholarship is disseminated and comprehended

Open Access – The Driver(Creative Commons License)
All published materials available on-line free to all (author pays model)
Unrestricted access to all published material in various formats eg XML provided attribution is given to the original author(s)
Copyright remains with the author
Open Access

Open Access – The Driver(Creative Commons License)
All published materials available on-line free to all (reader pays model)
Unrestricted access to all published material in various formats eg XML provided attribution is given to the original author(s)
Copyright remains with the author
Open Access: Taking Full Advantage of the Content
PLoS Comp. Biol. 2008 4(3) e1000037
Open Access

Why is OA Important?It enables scientists to take matters into their own hands –We have done so for a long time with biological databases, why not with the biological literature?

Why is OA Important?
In the time I have been talking ~20 papers have been indexed by PubMed

We Cannot Possibly Read a Fraction of the Papers We Should
Renear & Palmer 2009 Science 325:828-832

We Are Scanning More Reading Less
Renear & Palmer 2009 Science 325:828-832

We Need Tools Beyond the Aggregation Provided by PubMed, ISI etc. to Digest the Literature .. The Development of Such Tools Require Open Access to the Literature
But Wait There is More….

More Drivers of Change
Scientific publication has not changed since the invention of the printing press – the Internet changed the mode of delivery is all. Hence even in an eScience environment:
The publication is divorced from the experiments that produced it
Data and the publication are not integrated
A printed format may be the worst way to comprehend the science

Data and Knowledge are Disparate Which Makes no Sense in the Digital Age
1078 databases reported in NAR 2008
MetaBase http://biodatabase.org reports 2,651 entries edited 12,587 times
PubMed contains 18,792,257 entries
~100,000 papers indexed per month
In Feb 2009:
67,406,898 interactive searches were done
92,216,786 entries were viewed
Data as of April 14, 2009
We need data and knowledge about that data to interoperate
PLoS Comp. Biol. 2005 1(3) e34

Journals are Becoming More Like Databases and Databases are Becoming More like Journals
Electronic
Supplements
Biocuration
Unstructured data are
submitted as supplements
A great deal of money
is spent extracting from the
literature to structure in databases
Databases vs Journals

Lets Do A Mashup!
PLoS Comp. Biol. 2008. 4(7): e1000136

We Are Making Progress But it is Incremental
UKSG 2011

The Database View
www.rcsb.org/pdb/explore/literature.do?structureId=1TIM

The Literature View – Web 3.0?
PLoS Comp Biol2010 6(2) e1000673
http://www.rcsb.org/pdb/static.do?p=widgets/widgetShowcase.jsp

The New Reader Workflow
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
User clicks on thumbnail
Metadata and a webservices call provide a renderable image that can be annotated
Selecting a features provides a database/literature mashup
That leads to new papers
4.
1.
3. A composite view of
journal and database
content results
1. A link brings up figures
from the paper
3.
2.
2. Clicking the paper figure retrieves
data from the PDB which is
analyzed

Cardiac Disease
Literature
Immunology Literature
Take This Notion to its Logical ConclusionData Clustering via the Literature & Databases
Shared Function

Lets Do Another Mashup!
PLoS Comp. Biol. 2008. 4(7): e1000136

More Drivers of Change
Drivers of Change

So What Will Happen? – Integrated Multimedia
Present - www.scivee.tv

Why Do I Want This?Integrated Rich Media Can Improve Comprehension
Already happening but post publication not Prepublication
Lab discussions, presentations of the work etc. are part of the new discourse
23
UKSG 2011

So Lets Take This to Its Logical Conclusion …

The Research Article of the Future …
.. will be the select parts of
of a container that holds the
complete academic work flow
PLoS Comp Biol 2010 6(5): e1000787

Open source cohesive tools
New standards
Business rights and IP
Attribution/evaluation/archiving
A “publisher” to take the plunge
Beyond the PDF
26
What Will It Take to Get There?
https://sites.google.com/site/beyondthepdf/

What Will It Take to Get There?You as advocates of OA and of change

pbourne@ucsd.edu
Questions?

Open Access NBIC Workshop April 19, 2011

by Philip Bourne on Apr 22, 2011

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Open Access NBIC Workshop April 19, 2011 — Presentation Transcript