Some Thoughts on Open
Science
Philip E. Bourne
University of California San Diego
pbourne@ucsd.edu
“.. as we enjoy great advantages from the
inventions of others, we should be glad of an
opportunity to serve others by any invention of
ours; and this we should do freely and
generously.”
The Autobiography of Benjamin Franklin
April 28, 2009
BioIT World, Boston
In the next few minutes I would
like to give one person’s view of
the possibilities that await us
I readily acknowledge that talk is
cheap and action expensive
Well done is better than well said
Benjamin Franklin
April 28, 2009
BioIT World, Boston
Today’s Academic Workflow
Reviews
Curation
Feds
Research
[Grants]
Journal
Article
Publishers
Poster
Session
Conference
Paper
Societies
Community Service/Data
Blogs/Wikis
3
uzar.wordpress.com
Take Home Messages from the
Workflow
• Different products arising from the workflow are
valued very differently – data, software and
knowledge are good examples
• A publication is like a baton in a relay race – it is
handed off and one’s work is considered over
• Only we are aware of our scholarly output – no
aggregator, organization etc. knows it all
I am in the prime of senility
Benjamin Franklin
April 28, 2009
BioIT World, Boston
There are Signs of Change …
Is a Database Really Different from a Biological Journal?
PLoS Comp. Biol. 2005 1(3) e34
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
6
There are Signs of Change …
First Lending Library established
Benjamin Franklin
An Electronic Public Library
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
12 July 2016
Open Access
(Creative Commons License)
1. All published materials available on-line
free to all (reader 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
12 July 2016
Open Access: Taking Full Advantage of the Content
PLoS Comp. Biol. 2008 4(3) e1000037
Mashup of Rich Media with Traditional
Publishing
www.scivee.tv
ICTP Trieste, December 10, 2007
11
So Where Do We Go From
Here?
Only we are aware of our
scholarly output – no aggregator,
organization etc. knows it all
I an Not a Scientist I am a Number
PLoS Comp. Biol. 4(12) e1000247
April 28, 2009
BioIT World, Boston
April 28, 2009
BioIT World, Boston
A Unique Identifier is Going to
Happen
• It is DOIs for people
• Some scientists will
resist
• The winner is not
clear yet:
–
–
–
–
–
OpenID
MyBibliography
ResearcherID
ScopusID
CrossReg
Ideally the ID will be tagged to
every piece of scholarly
communication
I an Not a Scientist I am a Number
PLoS Comp. Biol. 4(12) e1000247
How This Might Work for
Authors
Scientist
submits a paper
through the JMS
using an existing or
newly requested ID
Central
authentication server
validates the authors
Publisher uniquely
Identifies the authors
and provides author
related statistics
I an Not a Scientist I am a Number
PLoS Comp. Biol. 4(12) e1000247
How This Might Work for
Authors
Represents a new
contract between
author and publisher
Scientist
submits a paper
through the JMS
using an existing or
newly requested ID
Central
authentication server
validates the authors
Publisher uniquely
Identifies the authors
and provides author
related statistics
A publication is
like a baton in
a relay race – it
is handed off
and one’s work
is considered
over
April 28, 2009
BioIT World, Boston
uzar.wordpress.com
Tomorrows Research Contract
• The research product will be different
• The relationship between scientist and
publisher will be different
• The publisher could be a warehouse for
the workflow of scientific endeavor not just
a repository for one type of end product
Energy and persistence conquer all things
Benjamin Franklin
19
Publishers as a Contractor for All
Aspects of Scholarly Output
Scientist
Idea
Experiment
Data
Product
20
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
– Orwik
21
In Summary …
• Encourage open
science with the
realization that there
must be a business
model
• Examples:
– Support the notion of
a userid
– Support new contracts
between author and
publisher
April 28, 2009
BioIT World, Boston
Acknowledgements
This political cartoon (attributed to Benjamin
Franklin) originally appeared during the
French and Indian War
April 28, 2009
BioIT World, Boston
pbourne@ucsd.edu
Questions?
A slip of the foot you may soon recover, but
a slip of the tongue you may never get over
Benjamin Franklin
April 28, 2009
BioIT World, Boston
April 28, 2009
BioIT World, Boston
• A slip of the foot you may soon recover,
but a slip of the tongue you may never get
over
• Energy and persistence conquer all things
• He that lives upon hope will die fasting
• .
April 28, 2009
BioIT World, Boston