PLoS - Why It is a Model to be Emulated

The Public Library of Science (PLoS) Why it is a Model to be Emulated Philip E. Bourne University of California San Diego [email_address] www.sdsc.edu/pb

My Two Lectures
The promise - Open Access, Open Science with particular reference to PLoS
The fulfillment - What Open Access facilitates and examples of how it benefits science

The promise - Open Access, Open Science with particular reference to PLoS
What you might get from this lecture:
Further insights into open repositories
Further insights into open access
What is happening with open journals
Some ideas for how you might proceed …

My Perspective
I am a domain scientist (computational biology)
I got involved with the Public Library of Science (PLoS) and subsequently the promise of open access
I co-founded a company, SciVee Inc., that is attempting to leverage the perceived changes in scholarly communication
I support a small academic scholarly communication group

Scholarly Communication Group
Can we improve the way science is disseminated and comprehended?
Through openness can we increase the number of people interested in science?

What is Open Access?
A spectrum of things!
Free, relatively fast online access
Usage with less restrictions
Author retains copyright
Attribution must be given
Green – Authors make papers publically available
Gold – Publishers make papers publically available

Why is Open Access Important?
Authors
access to the largest possible audience
Readers
access to the entire literature
Reuse of articles
download, copy, print, archive
Full-text searching and mining
beyond Boolean text searches

The journals crisis Journal prices CPI/inflation Journals purchased Source: Association of Research Libraries

Examples of International Support for Open Access
Berlin Declaration on Open Access
Dozens of major European Funders
Stipulates that articles ’ copyrights should permit virtually unrestricted redistribution
NIH proposal to increase access, investment in PubMed Central
UN ’s World Summit on the Information Society endorses open-access publishing

Sources of Funding Publishing is the final step in a research project Researcher Publisher Reader £ Public Digital Library Gov Funders Charity Business Institutions £

The Human Face of Open Access

Josh Sommer – A Remarkable Young Man Co-founder & Executive Director the Chordoma Foundation http://sagecongress.org/Presentations/Sommer.pdf

Chordoma
A rare form of brain cancer
No known drugs
Treatment – surgical resection followed by intense radiation therapy
http://upload.wikimedia.org/wikipedia/commons/2/2b/Chordoma.JPG

http://sagecongress.org/Presentations/Sommer.pdf

Adapted: http://sagecongress.org/Presentations/Sommer.pdf Isaac If I have seen further it is only by standing on the shoulders of giants Isaac Newton From Josh’s point of view the climb up just takes too long > 15 years and > $850M to be more precise

http://sagecongress.org/Presentations/Sommer.pdf

http://fora.tv/2010/04/23/Sage_Commons_Josh_Sommer_Chordoma_Foundation

Committed to making the world ’ s scientific and medical literature a public resource

PLoS Represents the Purest Form of Open Science – CC-BY

Some PLoS History…

PLoS Founding Board of Directors Harold Varmus PLoS Co-founder Nobel Laureate, Director NCI Patrick O. Brown PLoS Co-founder Howard Hughes Medical Institute & Stanford University School of Medicine Michael B. Eisen PLoS Co-founder Lawrence Berkeley National Laboratory & University of California at Berkeley

What is the Public Library of Science?
By driving a change in the publishing model to open access publishing
By generating tools for mining the scientific literature
By making it comprehensible to the non-specialist
A nonprofit organization of scientists committed to making the world ’ s scientific and medical literature a public resource

PLoS – A Brief History
Founded in October, 2000
Circulated an open letter urging publishers to increase access to research literature
>30,000 signatories
Some positive effects, but overall response from publishers fell short of demands
In December, 2002, $9 million grant from Moore Foundation to launch open access journals.

PLoS Biology October, 2003 PLoS Medicine October, 2004 PLoS Community Journals June-September, 2005 & October, 2007 (NTDs) PLoS ONE December, 2006 “ a very large compendium of papers that have been vetted for scientific quality, but which will not be confined in terms of their likely importance." Harold Varmus, Oct 2005 on PLoS ONE IF ~12 $$$ IF 5-10 $$ IF ~4 $

PLoS ONE is the first so-called “ mega journal ”

Covering all of Science (but mostly bio and health sciences)
Rapid editorial decisions
Publishing daily (currently ~70 per day)
Full colour throughout (no extra charge)
Papers of unlimited extent (no extra charge)
Unlimited supplementary materials (no extra charge)
Utilizes many ‘Web 2.0’ features (Comments, Notes, Star Ratings)
Utilizes many web 2.0 tools (Editorial Board discussion forum; everyONE blog; Twitter; FriendFeed; Facebook)
Encouraging of debate and commenting
Uses the most liberal ‘CC BY’ copyright license
Open source platform & 2 ‘open’ APIs (Search and ALM)
Some of the Features of PLoS ONE

Objective Editorial criteria
Scientifically rigorous ; Ethical ; Properly reported ; Conclusions supported by the data
Accepts negative results
Editors and reviewers do not ask subjective questions such as:
How important is the work?
Which is the relevant audience?
Everything that deserves to be published, will be published
Therefore the journal is not artificially limited in size
Online tools are used to evaluate, sort & filter the content after publication, not before
The ‘ full ’ PLoS ONE Model

Looking at all PLoS ONE articles one year or older:
76% already have at least one citation
20% have 9 or more citations
10% have 15 or more citations
Some articles already have more than 200 citations
(n=16,976 articles. Citation data from Scopus.)
250 articles have more than 10,000 downloads
Many Nobel Laureates have published (and one Ignobel!)
Several articles have won ‘best of’ awards from their societies
Quality Output

What is PLoS Doing With Its Open Access Content?
Collections
A journal within a journal
Hubs
Virtual aggregations
Using expert selection
‘ Alt Metrics ’ (aka Article Level Metrics)
Automated quality indicators
Integrated into search / browse

Article Level Metrics

The PLoS/PMC Corpus – Under the Hood
Conforms well/partially to the NLM DTD – little markup of content
PMC – some PDFs !
The lack of conformance will come back to haunt us!

What is PLoS Computational Biology Doing Specifically?
Mission:
To serve the community of computational biologists by providing a means for communicating their best research
To serve the community of life scientists by making them aware of the power of computation in advancing their science
Introduce innovation in education, software, and data to these communities

The Wikipedia Experiment – Topic Pages
Identify areas of Wikipedia that relate to the journal that are missing of stubs
Develop a Wikipedia page in the sandbox
Have a Topic Page Editor Review the page
Publish the copy of record with associated rewards
Release the living version into Wikipedia

PLoS Comp Biol Software
Requires source be deposited in an open source public repository
Encourages a copy of record be deposited with the article
Requires that the reviewer be able to test the software if they wish (implies data, documentation, test parameters and output be provided for checking
Motivation: S.Veretnik, J.L.Fink, and P.E. Bourne 2008 Computational Biology Resources Lack Persistence and Usability. PLoS Comp. Biol. . 4(7): e1000136

PLoS Comp Biol Software Guess What We Don’ t Have Many Papers So Far!

PLoS Comp Biol – Lessons Learned
It takes a lot of time
You have to believe (publish) in it
The community has to believe in it
Dedicated editors are a must e.g. Fran Lewitter (Education)

What About the Future?

A paper when complete is thrown over a high wall to a publisher and essentially forgotten – Perhaps it is time to climb the wall?
uzar.wordpress.com The Future – Requires a different kind of publisher than we have today

My Wish…
As a scientist I want an interaction with a “publisher” that does not begin when the scientific process ends, but begins at the beginning of the scientific process itself
What I want from a Publisher of the Future PLoS Comp Biol 2010 6(5): e1000787 UKSG 2011

What Does That Mean? The “Publisher” becomes Part of the Scientific Workflow Scientist Idea Experiment Data Conclusions Publish Laboratory Publisher Maybe The Line is Somewhere Else? UKSG 2011 uzar.wordpress.com

Maybe The Line is Somewhere Else? Scientist Idea Experiment Data Conclusions Publish Laboratory Publisher Institution? Lab Notebook UKSG 2011 ?

If All This is Realized What Could the Future Hold?
The worlds scientific literature delivered to all at a minimal cost
The ability to make the most of that knowledge by all concerned

Questions? [email_address]

PLoS - Why It is a Model to be Emulated

by Philip Bourne

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