The Public Library of Science (PLoS)

Why it is a Model to be Emulated

Philip E. Bourne

University of California San Diego

pbourne@ucsd.edu

www.sdsc.edu/pb

My Two Lectures

1. The promise - Open Access, Open Science with particular reference to PLoS

2. 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 articlesdownload, copy, print, archive

• Full-text searching and mining beyond Boolean text searches

Journal prices

CPI/inflation

Journalspurchased

The journals crisis

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

Publishing is the final step in a research project

Researcher

Publisher

Reader

£

PublicDigitalLibrary

GovFundersCharityBusinessInstitutions

£Sources of Funding

The Human Face of Open Access

Josh Sommer – A Remarkable Young ManCo-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

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

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://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 VarmusPLoS Co-founder Nobel Laureate, Director NCI

Patrick O. BrownPLoS Co-founderHoward Hughes Medical Institute & Stanford University School of Medicine

Michael B. EisenPLoS Co-founderLawrence 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 BiologyOctober, 2003

PLoS MedicineOctober, 2004

PLoS Community JournalsJune-September, 2005

& October, 2007 (NTDs)

PLoS ONEDecember, 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

http://hubs.plos.org/web/biodiversity/

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 FuturePLoS Comp Biol 2010 6(5): e1000787

UKSG 2011

What Does That Mean? The “Publisher” becomes Part of the

Scientific WorkflowScientist

Idea

Experiment

Data

Conclusions

Publish

Laboratory

Publisher

Maybe The Line is Somewhere Else?45UKSG 2011

uzar.wordpress.com

Maybe The Line is Somewhere Else?

Scientist

Idea

Experiment

Data

Conclusions

Publish

Laboratory

Publisher

Institution?

Lab Notebook

46UKSG 2011

?

Scientist

Idea

Experiment

Data

Conclusions

Publish

Laboratory

Publisher

Institution?

Lab Notebook

Maybe The Line is Somewhere Else?

UKSG 2011 47

?

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?

pbourne@ucsd.edu