Title: Open Access: Is it the future for all Scientific Publications?
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Title: Open Access: Is it the future for all Scientific Publications?
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Language: English
Creator: McFadden, Grant
Publisher: Grant McFadden
Place of Publication: Gainesville, FL
Publication Date: October 19, 2009
Copyright Date: 2009
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Open Access: Is it the future for all
Scientific Publications?

Dr. Grant McFadden
Sr. Editor, PLoS Pathogens
Department of Molecular Genetics & Microbiology,
College of Medicine, University of Florida

Open Access What is it?

* Free,

* Unrestricted
* Author retains

* Papers are

distribution and re-use


immediately deposited

online archive, such as PubMed Central

Bethesda Principles, April 2003


immediate access online

rights to

in a public





* Gold path the entire journal contents are open
and available. Open journals are usually
supported through the payment of author fees.
* Green path authors submit a copy of their
articles to an open repository, e.g., PubMed
* Traveling either path necessitates the author's
management of his licensing agreements:

an author addendum to a publishers copyright, or

a creative commons license.

Creative Commons
Attribution License

*Copyright: 2004 Moorthy et al. This is an open-
access article distributed under the terms of the
Creative Commons Attribution License, which
permits unrestricted use, distribution, and
reproduction in any medium, provided the original
work is properly cited.
*Goal: overcome access barriers and encourage
creative uses.

*Used in plos journals.

Facts about Open Access:

* Open access is not a business model; it is a
property of publication
* Ability to pay plays no role in editorial
* Ensures stable model of global
* Fully OA or hybrid models of publishing
* Open access embodies the concept of peer
* Catalysts for change

Why Open Access?

* Maximum impact for authors
access to the largest possible global audience
visibility of each paper to be measured in its own

* Greatly expanded access to research
for scientists, educators, physicians, the public

* New ways to access and use literature
full-text searching, data integration, and mining

How is OA Growing?

* OA is still

in its infancy

* Some traditional

publishers are

experimenting with OA format journals as
part of their portfolio
* Hard to predict if any one format will
predominate in the future


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Growing list of OA mandates

* Internationally
The Swedish Research Council requires free access to research
Dutch Scientific Research must make their scientific research
available on the internet and accessible to everyone

U.S. Institutional and Federal Level
5 Premier Institutions sign compact for Open-Access
Federal Research Public Access Act (FRPAA) introduced at the
Senate level and will likely be introduced in the House shortly

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PLoS Founding Board of Directors

Harold Varmus
PLoS Co-founder and Chairman of the Board
President and CEO of
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Howard Hughes Medical Institute
& Stanford University School of Medicine

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Lawrence Berkeley National
& University of California at


Open Access is still in its early days

A grassroots initiative by scientific
community to enforce deposition of published
research into a public repository (Pub Med
Circulated an open letter urging publishers to
increase access to research literature (>30,000
In December, 2002, $9 million grant from
Moore Foundation to launch open access

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My Own role at PLoS Pathogens

* I was invited in 2005 to join the Board by
John Young, the first Editor-in-Chief
* Started as Associate Editor, then Section
Editor for Virology, and now Deputy EIC
* I found the journal's emphasis on
pathogen-host interface appealing
* In 2009, the journal continues to grow
rapidly (Current Impact factor of 9)
* Is still defining its scientific "space"

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PLoS Pathogens is an open-access journal
that publishes important new ideas on
bacteria, fungi, parasites, prions, and
viruses that contribute to our understanding
of the biology of pathogens and pathogen-
host interactions,

1 NMA'1V1V1Wphif.'

Our peer-reviewed
journals are:

- Open access
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access policies
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Pathogens Top Downloaded Content

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C ^ Lujo Virus, a New Hemorrhagic Fever-Associated
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I Lyme Disease Spirochete Adhering to and
Escaping from the Vasculature of a Living Host
(Moriarty et al.)

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Sensors of Protozoan Parasites (Ng et al.)

Pathogens Top Downloaded Content

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Virus Since 1918 (Nelson et al.)

-~ _

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Gene Mutation (Richt and Hall)

Suppression of Plant Resistance Gene-
Based Immunity by a Fungal Effector
(Houterman et al.)

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PLoS Pathogens Pearls

Open Access

compendium of the

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professors ai



nd graduate students

"Virus and Host Determinants of
West Nile Virus Pathogenesis."
By Michael S. Diamond




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2009 ALPSPAward for
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* The 2009 winner was PLoS ONE from the
Public Library of Science. This combines the
traditional values of the journal with
innovative online features to create an
inclusive and efficient publication channel. It is
bold and successful and shaping the future of

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The Diploid Geniome Sequence of an Individual Human

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Opportunity at the Article Level

What Does this Mean for My Research?

Expanding access means more

* As part of the tenure and promotion
process, faculty quantify the significance
of their work to their discipline.

Traditional measures include:

* Ranking of the journals in which you
publish known as the Impact factor.
* Number of times other scholars have
cited your works.

Citation advantage of open-access?
Numerous studies offer mixed results
and discipline variations

Norris, M.and others studied citation rates in Open Access vs Toll
Access (Subscription) journals for ecology, applied mathematics,
sociology, and economics.
"Of a sample of 4,633 articles examined, 2,280 (49%) were OA and
had a mean citation count of 9.04 whereas the mean for (toll
access) TA articles was 5.76. There appears to be a clear citation
advantage for those articles that are OA as opposed to those that
are TA." [Abstract] Rates varied for each discipline.

The citation advantage of open-access articles.Journal of the American Society for
Information Science and Technology, Vol. 59, No. 12, 2008, 1963-1972, published
online: 9 July 2008







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An official journal of the International Society for Computational Biology

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Ten Simple Rules for Getting Published

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Comments: 3

Philip E. Bourne

ICitation: Bourne PE (2005) Ten Simple Rules for Getting Published
PLoS Comput Biol 1(5): e57. doi:10,1371/journal.pcbi.0010057

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Published: October 28, 2005

Copyright: 2005 Philip E. Bourne. This is an open-access article distributed under the terms of the
Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any
medium, provided the original author and source are properly credited.

Philip E. Bourne is Editor-in-Chief of PLoS Computational Biology. E-mail: bourne@sdsc.edu

BThe student council (http://www.iscbsc.orq/) of the International Society for Computational
Biology asked me to present my thoughts on getting published in the field of computational biology at
the Intelligent Systems in Molecular Biology conference held in Detroit in late June of 2005. Close to
200 bright young souls (and a few not so young) crammed into a small room for what proved to be a
wonderful interchange among a group of whom approximately one-half had yet to publish their first
paper. The advice I gave that day I have modified and present as ten rules for getting published.

Rule i: Read many papers, and learn from both the good and the bad work of others.

It is never too early to become a critic. Journal clubs, where you critique a paper as a group, are

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This is a course about professional ldeelopment. It teaches \ou all the things vital to a successful scientific career that you
ne\er nonnall\ get taught For example. ho\\ to give a good talk. \\rite a good paper or grant etc. As such the student is only
expected to attend and learn from the experience.
Mllore than anm thing else this \\ill be a discussion period in \\nch there is an active discussion around the topic for that week.
There \\ill be prerequisite reading and this \\ill form the basis of the class.

Source Material: \\hat textbooks, journals, or handouts w-ill be used or recommended? The use of Medline and other
computerized reference searching by students is strongly encouraged.
I have % written a series of "Ten Rules" Editorials that have been very popular- some have been downloaded awover
30,000 times. The open access collection is at htt p://collections. Ilos.org/ Iloscompbiol/tensim lerulei n
indexed in PubM ed. These will form the basis of the course material.

There \\ill be one lecture per week on the following topic. I will invite faculty and students
respect\ e experience of the \eek to come and be palt of the dialog and discussion.
Elements of scientific success according to Hamming and others
Getting the most from the graduate student experience
Rules for gi\ ing good oral presentations
Rules for preparing and presenting posters
Rules for good scientific paper writingllii
Rules for imakinlg good scientific illustrations
Rules for establishing a successful collaboration
Rules for re\ie\\ing scientific articles
Rules for getting your first postdoctoral position
Rules for getting your first grant or fellowship

Tenl Simple Rules To Combine Teaching and Research

Article Related Content Comments: 3

Quentin Vicens, Philip E. Bourne*
1 University of Colorado, Boulder, Colorado, United States of America, 2
Skaggs School of Pharmacy and Pharmaceutical Science, University of
California San Diego, La Jolla, California, United States of America

Citation: Vicens Q, Bourne PE (2009) Ten Simple Rules To Combine
Teaching and Research. PLoS Comput Biol 5(4): e1000358.

Published: April 24, 2009

Copyright: 2009 Bourne, Vicens. This is an open-access article
distributed under the terms of the Creative Commons Attribution
License, which permits unrestricted use, distribution, and reproduction in
any medium, provided the original author and source are credited.

Funding: The authors received no specific funding for this article.

Competing interests: The authors have declared that no competing
interests exist.

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Jump to
Rule 1: Strictly Budget...
Rule 2: Set Specific...
Rule 3: "Don't Reinvent...
Rule 4: Don't Try To...
Rule 5: "Be Shameless in..
Rule 6: Getthe Most in...
Rule 7: Compromise...
Rule 8: Balance...
Rule 9: Start Teaching...
Rule 10: Budget Time for...

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PLoS Computational Bioloqv

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I E-mail: bourne@sdsc.edu

The late Lindley 3. Stiles famously made himself an advocate for teaching during his professorship at
the University of Colorado: "If a better world is your aim, all must agree: The best should teach'
(http://thebestshouldteach.org/). In fact, dispensing high-quality teaching and professional education
is the primary goal of any university F11. Thus, for most faculty positions in academia, teaching is a
significant requirement of the job. Yet, the higher education programs offered to Ph.D. students do not
necessarily incorporate any form of teaching exposure. We offer 10 simple rules that should help you
to get prepared for the challenge of teaching while keeping some composure.

Rule 1: Strictly Budget Your Time for Teaching and for Doing Research Ti

Thic ri Ild mn=/ coco m cti-rinht-fnr.n =rH hi rocnortinn it nrh inlhl roni liroc mnro Hjicrinlino nnrl nH rill th n ii

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An official journal of the International Society for Computational Biology


Ia eun s*a a 5 6 erg.aa

Ten Simple Rules Collection

Written by PLoS Computational Biology Editor-in-Chief Philip E, Bourne, sometimes with collaborators, the "Ten Simple
01 Rules" provide a quick, concentrated guide for mastering some of the professional challenges research scientists face in
their careers,

ri l e Downlo-t en Simple Rules Collection: Screen PDF (400 KB) I Large PDF (1.3 MB)

Download the Ten Simple Rules Collection in Chinese: PDF (589 KB)
Translated by members of the EpiMan Forum, coordinated by Qiguo Lian (qglian [at] fudan.edu.cn). Please note that the
translation is the work of the authors and PLoS is not responsible for any inaccuracies or additional content.

Ten Simple Rules To Combine Teaching and Research
Vicens Q, Bourne PE
doi: 10.1371/journal.pcbi. 1000358

Ten Simple Rules for Organizino a Scientific Meeting
Corpas M, Gehlenborg N, Janga SC, Bourne PE
doi:10,1371/journal.pcbi. 100080

doi:10.1371/journal.pcbi. 100024

Ten Simple Rules for Aspiring Scientists in a Low-Income Country
Moreno E, Gutibrrez J-M

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Containing translations of the entire collection from October 2005 to June 2)0OS8.

Translated by members of the EpiMan Forum :lImp: toniri.epiiii.ni Cl i. coordinated by
Qiguo Lian (qgliaillj ftinan edii.cu

Please note that the translation is the work of the authors and PLoS is not responsiblefor
any inaccuracies or additional content.

Citing this work: This translation is not an official publication ofPLoS Computational
Biology. The work may be cited using the URL of the Ten Simple Rules ;ollecriorn page
(lhip \,ollections.plos org ploscompbiol rensimpleni-des.php).

Citations of the original work:

Gu J, Bourne PE (2007) Ten Simple Rules for Graduate Students. PLoS Comput Biol 3(11): e229.

Erren TC, Cullen P, Erren M, Bourne PE (2007) Ten Simple Rules for Doing Your Best Research,
According to Hamming. PLoS Comput Biol 3(10): e213. doi: 10.1371/journal.pcbi.0030213

Erren TC, Bourne PE (2007) Ten Simple Rules for a Good Poster Presentation. PLoS Comput Biol 3(5):
el02. doi:10.1371 joumal pcbi 0030I102

Bourne PE 001 7) Ten Simple Rules for Making Good Oral Presentations. PLoS Comput Biol 3(4): e77.

Vicens Q Bourne PE (2007) Ten Simple Rules for a Successful Collaboration. PLoS Comput Biol 3(3):
e44. doi:10.137 1/joumal.pcbi.0030044

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Ten Simple Rules for Good Presentations
Professor Philip Bourne, Editor-in-Chief of Public Library of Science
(PLoS) Computational Biology, talks about the ten basic principles of
making good presentations.
Authors: Philip E Bourne
submitted by: Phil
submitted: September 27, 2007 I views:23078
watch view paper listen

Ten Simple Rules for Getting Grants
This piece follows an earlier Editorial, "Ten Simple Rules for Getting
Published" [1], which has generated significant interest, is well read,
and continues to generate a variety of positive...
Authors: Philip E Bourne, Leo M Chalupa
linked profiless: Leo; submitted by: Phil
submitted: September 24, 2007 I views:4489


view paper


Ten Simple Rules for Getting Published
Professor Philip Bourne, Editor-in-Chief of Public Library of Science
(PLoS) Computational Biology, talks about the Ten Simple Rules for
Getting Published.
Authors: Philip E Bourne
submitted by: Phil
submitted: August 24, 2007 I views:7337
watch view paper listen

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a peer-reviewed open-access journal published by the PLoS Neglected Tropical Diseases

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Impact of Environment and Social Gradient on Leptospira
Infection in Urban Slums

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Published in the April 2008 Issue of
Comments: 1 PLoS Neq/ected Tropical Diseases

Renato B. Reis"-, Guilherme S. Ribeiro*, Ridalva D. M.
Felzemburgh1, Francisco S. Santana-1'2 Sharif Mohr!, Astrid
X. T. O. Melendez1, Adriano Queiroz1, Andreia C. Santos-,
Romy R. Ravines-, Wagner S. Tassinari34, Marilia S.
Carvalho3, Mitermayer G. Reis1, Albert I. Ko1'5*
1 Centro de Pesquisas Gongalo Moniz, Fundag o Oswaldo Cruz, Ministerio da
Sadde, Salvador, Brazil, 2 Secretiria Estadual de Saude da Bahia, Salvador,
Brazil, 3 Escola Nacional da Saude Publica, Funda go Oswaldo Cruz, Ministerio
da Saude, Rio de Janeiro, Brazil, 4 Universidade Federal Rural do Rio de
Janeiro, Rio de Janeiro, Brazil, 5 Division of International Medicine and
Infectious Diseases, Weill Medical College of Cornell University, New York,
New York, United States of America

Abstract Top


Leptospirosis has become an urban health problem as slum

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I Home BrOMIU~e Artll~eS 0 or eaffers For AUTHOR ana Reviewers journals HUlDS iFLOS.Org Illlc'll

lurn all highlightt^ I nB_ li.ibi'' | institution | asf l person place I prolein taxon
To I Abstract | Author Summary Introduction I Methods I Results I Discussion I Supporting Information I Acknowledgements References I Data Fusion Supplements

Impact of Environment and Social Gradient on in Urban Slu documentsummary

Renato B. Reis 1# Guilherme S. Ribeiro Francisco S. Santana 1.2, Sharif Mohr 1, Astrid X. T. 0. Melendez 1,
Adriano Queiroz Andrbia C. Santos 1, R., Wagner S. Tassinari Marilia S. Carvalho 3, Mitermayer G. Reis Albert I. Ko 1,
I Centro de Pesquisas Goncalo Moniz, Fundacao Oswaldo Cruz, Ministerio da Saude, Salvador, Brazil 2 Secretaria Estadual de Saude da Bahia, Salvador, Brazil 3 Escola Nacional da Saude Publica, Fundacgo
Oswaldo Cruz, Minist6rio da Sadde, Rio de Janeiro, Brazil 4 Universidade Federal Rural do Rio de Janeiro, Rio de Janeiro, Brazil 5 Division of International Medicine and Infectious Diseases, Weill Medical
College of Cornell University, New York, New York, United States of America



l has become an urban health problem as slum settlements have expanded worldwide. Efforts to identify interventions for urbanhave been hampered by
the lack of population-based information on Leptospira transmission determinants. The aim of the study was to estimate the prevalence of and identify risk
factors for infection in the urban slum setting.

Methods and Findings

We performed a community-based survey of 3,171 slum residents from -.;I., a.l.:.. Ei ii Leotospira agglutinating antibodies were measured as a marker for prior infection. Poisson
regression models evaluated the association between the presence of .ep0o3p"-r antibodies aId ci_,. ..ii,,ei.tr l arr ,,iurI: obtained from Geographical Information System surveys
and indicators of socioeconomic status and exposures for individuals. CO. raii pr.r. alen.e .r Leptosp.r antibodies **. a: 1 4% (95% confidence interval [CI], 14.0-16,8). Households
of subjects with clustered in squatter areas at the bottom of valleys. The risk of acquiring was associated with household environmental
factors such as residence in flood-risk region ?F ith open sewers (prevalence ratio [PR] 1.42, 95% CI 1,14-1,75) and proximity to accumulated refuse (1,43, 1,04-1,88), sighting
rats (1.32, 1,10-1,58), and the presen:- .:.r chickens (1,26, 1.05-1.51). Furthermore, low income and black race (1.25, 1.03-1.50) were independent risk factors. An increase of
US$1 per day in per capital household income was associated with an 11% (95% CI 5%-18%) decrease in infection risk.


Deficiencies in the sanitation infrastructure where slum inhabitants reside were found to be environmental sources of Leptospira transmission. Even after controlling for
environmental factors, differences in socioeconomic status contributed to the risk of indicating that effective prevention of t may need to address
the social factors that produce unequal health outcomes among slum residents, in addition to improving sanitation.

Resume portugues Portuguese Abstract

Resumo traduzido para no portugues pelo Dr Guilherme Pibeiro (Abstract translated into Portuguese by Dr Guilherme Pibeiro1.

Author Summary

B, a life-threatening has become an important urban slum health problem. Epidemics of now occur in cities throughout the developing v

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WT MC MR. Top I Abstract I Author Summary I Introduction I Methods I Results I Discussion I Supportinq Information I Acknowledgements I References I Data Fusion Supplements


Citation typing and downloadable reference list
The citations in this paper have been typed using terms from CiTO, the Citation Type Ontology, an ontology for describing the nature of reference citations in scientific research articles and other
scholarly works on the Semantic Web. CiTO was created by Da .d Shotton with assistance from I atle Portwin and Aliltair Miles, and is available from http://purl.org/net/cito/, which uses content negotiation
to deliver to the user an OWLDoc Web version of the ontology if accessed via a Web browser, or the OWL ontology itself if accessed from an ontology management tool such as Prot6g6
In consultation with the authors of this article, each cited reference has been assigned:
(a) One or more CiTO terms describing the relationship between this citing paper and the cited work, from the point of view of this citing paper (Relationship Object Properties in CiTO).
(b) A CiTO term describing the nature or type of the cited work (Sub-classes of Work in CiTO).
(c) A CiTO term describing the nature or type of the expression of the cited work (Sub-classes of Expression in CiTO).
(d) A CiTO term describing the nature or type of the manifestation of the cited work's expression (Sub-classes of Manifestation in CiTO) (Optional used where useful),
(e) A CiTO term describing the peer review status of the cited work (Boolean true / false value of Object Property peerReviewed in CiTO).
The human-readable terms used here are the labels of the respective object properties and classes within CiTO, 'humanized' by the addition of spaces to make them more readable (e.g. Journal Article
rather than JouralArticle),
This citation typing information is revealed in the reference list below by clicking the Turn citation typing on button below.
The complete reference list from this article, with these citation typings and with metadata recording numerical citation frequency information, is downloadable in RDF (Notation3) from
doi:10,1371/iournal.pntd.0000228.x004, to which there is an additional link at the end of this document. The numerical citation frequency information includes both the number of in-text citations of each
referenced work within this article, and the number of citations each reference has received globally, as determined from Gooole Scholar and the ISI Web of Knowledge on 11 March 2009,

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1. United Nations Human Settlements Programme (2003) The challenge of slums: Global report on human settlements W London: Earthscan Publications Ltd. Link

2. Riley LW, Ko AI, Unger A, Reis MG (2007) Slum health: Diseases of neglected populations. BMC Int Health Hum Rights 7: 2. DOI PubMed PubMedCentral

3. Sclar ED, Garau P, Carolini G (2005) The 21st century health challenge of slums and cities. Lancet 365: 901-903, DOI PubMed

4. The General Assembly of United Nations (2000) United Nations Millennium Declaration. Link.

5. Bartram J, Lewis K, Lenton R, Wright A (2005) Focusing on improved water and sanitation for health. Lancet 365: 810-812. DOI PubMed

6. Ko AI, Reis MG, Ribeiro Dourado CM, Johnson WD Jr, Riley LW (1999) Urban epidemic of severe in Brazil. Salvador Leptospirosis Study Group. Lancet 354:
820-825, DOI PubMed

7. McBride AJ, Athanazio DA, Reis MG, Ko AI (2005) Curr Opin Infect Dis 18: 376-386. DOI PubMed

8. Bharti AR, Nally JE, Ricaldi JN, Matthias MA, Diaz MM, et al. (2003) : A of global importance. Lancet Infect Dis 3: 757-771. DOI PubMed

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Adventures in Semantic Publishing: Exemplar Semantic
Enhancements of a Research Article

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David Shotton-, Katie Portwin, Graham Klyne, Alistair Miles
Image Bioinformatics Research Group, Department of Zoology, University of
Oxford, Oxford, United Kingdom

Abstract Top

Scientific innovation depends on finding, integrating, and re-using
the products of previous research. Here we explore how recent
developments in Web technology, particularly those related to the
publication of data and metadata, might assist that process by
providing semantic enhancements to journal articles within the
mainstream process of scholarly journal publishing. We exemplify
this by describing semantic enhancements we have made to a
recent biomedical research article taken from PLoS Neglected Tropical
Diseases, providing enrichment to its content and increased access
to datasets within it. These semantic enhancements include
provision of live DOIs and hyperlinks; semantic markup of textual terms,

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Published in the April 2009 Issue of
PLoS Comoutational Biology

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An official journal of the International Society for Computational Biology

ISearch articles ...

Session on

Special Interest Group
the Future of Scientific

Presentation made by David Shotton

At the ISMB-ECCB 2009 Annual Meeting
Stockholm, Sweden
June, 2009

Fundamental Shifts
Open Access Publishing

*Static document to living resource
*Journal level to article level
oPrepublication review and postpublication
*Reader/authors decide value and impact
*Community takes back the content
*Knowledge is shared globally to all who
choose to benefit

"My aim is to excite the imaginations
of researchers and publishers,
stimulating them to explore the
possibilities of semantic publishing
for their own research articles, and
thereby break down present barriers
to the discovery and reuse of
information within traditional modes
of scholarly communication."

David Shotton

Take Control of Your Research

1. Educate yourself about open access
2. Know your rights as authors

3. Publish your best work in

OA Journals

Tenure and promotion issues

* Still to early to evaluate impact
* May be more significant for future
funding at various sources (federal,
private, etc)


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