Björn Brembs, Freie Universität Berlin
http://brembs.net
http://www.slideshare.net/brembs/whats-wrong-with-scholarly-publishing-today-ii

1665: One journal: Philosophical Transactions of the Royal
Society of London (Henry Oldenburg)

• 24,000 scholarly journals
• 1.5 million publications/year
• 3% annual growth
• 1 million authors
• 10-15 million readers at >10,000
institutions
• 1.5 billion downloads/year
Source: Mabe MA (2009): Scholarly Publishing. European Review 17(1): 3-22

19th century publishing for a 21st
century scientific community

At least three different search tools to be
sure not to miss any relevant literature?

When we finally find the literature, we have
to ask friends with rich libraries to send it to
us?

We have to re-format our manuscripts every
time an ex-scientist tells us to submit to
another journal?

We have to pay ridiculous amounts of
money, just to find out who cited us, instead
of having that list directly on our papers?

We have to send hardcopies and CDs with
copies of the already submitted files by
express-mail to the publisher?

Every homepage has had an access counter
since 1993 but we don’t know how often our
paper has been downloaded?

Nothing happens when we click on the
reference after "we performed the
experiments as described previously"?

Nothing happens when we click on the
reference after "we performed the
experiments as described previously"?
First demonstration: 1968 WWW: 1989
Stanford Research Institute: NLS Tim Berners-Lee: CERN

Who„s to blame that our
publishing system is so lame?

We decide how and where to publish!

We are producers and consumers in
personal union!

We chose to outsource scientific
communication to publishers!

A public good in private hands

Rofecoxib=Vioxx (Merck)

“Merck paid an undisclosed sum to Elsevier to produce several volumes of
[Australasian Journal of Bone and Joint Medicine], a publication that had the look of a
peer-reviewed medical journal, but contained only reprinted or summarized articles—
most of which presented data favorable to Merck products—that appeared to act
solely as marketing tools with no disclosure of company sponsorship.”
“It was a stealth marketing campaign to Australian doctors under the guise of a regular
journal. “
The Scientist
“In issue 2, for example, 9 of the 29 articles were about Vioxx, and 12 of the remaining
were about another Merck drug, Fosamax. All of these articles presented positive
conclusions, and some were bizarre: like a review article containing just 2 references. “
Ben Goldacre, “Bad Science” The Guardian
“It has recently come to my attention that from 2000 to 2005, our Australia office
published a series of sponsored article compilation publications, on behalf of
pharmaceutical clients, that were made to look like journals and lacked the proper
disclosures. This was an unacceptable practice, and we regret that it took place.”
Michael Hansen, CEO Of Elsevier's Health Sciences Division

“Merck paid an undisclosed sum to Elsevier to produce several volumes of
[Australasian Journal of Bone and Joint Medicine], a publication that had the look of a
peer-reviewed medical journal, but contained only reprinted or summarized articles—
most of which presented data favorable to Merck products—that appeared to act
solely as marketing tools with no disclosure of company sponsorship.”
“It was a stealth marketing campaign to Australian doctors under the guise of a regular
journal. “
The Scientist
“In issue 2, for example, 9 of the 29 articles were about Vioxx, and 12 of the remaining
were about another Merck drug, Fosamax. All of these articles presented positive
conclusions, and some were bizarre: like a review article containing just 2 references. “
Ben Goldacre, “Bad Science” The Guardian
“It has recently come to my attention that from 2000 to 2005, our Australia office
published a series of sponsored article compilation publications, on behalf of
pharmaceutical clients, that were made to look like journals and lacked the proper
disclosures. This was an unacceptable practice, and we regret that it took place.”
Michael Hansen, CEO Of Elsevier's Health Sciences Division

“Merck paid an undisclosed sum to Elsevier to produce several volumes of
[Australasian Journal of Bone and Joint Medicine], a publication that had the look of a
peer-reviewed medical journal, but contained only reprinted or summarized articles—
most of which presented data favorable to Merck products—that appeared to act
solely as marketing tools with no disclosure of company sponsorship.”
“It was a stealth marketing campaign to Australian doctors under the guise of a regular
journal. “
The Scientist
“In issue 2, for example, 9 of the 29 articles were about Vioxx, and 12 of the remaining
were about another Merck drug, Fosamax. All of these articles presented positive
conclusions, and some were bizarre: like a review article containing just 2 references. “
Ben Goldacre, “Bad Science” The Guardian
“It has recently come to my attention that from 2000 to 2005, our Australia office
published a series of sponsored article compilation publications, on behalf of
pharmaceutical clients, that were made to look like journals and lacked the proper
disclosures. This was an unacceptable practice, and we regret that it took place.”
Michael Hansen, CEO Of Elsevier's Health Sciences Division

“Merck paid an undisclosed sum to Elsevier to produce several volumes of
[Australasian Journal of Bone and Joint Medicine], a publication that had the look of a
peer-reviewed medical journal, but contained only reprinted or summarized articles—
most of which presented data favorable to Merck products—that appeared to act
solely as marketing tools with no disclosure of company sponsorship.”
“It was a stealth marketing campaign to Australian doctors under the guise of a regular
journal. “
The Scientist
“In issue 2, for example, 9 of the 29 articles were about Vioxx, and 12 of the remaining
were about another Merck drug, Fosamax. All of these articles presented positive
conclusions, and some were bizarre: like a review article containing just 2 references. “
Ben Goldacre, “Bad Science” The Guardian
“It has recently come to my attention that from 2000 to 2005, our Australia office
published a series of sponsored article compilation publications, on behalf of
pharmaceutical clients, that were made to look like journals and lacked the proper
disclosures. This was an unacceptable practice, and we regret that it took place.”
Michael Hansen, CEO Of Elsevier's Health Sciences Division

• Name from Dutch publisher (1580):
“House of Elzevir”
• 250,000 articles per year in 2000 journals
• 7,000 journal editors, 70,000 editorial
board members and 300,000 reviewers
are working for Elsevier
• Part of Reed Elsevier group

Average periodical profit margin: 5%

2003 U.S. Sales (in billions)
Thomson L & R $2.639
Reed Elsevier $1.764
Wolters Kluwer $1.158
Other $1.250 (est) Thomson 38.75%
Reed Elsevier 25.90%
Total $6.811 Wolters Kluwer 17%
Other 18.35%

250
200
150
% Change
100 Subscription prices
CPI/inflation
50 Journals purchased
0
-50
1989
1993
1997
2001
1986
1987
1988
1990
1991
1992
1994
1995
1996
1998
1999
2000
2002
Modified from ARL

Chemistry $3,254
Physics 1,756
Astronomy 2,850
Engineering 1,548
Geology 1,724
Biology 1,323
Math & Computer Sci 1,278
Zoology 1,259
Botany 1,238
Health Sciences 1,132
Library Journal Periodical Price Survey, April 2006 Ray English
MPG: 18 Mio €/y for literature. 95% to the
three main publishers.

• People produce your product for you
• They check it for quality
• They’re even kind enough to give you their
intellectual property (copyright!)
• You polish it up and distribute it
• And you charge those same people handsomely to
make their product available back to them
• They think they must have your product, even
though they created it, so you’re free to raise
prices

What a magnificent ship! What makes it go?
Cartoon by Rowland B. Wilson

• Request increased
budgets
• Cut subscriptions
• Collective purchase of
electronic journals
• Rely on document
delivery or ILL
Ray English

Compared to now, was journal access 5 years ago…
60
40
20
0
lot worse worse same better much better
David Nicholas

• Substantial portion is
– funded by taxpayers
– supported publicly
– created in non-profit sector
• Journal literature is freely given away by
authors
• But journal publishing is largely under
corporate control
• A public good in private hands
Ray English

Peter Suber
“Open-access (OA) literature is
digital, online, free of charge, and
free of most copyright and licensing
restrictions.”

• First route: authors deposit copy of pre-print or post-print in
an “institutional repository” or other open web-site
– About 1400 open repositories already established world-wide
• Second route: authors publish in peer-reviewed journals
funded by publication charges rather than by library
subscriptions
– Over 4227 peer-reviewed open access journals now listed in the Lund
Directory of Open Access Journals www.doaj.org
ROAR
DOAJ
RoMEO

Traditional System
Subscriber Pays
Toll Access
Author
Page
Money Charges
Color Fees Information
Flow Publisher Flow
Subscriptions
Site Licenses
Pay-per-view Agent
Reprints
Library
Reader
Model adapted From Public Library of Science www.plos.org

Open Access System
Author-Pays Sponsor
Free Access
Money Flow Author
one time Information
publication charge Flow
Publisher
Library/Search Engine
Reader
Model adapted From Public Library of Science www.plos.org

Yesterday Today
Paper Bits and bytes
Brick and mortar libraries Cyberspace
Institute library address Uniform resource identifiers (URIs)
High cost of printing and distribution Publishing costs fallen by orders of
magnitude
Only comprehensible to a few humans Read and indexed by machines (e.g.,
Googlebot)
Restricted access to a few subscribers Increasingly public

www.scopus.com
www.pubmed.gov
http://ukpmc.ac.uk
isiknowledge.com
scholar.google.com
Duncan Hull

• Isolation
– each discipline has its own data silo
• Impersonal and unsociable
– “who the hell are you”?
– Where are “my” papers? (authored by me, or of interest to me)
– What are my friends and colleagues reading?
– What are the experts reading? What is popular this week / month /
year ?
• “Cold”: Identity of publications and authors is inadequate
• Obsolete models of publication, not everything fits publication-sized holes
– Micro-attribution
– Mega-attribution
– Digital contributions (databases, software, wikis/blogs?)
Duncan Hull

How can I find anything?
Identity Crisis

1. http://pubmed.gov/18974831
2. http://www.ncbi.nlm.nih.gov/pubmed/18974831
3. http://ukpmc.ac.uk/articlerender.cgi?accid=pmcA2568856
4. http://ukpmc.ac.uk/picrender.cgi?artid=1687256&blobtype=pdf
5. http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000204
6. http://www.dbkgroup.org/Papers/hull_defrost_ploscb08.pdf
7. http://dx.doi.org/10.1371/journal.pcbi.1000204
• One paper, many URIs. Disambiguation algorithms rely on getting metadata for each
– Big problem for libraries is these redundant duplicates
• Matching can be done by Digital Object Identifier (DOI) and PubMed ID (PMID);
– these are frequently absent < 5% (Kevin Emamy, citeUlike)
Duncan Hull

• Difficult with fragmented information silos
• Several initiatives
• Crossref: DOI, ContributorID
• PubMed: PMID
• …

• Machine-readable meaning
• Technically non-trivial
• Promising progress
Tim Berners-Lee
http://www.w3.org/2000/Talks/1206-xml2k-tbl/Overview.html

URI Uniform Resource Identifier, like:
http://id.animals.edu/mammal/dog
+ XML Customized tags, like:
<dog>Nena</dog>
+ RDF Relations, in triples, like:
(Nena) (is_dog_of) (Kimiko/Stefan)
+ Ontologies Hierarchies of concepts, like
mammal -> canine -> Cotton de Tulear -> Nena
+ Inference rules Like:
If (person) (owns) (dog), then (person) (cares_for) (dog)
= Semantic Web!

Or filter failure?
Information (Overload) Crisis

• Publish or Perish: number of
publications
• Where are you published?
– ~24,000 scholarly journals (~6,000 with IF)
– ~1.5 million publications/year
– 60-300 applicants per tenure-track position
• Reading enough publications is
impossible!

• Thomson Reuters: Impact Factor
• ScImago JournalRank
• Eigenfactor

Publikationstätigkeit
(vollständige Publikationsliste, darunter Originalarbeiten als Erstautor/in,
Seniorautor/in, Impact-Punkte insgesamt und in den letzten 5 Jahren,
darunter jeweils gesondert ausgewiesen als Erst- und Seniorautor/in,
persönlicher Scientific Citations Index (SCI, h-Index nach Web of
Science) über alle Arbeiten)
Publications:
Complete list of publications, including original research papers as first
author, senior author, impact points total and in the last 5 years, with
marked first and last-authorships, personal Scientific Citations Index
(SCI, h-Index according to web of science) for all publications.

There is no replacement for
reading papers!

• Who knows what the IF is?
• Who uses the IF to pick a journal
(rate a candidate, etc.)?
• Who knows how the IF is calculated
and from what data?

• 50,000 employees
• US$600 million profit/quarter
• Thomson family owns 53%
• €30,000-130,000/year subscription rates

Introduced in 1960’s by Eugene Garfield: ISI
citations articles
2008 2006 and 2007
IF=5
Articles published in 06/07
were cited an average of 5 times in 08.

Journal X IF 2008=
All citations from Thomsons Reuters journals in 2008 to papers in journal X
Number of citable articles published in journal X in 2006/7

• Negotiable
• Irreproducible
• Mathematically
unsound

• PLoS Medicine, IF 2-11 (8.4)
(The PLoS Medicine Editors (2006) The Impact Factor Game. PLoS Med 3(6): e291.
http://www.plosmedicine.org/article/info:doi/10.1371%2Fjournal.pmed.0030291)
• Current Biology IF from 7 to 11 in
2003
– Bought by Cell Press (Elsevier) in 2001…

• Rockefeller University Press bought their
data from Thomson Reuters
• Up to 19% deviation from published records
• Second dataset still not correct
Rossner M, van Epps H, Hill E (2007): Show
me the data. The Journal of Cell Biology, Vol.
179, No. 6, 1091-1092
http://jcb.rupress.org/cgi/content/full/179/6/1091

• Left-skewed distributions
• Weak correlation of individual article citation
rate with journal IF
Seglen PO (1997): Why the impact factor of journals should not be used for evaluating research. BMJ 1997;314(7079):497 (15 February)
http://www.bmj.com/cgi/content/full/314/7079/497

“Nearly all the grandest discoveries
of science have been but the rewards
of accurate measurement”

• Expensive
• Why Thomson?
• IF from what year?
• No correlation
• Why not actual citations?

Where you publish is more
important to us than what you
publish!

refworks.com
zotero.org
hubmed.org mendeley.com
2collab.com
connotea.org citeulike.org
Re-couple metadata that has be de-coupled from data
www.mekentosj.com
“iTunes for PDF files”

Your article:
• Received X citations (de-duped from Google
Scholar, Scopus, and Web of Science)
• It was viewed X times, placing it in the top Y% of
all articles in this journal/community
• It received X Comments
• It was bookmarked X times in Social Bookmarking
sites
• Experts in your community rated it as X, Y, Z
• It was discussed on X ‘respected’ blogs
• It appeared in X, Y, Z International News media
Peter Binfield

• Largest journal in the PLoS group
– 2 ½ years old
• Almost doubling in volume each year
– 2007: 1,231 articles
– 2008: 2,722 articles
– 2009: ~4,300 articles
– 2010: ~1% of PubMed?
• Largest journal in the world
• More than 800 Academic editors
• More than 30,000 authors
• Fully peer reviewed
– but the review / acceptance process does not concern
itself with „impact‟, „novelty‟ (or other subjective
measures)

"Not everything that can be counted
counts, and not everything that
counts can be counted."

• Won„t go away
• Should always be a last resort
• They are much too valuable to be satisfied
with the current pitiful state of affairs
• Let„s make them as good as we possibly can!

• No more publishers – libraries archive everything according
to a world-wide standard
• Single semantic, decentralized database of literature and
data
• Personalized filtering
• Peer-review administrated by an independent body
• Link typology for text/text, data/data and text/data links
(„citations“)
• Semantic Text/Datamining
• All the metrics you (don„t) want (but need)
• Tagging, bookmarking, etc.
• Unique contributor IDs with attribution/reputation system
(teaching, reviewing, curating, blogging, etc.)
• Technically feasible today (almost)
http://www.slideshare.net/brembs/whats-wrong-with-scholarly-publishing-today-ii