E-biomed

From: Harold_Varmus@nih.gov
Date: Thu Apr 22 1999 - 21:52:57 BST


 I have been continuing to think about more effective use of electronic
methods for disseminating the results of biomedical research. I hope that
you will read this latest draft proposal and send me any comments by email.
Thank you.

            APRIL 22, 1999 DRAFT

           E-BIOMED: A PROPOSAL FOR ELECTRONIC PUBLICATION
                     IN THE BIOMEDICAL SCIENCES
           http://www.nih.gov/welcome/director/ebiomed/ebiomed.htm

Comments: http://www.nih.gov/welcome/director/ebiomed/comment.htm

Prologue

Electronic communication is making dramatic changes in the way information
is exchanged among scientists, including biomedical scientists. Indeed,
many such changes have already happened and are continuing to happen at a
rapid rate. Over the past decade, steeply increasing numbers of
scientists on all continents have abandoned traditional mail and faxes in
favor of electronic mail. Many log-on to GenBank and many other data
repositories on a nearly daily basis. The titles and abstracts of
papers published in most scientific journals are available "on line" from
the date of publication and sometimes even before; some full texts can be
accessed electronically and downloaded, with or without subscription fees;
and convenient, freely accessible resources, such as PubMed
(http://www.ncbi.nlm.nih.gov/PubMed/), provide powerful engines for
searching the biomedical literature. In at least one field, physics,
preprints are made freely available electronically to interested readers,
through a server called "e-print"
(http://xxx.lanl.gov). In other fields, including biology, many
laboratories maintain World Wide Web pages that offer their colleagues
deeper views of the data that support published findings, describe methods
in detail, illustrate the most recent talks given by lab members, and serve
as important sources of specialized information and links to other Web
sites and citations.

Despite these welcome and transforming changes, the full potential of
electronic communication has yet to be realized. The scientific
community has made only sparing use thus far of the Internet as a means to
publish scientific work and to distribute it widely and without significant
barriers to access. Informative and even visionary essays have explored
this topic (see, for example, articles by Ginsparg
[http://xxx.lanl.gov/blurb/pg96unesco.html], Walker
[http://www.amsci.org/amsci/articles/98articles/Walker.html], and Harnad
[http://www.princeton.edu/~harnad/nature.html], and references cited
therein, as well as other recent proposals
[http://library.caltech.edu/publications/scholarsforum and
http://www.arl.org/newsltr/202/intro.html]).

In this essay, we propose a system for electronic publication of new
results and ideas in the biomedical sciences. We do this with the
conviction that such means of publication can accelerate the dissemination
of information, enrich the reading experience, deepen discussions among
scientists, reduce frustrations with traditional mechanisms for
publication, and save substantial sums of public and private money.

Before describing our proposal, it is important to acknowledge the
strengths of the current system for published scientific work, because it
has served the scientific community well for over 300 years. Printed
journals, particularly the few hundred leading representatives, do more
than just transmit results to our community. They subject the reports to
peer review and editing, a process that reassures busy readers that papers
have been carefully scrutinized and affords the authors an opportunity to
improve their work based on the (generally anonymous) advice of their
colleagues. The perceived hierarchy of the journals can be useful for
conferring status and grounds for career advancement on the authors of
papers accepted by the most prestigious journals, and it provides a useful
guide to readers besieged by the proliferation of published work.
Moreover, current journals often present their reports in attractive
formats, bound between colorful covers and accompanied by research
commentaries, reviews, and various kinds of news, advertisements, and
technical advice. In addition to being conducive to concentrated study,
pleasurable reading, and skimming, journals are usually convenient to
carry, fitting nicely into briefcases and adapting to activities like
riding the subway or sitting on the beach. Finally, their very existence
as "periodicals" implies a rhythm that can (in the best of circumstances)
stimulate anticipation of forthcoming issues and their contents.

No proposal to change the way scientists publish their results and ideas
should ignore these and other virtues of the current system. But we
believe that current practices also have many liabilities and that these
can be addressed by an evolutionary approach that need not threaten most of
the benefits attributable to the print-based publication system that is now
in place. More importantly, electronic publication can offer several
remarkable benefits that could never be achieved through the current
system. Many of these benefits depend on low-cost, barrier-free access
by scientists to all of the contributions of their fellow scientists in a
conveniently displayed electronic format.

A proposal for E-biomed

In the plan presented here, the National Institutes of Health----through
the National Center for Biotechnology Information, a component of the
National Library of Medicine at the NIH---would facilitate a
community-based effort to establish an electronic publishing site, called
"E-biomed." It is important to emphasize at the outset that in no sense
would the NIH operate as the owner or rule-maker for this enterprise. We
are proposing this plan in an effort to accelerate much-needed public
discussion of electronic publication in the United States and abroad and to
provide the financial, technical, and administrative assistance to initiate
such a program.

In the plan we envision, E-biomed would transmit and maintain, in both
permanent on-line and downloaded archives, reports in the many fields that
constitute biomedical research, including clinical research, cell and
molecular biology, medically-related behavioral research, bioengineering,
and other disciplines allied with biology and medicine. The essential
feature of the plan is simplified, instantaneous cost-free access by
potential readers to E-biomed's entire content in a manner that permits
each reader to pursue his or her own interests as productively as possible.
We have attempted to endow the plan with the flexibility necessary for
evolution as patterns of use become established and as new opportunities
for enriching the system are proposed. And we suggest a mechanism for
governance (the E-biomed Governing Board) that involves all of the parties
concerned---the scientific community (readers and authors), editors,
computer specialists, and funding agencies.

Copyright to reports posted in E-biomed would be retained by the authors,
with the provision that intact versions would be freely available for
transmission, downloading, and publication. Portions of reports could be
reproduced only with the permission of the authors.

Scientific reports in the E-biomed repository would be submitted through
either of two mechanisms, as described in more detail in the succeeding
sections. (i) Many reports would be submitted to editorial boards.
These boards could be identical to those that represent current print
journals or they might be composed of members of scientific societies or
other groups approved by the E-biomed Governing Board. (ii) Other
reports would be posted immediately in the E-biomed repository, prior to
any conventional peer review, after passing a simple screen for
appropriateness.

(i) Submission to E-biomed through editorial boards

The first of the two mechanisms that authors would use to enter new
scientific reports into the E-biomed database is closely aligned with
current practice and retains scientific review as a prerequisite to
publication. Authors would submit reports electronically to the central
server, requesting review by the editorial board of an indicated journal in
an appropriate field. If, after review, the report is accepted for
publication in either its original or a revised form, the edited version
would be posted immediately in E-biomed, and its title and list of authors
would appear for a fixed period in the current table of contents for that
journal. Later, it would continue to be accessible through the E-biomed
search engine or through the journal's home page, annotated with the dates
of submission, revision, and acceptance.

If an editorial board judges the report unsuitable for inclusion among its
own listings, the authors could resubmit the report for review by another
board, defer further attempts to disseminate the findings, or publish in
E-biomed through the alternative mechanism described in part (ii).

Electronic publishing provides an opportunity to offer a third outcome to
the review process, one that provides a novel solution to one of the most
commonly encountered problems in current editorial practice. If a
submitted report is deemed by an editorial board to be worthy of attention
by some segment of the scientific community, but judged not to meet the
criteria set for inclusion among a limited number of prime listings, the
editorial board could still accommodate the report by choosing to maintain
one or more additional listings. These additional listings might be
grouped by specialty or simply designated as a larger, less exclusive
version of the primary listing. Authors of reports that meet the criteria
set for these listings---which, while less prestigious, still denote review
and endorsement by the journal's editorial board --- could then elect
immediate posting in E-biomed.

 (ii) Submission to E-biomed through the general repository

Authors would also have the option of entering scientific reports directly
into the E-biomed repository without soliciting endorsement by the one of
its editorial boards. Before publication in the database, each report would
need to be approved by two individuals with appropriate credentials.
These credentials, to be established by the E-biomed Governing Board,
should be broad enough to include several thousands of scientists, but
stringent enough to provide protection of the database from extraneous or
outrageous material. (Such credentials might be membership on any
approved editorial board or receipt of a research grant from a reputable
funding source. The Governing Board would establish mechanisms to ensure
that authors need not personally know two validators in order to have their
submissions considered for deposition in E-biomed.)

Criteria for approval of reports must be sufficiently firm to guard against
gross abuse of the E-biomed repository, but sufficiently flexible to permit
rapid posting of virtually any legitimate work. At any time thereafter,
the authors would be free to solicit review and endorsement from a specific
editorial board as a means to provide greater prestige and visibility to a
paper. Alternatively, interest in such reports could be enhanced by
attaching to them informative commentaries written by other investigators.

Initially, some authors might hesitate to try this route or might use it
only to report information perceived to be difficult to publish in current
journals. With experience, however, this mechanism is likely to become
commonly employed because of its simplicity, flexibility, and speed;
because electronic search engines are much more powerful than visual
scanning of tables of contents to find relevant articles; and because other
instruments (novel peer review mechanisms, appended commentaries, citation
counts, and accession data) can be used to enhance the status and
prominence of a report.

Inherent and prospective benefits of E-biomed

We contend that establishment of the E-biomed system would deliver several
powerful benefits to the scientific community, with very little risk and
with the opportunity to supplement the system with further improvements in
the near future. In this section, we describe some of the advantages that
we envision.

Open access to scientific reports and assembly of personalized journals

The single greatest attraction of E-biomed is that all of its scientific
content will be available without barriers to any user with Internet
access. This will maximize the dissemination and use of research results.

All reports filed in E-biomed would be searchable by a single search
engine. In this way, all new entries that address topics important to any
single reader or laboratory could be highlighted on a routine (even a
daily) basis. Readers could also be alerted each time that the editorial
boards of greatest significance to them post new selections. E-biomed
would allow each user to invent his or her own "virtual" or personalized
journal, by downloading the reports he or she would like to read that week.
Browsing could be done electronically by scanning tables of contents for
selected editorial boards. But it is likely that browsing could also be
conducted with printed materials in more comfortable settings, perhaps by
using new magazines created as guides to E-biomed or existing journals that
add surveys of new E-biomed entries to their current services.

Improved format for publication of modern biology

More general use of electronic publishing through E-biomed would expedite
the wider use of methods of presentation that are now slowly gaining
acceptance at web sites and in supplements to print publications. With
the dramatic expansion of space, it will be possible to present much larger
data sets (including detailed photographs and movies), provide more
extensive analysis, and describe methods in the precise detail necessary to
recapitulate experiments. Moreover, electronic formats allow layered
viewing at increasingly greater levels of detail, so that readers can first
get a concise message and then pursue information in proportion to need and
interest. Publication in E-biomed would also offer many of the other
advantages that are now obvious from the transfer of journal articles into
electronically accessible forms: hyperlinks to relevant literature,
databases, and websites; registration for future retrieval of related
papers by interested readers; and other conveniences.

More rapid dissemination of scientific information

E-biomed would markedly speed up both the review and production processes
currently used in scientific publishing. This would be especially so for
reports that are entered directly into the E-biomed repository without
traditional editorial review. But even those reports reviewed and
listed by editorial boards would be available earlier to the reading public
because they would all be posted at the time of acceptance, eliminating the
lag time now ascribable to publication on paper. Moreover, many fewer
reports would be sequentially reviewed by more than one editorial board in
order to find a publishing outlet; this too would significantly decrease
the time that elapses between the drafting of a report and its transmission
to interested readers. It is also likely that more uniform electronic
publishing will speed the review period, because electronic methods will
probably be more generally employed to submit, transfer, review, alter, and
edit the reports. In fact, those editorial boards that develop the most
efficient and most accessible review processes will compete most
effectively for the best reports.

Reduced costs

Scientific journals are inherently costly. The price of publication and
distribution is presently levied on users in a variety of ways:
subscriptions to libraries and individual readers for print and electronic
versions; page charges to authors; and the time and labor required to
maintain and use libraries. (The expenses currently incurred by
institutions have recently been the subject of a much publicized scholarly
report---accessible at http://jan.mannlib.cornell.edu/jps/jps.htm---and
have even been held responsible for the decline in publication of academic
monographs [see "The New Age of the Book" by Robert Darnham in The New York
Review of Books, pp.5-7, March 18, 1999
http://www.nybooks.com/nyrev/WWWarchdisplay.cgi?19990318005F].)

While our proposal cannot eliminate all of the costs associated with
scientific publishing, movement to an electronic format is likely to reduce
those costs dramatically (see an essay by Odlyzko for one account
[http://www.research.att.com/~amo/doc/competition.
cooperation.pdf]). The most crucial effect of cost reduction would be the
opportunity to remove price as a barrier to individuals seeking any of the
vast information deposited in E-biomed. It would also offer savings to
individuals, laboratories, institutions, funding agencies, and the editors
and publishers who move to electronic formats.

Other possibilities

E-biomed is designed to evolve in ways that might affect the way we
practice science.

o In an electronic publishing system, it is possible to engage
electively in a more open reviewing process---one in which critiques of the
scientific reports are accessible and possibly signed. This development,
if widely accepted, could offer many benefits: more responsible reviews, an
instructive and ongoing public conversation about published work, and
career rewards for useful commentaries about work done by others. These
reviews could be part of the vetting process that awards authors with a
place on a table of contents of an E-biomed journal or they could be
post-publication reviews appended to entries in the general E-biomed
repository.

o E-biomed might serve as a communal site for posting notices of
meetings and job opportunities; for providing synopses---or even full texts
with illustrations---of talks presented at scientific symposia; and for
engaging in world-wide discussions of a variety of scientific and political
issues.

o Electronic publication could allow the amendment of reports,
permitting authors to transmit additional information that might not
warrant a separate report. Versions of reports containing supplementary
information would be announced and clearly denoted as such, while the
original versions are preserved as a 1.0 file for the historical record and
downloaded for safekeeping

^ The active E-biomed process might be accompanied by a much-needed
effort to convert material already published on paper to digital text and
image format, with hyper-linked citations. This additional initiative
would ultimately allow all users of E-biomed to move seamlessly through the
entire body of reported information in biomedical sciences. And it would
also enhance scientific productivity and reduce burdens on library
facilities.

  o One further, less tangible benefit might also occur as a
natural outcome of shared
            use of E-biomed: a heightened sense of community among
biomedical scientists.
            This might be conducive to the adoption of uniform standards
for sharing the data
            and providing access to the research tools described in
E-biomed.

How do we guarantee equity in the new system?

Although the current system of scientific publishing can be criticized for
lapses of fairness, it has, in general, served us well. Thus any new
system must be developed with concern for the ambitions of trainees,
little-known scientists, or scientists at less prestigious institutions or
foreign sites. Clearly, electronic communication has enormous advantages
for people in all of these categories, because it is a democratizing force
that makes distance and wealth nearly irrelevant. However, it is
important to ensure that opportunities to enter reports into E-biomed are
just as rich as the opportunities to access the reports filed by others.
The editorial boards and the Board of Governors will need to give careful
attention to this issue; for instance, it will be imperative to provide a
means for any author, however remotely located or poorly known, to have
access to two "members" of the system to validate reports submitted to the
general repository.

How should E-biomed get started?

We offer this proposal---and hope to publish it in a widely read
journal---with the goal of stimulating a much broader discussion of
electronic publishing before initiating E-biomed. In this way, we hope to
engage the editorial boards and publishers of existing journals, members of
scientific societies, and the entire scientific community in a vigorous
international discussion over the next few months.

Several questions should be addressed, while recognizing that satisfactory
answers to some of them can be obtained only by empirical tests of the
E-biomed proposal:

o Does the plan make sense? Is it likely to achieve the benefits
we ascribe to it?
           Are there other (better) ways to achieve them?

o How should E-biomed be financed and managed? The NIH is
prepared to provide
           funds and expertise to initiate the project. Should other
funding agencies, in the
           U.S. and abroad, also support it? Or should funds be
developed through other
           mechanisms, such as "submission charges" paid by authors?

o What should be the composition of the E-biomed Governing Board?
And how much
           authority should the Governing Board have over the functions of
editorial boards
           that participate in E-biomed? What responsibilities should
the Board have beyond
           developing rules of operation, producing an annual budget
projection, negotiating
           with groups asking to establish editorial boards, and resolving
disputes?

Once these and other questions have been considered, the NIH will
publicize an appropriately modified proposal, assemble the Governing Board,
and establish the E-biomed site with the Board's guidance.

Summary

The advent of the electronic age and the rise of the Internet offer an
unprecedented opportunity to change scientific publishing in ways that
could improve on virtually all aspects of the current system. The NIH
has addressed this opportunity by proposing a new system, E-biomed, that
has many advantages over the existing means of disseminating research
findings: open access, greater speed, reduced cost, and enhanced depth of
presentation. We now welcome constructive comments from the scientific
community, with the intention of putting a suitably revised plan into
operation in the near future.

Note: This draft was written by Harold Varmus, with active assistance from
David Lipman and Pat Brown, and advice from several others. Comments
will be gratefully received by email (varmus@nih.gov,
pbrown@cmgm.stanford.edu, lipman@ncbi.nlm.nih.gov)



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