Electronic Publishing of Scientific Manuscripts
Stephen R. Heller
USDA, ARS
Beltsville, MD 20705
steve@hellers.com
Introduction
To write a chapter about a topic which is so new and developing so rapidly that
changes take place just about everyday is an interesting challenge. What I hope to
accomplish in these few pages is to explain what electronic publishing is and explore a
number of issues associated with this new area of information dissemination. Yes!, this
is a new area of dissemination! And perhaps this is the place to start - by defining
electronic publishing. Electronic publishing is a new form of communication.
Electronic publishing, for the purposes of scholarly scientific presentation of results, is
the creation of a scholarly work which is in a totally electronic (non-paper) form from its
creation to its publication or dissemination. An electronic journal is a product that was
specifically developed and designed for the Internet, a product which is not re-worked
printed material that is delivered electronically. As I hope to show in this chapter,
electronic journals and electronic publishing is much more than an alternative to print.
Electronic publishing is the way of future, but not the only way. Printed materials
will not disappear in the future, just as speech did not disappear when books were first
published. Print will have its place in the future (1) as the paperless office is likely as the
paperless bathroom. Electronic journals, and their relatives, the digital libraries, will
likely still be a H.G. Wells dream of the future for much of the next century (2). But
while this future world may be years away, electronic journals can make a difference and
an improvement in the very near future. Among the unique benefits and value to
electronic publishing is to make scientific research available more quickly, at a lower
cost, and to more people, especially scientists from non-developed countries. Electronic
publishing can reduce the gap between the have's and the have not's in science.
In the past few years there has been much written about electronic publishing and
the creation of digital libraries of all books and journals by both scholars and authors (3).
Most publishers of scientific and technical journals have or are currently making virtually
all of their print publications available in electronic form (4). This is all very nice and
useful, but only to a very limited point. What the publishers are providing are not
electronic publications, but rather electronic versions or electronic clones of their print
products. None of the products they are providing are products developed specifically for
electronic dissemination. The products are, for the most part, just a reworking of their
existing print products, with the added costs of electronic conversion and manipulation
being added to price charged to the reader. There currently are some minor
enhancements, such as Internet "hot links" to abstracts as the Journal of Molecular
Biology has some links to Medline (5), and the CLIC project of the UK e-Lib program in
the UK which adds some molecular structures and manipulation capability to already
published print articles. (6).
The reason for this lack of imagination and conservative approach is, in the
opinion of the author, due to two factors. One is a lack of understanding of this new
medium of information dissemination, and the second is the concern that of how to
continue their current level of income in electronic publishing. The goal of this chapter is
provide the reader with a better understanding of what will be technically feasible in the
area of electronic publishing in the near future. Included in this will be some discussion
of the non technical issues, primarily the sociological ones.
Background
Scientific journals have been around for over 300 years, when the Philosophical
Transactions of the Royal Society of London began publication (7). Scientific journals
were first published by learned societies and only in the 20th century did commercial
publishers become a factor. It was primarily after World War II, when English took over
as the international language of science, that the local learned societies in Europe did not
respond to this, and local language journals began their slow decline, coupled with the
growth of English language journals from commercial publishers in the USA, Europe,
and elsewhere. What follows is first what substantial benefits electronic journals can
(and soon will) provide to both the author and reader of a journal article. A few short
comments are presented about peer review and copyright, followed by a description of
those currently existing electronic journals in chemistry. Lastly a detailed outline of a
new completely electronic journal in chemistry, the Internet Journal of Chemistry, is
described in detail, as its' characteristics and features are truly in keeping with the future.
Benefits of Electronic Journals
Electronic Journals, and to a much lesser extent the electronic editions of print
journals, offer much to both the author and reader. The author benefits from the ability to
publish much more quickly, to not be limited by the constraints of the number of print
pages the publisher has budgeted for that year, to use color to emphasize certain aspects
of a structure, chemical reaction, apparatus, or instrument. Authors can include computer
readable copies of their computer programs so that readers can actually use the program
on their own data. Authors can include data, full spectra, and other experimental
information to make their presentations and arguments even stronger. 3-D structures can
be rotated in space so that the reader can see what the author wants to present - and then
with a bit more manipulation, perhaps the reader can see even more or take another
approach and view to the structure. In chemical education areas one can add sound to an
experiment section, so that the reader can hear as well as see what is going on. In
chemical reactions the author can present full motion videos making it easier for the
reader (be they a researcher or a student) to see what is happening. While I would be
delighted to give examples of some of these in this chapter, being a printed publication
this is not possible. Or put another way, print can shows "dead" or frozen information,
while an electronic manuscript can be a "alive".
One of the greatest assets to chemists is the extensive and broad literature at our
disposal. Chemists have long realized the value of this treasure, developing in-depth and
broad indices since the turn of the century. The vast majority of the chemical literature
appears as page oriented, printed journal articles, communications and reviews. The
advent of the Internet offers a new avenue for chemists to describe and
disseminate their
research. Traditional print media is in fact quite limited in its ability to present much
information of value to chemists. Foe example:
1. Molecules are three-dimensional objects which are difficult to represent in
two-dimensions. An author must choose a single representation, which might not be of
interest to all potential readers of an article. Associated structural information is often
lost, such as bond distances and angles. This is particularly acute in the area of x-ray
crystallography.
2. Publication costs of color images are quite staggering and usually discouraged,
and certainly discouraged in large numbers. Color is often useful in representing a third
(or fourth) dimension, such as in electron density maps, multi-dimensional NMR, protein
structures, and so forth.
3. Dynamical processes are impossible to represent in print. The solution is the
publication of video and/or movies.
4. With the increased cost of publication and demands to restrict article length,
spectra, spectral data, and large data files are, at best, placed in supplementary material,
are presented in a highly abbreviated form, or are deleted outright. Related to this is the
ability to store online numerical results, input data, computer output, and so forth, ready
for the reuse without retyping for further processing.
5. With publications not limited by (page) space electronic journals can
include comments, criticisms, and author replies to all published manuscripts. This
interactive communication between authors and readership allows for points to be
clarified, extensions to be drawn, and collaborations to be born. Electronic journals will
be able to facilitate these exchanges, thereby enhancing the impact of these new
publications.
Peer Review
Fear that the Internet will be littered with alchemy and not chemistry. Fear that
peer review will be abolished. These are valid, but mostly unfounded concerns that many
people have voiced. "Will Science Publishing Perish" is an extreme example of a red
herring, which was published by the American Chemical Society in 1996 (8). In fact,
there is no reason to think the journals (printed or electronic) of the future will have more
or fewer errors, more or less duplication, or more or less manuscripts withdrawn owing to
fraud and related misrepresentation. Considering the sad state of book sales in science
and the popularity (and low cost) of (non peer-reviewed) technical magazines (many of
which are of good and useful quality), not everything published (and widely read and
used) today has been put through the peer review process. Yet there is no outcry about
science publishing perishing. There is only an outcry about protecting the publishers turf,
income, and monopolistic position in disseminating scientific information.
Copyright
While it was in 1465 that Gutenberg first invented the printing press, it was until
1709 that the first copyright law was passed in England (9). While copyright has played
an important role in the financial aspects of publishing for almost 300 years, it is not clear
that copyright is the way of future of financial stability and success in electronic
publishing. Copying information in electronic form is such a basic and inherent part of
the technology that apply 300 year old concepts are likely to fail. There has been much
written and said about copyright, but it would not surprise many people if this becomes a
non-issue in electronic publishing the near future. Certainly as long as there are print
publications, there will be copyright, but a separate form of intellectual property rights or
information rights need to be developed for this medium. Functionally what is needed is
some form of protection so that the people or organizations can recover their costs and
either earn a living or make a profit to stay in business. Thus, no further discussion of
copyright will be included in this chapter.
Existing Electronic Journals
In 1996 the Association of Research Libraries published a printed directory of
Electronic Journals, Newsletters, and Academic Discussion Lists (10). The list consisted
of 1093 electronic journals or magazines and 596 electronic newsletters and electronic-serials. However upon just a cursory examination of this large number of items, there are
actually just a handful of peer-reviewed scholarly publications which are purely
electronic (and hence meet the definition of an electronic journal given at the beginning
of this chapter). In chemistry there are no fully electronic journals listed. Of the journals
that approach being fully electronic there are:
1. Chemical Educator
2. Journal of Molecular Modeling
3. Molecules
4. Electronic Journal of Theoretical Chemistry
The Chemical Educator, a Springer-Verlag journal, is a peer-reviewed journal for
educational professionals (4b). An archival CD-ROM version is planned. While it
claims to exploit the capabilities of the Internet, the journal really only stresses the ability
to publish more quickly and to be able to search and access material more quickly. While
the journal purports to cover areas including experiments, there is no information or
suggestion that authors consider the multi-media capabilities of the Internet to accomplish
this as evidenced by allowing authors to submit paper-based, hard copy manuscripts. The
non-electronic or print mentality is also seen in the use of the phrase "color photograph"
as opposed to "color image". The journal "will welcome, but does not require, the
submission of a short videotaped example of a successful demonstration". Submission of
manuscripts by providing an Internet url is not listed as an option. Supporting video
segments (asked to be kept short (less than one minute) owing to possible very large files
are considered as independent supplemental materials and are not part of the peer-review
process for the manuscript, but rather are reviewed separately. Overall it would appear
that while there are clear positive aspects to this journal, the print media "culture and
history" will limit its effectiveness. Further, by mixing electronic and print, coupled with
the existing processing scheme for handling manuscripts, no cost savings would be
expected. Lastly, by publishing bimonthly (six issues a year), the print culture mentality
delays, rather than speeds up, the publication of every article until the next "issue" is
ready to "go to press".
The Journal of Molecular Modeling, another Spring-Verlag journal, is very
similar in nature to the Chemical Educator in its policies and practices (4b). It is
described as "the first fully electronic journal in chemistry - the advanced way of
publishing. The Journal of Molecular Modeling further states it is "the first journal in
chemistry to offer network, print based, and CD-ROM editions. The Journal is fully
citeable with CAS-abstract, ISI citation and ISSN (0948-5023)." (4b) It does not state
how a printed based journal is fully electronic. Again, articles are not published when
ready (after peer-review and corrections), but rather as part of the print mentality of a
regular monthly issue.
This journal does already have a few clear benefits. The two main features of
value to the reader of this journal are that structures often come with x,y,z coordinate files
so they may be download and manipulated by the reader and there is a much more
rapid publication time for an article which means that means new information is made av
available much more quickly to the reader.
The Springer-Verlag journal Molecules has the same editorial policies and
procedures as the Journal of Molecular Modeling (4b) with regarding to manuscript
submission and processing and having a hard-copy edition.
The John Wiley & Sons journal, the Electronic Journal of Theoretical Chemistry
(ETJC) is similar to the above three journals, but there are some small differences (4a).
According to there Internet home page "EJTC publishes in electronic form only. The
publication model will be article by article with no preset frequency. New articles will be
announced on the EJTC Home Page and subscribers will be alerted by e-mail. An annual
CD-ROM archive of all manuscripts published during the year will form part of the
subscription package. Table of Contents and other information are available without
subscription via the `public access' area of the EJTC Home Page." (4a) While the table of
contents are free to non-subscribers, software and book reviews can be read only by
subscribers.
As to the ETJC being electronic, in the submission information it is noted that
"For the time being, we must have hard copy in addition to electronic submissions" (4a)
and "Changing proofs: proofs will be supplied to authors to ensure that no errors have
been introduced during processing, not to permit the introduction of new material. No
page charges will be leveled against the authors or their institution." (4a). In addition all
papers are readable only using the Adobe Acrobat reader; it is not possible to read a
manuscript using a web browser (such as Netscape or Explorer). All manuscripts are
print page oriented and have page numbers. These statements would seem to indicate the
publisher and editors have not yet freed themselves from the paper and the print
mentality.
Are these four journals really new and different? Do they offer something or
enough for authors to submit sufficient high quality manuscripts to enable these journals
to succeed and survive? In a few years the answer will be known.
A New Electronic Journal in Chemistry
While there are many sociological problems with having a truly all electronic
journal, from both the point of view of the authors who write the manuscripts, the
librarians who purchase most of the journals, and the scientists who read the published
journal articles, there is one new journal which is going ahead and starting to publish,
using the definition of an electronic journal which was given in the opening paragraph of
this chapter. Before describing this new journal, it is useful to comment on the concerns
of authors, readers, and librarians on such a radically different journal. As is well
known, the purpose of a journal is not just to be used as proof of competence and
justification for promotion and salary reward. The scholarly work in a journal is also a
record of the science which was performed and the conclusions which were found and the
place where scientists go to read about a particular subject matter of interest to them.
Librarians, as well as scientists, want to be able to know these scholarly works will be
there for future generations. In the case of a fully electronic journal there is considerable
concern about the future of this medium. Hence the potential reluctance of both the
scientist to publish in such a journal and the librarian to use precious and dwindling
resources to purchase it. Put another way, the electronic journal, representing change
(and hopefully progress) is anti-establishment. However, change, besides being difficult,
is mostly inevitable. In the case of electronic, the increasing costs, now and projected
into the future, make it clear to all parties involved, that something must be done. In the
case of the Internet Journal of Chemistry (IJC), the technical (computer systems),
scientific, financial, and social issues are all being addressed, with the belief that this will
substantially increase the likelihood of success. With the cost of print and distribution
rising, along with labor, most, if not all, print journals (certainly as they are currently
produced and distributed) must have a short lifetime remaining.
The Internet Journal of Chemistry (IJC)
The following has been primarily extracted from the Internet home page of this
newly established journal (11) and describes how this journals will be new and different
and truly an electronic journal, not an electronic version of a print or print oriented
journal. I have chosen to use the material almost verbatim because it describes a likely
scenario and plan for the future of electronic journals. Also, at present it is the only such
journal of its kind, as indicated by the description and discussion above of the current
electronic type journals now available. While I am very confident that by the time this
chapter is published there will be other similar journals in chemistry, the Internet Journal
of Chemistry is highlighted here for both its value and uniqueness.
The aim of the Internet Journal of Chemistry is to promote the use of the Internet
and development of network resources to enable chemists to better communicate. This journal provides a mechanism for chemists to publish their research in developing new techniques, new resources, new databases, and so forth on the Internet for use by chemists. Further, the journal publishes chemical research that includes materials that are difficult if not impossible to include in a traditional journal, especially those articles
where the non- traditional presentation is essential in understanding the work. The journal
is aimed for all areas of chemistry, since the Internet media provides unique opportunities
for all disciplines.
The IJC Commitment to Technology
The Internet Journal of Chemistry strives to be at the forefront of Internet
technology. The editor and editorial board of the Internet Journal of Chemistry are
committed to providing the Journal with as broad an impact as possible. They are
continually developing new resources in conjunction with the journal that will enhance
the utility and value of the Internet Journal of Chemistry. Developing text and structure
search utilities and archival technologies is one of the goals of the journal. The journal
will incorporate the Chemical Markup Language (CML) (12) and become involved (and
strongly encourage others) in the development of browser plug-ins, Java Scripts (13),
external applications, etc. that will assist in communicating molecular science. The
Internet Journal of Chemistry will support development of SGML (14) with the aim of
assuring long-term archival retrieval. A major aim of the Journal is to promote the
development of these types of resources and to actively encourage their use throughout
the chemical community.
The Internet Journal of Chemistry will focus on the use of the Internet by
chemists. This includes both presentation of chemical research that benefits from
publication on the Internet and developments of Internet resources. All manuscripts will
be peer-reviewed, utilizing only all electronic means, such as e-mail to encourage rapid
turn-around. The Internet Journal of Chemistry will be published only on the Internet,
with all articles available in HTML (and later on in SGML). The Internet Journal of
Chemistry will not be available in any print page form, such as the Adobe Acrobat pdf
file format. Manuscripts will appear as they are accepted, bringing the article to the
reader as quickly as possible. There will be no individual issues, or page numbers, only
manuscript numbers (along with the associated url) and year of publication. The Journal
will provide long-term archival retrieval of the manuscripts both on the Internet and by
alternative means, such as CD-ROM and library archiving.
Publication on the Internet offers many advantages for chemists. Documents can
contain color graphics, movies, chemical structures, spectra, raw data, and so forth, most
of which is difficult (if not impossible) or prohibitively expensive to include in traditional
publications. The Internet Journal of Chemistry will publish articles in any and all areas
of chemistry which take advantage of the special attributes of the Internet. The journal
will publish chemical research results whose presentation and information-content are
significantly enhanced by utilizing the resources of a distributed computing environment.
This includes (but is not limited to) articles that incorporate hypermolecules, video,
VRML, spectra in downloadable files, and interactive programs using Java or CGI
scripts. The journal will encourage authors to include their raw data as supplementary
material that can then be accessed and manipulated by the reader. Again, due to the
nature of the Internet, these large data sets can be readily managed and distributed.
A principal aim of The Internet Journal of Chemistry is to provide a means for
publishing original research on the development and implementation of Internet
resources for chemists. This includes developments of databases and tools to access
them, proposals for new MIME types (15), proposals for file standards, new software for
handling Internet data, new visualization tools, development and implementation of
VRML (16) tools for chemists, etc. The journal does not intend to set standards or
become a clearinghouse for standards, rather it aims to provide an avenue for the
publication of proposals, protocols, etc. that may proceed to become standards.
This chapter has defined electronic publishing, discussed the value of this new
way to publish, highlighted some issues associated with this new method of
dissemination, gave examples of existing chemistry journals which approach being
electronic journals, and lastly described a new truly electronic journal for chemistry. The
goal of this chapter was to educate chemists about electronic publishing and lobby to
chemists into wanting to use this new method for publishing their scientific research in
the future and for reading articles which take advantage of this new technology. This
future of electronic publishing is new and exiting. It is going to be a change for the
better, it is something that will come slowly, but something which needs
to be started.
The sooner chemists adopt this new technology the sooner they will be able to benefit
from it.
References
1. Nunberg, G.; Representations 24, Spring 1993, 13-37.
2. Wells, H. G., World Brain, Meuthen, London, 1938.
3. (a) Olsen, J; Electronic Journal Literature - Implications for Scholars; Mecklermedia; Westport, 1994.
(b) Borman, S., C&E News, March 27, 1995. The url for this
article is:
http://pubs.acs.org/hotartcl/cenear/950327/art07.html
(c) Heller, S. R.; J. Chem. Inf. Comp. Sci., 1996, 36, 205-213.
(d) Bolman, P.; Logos, 1996, 7, 86-92.
(e) Bachrach, S. M., Proceedings of the 1996 International Chemical Information Conference; Collier, H., Ed.; Infonortics; Calne, UK, 1996, 135-139.
(f) Schatz, B. R.; Science, 1997, 275, 327-334.
4. For example, see the following web sites:
(a) http://www.wiley.com
(b) http://www.springer-ny.com or
http://www.springer.de
(c) http://www.elsevier.com or http://
www.elsevier.nl
(d) http://www.apnet.com or
http://www.europe.apnet.com
5. The Journal of Molecular Biology url is: http://www.hbuk.co.uk/
6. More information on the CLIC project can be found at the following urls:
http://chemcom.clic.ac.uk/clic/
http://chemistry.rsc.org/rsc/clic.htm
7. Development of Science Publishing in Europe; Ed. Meadows, A. J., Elsevier,
Amsterdam, 1980.
8. "Will Science Publishing Perish? The Paradox of Contemporary Science Journals",
ACS Publications, Washington DC, 1996.
9. Goldstein, P.; Copyright's Highway; Hill & Wang; New York; 1996, page 43
10. Directory of Electronic Journals, Newsletters and Academic Discussion Lists;
Association of Research Libraries, 6th Edition, Ed. Mogge, D. Washington, DC;
1996.
11. http://www.ijc.com or http://ijc.com I would like to thank the Internet Journal of
Chemistry(IJC) Editor, Steven Bachrach for permission to quote extensively from
the IJC information material.
12.CML is an SGML-based approach to managing molecular information, especially over the Inter- and Intra-networks. For more information look at the url: http://www.venus.co.uk/omf/index.html and http://www.ch.ic.ac.uk/cml
13. Java is Sun Microsystems object-oriented, cross-platform programming language. For more information look at the url: http://www.sun.com/java
14. SGML is the abbreviation for Standard Generalized Markup Language. SGML is the parent language to HTML. SGML allows one to put more information in a markup of a document (in this case a scientific manuscript) so that it describes all the data elements (author, title, abstract, references, etc.) It is for this reason, that SGML describes the content and structure of your data independent of any output format, one can easily convert from SGML to any composition, presentation, or data management format, making SGML excellent for archive storage.
15. Henry Rzepa has done extensive work on MIME (Multipurpose Internet Mail Extensions). Rzepa H.; Science and the Internet : The World Wide Web, Science Progress, 1996, page 97. For an electronic copy of the manuscript look at the url: http://www.ch.ic.ac.uk/rzepa/science/
16. Virtual Reality Modeling Language (VRML). For an excellent general description of
VRML see Kreiger, J.; C&E News, December 9, 1996. The url for this article is:
http://acsinfo.acs.org/hotartcl/cenear/961209/virtual.html