CINF E-News
Volume 5 Number 1
Fall 2003
Edited byBruce Slutsky
Table of Contents
/ Editor's Note/ CINF Sponsors
/ Slides from the New York Meeting
/ Open Access Publishing
/ Photos from the New York Meeting
/ News about Awards
/ Applications for the CSA (Chemical Structure Association)
/ CINF Website in Transition
/ Publications Committee Report
/ Membership Report
/ CHMINF-L -- The Chemical Information Services Listserv
/ Chemistry Site Seeing (Web Sites of Interest)
/ Publisher Announcements
/ Chemical Abstracts Service
/ Highwire Press
/ CINF People in the News
/ News from other Professional Societies
/ Future Meetings
Editor's Note
by Bruce Slutsky
I hope that everyone enjoyed the recent ACS National Meeting in New York City. This was the first time since 1991 that the convention was held in the Big Apple. You could not have asked for nicer weather. It was a little strange for me to commute from my home in Queens to the Javits Center on the west side of Manhattan. It was nice to go to another city and just hop out of my hotel room and walk to the meeting. Some months ago I said on CHMINF-L that I would organize a trip to Shea Stadium to see a New York Mets game. Well, since the team played so poorly this season, I cancelled the event. It turns out that I had to go to work that night at the New Jersey Institute of Technology. So there are disadvantages to attending a national meeting in your home city.
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CINF Sponsors
submitted by Guenter Grethe
In 2003 the Division of Chemical Information again was fortunate to receive generous financial support from our sponsors to maintain the high quality of the Divisions programming at National ACS Meetings and to promote communication between members at Welcoming and Award Receptions.
The Division gratefully acknowledges contribution from the following sponsors:
Platinum Level / Chemical Abstracts ServiceMDL Information Systems, Inc.
Gold Level / ACS Corporation Associates
Derwent Information
Silver Level / Novartis
Bronze Level / Cambridge Crystallographic Data Center
GlaxoSmithKline
Contributor Level / Advanced Chemistry Development, Inc.
LION bioscience
Louisana Alliance for Biotechnology
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Slides from New York Meeting are Now Available for some Presentations
submitted by Kerryn Brandt
Slides from the CINF sessions at the Fall 2003 New York ACS meeting are being added to the CINF website as they are received. The slides, as PDF files, are available for the hyperlinked titles at the following URL:
This page is on an ACS development server as we continue work on moving the CINF website to a new home. The page can also be reached via the "Abstracts" link on the following page of the current CINF site:
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Open Access Publishing: A Report from the American Chemical Society Meeting, September 2003
submitted by Bonnie Lawlor, CINF Councilor
One of the many papers presented at the recent Fall national meeting of the American Chemical Society (ACS), held in New York City, NY from September 7-12, 2003, was a paper on open access publishing presented by Harold E. Varmus, co-founder of the Public Library of Science (PloS) and President and Chief Executive of the Memorial Sloan-Kettering Cancer Center. His paper focused on the coming revolution in the publication and dissemination of scientific works, and his intent was to persuade and encourage chemical scientists to participate in the movement of open access publishing.
Background
Varmus reviewed the evolution of print as the medium for scientific communication, beginning with the first printed journal in 1665 (Philosophical Transactionscontinually published and currently under the aegis of the Royal Society of Chemistry (UK)) -- to the present reality of thousands of scholarly and scientific journals.
The current publishing framework supports the peer review process, provides sophisticated indexing for access and retrieval, offers printed text for distribution, and a manageable format for archiving (print, microform). However, the costs associated with this print infrastructure have escalated and created what Varmus has described as a private library mentality as only those individuals and institutions who can afford subscriptions have ready access to current scientific communication. He contends that the Internet now provides the potential for developing the public library through which one electronic publication can be globally distributed and freely accessed by all. He listed the obvious attributes of this new publishing infrastructure as providing: 1) an improved format for data presentation; 2) a potential archive for both new and old publications; 3) a huge capacity for searching; and 4) an opportunity to build novel and innovative features into publications including multi-media. And he asked the audience to consider the difference between a printed genome database rather than the current electronic file that grows on a daily basis due to the direct input of researchers: Which model, he challenged, provides the better medium for access, retrieval and the rapid application of new ideas (and hence an acceleration in the scientific process overall)?
Varmus described what he termed the "Gutenberg Liabilities" of the print medium: The rising cost of print publications that is strangling libraries and resulting in the death of books; the high profit margins of print journals that, in his opinion, benefits only publishers; and the very obvious disadvantages of print versus electronic format in distribution and use.
Open Access Publishing
Varmus described open access publishing as publication on the web that allows for the full range of uses facilitated by the digital format free of charge, but subject to proper attribution. The publication is really an article (or a group of articles all peer reviewed) that is deposited immediately in a public online archive for access, search and retrieval. There is no elapsed time between publication and online availability. The potential benefits of this new publishing infrastructure were noted as follows:
Authors: / Their material is immediately available to the largest possible audience worldwide.Users: / They have access to all of the published literature, not merely affordable segments. They can download, copy, print and archive as needed. The ability to perform full-text searches and data mining is inherent in this model well beyond the limitations of standard Boolean text searches.
Current Online Publishing
Varmus pointed out that several online publishing models currently exist, but that he believes that their business models are less than optimum in the service of science. For example, while some publishers do provide free services to the poorest countries, most online journals require a paid subscription and are free only after a specified time period, and only if the publisher chooses to make them available. PubMed Central (also founded by Varmus when he was the Director of the National Institutes of Health (NIH), provides only limited open access as does BioMed Central which offers, as of this writing, 57 open access titles. Varmus argued that the Public Library of Science, of which he is a co-founder, offers the model with the greatest potential to ensure the broadest distribution of scientific research.
Public Library of Science (PloS)
This initiative was founded with a $9 million grant from the Gordon and Betty Moore Foundation in December 2002, as well as in-kind support from the Howard Hughes Medical Institute. The goals of this publishing project are to:
- Open the doors to the world's library of scientific knowledge by giving any scientist, physician, patient, or student anywhere in the world unlimited access to the latest scientific research,
- Facilitate research, informed medical practice, and education by making it possible to freely search the full text of every published article to locate specific ideas, methods, experimental results, and observations; and,
- Enable scientists, librarians, publishers, and entrepreneurs to develop innovative ways to explore and use the world's treasury of scientific ideas and discoveries.
The first journal --PLoS Biology-- will be published in October 2003, and a second in the field of medicine is planned for release in the Spring of 2004. Additional specialty titles and archival journals are planned for the future. The journals will cover material at the interfaces between biology, chemistry, medicine and mathematics. They will include opinion and commentary sections, and all material will undergo rigorous and constructive peer review. PloS Biology can also be ordered in print format with a charter subscription costing $160 for 15 issues (Allen Press). Varmus stated that PloS has a staff of excellent professional and academic editors, and that the project has been enthusiastically received within the scientific community. He believes that this project will overcome barriers to the introduction of novelty into the content and format of scientific publications.
How is this project funded? Well, in addition to the grant and in-kind support noted earlier, each submitted article is accompanied by $1,500 from the author (or the author's institution), under the assumption that publication of research results is part and parcel of the overall research expense. (BioMed Central has a similar structure, although their per author charge is $500). Varmus also stated that they have support from funding agencies, and that he firmly believes that they have a viable business plan. He commented that in the print model the average research article can require as much as $200K to produce, and he believes that when economies of scale are reached with the open access model, the cost of scientific communication will be reduced in aggregate. He has noted a growing movement towards open access publishing in other journals as well, and believes that the momentum for success has been created.
Resistance to Open Access Publishing
When asked what resistance the open access movement faces, Varmus noted that there are several challenges that must be overcome. First, people who have a dependency upon journals in paper format because of age, technology limitations, etc., are opposed to electronic journals in general. Certainly the established publishing houses that have a significant investment -- and revenue stream -- attached to the current publishing framework are very opposed to open access. Even non-profit Society publishers have business plans that are firmly entrenched upon journal revenues. And students and post-docs have a very real concern with regard to attribution of work that is published via open access models -- will their tenure opportunities be negatively impacted if they publish outside the current mainstream publishing houses? But Varmus believes that this resistance will weaken over time as the proven advantages of open access publishing become entrenched in the culture of science and eventually outweigh the initial concerns.
Open Access Publishing from the Perspective of Chemistry
Varmus's list of open access publishing advantages to chemists could actually be applied to any scholarly discipline. These are as follows: 1) the barrier-free retrieval of knowledge from enhanced digital archives; 2) the reduced cost of publishing; 3) more public access to chemistry as a discipline; and 4) the promotion of trans-disciplinary research. He suggested that perhaps a public digital library could initially be created for chemists by morphing Chemical Abstract Services' SciFinder with the delayed or immediate deposition of journals and articles. He also suggested that perhaps with the help of funding agencies, better digital libraries in chemistry could be created along with the requisite search tools. And he recommended that chemists serve as advocates for open access journals and articles beginning with the biological, physical and computational interfaces.
Are Traditional Indexes Awaiting Extinction?
When asked about the ability to effectively access, search and retrieve open access material, Varmus was vehement in his stated belief that improved search engines will be key, and that traditional indexing as currently performed will gradually disappear as the proven need for such indexing declines. Again, the defining moment, in Varmus's opinion, will be at the point in time when open access publishing ultimately reaches a critical mass of material that meets the requirements of the majority of researchers.
For more Information on the Public Library of Science go to:
For information on BioMed Central go to:
For information on Dr. Harold Varmus go to:
For a list of Alternative Publishing Initiatives go to:
Additional reading list:
All URLs were last accessed on September 23, 2003.
Copyright 2003: Reprinted with permission byNFAIS, 1518 Walnut St, Suite 307, Philadelphia, PA 19102. For more information contact Bonnie Lawlor, Executive Director atmailto:.NFAISis a registered Trademark.
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Some Photos from the New York Meeting
submitted by Bill Town
Frank Allen receives the Herman Skolnik Award from Chuck Huber
Andy Berks receives his pin from Chuck Huber for serving as CINF Chair
Grace Baysinger is thrilled as she receives an award for her participation in National Chemistry Week
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News About Awards
2004 Herman Skolnik Award Winner Announced
submitted by Bill Town
The Herman Skolnik Award of the ACS Division of Chemical Information, recognizing outstanding contributions to and achievements in the theory and practice of chemical information science, will be presented at the Fall 2004 ACS meeting in Philadelphia to Professor Peter Johnson.
Since 1980, Peter has had a long and distinguished career at the University of Leeds. He was Head of the School of Chemistry from 1998 to 2001, and has been Director of the Institute for Computer Applications in Molecular Sciences (ICAMS) since 1988 and Professor of Computational Chemistry since 1995. During his time there, he has made Leeds one of the world's leading centres for academic research in chemical information science and has made significant contributions to computer-aided synthesis design, reaction indexing and retrieval, and de novo ligand design.
However, he is equally well known as Managing Director of Orac Ltd (from 1987 until its acquisition by Robert Maxwell and subsequent demise following the collapse of the Maxwell empire in 1992) and for setting up a charitable organisation LHASA UK to promote the use of the LHASA program in the drug discovery programmes of leading pharmaceutical companies. Many of the key staff of Orac Ltd (all alumni of Peter's group) went on to form the specialist chemical database company Synopsys Ltd which was acquired by Pharmacopoeia Inc in 2000 and is now an important part of Accelrys.
Over the last decade, Peter's group at ICAMS has developed a number of key software systems including HIPPO (a system for analysis of the receptor site of a protein), SPROUT (a system for growing ligands in protein binding sites), CEASA (a system which evaluates the hypothetical structures generated by SPROUT) and CLiDE (a system for the automatic extraction of chemical information from the scientific literature). Fees from commercial licenses of these systems have made a substantial contribution to the funding of the ICAMS research group.
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Bill has also given the procedure for nominations for the 2005 Herman Skolnik Award which will be announced at the Fall 2004 National Meeting in Philadelphia:
Background:
The ACS Division of Chemical Information established this Award to recognize outstanding contributions to and achievements in the theory and practice of chemical information science. The Award is named in honor of the first recipient, Herman Skolnik.
By this Award, the Division of Chemical Information hopes to encourage the continuing advancement of chemical information science in areas such as:
/ Design of new and unique computerized information systems;/ Preparation and dissemination of chemical information;
/ Editorial innovations;
/ Design of new indexing, classification, and notation systems;
/ Chemical nomenclature;
/ Structure-activity relationships; and
/ Numerical data correlation and evaluation.
The Award consists of a $2000 honorarium and a plaque. The recipient is expected to give an address at the time of the Award presentation. In recent years, the Award Symposium has been organized by the recipient.
Procedure:
Nomination letters should describe the nominee's contributions to the field of chemical information and should include supportive materials such as a biographical sketch and a list of publications and presentations. Three seconding letters are also required. Preferably all of these materials should be submitted in electronic form (as emails and attached files). The deadline for nominations is June 1 in the year preceding the award presentation. Nominations should be sent to me () as CINF Awards Committee Chair.
Hence a rough timeline for the 2005 award will be as follows:
/ Spring 2004 - call for nominations will be issued/ June 1st 2004 - deadline for receiving nominations
/ Nominations will be assessed and previous Award winners may be consulted
/ Fall 2004 ACS meeting - jury will meet to select the 2005 award winner
/ 2005 award winner is announced after s/he agrees to accept the award
/ Planning for 2005 Herman Skolnik Award Symposium begins
/ Fall 2005 ACS meeting - 2005 Herman Skolnik Award will be presented
If there are any further questions regarding this procedure, I will be happy to answer them off the list and summarise them for the list at a later date.