Chemical & Engineering News,
November 13, 1995

Copyright © 1995 by the American Chemical Society.

Chemistry Sites Proliferate On The Internet's World Wide Web

Chemical community ponders issues arising from increasing size and expanding variety of the web's chemistry domain

James H. Krieger,

C&EN Washington

Want to download a three-dimensional image of a particular protein from a database? Want to join in an electronic conference on glycoscience? Want to observe or participate in development of virtual reality modeling language (VRML) for chemical use? Want to publish or read a paper in an electronic journal, download chemical education aids for a course in physical chemistry, check out some academic employment possibilities, or scan data from Facts & Figures of Chemical R&D 1995 from C&EN?

You can. These are just a few of the chemistry resources available on computer screens today through the Internet's World Wide Web.

Indeed, the chemical activity on the web over the past couple of years has grown plentiful. As it continues to unfold, the web phenomenon is almost sure to affect the doing of chemistry. It adds a new dimension to the ways that chemists get, exchange, and deal with information.

Yet development of the web's chemistry domain has only just begun. To some observers it is already a glass partially full. To others, anxious to exploit the potential, it is a glass partially empty. Either way, the glass is filling. And as it does, chemists involved are mulling over many of the issues that have arisen as a result.

Although web-astute chemists reflecting on the potential of the web for chemistry and science express an assortment of views, few doubt its eventual significance. For example, Thomas H. Pierce, a computational chemist at Rohm and Haas, Philadelphia, envisions the web as becoming something chemists reach for the way they would for a telephone.

"I think it will be in everyone's self-interest - or best interest, personal interest - to use the web to leverage their activities," he says. They would employ it" to quickly find out something they need to know. Quickly figure out where something is. Look something up. Find the current information on the topic of interest. Catch up with a new idea."

Steven M. Bachrach, an associate professor of chemistry at Northern Illinois University, DeKalb, and a chemistry-on-the-web pioneer, likens the web in importance and influence to the development of movable type. However, he sees the situation more as a societal revolution than as one impacting just science. "I think it suggests a new era of how communication in general will proceed, not just how scientists will communicate."

Stephen R. Heller, a research scientist in the Agricultural Research Service's plant genome program at the Department of Agriculture is another seasoned observer of the chemistry/computer scene, one who sees web applications lagging well behind the potential. Speaking at a Division of Chemical Information venue during the most recent national meeting of the American Chemical Society in Chicago, he struck something of a cautionary note about the web's chemistry resources.

Most sites, Heller said, have a number of common denominators. "They have been put together as a side project or hobby, they have little information, what little information is there is useful to an even more limited number of people, and there are links to many other web sites with the same characteristics. ... Finding something on the Internet is like trying to find the bathroom in a house with 250,000 unmarked doors."

But Heller also pointed out that the chemistry-on-the-web situation today is mostly only in the first stage of development. "All the technology is here," he said. "People are experimenting with what to do and how to do it."

One of the stronger opinions on this score was expressed at the Chicago ACS meeting by a participant in a" Chemistry on the Infobahn" symposium sponsored by the Division of Computers in Chemistry. "There can be few other developments in the history of science of such significance as the advent of the World Wide Web," in the view of Robert Stembridge, European sales development manager for Knight-Ridder Information, based in London. He placed the development among such milestones as the periodic table, splitting of the atom, and isolation of penicillin.


TO SIDEBAR:
Chemists urged to increase activity in web development


Chemical information accumulates

Quantity and quality are variables difficult to pin down in general terms for chemistry on the web. For example, Heller noted that there are a few hundred chemistry web sites available. The exact number, he pointed out, is impossible to determine since sites come and go.

For the Chemistry on the Infobahn symposium in Chicago, a "Best-of-the-Web" listing was put together by Bachrach, Pierce, and Henry S. Rzepa, a reader in organic chemistry at Imperial College, London. The listing totaled some 60 sites. And as even a casual visit to those sites and to others shows, an increasingly useful amount of information of value to chemists is beginning to accumulate on the web.

The 60 sites qualifying for inclusion on the 1995 Best-of-the-Web list make up just a portion of all the chemistry sites available. And those make up a tiny fraction of the entire web, a resource some estimates have put at more than 5 million documents - pages, in web terminology - and growing daily at a rapid pace.

That growth has taken place in just a few short years, especially since 1993. That was when the first web browser or graphical user interface software, Mosaic, came along from the National Center for Supercomputing Applications at the University of Illinois, Urbana-Champaign, to make the web easily available to a wide audience of users. Other browsers have become available since then, perhaps most notably Netscape Navigator, developed by Netscape Communications Corp., Mountain View, Calif., the first commercial offshoot of Mosaic.

The subsequent mushrooming growth of the web in general has had the effect of blurring distinctions among sectors of the Internet. For example, Gopher servers, which offer a hierarchical organization of files available for reading or transfer, and Newsgroups, with their bulletin board discussions, are often readily accessible using a web browser. Hence, in essence, the web and the Internet have become somewhat interchangeable terms for persons navigating on the web.

With browsers readily available, all manner of parties have been attracted to the web to contribute one type of chemistry resource or another. University chemistry departments were early providers, at first often simply dispensing faculty lists and course descriptions. More recently, companies and other organizations have joined in to put pages on the web as well. Today, university departments, government agencies, chemical companies, computer firms, software developers, scientific publishers, and chemical and other scientific societies are among those posting materials along the electronic filaments that make up the web's chemical domain.

Not only has the information available been building up in quantity, it has been growing increasingly diverse as well. One aspect of that diversity is evidenced in the Best-of-the-Web's categorization of sites into such groupings as "Pointers," "Chemical Internet Standards," "Value Added Processing of Chemical Information," "Conferences and Talks," "Visual Sources and Programs," "Teaching Resources," "Electronic Journals," and "Organizations."

Still, with all the development of the web so far, relatively few chemists are making use of it. Indeed, Bachrach ranks awareness as one of the main issues for chemists. Comparing notes, he and Pierce have come to a conclusion that the penetration of the web into the chemical community to where people are acclimated and making effective use of it is not more than 10%, even at universities.

"There are many chemical companies that still are not connected to the Internet," Bachrach points out. "There are many academics who don't have Internet connections. There are still academics who don't have computers on their desks."

Pierce observes that in his experience it takes about a year for people to become comfortable with the Internet. "It takes that long," he says, "to figure out how to find things, to figure how to surf the net. And it takes awhile for people to stop asking unanswerable questions - you know, ranking right up there with the meaning of life, which is 'Well, what's on the Internet?'"

Nevertheless, Bachrach notes that there have been some significant changes. As an example, he points to the first electronic conference a year ago when the organizers, in putting together plans for publishing the proceedings on a CD-ROM, believed it absolutely imperative to market the CD-ROM with a web browser included. If a CD-ROM is published for this year's conference, it will not carry browser software. "People now at least are aware of what a browser is," Bachrach says, "and probably most people who would buy this product would have a web browser already."

Quality of the material now on the web is another issue. There are excellent collections of chemical information on the web as the result of work by a few individuals, Rzepa maintains. "However," he adds, "developments in this area are by and large not yet fully recognized in terms of career achievements and, hence, the quality is very variable."

Although Bachrach notes some improvements in quality, he also says, "I think what you see on the web developed by chemists is really pretty mundane. There hasn't been a whole lot of creativity to take advantage of what the medium can do." Consequently, Bachrach views the web as an essentially untapped resource.

Heller suggested something similar in Chicago, noting that "while today there are vast amounts of 'free' chemical information on the Internet, there are two main issues that one must consider. They are: What exactly is the nature of the information there, and how long will it be there?"

Stembridge voiced a related concern. "The virtue of the World Wide Web is also its biggest vice," he said. "Amongst the wealth of information available, how do you find what's needed?"

Stembridge also noted that speed of access to sites on the web and reliability of connection continue to be issues. And as the quantity of information on the web grows exponentially, so the problem of knowing what to believe and rely on and what to discard will increase.

For Stembridge, a natural response is the growth of sites on the web with editorial control, from newsletters to well-known information providers and publishers. Many of these sites are now, and increasingly will be, made available by commercial organizations, he said. "The choice for the user then becomes no different from the daily experience of whether to believe what you hear through the grapevine for free or to trust your favorite scientific journal for which you have paid."


Publishing: A major issue

The tangle of issues involved in electronic publishing is complex, and the resolution of those issues is far from certain (C&EN, March 27, page 42, "Electronic Publishing Increasingly Offered as Alternative to Print Medium" by Stu Borman. But electronic publishing is one chemistry activity that could well experience a great deal of change stemming from the Internet with its web accessibility.

Bachrach is among those who see electronic publication of primary, secondary, and tertiary literature as a major issue for chemists. In his view, "The Internet is going to become important to chemists when the primary literature becomes distributed on the Internet."

Bachrach notes that most, if not all, the players in tertiary literature - the abstracting services - have products on-line and are beginning to develop web-aware and Internet-savvy packages. But primary literature - original articles such as research papers - is by far more available in hard copy. It's hard to predict the future, Bachrach says, but once primary literature becomes published electronically, "things are going to change very, very rapidly."

Among the issues raised by the idea of electronic publishing, Bachrach points out, is the definition of publication on the Internet. For example, what constitutes a publication? Is a posting on a newsgroup a publication? Is a paper in an electronic conference a publication? How does one track the literature?

How such questions are eventually answered will be among the concerns shaping the future direction of electronic publishing on the web. But there are a number of different forces at work that could well have a major impact.

For his Chicago audience, Heller provided a particularly provocative view of the process. "What I foresee," he said, "will be a totally different way of life for publishing in science. Just as the airplane has brought travel throughout the world to a level never dreamed of before the middle of the 20th century, publishing on the Internet will be a radical change from the world of the Gutenberg press."

Heller listed a few of the considerations underlying that change. He noted, for example, that the bulk of scientific manuscripts come from universities, government laboratories, research organizations, and to a much lesser extent, industrial companies. All of these establishments are undergoing reorganizing and downsizing and are looking for ways to keep their incomes up.

"What would happen," Heller asked, "if universities and the other organizations that create the manuscripts decide they want to receive compensation from publishing?" Heller then posed the further question: "What would happen if a university would require all faculty and staff - all departments - to publish their research in the university or company electronic press - and print press?"

Heller pointed out that "such electronic journals and software programs could become part of the academic, government, and industrial chemist's reward/promotion and tenure system." Should the issue of academic freedom to publish where a researcher wishes come up, Heller said, an offer by a university to share some of the revenues from the publishing activities would likely win over the faculty members, especially those who need funds for research.

Perhaps even more critical to a researcher than funding, Heller said, is how to guarantee that published results will be readily available for future generations of researchers. Today, professional societies and commercial publishers print the journals, which are purchased and stored in libraries. In the paradigm imagined by Heller, he foresees elimination of the middleman - that is, the publisher - with the library taking over the function of providing long-term stability and preservation of electronic scholarly works.

These are just a few of the considerations involved in any attempt to assess the impact of the web in the publishing arena. As Heller noted, what exists today is a system that has served the scientific community quite well. In the past, the technology of the world required scientists to publish their papers in the most highly recognized scholarly publications, to read papers in journals mostly in the library or in the lab, and to go to the library for access to the abstracting publications.

But today, Heller suggested, the Internet is a potentially powerful tool" that is likely to result in a massive restructuring in the way in which scholarly works are created, reviewed, and disseminated."


TO SIDEBAR:
'Best-of-the-Web' list underscores growth in chemical sites


Hyperlink lists ease access

Meanwhile, anyone scouting the web will find a growing accumulation of chemical wealth, though the value of any given site will naturally depend on the needs of the explorer. There is no one-stop shopping. But there are a number of lists of hyperlinkages - pointers, gateways, indexes, however a user might want to think of them - that provide entry to a wide variety of chemistry servers.

One of these pointers is called ChemDex (http://www.shef.ac.uk/uni/ academic/A-C/chem/chemistry-www-sites.html ). It is a global list of chemistry Internet sites that is supported by the department of chemistry at the University of Sheffield, England. The major categories of sites give an indication of its breadth: "Universities" (chemistry web sites by country), "Commercial" (also chemistry sites by country), "Societies" (again by country), "SuperList" (a list of lists), "Newsgroups" (Internet discussion groups), "Journals," "Software,"" FTP" (anonymous file transfer protocol sites), "Gophers," "Listservs" (topical discussion groups), "Telnet," "Highlights," "WebElements" (a periodic table site with data on elements also maintained by the University of Sheffield), and "Miscellaneous" (nonchemistry sites thought to be of interest).

Digging deeper, the current ChemDex university listing provides linkages to chemistry sites at nearly 250 universities in 31 countries. The commercial group includes linkages for some 50 companies in eight countries, mostly in the U.S. Likewise, the rundown of chemistry learned and professional societies includes 15 societies in seven countries plus numerous divisional sites for two of them - ACS and the Royal Society of Chemistry.

In the U.S., another comprehensive web index, called Chemical Information Sources from Indiana University (CIS-IU), is under development at the university's Bloomington campus ( http://www.indiana.edu:80/~cheminfo/). Intended as a guide to Internet and other information resources in chemistry, it evolved from a class project in "Current Topics in Chemical Information" during the spring semester this year and from another, earlier Internet list produced at the university called "Some Chemistry Resources on the Internet."

The prime mover behind CIS-IU is Gary D. Wiggins, head of the chemistry library at Indiana. He likens it to a book comparable to various guides to the printed literature "where you have a kind of tertiary source that guides you to the appropriate place in the library, whether it's a journal or a handbook or an encyclopedia."

Among CIS-IU's stated goals are to put into a useful classified arrangement the most significant chemical information resources on the Internet and to make Internet users aware of non-Internet resources that may be better suited for their information needs. It will also be a gateway to chemistry courses on the Internet.

CIS-IU has moved a good way toward its goals already. For example, it has an index consisting mainly of chapter and subchapter entries within a" Classified Arrangement" grouping, supplemented with additional keywords. At the highest level of the classified arrangement are chapter headings, ranging from a chapter on "Chemical Information Sources, Publications, and Databases" to one on "Current Awareness Reviews, Background Reading (Dictionaries, Encyclopedias, Treatises, and So Forth), and Document Delivery Sources for Chemistry."

A further subdivision of the chapter on "Chemical Information Sources, Publications, and Databases" provides linkages grouped under "Preprints" (for example, "Chemical Physics Preprint Database at Brown University")," Primary Journals" (for example, the Bulletin of the Chemical Society of Japan and the Journal of Biological Chemistry)," Conference Proceedings" (for example, the "Electronic Conference on Trends in Organic Chemistry," held last June), "Databases" (for example, the "Fullerene Database at the University of Arizona"), and "Miscellaneous Classification Tools" (currently containing an "Index to Some Library of Congress Classification Numbers Relevant to Chemistry").

But CIS-IU provides material besides just linkages to other servers. It is the repository for the Clearinghouse for Chemical Information Instructional Materials. CCIIM is a project initiated by the Special Libraries Association's chemistry division and the education committee of ACS's Division of Chemical Information.

Most libraries, Wiggins explains, provide paper handouts that give instructions on everything from how to search the paper version of Chemical Abstracts to how to do a CAS Online search on STN International, the scientific and technical information network on-line search service. The idea behind CCIIM, he says, is to have an on-line place where librarians or chemistry teachers can deposit such tools that they have produced. The hope, Wiggins says, is to move totally away from the paper-based handouts, of which there are a couple hundred. In addition, CCIIM is linking to informational material that might be provided by commercial sources. "We think it's important," Wiggins says, "to have one place where, if you were trying to teach about Beilstein, you could go to see what things are available from the Beilstein Institute."

Although there are as yet only a few dozen handout-type files on the web, an example of what's possible is a" Classified Arrangement" chapter on" Chemical Structure Searching." That chapter links to documents with tutorial type information on "Chemical Structure Searching on STN," "Biomolecular Sequence and Structure Searching," and" Other Structure Coding Systems." Typical of the documents in the first of these is one on tips for building structures for substructure searching. The group" Other Structure Coding Systems" has a linkage to a "SMILES Tutorial" (Simplified Molecular Input Line Entry System) for that chemical notation system, located on a server maintained by Daylight Chemical Information Systems, Irvine, Calif.


TO SIDEBAR:
Web site makes debut for structure searches


Diversity of sites

Developing areas of the web's chemical domain include sites devoted to education. One site that can be found there, for example, is at Virginia Polytechnic Institute & State University, Blacksburg ( http://www.chem.vt.edu/chem-ed/vt-chem-ed.html). The "Chemistry Hypermedia Project" at Virginia Tech is aimed at providing supplemental educational material to undergraduate chemistry students, determining effective hypermedia designs for chemical education, and evaluating the distribution of multimedia educational material over the Internet.

Virginia Tech chemistry professor Brian M. Tissue, originator of the project, notes that what's missing from the web now for educational application is content. But the potential is there. "I think the networked educational material will in the long run have a really big impact in continuing education," Tissue says. "Not this year or next," he adds. But he expects to see in the future a lot of short-course types of materials on-line.

As for the Chemistry Hypermedia Project, Tissue, an analytical chemist, says he sees it as a convenient way to put supplemental class material on-line. It is directed at laboratory work.

Putting material on the Internet in this way and incorporating a lot of graphics - pictures of instruments, pictures of endpoints, movie clips showing use of an instrument - accomplishes two things, Tissue says. One is to provide more effective prelab material so that students will have a better understanding of how to do an experiment when they come to a lab. The other is to increase cost-effectiveness, for the students as well as the professor, who would otherwise generally have to give numerous demonstrations at the beginning of a lab.

Moving beyond educational applications, web navigators can find an array of visual image sites. These range from entries in Brookhaven National Laboratory's Protein Data Bank database, accessible through the National Institutes of Health ( http://www.nih.gov/molecular_modeling/pdb_at_a_glance.html) to visualizations and animations in chemistry done at the Center for Scientific Computing in Espoo, Finland ( http://www.csc.fi/lul/chem/graphics.html).

The web is also being used to bridge communications between chemists and biologists. Late this summer, a web site was established by Current Biology Ltd., the U.K. publisher of Chemistry & Biology, to serve as a networking tool for chemists and biologists interested in fluorosensor design http://www.cursci.co.uk/fluoro/).

Described as an experiment in use of the web, the site was put up in response to a call from Anthony W. Czarnik, director of bioorganic chemistry at Parke-Davis Pharmaceutical Research and adjunct professor of chemistry at the University of Michigan, Ann Arbor. It is one part of a more encompassing web operation, called BioMedNet, being developed by the publisher as a worldwide club for biomedical scientists. Until the end of this year, nonmembers may search the BioMedNet library of various journals and browse the content pages free, although examination of full texts requires membership ( http://www.cursci.co.uk/BioMedNet/biomed.html).

According to Czarnik, there is an enormous list of biologically active small molecules for which fluorescent sensors would be desirable. Such sensors would enable biologists to study the internal functions of cells - for example, changes in concentrations of glutamate, adenosine 5'-triphosphate (ATP), and nitric oxide. Czarnik points out, however, that the chemists who could make the fluorescent molecules required for such sensors frequently don't know exactly what is needed, and the biologists who would like to use such sensors find it difficult to identify the chemists who might be interested in constructing them. The hope is that the new web site will serve that communication function.

This summer also saw the arrival on the web of Network Science (NetSci), which bills itself the Web Journal of Science & Computers ( http://www.awod.com/netsci). NetSci was created by Molecular Solutions, Isle of Palms, S.C., a consulting and executive placement firm dedicated to the chemical information and molecular modeling fields. Each month, NetSci highlights a specific topic and solicits papers from both end users and vendors involved in that area. The October issue, for example, examined the topic of bioinformatics. Mass screening, as used to rapidly analyze compound libraries and to target active chemical entities, is the topic for the November issue. Earlier issues focused on combinatorial chemistry, structure-based drug design, and 3-D databases.

In addition to papers, NetSci carries sections on industry news, product updates, people who have taken new positions, meetings, literature reviews, software availability, and, beginning with October, a biotechnology section. Access to the journal is free.

Commercial enterprises are making increasing use of the web, too. A web site would seem a natural for companies developing chemically related software. Indeed, they are there, and many have free software packages available. For example, MDL Information Systems, San Leandro, Calif. ( http://www.mdli.com), has available its ISIS/Draw structure drawing program, which it is offering free for academic use or personal use at home. And SoftShell International, Grand Junction, Colo. ( http://www.softshell.com), is providing free its ChemWeb chemistry drawing software for World Wide Web publishing activities.

The web would seem a natural as well for computer companies. And some of these have chemistry-related sites. In August, for example, a Chemistry and Biological Sciences home page from Silicon Graphics, Mountain View, Calif., made its debut during the Chicago ACS meeting ( http://www.sgi.com/ChemBio). The page offers hyperlinks to a collection of technical papers as well as to a large number of chemistry sites. An" Events" list provides information on an extensive list of upcoming worldwide conferences of interest to the computational chemistry community.

Not only software and computer companies but also chemical, equipment, and instrument companies help to make up the chemistry domain on the web. There are various types of activity that companies can mount, depending on their size, products, and the use they want to make of the web.

Many companies have home pages that describe the firms and their products. But Fisher Scientific, Pittsburgh, is an example of a company that goes a step further, providing its complete catalogs for general analytical reagents and for FisherBiotech reagents ( http://www.fisher1.com). A few clicks of a mouse will take users to a page for any chemical in the catalogs, where they will find tables of chemical specifications, product specifications, and prices. Information for ordering directly from Fisher is also provided.

The web can be a vehicle for other types of commercial activity as well. World Wide Chemnet, Tulsa, provides a site to bring buyers of chemicals together with manufacturers, distributers, and packagers ( http://www.chemnet.com). As the firm points out on its home page, corporate buyers in Akron, Ohio, can obtain quotes from manufacturers in Bangkok, Thailand, or any other source in the world through the web site. ChemNet charges a nominal search fee, but there is no charge if a desired product is not located.

ChemNet cofounder Phillip Bates says that six months of operation has convinced him that the Internet is an extremely useful tool for the chemical industry. Since June, he says, some 3,000 visitors have accessed the site, and requests for information on chemical manufacturers, sources, and quotations have come in from around the world.

The company plans to expand its page to include résumé postings for people seeking positions, job openings in the chemical industry, advertisements, new product information, live on-line chats with chemists, and a bulletin board area for leaving e-mail questions. The page will be available in Spanish very shortly, Bates says, and German and Japanese will follow not far behind.

And so it goes. With more chemistry sites appearing all the time, a user can appreciate the unanswerability of the question: "What's on the web?" But whatever the web's future development holds in store more broadly for commercial or scientific operations, it seems almost certain that it will play an increasingly pivotal role in disseminating the information involved. It will have a major influence on the chemical community and on the doing of chemistry.

Stembridge made that connection clear for science in his remarks at the Chicago symposium. The essence of science, he said, is discovery. The cornerstone of science, of discovery, is knowledge. And knowledge is gained through understanding - understanding that comes through questioning, probing, sharing, and discussion. These, Stembridge pointed out, are the two fundamental elements of the World Wide Web: a vast storehouse of information coupled with the vehicle for the dissemination and discussion of that information by other minds.

"Thus," said Stembridge, "the World Wide Web is already having, and increasingly will have, a profound impact on the way that science is done."


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