The Internet Journal of Chemistry: A Premier Eclectic Journal

Citation

McKiernan, G. (2001), "The Internet Journal of Chemistry: A Premier Eclectic Journal", Library Hi Tech News, Vol. 18 No. 8. https://doi.org/10.1108/lhtn.2001.23918haf.002

The Internet Journal of Chemistry: A Premier Eclectic Journal

Gerry McKiernan

American Chemical Society

In April 2001, the American Chemical Society (ACS) commemorated its 125th anniversary. Founded in 1876, ACS is the world's largest scientific society and is "recognized as a world leader in fostering scientific education and research, and promoting the public's understanding of science" (American Chemical Society. ChemCenter, 2001).

The ACS has a proud tradition as an innovator in the development and application of advanced electronic information systems. Through its Chemical Abstracts Service (CAS) division, ACS was among the first publishers to computerize their abstract and indexing services, and to create and develop electronic bibliographic databases. Chemical Abstracts (CA), the CAS database, is considered the most comprehensive index to a scientific literature currently available. The development of the CAS Registry Number system to uniquely identify chemical substances and its application for indexing the chemical literature for CA and other major bibliographic databases are widely recognized as major innovations in information access. Equally significant is the development of a query interface that allows users to search the CA database by chemical structure (Schwarzwalder, 1998, p. 64; Powell, 2000).

The ACS is a major publisher of the primary literature in chemistry and related areas. It publishes, co-publishes, or distributes more than 40 journals, all highly respected and with high impact (e.g. Analytical Chemistry, Journal of the American Chemical Society, Journal of Organic Chemistry, etc.). The ACS was among the first major scientific publishers to provide online access to the full-text of its journals. In addition, it served as a key participant in the landmark Chemistry Online Retrieval Experiment (CORE) project to evaluate enhanced networked access and navigation of electronic chemical journals (Entlich, 1995).

Today, ACS offers Web access to all of its primary journals, allowing users to read articles in a format that provides a replica of the print version (PDF) or one that is more dynamic (HTML). The HTML version not only allows users to read an article as they would on paper or in the PDF format, but, through links to cited work, also permits the reader to quickly assess the potential value of related work in context. In addition, in select cases, citations are linked to the full-text of the cited publication, or to an abstract with various full-text retrieval options. The HTML e-journal also has embedded thumbnail graphics linked to medium-sized images tables, charts, and molecular illustrations.

As is the case with an increasing number of "eclectic journals", select ACS journals offer electronic manuscript submission (American Chemical Society, 2001a), provide access to data or information that supplement or enhance a published article (American Chemical Society, 2001c), or allow readers to subscribe to services that provide e-mail notification of new or future content (American Chemical Society, 2001b). In addition, ACS has joined other electronic journal publishers in providing access to forthcoming articles (McKiernan, in press). While innovative in providing several select features and functionalities, ACS e-journals, to a large degree, closely resemble their print counterparts. The presentation of supplemental data and images are indicative of this conventional approach: supplemental data are primarily available in PDF format and images are static reproductions of print graphics.

As noted by Bachrach, ACS journals are typical of many electronic journals in that they "take little advantage of the opportunities [provided by the digital medium]" and "simply [provide] electronic delivery of the print counterpart ... [where] ... articles are usually made available as PDF files, though some offer HTML versions as well" (Bachrach, 2001). Bachrach further observes that in general, Interactive tools, 3D structures, full interactive spectra, color graphics, and animations are not included in any of these electronic versions. For most [electronic] journals, there is no procedure for authors to include electronic enhancements. [While] some electronic journals ... do allow for deposition of these electronic enhancements within the supplementary materials ... [t]hey are still not directly incorporated with the articles (Bachrach, 2001).

The Internet Journal of Chemistry is a significant exception to these and other conventions and practices.

Internet Journal of Chemistry

Scope and History

The Internet Journal of Chemistry(IJC) (ISSN 1099-8292) is an electronic-only e-journal (www.ijc.com) with the primary aim of publishing the results of high-quality research in all areas of chemistry. Although initially consideration was given to publishing IJC as a specialized journal, its editorial board decided that such a focused publication would duplicate the scope of other chemistry e-journals or have a limited audience. Manuscripts submitted to IJC must be original research and are assumed to be submitted for consideration on an exclusive basis. All submissions are peer reviewed. The first IJC article was published on January 1, 1998.

As an electronic-only journal, a concurrent aim of IJC is to fully utilize the inherent potential of the Internet and the World Wide Web to create an "enhanced chemical publication" that empowers authors as well as readers (Bachrach et al., 1998).Style

To facilitate the publication of IJC as an "enhanced" journal, authors are required to submit their manuscripts in the latest version of the HyperText Markup Language (HTML). Submissions that make use of PostScript, TeX, or other word processing software or formats, are not acceptable. All submissions must use a standard layout for the title, author(s), affiliations, and keywords (Instructions for Authors, Style, 1998).

While authors are allowed to format their submission as desired, they are encouraged to use a standardized structure. The following is the suggested IJC article outline (Example of an IJC paper, undated):

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  Abstract.

• •

  Introduction.

• •

  Lead Template.

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  Methods for Enhanced Presentation.

• •

  Tables.

• •

  Graphics.

• •

  Video.

• •

  Hypermolecules.

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  Java.

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  How to Cite References.

• •

  Conclusion.

• •

  Acknowledgments.

The background color for every submission should be white (body bg = "#FFFFFF") and tables must be prepared using the table tags as defined in the latest definition of HTML.

Graphics and Video

Within IJC, figures should be in either the GIF (Graphics Interchange Format) or JPEG (Joint Photographic Experts Group) formats, with small graphics (less than 20K) integrated within the text of the submission and larger graphics files represented by a thumbnail or linked from a notation.

Due to the incomplete implementation of the Math tags (Math Tags, 1997) in popular Web browsers, efficient handling of mathematical equations within IJC is not currently possible. Authors are therefore requested to create mathematical equations as images (.gif or .jpg format) and to embed these within a manuscript text in an appropriate location.

To enable readers to better understand the concepts and research presented, contributors to IJC are encouraged to incorporate animation in their submission. Clips can be in one of the common video formats (e.g. MPEG (Moving Picture Experts Group) (i.e. .mpg), SGI Movie (i.e. .movie) or Apple QuickTime (i.e. .qt or .mov).

Interactive Formats

In addition to video, authors are encouraged to include file formats that enable readers to manipulate data or change the nature of a presentation. Tutorials on using interactive tools are available (Creating Enhanced Web Pages for Chemistry, undated) (see below). "Hypermolecules" is a term used to describe interactive models of molecules. Instead of including only static images of molecules within an HTML manuscript, authors can embed molecular structures in three dimensions and empower readers to manipulate, resize, rotate, and magnify these virtual objects by using appropriate software and file formats. IJC accepts several hyperactive molecule formats (see Table I).

In general, authors are encouraged to utilize any and all Internet tools that will enhance reader interaction and comprehension, notably Chemscape Chime™, the chemical structure visualization plug-in that allows hypermolecules to be embedded directly within an HTML document (MDL Information Systems, c2001). Chemscape Chime™ can support many of the acceptable interactive file formats (i.e. files with the following file extensions: spt, .csm, .emb, .gau, .mol, .rxn, .mop, .pdb, .xyz). A detailed tutorial is available (Bachrach, undated).

Table I. List of acceptable hyperactive formats for IJC contributions

Authors who wish to include infrared (IR) or nuclear magnetic resonance spectra (NMR) should provide these in the JCAMP-DIX format (.jdx). Those who wish to use new MIME (Multipurpose Internet Mail Exchange) types other than those considered standard (Rzepa, 2001) are required to receive approval in advance; alternative MIME types are to be avoided (Instructions for Authors, c1998).

Java, Javascript, and CGI Scripts

IJC manuscripts may also include Java applets, JavaScript scripts or Common Gateway Interface (CGI) scripts, although alternative means of reading text are required for readers who lack Java- or JavaScript-enabled browsers. While authors can include links or forms that access CGI scripts, these are not stored on the IJC server and the contributor must assure their maintenance.

Supplementary Materials

Recognizing the value and potential interest of some readers, IJC encourages submissions that include data sets (including raw data) as supplemental files.

Submission and Refereeing Procedures

All articles must be submitted using the online Web submission form (Manuscript Submission Form for the Internet Journal of Chemistry, 1997). Among the data required are:

• •

  Title.

• •

  Author(s) name(s).

• •

  Contact author name.

• •

  E-mail of contact author.

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  Mail address of contact author.

• •

  Phone number of contact author.

• •

  FAX number of contact author.

Contributors are offered two options for submission: file transfer protocol (ftp) or Uniform Resource Locator (URL). Complete instructions on the submission process are available as a combined document (Help for IJC Article Submission Form, 1997) and separately through a linked information icon found adjacent to each field in the manuscript submission form (Manuscript Submission Form for the IJC, 1997).

All submissions to IJC are anonymously peer-reviewed, with referees instructed to evaluate contributions on their scientific and scholarly merit as well as their effective utilization of the electronic medium. Professor Steven M. Bachrach, the Dr D.R. Semmes Distinguished Professor of Chemistry, Department of Chemistry, Trinity University, San Antonio, Texas, USA, is the co-founder and editor in chief of the IJC. Three noted authorities in chemical informatics, Peter Murray-Rust, director of the Virtual School of Molecular Sciences at Nottingham University, UK, Dr Henry S. Rzepa, Reader in Organic Chemistry, Department of Chemistry, Imperial College of Science, Technology and Medicine, London, UK, and Steven R. Heller, guest researcher at the National Institute of Standards and Technology (NIST) and strategic planner for MDL Information Systems, and co-founder IJC, serve among the IJC senior editors. Members of the IJC advisory board include individuals associated with major North American and European research universities.

On acceptance of a submission, authors are required to complete an agreement that licenses their articles for commercial redistribution to IJC. Authors, however, retain non-commercial rights and may redistribute their articles at no cost. Authors also retain the copyright to their articles. IJC licensing and copyright policies were developed with the assistance of the Scholarly Publishing and Academic Resources Coalition (SPARC) (see also below).

Subscriptions and Access

While any user is provided access to the table of contents as well as to abstracts for all IJC articles, as of the year 2000, access to the full articles is available only to individuals with personal, institutional, or organizational subscriptions. Costs for a personal, educational institutional site license, or non-educational institution or commercial organization site are comparably low (for 2000, $49, $289, and $489, respectively). Individuals with personal, institutional, or organizational subscriptions have the option of accessing the full content as a non-registered or registered reader.

Customization

IJC offers a number of options for reader customization of select features, functionalities, and content. To select these options, readers are required to formally register with the journal by providing basic identification information (e.g. first and last name, e-mail, and affiliation) and a preferred log-in identification name and password. Readers have the option of also providing their e-mail signature. Future plans include an option to include a link to a personal portrait image file that would be appended to reader postings to an associated IJC discussion forum (see below). In IJC, customization is enabled through the use of "Magic Cookies" (see below).

Among the customization options available are:

• •

  Greek characters visualization. Readers with workstations running under Microsoft Windows, may have Greek letters displayed using the Symbol Font format or displayed as GIF images. Currently, only the GIF option is available to Macintosh and Unix systems.

• •

  Interactive chemical structures. Readers may choose to have interactive chemical structures displayed as standard GIF/JPEG images, as a link to a datafile, as an embedded object, or a Java applet.

• •

  Interactive features size and style. Readers may change the area size allotted for the display of hypermolecules as well as specify the display style (e.g. wire frame, ball-and-stick, spacefill, etc.).

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  Multimedia resources icons. Readers may choose to have specialized icons within IJ appended to their associated resource (see below).

• •

  Units conversion. Within IJC, temperature, energy, and length base units can be converted into other base units (e.g. Celsius to Fahrenheit) on-the-fly by the reader. Readers have the option of specifying their preferred base and the destination of this conversion as another frame or an independent window. In addition, a reader may choose that simple notation (e.g. 5,000,000.0) or scientific notation (5.0 x 106) be used for numbers.

• •

  Footnotes display destination. Readers also have the option of designating the location of the cited references in either a lower frame or an independent window.

• •

  References. Within the body of an article, readers may choose among five options for the link style for a reference. Within the reference list, readers can display the journal title in full or as a standard American Chemical Society (ACS) journal abbreviation, or display the order of author names in standard (e.g. J.A. Smith) or inverted order (e.g. Smith, J.A.). In addition, readers may choose to display references with or without a standardized icon indicating the publication type; for example, an icon for a book placed adjacent to the citation for that type of publication:

  • •

    H. Spath Cluster Analysis Algorithms for Data Reduction and Classification of Objects, Ellis-Horwood Ltd.: London, 1985. In addition, readers may chose to activate reference links by a click ("True Link") or by a click or mouse rollover ("Lazy Link").

• •

  Layout. Of all available customization options, the configuration choices for page layout are the most varied. Readers may choose from a "classic" format or one that provides for individual article browsing (see Figure 1), a classic format with references in an independent window, or one that provides for individual article browsing with references in independent windows (see Figure 2), or one of two "space saver" formats, among available options.

• •

  Color. Readers are provided with a wide range of options for selecting article background color, article text color, article new link color, article visited link color, and article link color. In addition, readers may also select the color background for interactive structures, as well as the color for table and references rows, and the article navigation bar background color.

• •

  Margin notes/annotations. Within IJC, readers may annotate individual sections of an article with personal annotations by selecting the "Edit User Note" icon in a top margin area above the text or other components of an article. Annotations may be displayed and read in a lower frame beneath the article or displayed in an independent window. A reader may choose to display the associated annotation by clicking on the icon associated with margin notes and annotations, or opt to display these automatically when a new page is opened.

Figure 1. Screen print of select article display options in IJC

The availability of customization options may vary depending on individual hardware and software configurations. For each customization option, a default is available.

Table of Contents

On entering the journal proper as a non-registered user, the reader is presented with three frame-based options: the table of contents for the current volume (right-side frame), journal information, access and navigation features (upper left-side frame), and index options and special content (bottom left-side frame). The right-sided frame ­ the largest of the frames ­ lists the table of contents for the current volume and year in reverse article number order (Figure 3). The reader may display the abstract for the article (in HTML or PDF format) or an outline for the article by clicking the article title. At the head of the outline will be the full title of the article, its authors, their affiliations and full addresses, date of publication, and assigned index terms or phrases ("Keywords"), which are hotlinked to a comprehensive index of all article keywords. The outline itself will include entries for all the major sections of the article (e.g. "Abstract", "Introduction" section headings) as well as lists of special elements or objects embedded within the article, (e.g. interactive chemical structures) along with their associated icons (see Figure 4).

Figure 2. Screen print of additional article display options in IJC

As noted, readers may customize the layout of articles, choosing from a variety of display options (see above) (see Figures 1 and 2). In the default mode, the article may be read by clicking any outline entry (e.g. "Abstract"). Subsequent article sections may be read by selecting the right or left arrow at the top of the section. As sections are selected they are displayed in the main right-side frame, replacing any previous content. Readers may also choose to review and read sections using a duplicate article outline that is displayed in the left-side bottom frame when the initial outline is displayed in the right frame (see Figure 4).

Readers may choose to retrieve other articles that may have been assigned identical keywords by clicking a hotlinked keyword (e.g. "Isoxazoles") from the article header. These terms or phrases are hyperlinked to their entry in an alphabetical listing of "Keywords." In general, entries will contain a concise citation providing the year of publication, the IJC volume number, article number with the volume and the full article title.

Search and Browse Options

From the bottom left-side frame, readers are provided five search and browse options (see Figure 3):

1. 1.

   Titles.

2. 2.

   Authors.

3. 3.

   Keywords.

4. 4.

   Web Reviews.

5. 5.

   Library.

Figure 3. Screen print of opening IJC page

Figure 4. Sample IJC article showing frame content and navigation options

This frame also provides access to IJC news and a link to previous Chemistry and the Internet (ChemInt) conference abstracts, meeting reports, slides, lectures, and Webcasts, as well an announcement about the forthcoming ChemInt conference, all IJC-sponsored events.

The "Titles" option will display the table of contents for the current IJC volume, with hotlinked entries for all previous volumes listed in the contents list. The "Authors" option provides a complete alphabetical listing of primary and secondary article authors. In general, each author entry includes the title of the article, its year of publication and associated volume, and the assigned article number in a specific volume. The "Keywords" option displays an alphabetical listing of keywords (subject terms and phrases). Beneath each keyword entry is an indented listing of the titles assigned the keyword. The year of publication, corresponding volume, and associated article number are provided for each. Title entries are listed chronologically, then therein in numerical order. Keywords are apparently not standardized (for example, "ab initio" and "Ab initio" are listed separately, each with its own group of entries). "Web Reviews" provides access to an alphabetical list of reviewed chemistry-related Web sites (e.g. ChemFinder, ChemWeb, Molecule of the Month, etc.), along with a star-rating and reviewer name. The full review is linked from the reviewer's name. The "Library" is a collection of previously published conference papers, mostly from the First Electronic Computational Chemistry Conference held in 1994.

Access, Information, and Navigation Options

Within IJC, the upper left-side frame offers the reader a number of information, access, and navigation options, including:

• •

  IJC Articles.

• •

  Legend.

• •

  Multimedia.

• •

  Personal Preferences.

• •

  Search this Article.

• •

  Search the Journal.

Selecting the "IJC Articles option" will display the table of contents for the current volume in the right-side frame (see Figure 3). "The Legend" option provides access to a listing of specific parts, elements, or objects incorporated or embedded with IJC with their associated icons (e.g. "Text, Figure, Scheme", "Mathematical equations", "Movies, videos, animations". Access is also provided to a list of notations for specific types of references (e.g. "Journal article", "Book", "Software, Program, Code") commonly found in the "References" section of IJC article, along with their associated icons. As previously noted, readers have the option of customizing reference displays to include the appropriate icon for the specific reference type.

The "Multimedia" option is an index of multimedia and non-multimedia elements within IJC and their associated icons. Multimedia components include interactive chemical structures; movies, videos, animations; and virtual reality modeling language (VRML) models. Non-multimedia elements include figures, graphic images, and references. Selection of the "Multimedia" option will display a list of all multimedia and non-multimedia elements, with the number of occurrences noted adjacent to the icon associated with the element (see Figure 5). The list is displayed in the bottom left-side frame. Clicking the number associated with an element will display a listing of article titles and entries for the individual element in the right-side frame (see Figure 6). Readers may access the specific element within the context of an article by clicking on the hotlinked entry associated with the element icon.

As noted, registered readers are provided a variety of customization options within IJC (see above). The "Personal Preferences" entry in the upper left-side frame provides a ready opportunity to modify these customization and personalization options for current reading or to create new overall default. From within this frame, readers may also search the current article ("Search this article") or concurrently search the contents of the entire article ("Search the Journal") using identical search forms that allow standard search statements, Boolean combinations, and truncation options. Users have the option of matching the whole word only or the "word case". The search engine can search article text only; it does not currently support citation or multimedia searches. Advanced search functionalities are planned.

Figure 5. Index to multimedia and non-multimedia components in IJC articles

Figure 6. Sample listing of articles containing interactive chemical structures with linked access to article full-text and embedded multimedia components

Alerting Service

Registered readers of IJC have the option of receiving e-mail notification of new articles or the current table of contents on a bi-weekly basis. Such notification may be sent as plain text (ASCII) or as a hyperlinked HTML document. In addition, registered readers can receive e-mail copies of postings to subscribed discussion forums (see below) within minutes of their posting, or daily digests for individual sections or all subscribed sections.

Discussion Forum

IJC readers can choose to participate in an electronic discussion forum established for each article through the IJC "Discussion Page". This page is divided into three areas:

1. 1.

   Sections List. A list of the discussion sections for each of the published articles.

2. 2.

   Posts Lists. A list of postings to a given section for an article.

3. 3.

   Messages. The current message for the current section.

The "Sections List" includes the title and number of the corresponding article, an option to subscribe to a discussion for an article, and the total number of postings for each. This list may be sorted alphabetically by title, or in descending order by the total number of posts. In addition, a list of subscribed sections can be displayed first, as can a list of unread postings in descending order by the number of postings. The "Posts Lists" links the author, subject and date of postings to a discussion section. These postings may be sorted by date, author, or subject. A "Post Composer" facilitates participation in the discussion forum.

The Lancaster Continuum

Nearly a generation ago, and more recently, Lancaster outlined the inevitable replacement of print on paper by electronic publication (Lancaster, 1985, p. 553). As summarized by Shum and Sumner (2001), Lancaster viewed the development of the journal as a continuum based on the utilization of computer technology:

• •

  computers used for print production;

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  journal distributed in both print and electronic formats;

• •

  publication design is rooted in print, but articles are developed solely for electronic distribution;

• •

  interaction between authors and readers is possible; publications can evolve as a result of such interactions;

• •

  the inclusion of multimedia content;

• •

  both interactive participation and multimedia capabilities are supported.

Lancaster not only concisely outlined the general evolution of the electronic journal and other publications, but he, and others, also clearly anticipated the emergence of the eclectic journal that would offer alerting services, user annotation and commentary, data manipulation, electronic discussion forums, electronic manuscript submission, font, format, and display control, modeling, multimedia components, personalization, and reader participation (Lancaster, 1978, 1985, 1989, 1995) and other innovative features, functionalities, and content (McKiernan, in press) exemplified by IJC.

In describing the underlying design of the IJC, Bachrach and his colleagues provide insight in their reconceptualization of the scholarly journal:

In a sense, we are dramatically remaking the concept of ... [the] scientific journal. The traditional print model has a single delivery mode of text and graphics, forever fixed upon the page, delivered in immutable form to isolated readers. In our model, the journal becomes a large inter-connected collection of objects, cross-linked and cross-referenced into a single Web (Bachrach et al., 1999, p. 84).

For Bachrach and his co-authors, their journal is one "large object" made up of article objects, individual request objects, a server object, solution objects, page objects, and reference objects, and other objects that interact with each other, the network, and the hardware environment to "create the 'journal' that is delivered to each reader." Indeed, in their view, the reader is an integral part of the journal, dynamically participating in its creation (Bachrach et al., 1999, p. 84).

Future Developments

As part of its commitment to be at the "forefront of Internet technology", those involved with the management of IJC plan to continually develop new resources that will enhance its utility. They anticipate the development of text and structure search utilities, adoption of the Chemical Markup Language (CML), active participation in the development of browser plug-ins, Java scripts, and external and related applications that will assist in the publication and communication of molecular science. IJC staff also plan to support development of SGML applications to assure long-term archival retrieval of the journal (Statement of Purpose. Commitment to Technology, 1998).

Technical Considerations

Customization is made possible in IJC through the use of "Magic Cookies" or "Cookie". A cookie is an HTTP (HyperText Transfer Protocol) text file that contains the "domain, path, lifetime, and value of a variable" that is stored in a reader's browser. It is IJC policy to store a single cookie once during each session. Information provided in the registration and log-in is used only for "maintaining functionality and integrity of the IJC server system." Reader-supplied data and information will "not be sold, lent, distributed, shared, or provided in any other way to any third party for any purpose" (IJC and Privacy, undated).

Assistance

IJC provides detailed assistance for authors interested in creating enhanced submissions by incorporating Chemical MIME types and developing Chime™ and VRML dynamic interactive images (Creating Enhanced Web Pages for Chemistry, undated).

Indexing

The IJC is indexed by Chemical Abstract Service (CAS) and by the Institute for Scientific Information (ISI) in its Chemistry Citation Index and Science Citation Index Expanded.

Support

Early development of the Internet Journal of Chemistry was supported by a Henry and Camile Dreyfus Chemical Informatics Award. The IJC is an InfoTrust Production.

Acknowledgment

The author wishes to thank Dr Steven M. Bachrach, editor in chief, Internet Journal of Chemistry, and Dr D.R. Semmes Distinguished Professor of Chemistry, Department of Chemistry, Trinity University, San Antonio, Texas, for his assistance in preparing this review and for permission to publish selected screen prints from the journal.

SPARC Leading Edge Program

In October 1999, SPARC (Scholarly Publishing and Academic Resource Coalition), an initiative of the Association of Research Libraries (ARL), announced the Internet Journal of Chemistry as a "Leading Edge Partner" (Latest Features, undated) (Buckholtz, 1999). The "Leading Edge" program "encourages and supports projects that represent a paradigm shift in technology use, introduce an innovative business model, and/or meet the scholarly and research information needs of an emerging or fast-growing STM field" (Scholarly Publishing and Academic Resource Coalition, 2001).

Note

This profile of the Internet Journal of Chemistry is based on an analysis of available documentation and literature, and a review of operational features, functionalities, and content.

Gerry McKiernan(gerrymck@iastate.edu) is a Science and Technology Librarian and Bibliographer, Iowa State University Library, Ames, Iowa, USA.