Chemical Information Sources/The Publication Process

Primary, Secondary, and Tertiary Sources

Introduction
Traditionally, scientific research work is first published in journal articles (known as the primary literature). It is then picked up in various secondary tools whose purpose is to better organize the primary literature and make the retrieval of items of interest much easier. Most important of these are the abstracting and indexing (A&I) services such as Chemical Abstracts Service, the Web of Science, Reaxys, and Scopus. There are differences among secondary A&I services both with respect to the depth and breadth of coverage of chemistry and with respect to the swiftness with which the average reference to a new primary work makes its way into the A&I databases. A very significant change in scientific publishing is now underway. Innovations such as the American Chemical Society's "As soon as publishable" process for new journal articles make possible the appearance of Web editions of original research articles several weeks before the corresponding print versions. The shift to electronic journals as the archival record of science is nearly complete. Many chemistry libraries have decided to stop subscribing to printed journals. With so much new information available, there are other sources that help to sift through, condense, and re-package the most important discoveries. For example, some people write reviews of what has been happening in a given scientific area over a period of time. Of course, once the new discoveries have been validated and deemed important enough, they will find their way into various books, encyclopedias, and other secondary sources.

Types of Primary Literature
PRIMARY LITERATURE refers to the first place a researcher will reveal to the scientific community in a publicly accessible document the results of scientific investigations. In many cases, the document that describes these results has undergone rigorous review by one or more peers who help insure the integrity of scientific knowledge. Increasingly, however, we are seeing appear on the Web PREPRINTS, unreviewed literature that is posted by the original author. More traditional primary publications include scientific journal articles, published conference proceedings, technical reports, dissertations or theses, and patents. All of these are collectively called DOCUMENTS.

Different types of information and different levels of detail are found in each of the DOCUMENT TYPES of primary literature (journal article, patent, dissertation, etc.). Since that is the case, it is sometimes important to distinguish the document type when a search is being conducted. Therefore, the type of primary document may be coded in a database or printed abstracting or indexing journal that covers more than one type of document in order to aid in retrieval.

Let's look at a few journal titles that one might expect to find in any respectable chemistry library. The American Chemical Society Committee on Professional Training publishes a Recommended Journal List for Undergraduate Programs. On the list are commercial news journals such as Science and Nature, primary research journals such as Inorganic Chemistry, and primary journals designed to rapidly communicate new research results such as Chemical Communications and Tetrahedron Letters. Also on the list are some secondary sources, such as Chemical Reviews.

On the other hand, a new movement in scientific publishing is OPEN ACCESS, defined by the Budapest Opean Access Initiative as the free availability of literature on the open internet permitting users to read, download, copy, distribute, and print the full-text. In lieu of subscription income, open access (OA) journals are funded in a variety of ways including article processing charges (APCs), grants, and direct support from societies or institutions. APCs are paid by the authors of accepted manuscripts from personal, institutional, or grant funds. However, many OA journals have no APCs or waive fees for authors with limited funding, making the article free for both readers and authors. In addition, many OA journals require that manuscripts undergo the same rigorous peer review process traditionally used by subscription journals. The potential audience for an open access article is much greater than that in a subscription based journal article. Compared to articles requiring a subscription to read, OA articles typically have many more downloads and, quite possibly, more citations. However, unlike some fields, most of the prestigious journals in chemistry are still subscription based making them more attractive to authors.

The Directory of Open Access Journals contains many thousand OA journal titles, some of them in chemistry. Many publishers of subscription journals now permit authors to pay an article processing charge which allows their article to be made open access as soon as it is published. Journals containing a mix of OA and subscription-required articles are known as hybrid open access journals. Examples of two such programs are the Royal Society of Chemistry's Open Science and the AuthorChoice option of the American Chemical Society.

SPARC (Scholarly Publishing and Academic Resources Coalition) was developed by ARL (Association of Research Libraries) to advocate changes in scholarly communication. There is an Open Access Working Group initiated by SPARC that is building a framework for the collective advocacy of open access to research.

Other types of primary literature include most technical reports, dissertations and theses, patents, and market research reports which are discussed in other chapters of this book.

Writing and Publishing a Journal Article in Chemistry

Before a chemist writes a paper he/she must determine its intended audience and what journals reach it. If the author picks the wrong journal it may be returned with the comment that the “work is not appropriate for this journal.” An author should do a literature search on the topic to determine which journals have published papers in that area. When selecting a journal its prestige, access, speed of publication, target audience, and impact should be considered. One way of determining those factors is to consult a subscription database called Journal Citation Reports published by Thomson Reuters. It offers a systematic, objective means to critically evaluate the world's leading journals, with quantifiable, statistical information. One important criterion is the Journal Impact Factor, a measure of the frequency with which the "average article" in a journal has been cited in a particular year or period. Thus, authors may wish consult Journal Citation Reports to find journals in their specialty with high impact factors, but this should not be the sole determining factor as indicated above. There are now a number of free web sites that evaluate the impact of journals including Eigenfactor, SCImago, and Google Scholar Metrics for Journals.

Once a journal is chosen the chemist must consult the “Instructions for Authors” page which is on the journal’s web site. An author should submit a manuscript to only one journal at a time. If it is rejected he/she may offer it to another periodical for consideration.

Two recommended sources: Robinson, M. S. (2008). Write like a chemist: A guide and resource. Oxford: Oxford University Press.

Day, R. A., & Gastel, B. (2011). How to write and publish a scientific paper. Santa Barbara, Calif: Greenwood.

The Secondary Literature
The terms "primary," "secondary," and "tertiary" literature are interpreted differently by different authors. We will call SECONDARY LITERATURE such things as textbooks, treatises, monographs and "edited texts" (books with chapters written by different authors), encyclopedias and dictionaries, handbooks and data compilations, review articles and review serials, bibliographies, and indexing and abstracting services.

All of these secondary works have in common the goal of repackaging and better organizing the new information reported by researchers in the primary literature. Since there is additional work involved in creating the secondary works (that is, they gather their information and facts from the primary works), they are always less current than recently published primary literature.

The Temporal Relationship Between New Primary Literature and the Secondary Literature
Depending on the type of effort expended in their compilation, the secondary works require varying periods of time to repackage or explicate new knowledge. Thus, there is a definite flow of scientific information from the inception of a research idea through the various types of secondary sources. One can typically expect to find the repackaged new knowledge or pointers to/summaries of new primary works in:

It is important to understand that the lag time is only partially linked to the frequency of updating of the secondary publication or database. Taking examples from several decades ago, the time lag for two journal articles entered in the Chemical Abstracts Service database, which at the time was only updated weekly, can be seen in the following abstracts:
 * Indexing tools: a few days to several weeks after the new primary work appears.
 * Abstracting tools: one to nine months or more after the new primary work appears.
 * Review articles: one to three years or more after the new primary work appears.
 * Various collected works: repackaged in the form of handbooks, dictionaries, encyclopedias, etc., the most important facts and data appear two to five years or more after new primary works are published.

Thus, the fact that an abstracting or indexing journal is updated every week or even daily does not necessarily mean that the primary literature covered in that A&I update is the new primary literature that appeared that week. Quite the contrary, there is almost always some lag time between the appearance of the new primary literature and its coverage in the secondary sources. However, with some abstracting or indexing sources, notably ingenta (formerly, UnCover), the time lag is quite small, on the order of a few days.
 * 1) CA abstract 93:25540j appeared in the volume 93 no. 3 (July 21, 1980) issue of Chemical Abstracts, but the original journal article was in the v. 102 no. 7 (March 26, 1980) issue of the Journal of the American Chemical Society. Time lag: apparently 117 days.
 * 2) CA abstract 106:205033s appeared in CA issue v. 106 no. 24 (June 15, 1987), but in the v. 37 no. 1 (April 1987) issue of the Journal of Photochemistry. Time lag: perhaps 60-75 days.

A development that is reducing the time lag between the publication of new primary literature and its inclusion in A&I services is the electronic publishing of new journal articles long before the appearance of the print versions. The "As Soon As Publishable" (ASAP) policy of the American Chemical Society and similar early publication policies of other primary publishers (e.g., Springer) have tended to drastically reduce the lag time. Under ASAP, the articles published in ACS journals appear in the electronic versions of the primary journals some two to six weeks prior to the corresponding print title. The references to the articles are also fed into the Chemical Abstracts database (which is a part of the ACS) much earlier than those for the primary journals of other publishers.

Other categories of secondary works are directories, buyers' guides, biographical works, etc. These cannot be related easily to the primary literature in a temporal sense.

Types of Electronic Sources
There are databases that correspond to the different primary and secondary printed sources. They can be categorized as:


 * BIBLIOGRAPHIC - provide a bibliography of documents, perhaps with abstracts (summaries), and increasingly with links to the full texts of the primary documents. Each record includes the elements needed to identify the document including journal title, author(s), article title, volume number, issue number, pages, and year of publication.
 * NON-BIBLIOGRAPHIC - numeric, text, dictionary, and directory databases.

Non-bibliographic databases are sometimes called FACTUAL or SOURCE databases, as opposed to bibliographic databases that traditionally give only pointers to primary publications that have facts in them.

The Internet, especially applications based on the World-Wide Web, is accelerating the creation of true full-text databases and blurring the distinction between abstracting/indexing databases and primary journals. Scientific full-text databases on the Web include graphics, for example, the Web versions of the American Chemical Society journals. Both HTML versions and pdf versions of the articles are found in some databases. The HTML versions may have enhanced features such as links in the references of the bibliography of an article to ABSTRACTS (summaries) of the cited articles in an A&I database, with further links to the full-text Web version of the cited older articles. For example, it is now possible to link directly from the various options for searching the Chemical Abstracts database to over 1,000 primary journals through the ChemPort option. A project (CrossRef) provides direct links from the citations in an article to the cited article without having to visit an A&I service as an intermediate step. CrossRef is also the official DOI (Digital Object Identifier) registration agency for scholarly and professional publications. Thus, if we find a DOI identifier, such as 10.1021/ci050354f, you can link to the full text of the article by entering in your browser the DOI preceded by http://dx.doi.org/, as in: http://dx.doi.org/10.1021/ci050354f.

A revolutionary step in the publishing of electronic journal articles was taken in 2007 by the Royal Society of Chemistry when they introduced their RSC Prospect project. This provides hyperlinks from words in the article to their definitions in such works as the IUPAC Compendium of Chemical Terminology (the Gold Book) and various bioscience ONTOLOGIES (schemes that show the relationship of all of the concepts and terms in a subject field). In addition, compounds are linked to structural depictions and other data about them. The American Chemical Society has developed a similar program of enhanced full-text articles, ActiveView PDF.

Note that some publishers have made the electronic version (rather than the printed version) of the article the official copy of record. In addition, some publishers, especially of online only journals, have dropped identification conventions from the print world such as volume and issue numbers or even page numbers, assigning an article number in their place.

Most primary chemistry journals are now available on the Web. See the list of WWW versions of Chemistry Electronic Journals list accessible through the Indiana University Chemistry Library.

Options for Database Searching
The options for database searching include:

VENDORS of online search services (for example, STN International) lease or acquire databases from the database PRODUCERS (such as Chemical Abstracts Service or Thomson Reuters) and make them available on remote computers. For a given vendor, which may have dozens or hundreds of databases on its computers, the databases are all searched by a common COMMAND LANGUAGE or graphical user interface (GUI). In some cases, especially in industry, pay-as-you-search fees are accessed based on connect time, number of queries, and records displayed, printed, or downloaded. However, especially in academia and large corporations, an annual site-wide flat-rate license has been negotiated by the library or other entity that allow everyone in the organization unlimited access to the database. Since access is often based on IP address authentication that is transparent to the searcher (no authentication required), some user may think the database they are searching is free of charge. Another option is to search free chemistry databases on the Web. The quality and range of search features of some of free Web databases may be more limited than those of the commercial databases. Nevertheless, free web databases should not be ignored, even when one has access to many subscription databases. Examples of excellent free chemistry web databases include ChemSpider which is supported by the Royal Society of Chemistry and the National Institute for Standards and Technology's NIST Chemistry WebBook.
 * ONLINE SEARCHING of remote databases outside the boundaries of the organization where the search is performed.

Large organizations may load databases on their own computers. Several new models of providing database searching are now being explored with the advent of client/server computer systems and WEB SERVICES.
 * IN-HOUSE SEARCHING of databases within the organization.

Tertiary Sources: Guides to the Literature
We will consider works that are designed to teach you how to use primary and secondary works to be TERTIARY works. Many of these are GUIDES of one sort or another, and indeed, this Wikibook is an example of a guide. Guides are covered more thoroughly in another chapter.

Summary
There are many different types of publications and databases in which the vast literature of chemistry is published. From the primary literature (places where original research is first published) through the secondary literature (which repackages the important findings first reported in the primary literature), the searcher has many options from which to choose. It is the goal of Chemical Information Sources to acquaint you with those tools so that you can make intelligent choices about how to efficiently satisfy your chemical information needs. While you may not consider yourself a master of all of them, you will at least have an awareness of the existence of the best tools to answer your questions once you have worked through all of the chapters of this guide.

SIRCh Links for The Publication Process

Problem Set on this topic