Managing Biological Journal Citations: The Use of a BIBTeX Journal Titles and Abbreviations Database in Conjunction with LaTeX Type-Setting System

Abstract

We applied a method to automate bibliographic management for biomedical and environmental scientists/professionals using a BIBTeX database of the titles and abbreviations of 4,387 mostly biological journals. This database is readily usable to meet the requirements for journal title format by many of today's leading scientific publishers. This article also provides links to additional tools and tutorials for using the proposed database.

Introduction

Today, various software packages, such as EndNote (Combs 1998; Siegler and Simboli 2002), ProCite (Rohmann 1999; Wachtel 1987), Reference Manager (Neal 1993; Shmaefsky 2000; Wachtel 1987), and BIBTeX (Harrison and Munson 1989; Lamport 1994), etc., are widely used to aid the management of scientific literature citations. In this article, we describe the use of a BIBTeX-based journal title and abbreviations database, which was translated from the biological journals database of Patton (2006), in order to assist writing and publishing in biomedical and environmental sciences. The method for the automated handling of literature citations based on BIBTeX was perhaps first proposed by Patashnik (1988) and there are discussions on the Internet on the use of this method (such as at http://www.latex-community.org/forum/viewtopic.php?f=5&t=690). However, to our best knowledge, Patashnik's idea has not been turned into a full-scale application for the management of citations of the rapidly expanding biological journals using LaTeX. We believe that our work is a first attempt to fill this gap for the benefit of the biological research community.

Scope and Methods

The journal titles and abbreviations database needs to be used in combination with a literature database within the LaTeX type-setting system (Figure 1). There are three components for using the proposed database in LaTeX: (1) the LaTeX template and source code for generating the document; (2) the journal titles and abbreviations database; and (3) the literature database. We briefly describe how to use the database, but will not discuss in detail the basics of using LaTeX, because this is available elsewhere (Lamport 1994; Williams 2001; Dodson 2001; Greenberg 2005).

Figure 1. A schematic diagram for the relationship among the journal titles/abbreviations Database, the literature Database and the LaTeX type-setting system.

Table 1. A list of additional documents downloadable from {https://web.archive.org/web/20130311160032/http://www.infoclearinghouse.com/tiki-index.php?page=LaTeX+Applications}

A typical LaTeX source file for producing a technical document can be something like:

Box 1:
\documentclass[a4paper,12pt]{article} %Line 1
\usepackage{natbib} %Line 2
\begin{document} %Line 3
In grasslands, surface soil dryness can greatly influence %Line 4
respiration~\citep{Redmann:Aa1978a}. %Line 5 
\bibliographystyle{kluwer} %Line 6
\bibliography{Jshort,MyRef} %Line 7
\end{document} %Line 8 

Line 1 is for document type, font size and paper size; line 2 evokes the “natbib” package, which is a LaTeX macro able to handle both the author-year and the numerical styles of literature citations. Lines 3 and 8 mark the beginning and end of the document, respectively. Line 5 is to parenthetically cite a paper located in the literature database (Supplementary 1 of Table 1). Line 6 instructs BIBTeX to use a popular author-year bibliography style of kluwer.bst (see BioJournalOK.pdf of Table 1). Line 7 is especially important because it instructs BIBTeX to use an abbreviated version of the journal title database (Jshort.bib, see Supplementary Material 2) and a literature database. One important thing to note here is that the journal name database file should always be followed by the literature database file. The LaTeX output is shown in Box 2.

In Box 2, we find that the cited paper is listed at the end of the document automatically with only one instruction: “\bibliography{Jshort,MyRef}” from Box 1. Also note that the journal titles are abbreviated. When necessary, the author can also use two other versions of the journal titles: the abbreviated-dotted version (Jshort_dot.bib as listed in Supplementary Material 3) or the full version (JLong.bib as listed in Supplementary Material 4). In the latter two cases, the listed journal titles will be changed accordingly with the rest of the citation remaining the same. Now let's extract a portion of the bibliography file Jshort.bib to see what it looks like.

 ...
 ...
 @string{CanJBot = {Can J Bot}}
 ...
 @string{CanJSoilSci = {Can J Soil Sci}}
 ...

All the entries have a common format: “@string{A={B}}”, where A is the title key (a unique nickname for the particular journal), and B is for the abbreviated name for this journal. Next, let's show how the database MyRef.bib looks in Box 4.

...
@ARTICLE{Redmann:Aa1978a,
AUTHOR = {R. E. Redmann},
TITLE = {Seasonal dynamics of carbon dioxide exchange in a mixed grassland ecosystem},
YEAR = {1978},
JOURNAL = CanJBot,
volume = {56},
number = {},
pages = {1999--2005},
month = {},
}
...

Box 4 lists only one article that is cited in this sample document fragment of Box 2; however, one can have hundreds of articles and other reference materials listed in this same file (see Supplementary Material 5). After “LaTeXing” the source file, only those papers (or other materials) that are actually cited in the main text will be listed under the reference section of the document. While most of the entries are self-explanatory, two points in particular are important here. First, each article has a unique “key” that is to be referred to in the main text (this is different from the title key of a journal). These keys help LaTeX to find the correct papers from the literature database. Here the key for the cited article is: “Redmann:Aa1978a”.

One important entry in Box 4 is the journals' title key, namely, “Journal = CanJBot”. This unique title key is where the literature database and the journal title database are linked (see Figure 1). The statement of “Journal = CanJSoilSci” provides all the information LaTeX/BIBTeX needs in order to find the real name of the journal, whether it is a full name, abbreviated, or abbreviated-dotted, in the journal title database. The reason the literature database should be preceded by the journal title database in Box 1 line 7 (namely, first Jshort, then MyRef) is that LaTeX first needs a definition of which journal each of the journal nicknames represents before it can find the complete information for each of the cited papers as listed in Box 4. Most of the title keys (nicknames) are simply the concatenated version of the abbreviated journal titles as used by Patton (2006). However, when the journal titles are very long, the concatenated words are shortened, but still uniquely defined.

The bibliography style file used in Box 1 is "kluwer" (visit http://bst.maururu.net/faq.html for an explanation of how to use different types of style files). The style file determines the appearance of all the bibliography items in an article in both the in-text citation and the bibliography listing. It can be obtained from various web sites or can be generated easily (see Supplementary Material 6).

What about Citing Books and Documents?

Titles of books and technical reports usually are not abbreviated in the bibliography listings of scientific journals. So, these reference materials are cited in the LaTeX's usual way as shown in details elsewhere (Williams 2001). As a result, only the literature database matters in citing technical documents other than journal articles.

Advantages and Disadvantages

There are a few apparent advantages in using the proposed journal titles/abbreviations database introduced in this paper:

• The database is freely available and can be easily updated to include many journal titles one wishes to use.
• As long as the database is properly updated, it can be reused not only save time for scientists but also maintain a consistent and error-free method for handling literature citations.
• While using this database, one can enjoy numerous other benefits of using the LaTeX type-setting system for professional document preparation.

There are disadvantages of using the proposed database for citation management:

• It can only be used along with the LaTeX system; so, for those who are not used to or don't like to using the LaTeX system, the database might be of no value.
• At present, one has to manually update both the journal title database and the literature database.
• The method cannot generate all possible formats of literature citations. Often one has to do some small editing or cleaning before the document is finalized.

Future Plans

For those in biomedical and environmental sciences, the journal titles and abbreviations database is probably already quite inclusive. In the meantime, we hope to include more journal titles in wider disciplines so that this database will be useful for a larger number of researchers. For example, we may want to include all the over 6,000 journals covered by the Journal Citation Report of Thomson Reuters. Furthermore, we need to develop a stand-alone computer program to enable the automated generation of the literature database, to save time for those who manually prepare their literature databases.

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