Writing Manual for Scientific Papers

2. The References Section

General
Journal Citations
Making the reference list
Reference systems
Periodical title abbreviations
Multiple author papers
Book Citations
Use of EndNote^®
The References or bibliographic section of a paper or thesis (also sometimes called Literature Cited, Bibliography or References Cited) is often the most neglected area of all. Make sure that your paper or thesis has an adequate number of references to document the points you make or to give further details of the methods that you used, without quoting too many. Reference lists that are too long are as unsatisfactory as a paper lacking key references, and show a lack of discrimination in the author. If you are uncertain, err on the side of quoting too many. The editors will delete, or ask you to delete, some of them. But in general, YOU SHOULD NOT RELY ON THE EDITORS TO DO THE AUTHOR'S WORK FOR YOU.
There are two different kinds of entries in a reference list: BOOK citations and PERIODICAL (JOURNAL) citations.

1. Journal Citations

In principle these are easy because in general, the same information is required whatever journal you are writing for. These are:
Surnames of authors and full initials
Title of journal
(Title of paper)
Volume number of journal
(Issue number of journal)
First (and last) page numbers of the article
Year of publication
Some journals do not require the parenthesized items. However, just to make the would-be author's life more difficult, there is no standard way of quoting this information. Every possible permutation of the order of the information seems to be used by some journal or other. Contrast the following examples:

(Journal of Bacteriology and other ASM journals):
Zinder, S.H., K.R. Sowers, and J.G. Ferry. 1985. Methanosarcina thermophila sp. nov., a thermophilic acetotrophic methane-producing bacterium. Int. J. Syst. Bacteriol. 35:522-523.
(Microbiology):
Zinder, S.H., Sowers, K.R. & Ferry, J.G. (1985). Methanosarcina thermophila sp. nov., a thermophilic acetotrophic methane-producing bacterium. Int J Syst Bacteriol 35, 522-523.
(World Journal of Microbiology and Biotechnology)

Zinder, S.H., Sowers, K.R. & Ferry, J.G. 1985 Methanosarcina thermophila sp. nov., a thermophilic acetotrophic methane-producing bacterium. International Journal of Systematic Bacteriology 35, 522-523.

RULE NO. 1: Find out from a recent issue of the journal and/or its Instructions to Authors, the exact order of the above items and the various typefaces and layout of the references for the target journal. This rule applies whether you are using a computer-based reference list or a card index list, but may not be necessary if you are writing for a journal with a style in the styles database of EndNote.
RULE NO 2: Go through your manuscript and tick each reference off with your draft reference list. Make sure that all the references in the text also appear in the list and vice versa.
Making the reference list

How do I get all the references in the text into the list? The answer to this depends on how you are writing the paper. If your target journal uses the Harvard (name and date in text) system of references, it is relatively easy. Some word-processing systems (e.g. MS Word) have an indexing system that allows you to mark each reference and it will produce on demand an alphabetical list of the names at the end. Otherwise you must copy and paste each set of names in the text via the memory into a list at the end of the manuscript and then arrange it manually (or using appropriate computer software) into alphabetical order. Having done that you must then find the accurate bibliographical information on the name list (say from your bibliographic data base, your card index, your reprint collection, or by going to the library and looking at the original paper), and type or import it in the correct format into your Reference list. Note that for journal names that occur frequently, it is convenient when typing to use a two- or three-letter abbreviation and to change to the full title or the standard abbreviation for the title when the list is finished, using the search-and-replace facility.
Reference Systems

For numbered references, what you do depends on the system used by your target journal. ASM journals use numbered references listed alphabetically. For these, leave the references in the text until the last minute. Then number the list in alphabetical order and assign numbers to the named references in the text. Only when this has been done should you delete the names and dates from the text. If the journal uses references numbered in order of citation, then no alphabetical arrangement is needed. Copy and paste the authors' names as they appear in the text, then number the references. Then add numbers to the references in the text. Because some references will be cited more than once, the numbers in the text will not always be in numerical order. Check that every reference in the text has a number, and right at the last minute delete the names and dates from the text. Because adding new references in a numbered system is difficult, the numbering should be the last operation in preparing the manuscript.
Periodical Title Abbreviations

Some journals use unabbreviated journal titles in their reference lists, others use standard International List system abbreviations as used by Chemical Abstracts (CA) , Biological Abstracts and Index Medicus.. Some journals use their own abbreviations. Stick rigidly to the convention used and NEVER make up your own abbreviations. One-word periodical titles are never abbreviated. If unsure of a title or abbreviation, check it using CA Index Guide, Science Citation Index (SCI) or Current Contents. You can check abbreviations for biological periodicals on line using the WWW site Jointly Administered Knowledge Environment of Yale University.

If writing a thesis, decide which system you prefer for periodical titles and stick to it rigidly and consistently.

Multiple Authors

Note the journal's rules for multiple authors of a paper. Most Harvard System journals use one or two authors' names only in the text. For papers with three or more authors, the style is (first author) et al. and the date. If there are two papers of the type Smith and Jones (1972), quote them in text and list as Smith and Jones (1972a) or Smith and Jones (1972b). If there are more than one paper of the type Smith et al. in a year, quote them as Smith et al. (1973a) etc., even when the authors (except the first) are different. In the list, papers by a single author (e.g. Smith, 1978) come before those with two authors (e.g. Smith and Black, 1993), which in turn come before those with three or more. The lists are alphabetized according to the first letter of the second author, thus Smith and Jones (1963) comes before Smith and Thompson (1959), but references that use et al. in the text are arranged in chronological order, so that Brewer, Brown and Jones (1953) comes after Brewer, Stewer and Cobley (1951).

2. Book citations

It is a tribute to the slowness of journal editors to respond to sensible innovation that only one journal that I know of (the World Journal of Microbiology and Biotechnology) uses the one unique identifier for a book that would make it very easy to trace, namely the International Standard Book Number (ISBN). Most are instead obsessed with authors/editors and publishers as well as the well-nigh useless place of publication. Many cited books are compilations by an editor of a series of chapters contributed by different authors. Such items appear in your list under the contributing author's name, with the names of the editor(s) cited later, e.g.

(Journal of Bacteriology and other ASM journals):
Baker, E.N. and J. Drenth. 1987. The thiol proteases: structure and mechanism, pp. 312-368. In J. McPherson (ed.), Biological Macromolecules and Assemblies, vol. 3, Active Sites of Enzymes. Wiley, New York.
(Microbiology):
Baker, E.N. & Drenth, J. (1987). The thiol proteases: structure and mechanism. In Biological Macromolecules and Assemblies, vol. 3, Active Sites of Enzymes, pp. 312-368. Edited by J. McPherson. New York: Wiley.
(World Journal of Microbiology and Biotechnology)

Baker, E.N. & Drenth, J. 1987 The thiol proteases: structure and mechanism. In Biological Macromolecules and Assemblies, vol. 3, Active Sites of Enzymes, ed McPherson, J. pp. 312-368. New York: Wiley. ISBN 0-471-85142-6.

Note that once again every possible order of the required information seems to be used by different journals. Make sure that you get the chapter, page and volume numbers correct. If you cite the whole book, then it appears in the list under the editor's name. Book citations can only really be checked against the original book or a photocopy of the relevant chapters. The author/editor, publisher, ISBN and date of publication can be checked quickly and easily online via LOCIS, the Library of Congress Information Service .

3. Use of EndNote®

If you keep all your references in an EndNote library, then writing a paper is easy. Every time you need to cite a reference, you go into your EndNote library, highlight the reference, copy it, return to your word-processing system and paste it in. EndNote introduces a marked temporary reference in the text. When you have finished writing and are ready to compile the Reference list, you get EndNote to do it for you. If you are writing for a journal with a style in the EndNote Style database, you tell EndNote that you want your references formatting in the style of say, Nature, and it does it for you, in both text and list. If your journal of choice does not come in the EndNote Style database, you will have to choose a style as similar as possible and manually edit the formatted reference list. You need to read the EndNote manual to make proper use of the formatting facility. It is possible to compile an EndNote Style for any journal you wish, but unless you plan to write a lot of papers for that particular journal, it is probably not worthwhile. Note also that EndNote supports all common word processors, including AppleWorks, although it is optimized for use with MS-Word and the new Cite While You Write system. EndNote also enables you to search WWW databases and online library OPACs and import any relevant references into your EndNote library. This marvellous new feature makes the cost of EndNote well worth while.

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