Citations and Reference Formatting in Manuscripts

This is the next post in a series of tutorials I’m writing for my students related to scientific manuscripts. This series is compiled on the page A Beginner’s Guide to Writing Scientific Manuscripts.

For every statement of fact in your introduction, results or conclusions sections or for every method, it is important to cite the appropriate reference, which provides the basis for this fact or method resource. Thus, references are given throughout the manuscript to direct the reader to previous literature to independently verify the facts or otherwise track down more information. Providing references for information in a scientific manuscript is somewhat different than providing references in a research paper for the humanities. While there may be some similarities with MLA style, there are specific requirements for scientific manuscripts that are determined by the choice of journal for submission.

Acceptable references are books and other peer-reviewed articles. You’re not allowed to get facts from random sites on the internet and other unreliable sources. Scientific literature is vetted by a peer-review process, in which other scientists evaluate the merit of submitted work. While it’s not perfect, this arduous process of evaluation and revision is science’s way of validating reports of experimental work. It means you can trust the information within peer-reviewed journal articles more than you can the random blog post or Wikipedia entry.

Specific formatting for references can be found in the instructions for authors. Some journals prefer using numbers in parentheses, some use superscripts, and some use an (author, year) formatting within the text of the manuscript. Reference lists are likewise variable according to journal- numbered lists, alphabetical lists, include titles, no titles, full journal names, abbreviated journal names etc. etc. In any case, the format will include enough basic information for a reader to look up the exact reference and check your facts. You have to follow the exact style for the journal of choice or the editor in charge of looking over new manuscript submissions will notice and kick your manuscript back to you- not reviewed, not accepted, not any further beyond your lab notebook than your computer files.

Citation management software should be your new best friend. Chances are the previous written assignments you’ve had haven’t required dozens of citations backing up various facts in your manuscript. You also probably worked on all of your previous manuscripts from start to finish in the order in which they will appear. As stated in my previous tutorial, you generally work on the sections of your scientific manuscript in a very different order than the one in which it will be finally assembled. Not to mention that working with multiple authors means merging sections from different writers and major rearrangements of written work. All of these complications mean that it is futile to try to manually keep track of all of the references that go along with these edits.This is a waste of your time and will lead to errors. Use citation management software. Citation management software like EndNote allows you to search for literature, manage all relevant information for a citation and integrate it into your handy text editing software (MS Word) in a way that lets you point-and-click which references to incorporate. This software will re-order citations in the reference list as sections are rearranged. The citation management software also already knows the exact details of each journal’s citation style. Simply select the appropriate journal option in the citation management software and EndNote will keep track of journal abbreviations, what should be italicized, what things are separated by commas and where periods should go. And if you decide to switch the journal for submission, all you have to do is click a different button and at least the reference section is done. Using citation management software ensures that no random numbers in parentheses are forgotten in the middle of your text.

Here’s a brief tutorial for using EndNote.

The EndNote software allows you to create a library of citations that can be used in your writing projects. There are two general strategies for EndNote library usage. (1) A single EndNote library containing every citation you will ever use. (2) Multiple EndNote libraries with one for each writing project. Each has its own merits and drawbacks. I know people that use both successfully, so if you feel strongly one way or the other, go with the one that seems most intuitive to you.

Citations can be added to your EndNote reference library by using the on-line search function. The most useful searches for scientific manuscripts are the PubMed (NLM) and Web of Science (ISI) searches. If you enter an author, publication year, journal name and some relevant keyword, EndNote should easily identify the necessary reference, which can then be saved in your library. It should be noted that I find this search feature useful for finding specific references (like those you’ve already read and know you want to use) rather than a general search to keep up with the literature (then again, I’m a type 2 EndNote user).

Reference entries can be added manually to an EndNote library also. If the paper is ancient or otherwise impossible to find with the search tools, you can manually type in all of the fields.

Duplicate entries within a library can be identified and eliminated. This should be done or it can cause problems when trying to use these entries while writing in MS Word.

The EndNote program also integrates itself as an add-on feature in MS Word. Once installed, it will have its own tab in the top toolbar. While working on a manuscript in MS Word, open the EndNote program and the appropriate library. From the EndNote tab in MS Word, all you have to do is click the ‘Insert Citation’ button to select the appropriate reference from the library. Note, the reference must be a part of the library at this point (already captured from an on-line search) because you can’t do an on-line search via EndNote from MS Word. Once selected, a reference placeholder will appear in the text (whether (#) or (author, date)) and a reference list will be started at the end of the text portion of your MS Word file. All of the details are determined by the designated style, given in terms of the journal title, which can also be changed from a drop-down style menu in the EndNote tab in MS Word.

Finer points of citation formatting with EndNote…

You can make some changes to the style if it’s not exactly correct based on the most up to date info on the journal’s website.

If you are citing multiple references at the end of a particular sentence, you can reorder them according to the stipulations of the journal style (usually in chronological order, oldest to most recent).

An EndNote library can be exported from an MS Word file. So, if you get a written portion from another author, you can recreate their EndNote library of citations even if they didn’t send you their library file.

A note on plagiarism: Don’t do it. Just because you are citing a reference in order to substantiate a statement in your manuscript doesn’t mean that you can copy their exact words. Use your own words and incorporate their work as it relates to yours. Don’t sweat whether minor wording changes are enough. Since you are building on these previous facts, the context will be different than the original paper, but there’s no excuse for copying things word for word. Sure, there are limited numbers of ways of saying any given truth clearly and concisely, but you can find a way of stating a necessary fact in your own words. Plus, you should really understand the previous literature well enough to restate necessary information in the context of your research manuscript without stealing someone else’s words.

Share your reference, citation and EndNote pro-tips in the comments section below.

Johnna

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