How to………. 4: cite and reference

Before, I gave hints on how to structure a paper and on how to get a paper ready for submission. The one thing I didn’t dwell on was how to handle citations (when you refer to someone else’s work in the text) and references (the list of sources at the end of the paper). Boring as it sounds, that’s a huge amount of work, and doing it right from the start means saving a lot of time and effort later on.

As a style editor for Palaeontologia Electronica I have seen all possible ways of doing this suboptimally. This includes having lists of papers in one or several word processor documents from which you copy and paste, using c&p from other people’s papers, hand-typing the list afresh, and so on. Many people use reference managers, but inefficiently, so that the end result is not much better than it would be without using a reference manager.

What’s a reference manager, and why do I need it?

In short, you need it so that you do not get a paper back looking like this:

(formatting based on style of Palaeontologia Electronica. Click for full size, readable version).

What happened here is fairly simple: sloppy reading of the style guide, or simply being too tired when proof-reading the text, led to commas being missed, spaces being added, and many other small things. Additionally, some of the entries look like they were copied from other papers with similar, but not identical formatting. The worst possible error, a missing ref or a supernumerary one in the list, isn’t even there. This is a list I am likely to get as style editor: a well-meaning author has done an OK job (if tired), or a somewhat sloppy job, but has tried to deliver a good list.

So what does a reference manager do to improve this situation? First, you enter the papers and books you cite into its database. This means that you enter the data once, and do not need to re-type it for the next paper. Then, the program asks you how you want citations in the text and the reference list to look like. Once you tell it (more on that below) it takes the data sets you entered and formats them accordingly. Therefore, the formatting is correct (assuming you didn’t mess up the data entry in the first place). As an added benefit, there will be a 1-on-1 correspondence between the citations and references.

If you alter your text later, by adding or removing citations, the reference list will get updated, too. Very handy, that! For example, if I remove a citation of Huene (1908) from page 2 I do not have to search through all the rest of my paper to find out if I also need to remove Huene 1908 from the reference list.

Admittedly, up-to-date programs do a lot more, like managing your PDFs for you, extracting data sets from PDFs and web pages, and what not. But that’s not the point of this post, we’ll stick to the basics!

How do I do this?

First of all, you need to enter your data. I’ll show you how this is done on the example of the free program zotero, but there are many others. You can get zotero, which works for MS Word and for OpenOffice, from the project’s download page. There are two parts: the reference manager, which is a plug-in for Firefox, and another plug-in that integrates with your word processor of choice. Alternatively, if you do not use Firefox, there is a Beta of a stand-alone version. A quick-start guide can be found here.

Once you install the program you can start adding data sets. zotero can run as a partial screen, so you can have a web page open in the upper half, and add data from it below, or it can run as a full tab.

(Click for full size, readable version)

This is what zotero looks like in tab mode. On the left you have your libraries, which you can use to sort your data sets, in the middle is the searchable list of entries in the library selected on the left, and on the right are the details of the selected entry. There is a wide variety of pre-formatted types available, with the most useful ones being “journal article”, “book” and “book section”. All you have to do to add one is select the “add” button on the top, select the proper type from the pull-down list, then copy and paste or type the data into the fields provided on the right. That’s all – roughly the same amount of work as adding it to a reference list for the first time. And don’t think you can cheat by copy- and pasting into the word doc instead, because you’d copy the mistakes as well.

Now you go to your word processor file, where you find an icon to add a citation. Click it, and zotero presents you with a pop-up window. In the main part, you get a search field and the results of your search, where you can select the paper you want to cite. “Wait a minute, I need to cite more than one” you say? No problem: click “Multiple sources” and you get a dialog that allows adding more.

(Click for full size, readable version)

Once you are ready, scroll to the end of your document and click the icon that creates a reference list. Presto!

Seriously, it can really be this easy!

“But I need the right style!” Well, yes, it is important to have style. Which is why there is the zotero style repository, where you can find styles for many journals. Also, because everything is licensed under the Affero General Public License, you can easily adapt an existing style to fit your purpose. Or you can write one from scratch. That’s a bit complicated, but the former option I was able to manage repeatedly. Yeah, little programing-noob Heinrich did this!

Importing and sharing datasets

If you register for zotero you can store your datasets on their servers, and you can create and join public libraries. That means that you may be able to save yourself the trouble of entering data! Also, you can import from other reference managers, again making sharing already-entered data easy.

No more excuses

So now you have no more excuses. Use a reference manager, and deliver perfect reference lists!

Obviously, not all is gold that glitters, and all programs have their little flaws and bugs. Also, you will find a gazillion ways of messing up when using them. However, once you have either gotten back a paper with no mistakes, or (even more time-saving), once you have re-formatted a manuscript’s citations and reference list for submission to a different journal than planned, you’ll LOVE your reference manager.

For the persistent here’s a pretty fossil.

Gastonia cast mounted at the Museum of Ancient Life at Thanksgiving Point.

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About Heinrich Mallison

I'm a dinosaur biomech guy working at the Museum für Naturkunde Berlin.
This entry was posted in Ankylosauridae, Dinosauria, How to, Ornithischa. Bookmark the permalink.

7 Responses to How to………. 4: cite and reference

  1. Cheers again Heinrich! Gonna give this Zotero a whirl, never liked all these reference managers and the like (Mendeley is wank)..

    You’ve painted a massive target on your head now too, people will be sending you unfinished manuscripts of all sorts to check for reference/citation consistency ;)

  2. Andy Farke says:

    I’ve used Zotero more than a few times – the point where it gets complicated is when there are multiple authors, most of whom don’t use a reference manager (or use a different reference manager). In this case, I’ve found the best solution is to either copy/paste their changes into the “real” MS, or else cross my fingers that their edits don’t completely bork the codings in the MS file.

    • Oh yes, that can be a real bother! I once had the luck of two very cooperative co-authors on a research grant. They used strike-outs an added new citations with a yellow background color, and I added or removed the zotero fields accordingly. Worked fine, but only because they were very thorough.

  3. dmaas says:

    ooooh… pretty fossil!



    yeah, yeah. I’ll go back and read the article. :-|

  4. Mike Taylor says:

    Shame that the reference manager didn’t help with the error in the reference that actually matters: the misspelling of “hyposphene”!

    What a monumental waste of everyone’s time and energy all this is. The world should have one (1) reference format, and all journals should use it. There, done. See also http://reprog.wordpress.com/2010/08/03/the-second-stupidest-thing-in-the-world/

    Yes, reference managers help with this problem. But it’s a stupid problem in the first place. We shouldn’t need help with it.

    • I agree that one format for all would make life a lot easier. I do understand that journals often try to reduce space usage and thus printing and shipping costs in conventional, dead-tree printing. Online journals, however, should always opt for as much info as possible, and for a comfy way of presenting it (JEB is a prime example of how to do it).

  5. Pingback: Stas Meshkov is a thief! | dinosaurpalaeo

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