Citation Format Wars

Over at SV-POW!, Mike Taylor recently addressed the issue of how to format in-text citations. Writing in his inimitable style, he makes the case that PLoS ONE is simply doing it all wrong; the majority of commenters there have agreed. I posted a lengthy comment there, but realized that it would be appropriate to revise and republish those thoughts here too.

First off, let's have a quick recap of the issue. When writing a scientific paper (or any paper, for that matter), it is essential to credit the sources of information and ideas. Not only does it allow the reader to learn more about the topic, it's the ethical thing to do. Rather than a simple reference listing at the end of the paper, most scholarly works also reference the relevant works within the text. This is called an in-text citation, and allows the reader to know precisely which information was associated with which author.

Two Worlds
Two styles of in-text citation dominate the scientific literature. The first of these is author-year, which looks something like this: (Farke, 2010). The second is numbered, which looks like this: [1]. This number then refers to a specific bibliographic entry at the end of the paper. Many variants of each style exist.

PLoS ONE uses numbered citations, in common with many other high profile journals (such as Nature), and in marked contrast to most of the paleontological, geological, and anatomical literature (such as Journal of Vertebrate Paleontology, The Anatomical Record, Geology, and others). The SV-PoW! post, of course, argues that the numbered format is vastly inferior to the author-year format. Let's boil the argument down to its essentials, and delve into the pros and cons of both formats in more detail.

Two essential reasons are given for why the author-date format are preferable: 1) ease of reading for authors familiar with the literature; 2) paleontologists don't like it. PLoS ONE thus chose a numbered reference format simply because they wanted to copy the glamour magazines. Do any of these arguments hold up?

Advantages of Author-Year (and disadvantages of Numbered)
Of course, there are some significant advantages to the author-year format. These include:

1. It's easy for readers who are familiar with the literature to know exactly what's being discussed. If I quote from my 2010 JVP paper on ceratopsian sinuses, "Less detailed descriptions have been published for other chasmosaurine and some centrosaurine ceratopsids (e.g., Gilmore, 1917; Lehman, 1990; Sampson, 1995; Sampson et al., 1997)," a long-time ceratopsian worker will know right off the top of her or his head that I'm talking about the Gilmore Brachyceratops monograph, Tom Lehman's paper in the Dinosaur Systematics volume, Scott Sampson's description of the Two Medicine centrosaurines in JVP, and the ZJLS paper with Scott, Michael, and Darren. I see pages from those papers when I close my eyes, and I could almost write the citation for each of them off the top of my head.
2. You don't have to flip back and forth between the main text and the reference list. For the ceratopsian expert described above, there's no need to waste time skipping around the paper (or PDF). It's just easier.
   
3. It helps readers new to the field to become familiar with the major names and papers. See the names "Wedel," "Taylor," "Wilson," "Curry-Rogers," and others often enough, and you probably have a good picture of a few of the major recent workers in sauropods.
   
4. It's easier for authors to keep their references straight. When writing and revising without use of a citation manager, the numbered system can get very unwieldy. If you add a reference in the middle of the paper, you not only have to renumber the entire bibliography after that reference, you also have to change the numbers within the manuscript itself. Miss one, and your readers are going to be grumpy when the number and citation don't match up.
5. It's familiar to the paleontological community. As mentioned above, "It's Got What Paleontologists Crave."
   

Disadvantages of Author-Year (and Advantages of Numbered References)
As you might have guessed, there are some disadvantages, too:

1. The author-year format is helpful only if you are already familiar with the relevant literature. Otherwise, you're still in the game of flipping back and forth to the reference section. Anticipating that most of my readers are savvy to vertebrate paleontology, but not to the latest in tectonics, contrast my above example in point 1 with this example (Najman et al., 1997, Geology 25:535-538): "Why is this so, as crustal thickening and metamorphism are thought to have occurred by this time (Frank et al., 1977; P. Zeitler in Hodges and Silverberg, 1988; Inger and Harris, 1992; Searle, 1996, and references therein; Vanny and Hodges, 1996)?" Although I understand the meaning of the sentence, the names and dates have absolutely no meaning to me, other than to help me find the appropriate citation in the back. I'm not familiar with that literature, so I'm annoyed by the extra text.
   
2. Not every reader wants to become an expert on a given subspecialty. Believe it or not, I may not be reading a plate on Indian tectonics (or sauropod vertebrae) because I want to become an expert on said subject. Let's say that I'm chasing the above-mentioned example from Najman because I want to know the context for some fossils I found in a format described in that paper. I just want the bare minimum of info, and I don't care about Frank, or Zeitler, or Hodges, or Silverberg, or Inger, or Harris, or Searle, or Vanny. Sure, maybe I'll chase some of those references for alternate opinions, but once that's done the names will probably never cross my mind again. This leads to the next point. . .
3. The author-year format clutters the text. I'm not the first person to state this, and I'm not the last. By editing my ceratopsian quote above, you now get: "Less detailed descriptions have been published for other chasmosaurine and some centrosaurine ceratopsids [1-4]." Try the same with the Najman quote. Much shorter and more easily readable. A comment on the SV-POW! post by Zen Faulkes gives some more nice supporting opinions.
4. Most of the rest of the scientific world uses numbered citations. I think people are giving Science and Nature a little too much credit for driving the numbered citation game. Yes, they certainly are the most visible journals to those of us in paleo/geo/zoological sciences, but that's a rather myopic view. I did a quick survey of the other 99 percent of the scientific literature, and numbered citations simply dominate. Even arXiv - the epitome of digital presentation with no real standard format - has a vast majority of papers with the [1,2,3] style (in fact, the only counterexamples I found were in a handful of biologically-oriented papers). The medical literature (medically oriented papers are the great majority of PLoS ONE submissions), computing literature, physics literature, etc., most often use numbered citations. Let's face it - paleontologists are not the biggest fish in the sea. It doesn't mean we're wrong or can't change things, just that it's a very uphill battle.

Closing Words
So, I have to say that the arguments for author-year and against numbered references are not as simple as one might hope. Major advantages and disadvantages characterize both formats. In the end, I suspect much of it comes down to "what we were born into." I like the author-year format because that's all I've ever known. My spouse, who is a physicist, surely thinks otherwise, but then again all she has ever known is the numbered format. She also thinks paleontologists are silly because we don't use LaTeX (and good luck getting that instituted, no matter how easy it would make things for us).

Interestingly, I came into this with a strong preference towards the author-year citation format, but after thinking about it I'm not sure that numbered citations are the Great Evil that they have been made out to be. What are your thoughts?

Update: The above-mentioned Zen Faulkes has a post strongly coming down on the side of numbered references. He argues that numbered references decrease overall manuscript length, greatly improve readability, and level the playing field for both readers and cited authors. The last argument is particularly novel, and strikes at the heart of the true purposes of citations. I'm not sure I totally agree, but it's definitely food for thought. [12 January 2011]

(As an interesting side-note, the author-year referencing style may be so common in the paleontological and zoological literature because of a historical accident - the format was apparently invented by a Harvard zoologist, and spread throughout the zoological part of the literature. I suspect the weight of the Harvard name didn't hurt.)

Disclaimer: Although I am a volunteer editor at PLoS ONE, this posting is written strictly as my private opinion.

Thank you to the many commenters at the SV-POW! blog, whose thoughts inspired this post.

A New Reference Manager to Watch

Nearly two years ago, I ran this series on a bunch of reference managers available in both commercial and open source models. Some things have changed since then, and others have not. OpenOffice.org Bibliographic has pretty much stagnated, Bibus has undergone incremental improvements, and Zotero has leap-frogged ahead to a function-rich 2.0 beta and survived a lawsuit from the makers of Endnote (which remains the commercial standard for reference management).

Today, a post at Bora Zivkovic's Blog Around the Clock higlights yet another new bibliographic offering, Mendeley. It is free, but not open source, and still in the beta stage, but it looks like it might offer some interface improvements over programs like Zotero and Endnote. Definitely worth following - do any of you readers have experience with Mendeley?

Zotero in the news. . .

And this time, because of a lawsuit from Thomson Reuters. Here's hoping this turns out for the best! Thanks to Mike Taylor for pointing out this news item (also here on Nature).

The basic gist of the lawsuit, apparently, is that the latest beta version of Zotero imports the Endnote style files, an alleged violation of the Endnote user agreement, among other things. Thomson Reuters alleges that the "reverse engineering" of their files (and allegedly, part of the software) is illegal. . .we'll see how this pans out, but I am not sure if I see the difference between what Zotero did and the file format translation capabilities of programs like Microsoft Office, etc.

JVP - Zotero Style!

In a previous post, I lamented how difficult it is to create custom style files in the program Zotero. As a brief recap, this reference manager does a fantastic job of downloading references from the web and creating citations and bibliographies in Word or OpenOffice.org Writer. But, if you want to venture beyond the default style library (which is steadily expanding with a number of add-ons), you have a little style-file writing to do.

Creating a Zotero style file is not for the faint-of-heart. These are written in an XML scripting language called "CSL" (for "Citation Style Language"). As I was writing my dissertation, I needed to format one of my chapters with the format for Journal of Vertebrate Paleontology. Of course, Zotero didn't have a style available for this, and I wasn't in any mood to format everything by hand. So, I decided to invest an afternoon in learning enough CSL to be dangerous.

In actuality, I didn't learn much CSL at all. I took an existing style (American Psychological Association) and retrofit it for JVP. The APA style was close enough to start, and I had to tweak author orders, abbreviations, etc. The result is uploaded here. Caveat emptor!!! As you will find, my work is nowhere near perfect - I got the citation styles down pretty well for journals and edited volumes, and beyond that things might be a little wonky. Anyone who wishes to do their own tweaking is welcome to do so - and I would appreciate it, in fact!

Because I'm not a real code-head, I had to rely on a few "crutches" to limp through modifying the style file. First, a style preview tool, written by Dan Stillman, was invaluable. Follow the directions here in order to use that. Second, I relied on the CSL schema, which was the final authority on what various parameters meant. After that, it was tweak, test, re-tweak, and re-test, until I got something I could live with. It took a few hours of time, but was well worth it.

Good luck! Anyone else have their own style files they've written?

The Open Source Dissertation

My university has done a wonderful thing, in accepting only PDF files for deposition of a thesis or dissertation with the graduate school. Gone are the days of printing 5 copies of a 300-page document on acid-free paper that costs 20 cents a page (and then finding out that one of the margins is 0.1" too wide, so please correct and resubmit before the deadline in three hours). The transition is a wonderful step forward, and also means that it is much easier to distribute the dissertation.

As a proponent of free and open source software (having made the big switch about a year ago), I wanted to do as much as I could within the realms of that universe. This posting summarizes the software I used, with the hope of inspiring others to follow a similar path (whether in whole or in part).

Data visualization: I processed all of my CT scan data in 3D Slicer. For segmenting structures, generating surfaces, and measuring volumes, look no further! [I still need to do a more complete post on this one.] Additional analysis was done in ImageJ.

Data analysis: Initial data entry in OpenOffice.org's Calc, with analysis primarily in R and an occasional venture to PAST.

Figures: Raster image editing was done in the GIMP, and line drawings or composite figures were assembled in Inkscape.

Word processing: All done in OpenOffice.org's Writer. The PDF output function was very nice for sending drafts to committee members and advisors, and the software's Microsoft Office compatibility is such that I could also send and receive marked-up documents (in .doc format) pretty easily. For the final document, I exported each chapter in PDF format.

Referencing: All of my references were sorted, organized, and rendered as bibliographies with Zotero. Along the way, I created custom styles for Journal of Vertebrate Paleontology and Zoological Journal of the Linnean Society. More on this process in another post.

Document assembly: To assemble all of my dissertation's chapters into a single PDF document, I used Ghostscript. The output was quite pleasing, and easily accomplished through the command line in a matter of seconds.

Presentations: For my oral dissertation defense, I created my presentation using OpenOffice.org's Impress.

I Win!

In a previous post, I lamented the fact that BioOne forced all of its article titles into all-capitals. This was a serious annoyance for anyone exporting references into their favorite bibliographic manager, because you had to retype the title for inclusion in bibliographies. But, I just went to download the reference for the latest paper on Triceratops cranial ornamentation and found a pleasant surprise. The titles are now in upper- and lower-case! Sure, you still have to do a little editing mid-title, but at least it's not a case of complete retyping. Unfortunately, it seems like the old references are still in all-caps. Ah well.

Old Format:
THE SMALLEST KNOWN TRICERATOPS SKULL: NEW OBSERVATIONS ON CERATOPSID CRANIAL ANATOMY AND ONTOGENY

New Format:
Ontogeny of Cranial Epi-Ossifications in Triceratops

I like to think that BioOne changed this due to all of the angry readers of this blog who wrote in, or that some editor had a change of heart after reading my post. Yeah, I'll go on thinking that. . .

Zotero 1.0.3 now available

Some readers may remember my endorsement of the Firefox plug-in Zotero as one of the best open source options for reference management. You will be pleased to know that a nice little upgrade - from 1.0.3 from 1.0.2 - is now available. It includes some added functional support for downloading references from some major sites, such as PubMed, updated output styles, and some handy fixes for a few bugs in word processor integration. Zotero 1.0.3 is a must-have release for anyone who uses this program (and is worth a look for those who don't use it yet!).

Reference Managers on Parade - The Conclusion

Other Options
My wife, a physics graduate student, is constantly puzzled by the fact that the paleontology community hasn't adopted LaTeX. Odds are that most of you reading this (someone does read this blog, right?) have never heard of LaTeX. It's somewhat akin to HTML, in that it's essentially a markup language for scientists. Thus, it's a little scary for those who have never ventured beyond the confines of their word processor. But. . .it's incredibly powerful. There are a whole host of bibliography management tools for LaTeX - JabRef is one example. The main reason LaTeX hasn't entered my sphere is because I collaborate with a lot of people who don't use it - so, there isn't a lot of incentive for me to learn it. Maybe one day, though. . .

Closing Thoughts
There isn't really a "perfect" open source reference manager out there yet. All of the packages have significant strengths, but also sometimes significant weaknesses. I think that the next year will experience major gains in open source reference managers, and hopefully by this time next year there will be several extremely good options. For the time being, I recommend experimenting to find one that works for you. Zotero is my current reference manager of choice - its integration with Firefox and capability to easily dump formatted references into a word processor move it to the top of the pack.

Reference Managers on Parade - Part IV

OpenOffice.org Bibliographic (OOoBib)
First, a disclaimer: This software doesn't exist yet. But, I've included it here just to generate a little excitement for what could be a great addition to OpenOffice.org.
Pros: According to the project website, this will greatly augment the bibliographic features for OOo Writer. We'll have to see what this entails in the long run.
Cons: Microsoft Office users are probably out of luck here. Switch to OpenOffice.org if you want to give it a spin! And the biggest current downside: this program isn't functional yet.
The Bottom Line: Look for this to appear sometime in the second half of 2008.

Reference Managers on Parade - Part III

Zotero
Zotero is a very nifty little plug-in for Firefox that has very, very quickly become my reference manager of choice. It is in quite active development, and has a very promising future ahead of it, I think.
Pros: Web integration is insanely good! So you find the webpage for the latest article in Nature. A little icon appears in the browser's navigation bar. You click the icon, and all of the article's information - authors, abstract, direct URL, etc. - is dumped into your database. Zotero also accepts the standard "reference export" option, for sites that don't yet support direct export. Also, Zotero has two very functional plug-ins that allow users to "cite while you write" in Microsoft Word and OpenOffice.org Writer, and it functions in any operating system that supports Firefox. You don't have to be connected to the internet to use Zotero, either (because all files are stored locally).
Cons: The two biggest downsides that I've run into are 1) it is insanely difficult and not at all intuitive for the average user to create output styles in the current version, and the available output styles are quite limited (although they promise to correct this in the near future); and 2) character formatting (italics, underlining, etc.) is not an option within the database. Some journal homepages (notably JVP's BioOne page) aren't yet supported for direct linking. But. . .you can still import references using the standard "reference export" option (exactly as you do in Endnote).
Note: If you export from the BioOne website, use the Procite or Reference Manager format - the Endnote format doesn't seem to capture all relevant data. And BioOne, if you're listening, it's really, really annoying that you force the titles and author names of your reference exports into all caps. No journal on earth uses this format!
The Bottom Line: Zotero is *the* open source option for reference management, and it's only going to get better.

Reference Managers on Parade - Part II

Bibus
Bibus is one of the more functional open source bibliographic managers. Based on an SQL backend, it will run in Linux, Mac, and Windows OSes.
Pros: The interface is pretty intuitive, and it is easy to create style files for output in specific journal formats. Bibus also includes a feature akin to "Cite While You Write," compatible with both Microsoft Word and OpenOffice.org Writer. Manual input of references is pretty easy.
Cons: The Bibus development team is quite small, and it can be a looooong time between updates. There is no support for character formatting in the database either (italics, underlining, etc.), which is quite annoying if your references have scientific names in them. Additionally, it's not entirely straightforward (although certainly possible) to import bibliographic information from journal websites. In the current version of Ubuntu Linux, lots of folks are having trouble getting it to link in with OpenOffice.org. This is the main reason I abandoned Bibus for the package discussed in my next post. . .
The Bottom Line: Bibus is pretty functional, but has its quirks. It's a good choice for Windows and some Linux users, but requires a little effort sometimes.