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?

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?

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 - Part I

Everyone has a massive reference library, but few know how to manage it. Ideally, you want an application that will let you record all of your papers and import formatted citations into a document. In the upcoming series of posts, I'm going to review some reference managers, both open source and commercial.

Endnote
This program is the classic reference management program, and probably one of the most widely supported by publishers. It has been around for years now, and it shows the polish and feature richness that you would expect for a mature program. This is not an open source or free program, but I include it here just as a standard of comparison.
Pros: The Cite-While-You-Write feature is quite handy; this tool allows you to build your paper's reference list automatically while you type the paper (hence the name for this feature!). Also, Endnote has a very broad output styles database, and it is quite easy to build reference styles (JVP even has a style available from the journal website). You can format italics within each bibliographic entry. It is quite easy to import references from journal websites, too. Available for both Windows and the Mac OS.
Cons: It's expensive - $250 to download, and $300 (oops, I mean $299.95) to have a physical copy shipped to you. Also, there are occasional functionality issues if you try to run the program under WINE (and Cite-While-You-Write doesn't work in OpenOffice.org). No native Linux version is available.
The Bottom Line: If you can afford it, Endnote is the way to go. It has polish and pizazz, and it is widely supported. Linux users are better off looking elsewhere, though.