My take on the battle of bibliographic software

Time was when managing a reference bibliography required a stack of cards, either plain 3 x 5s or, if you were very technologically advanced, bigger ones with holes punched around the edge, and a secretary or, if you were technologically advanced but lower than pond-scum on the hierarchy, a knitting needle, a typewriter and a big bottle of correction fluid.

Time was when the worst part about having a paper rejected by Nature, and considering resubmission to Science, was the thought of having to reformat both the citations and the references themselves.

Today, though, these nightmares are all but forgotten.

There are several packages that will manage your sources and help you to create citations and references in the papers you are churning out. I've used one of them, Bookends, a paid-for option for the Mac, for a few years now, and would not be without it. Recently, though, I had need to corral a bunch of authors and their disparate systems into a smooth-reading whole. So I turned to Mendeley, which offers onlineness and social tools. With Mendeley, you can create groups (open or closed) and use them to gather references from the several authors. If they've heard of Mendeley. And if they know vaguely how to use it. It seemed, at first, like an ideal solution.


In theory, one of the great things about Mendeley is that you can search the papers others have inserted to find one you need, and then copy that to your own library. Unfortunately, there are often duplicates. Furthermore, the differences between two instances of what must be the same original source are not trivial; if you actually care about this sort of thing, Mendeley may add work, as it forces you to go elsewhere to get the "correct" details. These are my qualitative impressions -- I have not backed them up with analysis as an old chum did a while back -- but they are enough to make me wary of relying on Mendeley as a source of sources, ITSWIM. 1

An even bigger problem, for me, came when I tried to use Mendeley to insert citations into a Word document and then produce the bibliography. In a nutshell, it was hopeless. There did not seem to be any kind of fine-grained control over the output, with author names, for example, being all over the shop and some of the formatting impossible to alter.

Bookends is completely different, offering extremely fine-grained control of output (You'ld like to use § as a delimiter? Certainly.) and formatting for citations and references. It also inserts no unwanted cruft into the document itself, something I noted only after switching from Mendeley to Bookends and wondering why Bookends kept barfing about non-existent citations that weren't citations at all; they were Mendeley's undigested pearls.

In the end, I used Mendeley to gather material from some of the other authors, and exported from there into Bookends for the final runs. And that showed up yet another weakness of Mendeley, the way it handles utf-8 stuff, including diacriticals. Øȟ ẙȅṩ indeed.


With the document in question done and dusted, at least for now, I thought it might be worthwhile thinking about future efforts of the same kind. As I said, one of Mendeley's great strengths is that it shares bibliographic information. The downside is the quality of that information, about which, to be fair, Mendeley makes no claims. Its other great weakness, at least in the free version I used, is that it offers almost no formatting abilities. Bookends has great and almost infinitely flexible formatting. Ironically, the one "social" aspect of Bookends is that users can share their formatting templates for specific publications and for importing from specific databases. That is a tremendous benefit.

What if Bookends allowed users to share bibliographic information?

Not the PDFs themselves because there would be rights issues. But the actual metadata. One advantage I can see is that because I do care about accuracy, I know the details I have are mostly correct. I could share with confidence. And I could hope that other people who have actually paid for the software might be similarly diligent. It would also be possible to do something better than Mendeley about disputed items. Mendeley currently flags some things as needing attention, but doesn't actually tell me where to look. Anyway, that's just a thought. A second thought is that maybe Bookends already allows this, and I have not discovered how. Given its many complexities, most of which I have not yet discovered, this is not beyond the realms of possibility.

I suppose another solution might be for Mendeley to start doing a better job of curating the accuracy of its entries, but somehow that doesn't seem nearly as likely.


There are, of course, other solutions that allow sharing for the discovery of sources. Citeulike still has a lot going for it, although I have neglected it of late. 2 It certainly offers an alternative for collecting references from a group of authors. I've no idea how it performs in generating citations and bibliographies, but it could easily replace Mendeley as the corral, with an easy export to Bookends. Others I haven't used at all. For now, I'm sticking with Bookends. And paying for it. Happily.

  1. The same chum is first author on Defrosting the Digital Library: Bibliographic Tools for the Next Generation Web, which although it is now over three years old remains an excellent introduction to the costs and benefits of online libraries.  

  2. Maybe I should consider synchronizing Bookends and Citeulike on a regular basis.  

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