Bibliography Management (BibDesk)


In a previous post I discussed some of the benefits I discovered in using LaTeX with LyX as a front-end. Another extremely useful tool to learn how to use is a Bibliography manager. If you are like I was, and often develop a new bibliography for each paper you write, this is something you might want to consider. On the other hand, you might be used to Microsoft applications and already be familiar with bibliography managers (such as Zotero) that integrate pretty well with the MS Office family.

As I started my PhD and began writing more papers, I noticed that many of my citations were the same. Rather than copy-pasting from previous papers and then adjusting the formatting for each submission, I realized it would be much easier to have a centralized location for all the papers I wanted to cite, and have the computer deal with the formatting according to the style sheet I needed to use.

Fortunately, support for this is ‘baked-in’ to LaTeX/LyX. There are various good tools that integrate with BibTeX (as the bibliography manager in LaTeX is called), but the one that I found to be most useful for my purposes is BibDesk. Rather than explain how I do it, I’ll point you to this excellent tutorial for Mac, which describes how to set it up. In the rest of this post I’ll simply give my reasons for using BibDesk.

  1. It centralizes bibliography management.

      Using BibDesk allows me to have a single repository for all the details of every publication I will ever need to cite. I keep this single (small) text file in a cloud folder, so I will (ideally) never lose it. All of my academic writing accesses this same text file database.

      As I read new publications and decide that I want to cite them, I add them to my main bibliography database. I will never face the problem again of having to build a completely new bibliography, unless I decide to change fields completely.

  2. It forces me to be more exacting about my workflow and citation data.

      Previously, I might let one citation slip through that only had a first initial, or another minor error. Since I’m forced to fill out the same form for each citation, I also have to be more precise about the details of the reference.

      I now try to find each author’s full names (sometimes this is impossible, unfortunately), because I know some bibliography styles require full first names, etc. The same goes for full names of journals or a series - the particular style will define how things get abbreviated, if at all. And this has actually led to some interesting discoveries - by forcing myself to find the full names, I have been led to other relevant publications that were ignored by previous writers on a particular topic.

  3. It allows me to annotate and auto-file relevant documents.

      Annotations such as notes to myself (of quotable quotes, page numbers, keywords, etc..) make a particular publication much easier to find. Not only that, but if I can attach a relevant document like a webpage or a PDF, I can much more easily re-read the article. Having a searchable database is incredibly useful, particularly if the article itself is open-source and machine-readable. BibDesk can take an existing document and re-file it for you according to conventions defined by you (the user), which means that you can have a single folder housing all relevant publication documents.

      I work with quite a number of old documents that are out of copyright, and it is extremely useful to be able to download an old scan (from Google or and have it re-named and re-filed simply by dragging it onto the relevant bibliography entry in BibDesk. If I have an OCR’d version, then searching for keywords in the BibDesk search bar can bring up entries that I didn’t realize were even relevant.

Each of these reasons alone are worth getting your act together and creating a single bibliography repository. You can likely think of other good reasons, which just means there is no excuse to not do so.

Another issue that I am thinking about is how to make my library of citations/documents available on any computer with internet access via the cloud. This would ensure at the very least that I wouldn’t worry as much about losing it if my computer dies (though I’m still going to make backups regularly). A fellow academic and friend of mine has managed to integrate all of his citations and PDFs with Zotero, and make it available on his phone in an app like Google Drive, so that at conferences he can remember a publication or search for one in a conversation and pull up the reference and/or associated document to show people. This is super cool and super useful - I’ll write about it if I can figure out how to pull it off on my own, or maybe I’ll get him to write about it.