Zotero

In my line of work, good reference management is essential. In grad school I had an elaborate system of manila file folders organized by subject, in which I had copies and printouts of every paper I might need to cite. Needless to say that system became cumbersome quickly, especially once I started to work in multiple fields of research.

At NRL EndNote was available to me, so I spent quite a bit of time entering all my references into a database. It was then I realized how useful reference software could be. Not only were my references all searchable now, I was able to automatically cite references and create a bibliography automatically in Word (using a plugin). These are the two criteria upon which to judge good reference software: 1) ease of database management (adding references, searching references, organizing references, etc.) and 2) ease of use in Word (citing references, building bibliographies, editing reference styles, etc.). EndNote is actually pretty great at #2. I recently submitted a paper to Science, and after changing style settings in the EndNote Software, I only had to make one edit to my bibliography list (instead of having to make a bunch of edits for almost every reference, which is the biggest complaint I hear about reference software). But EndNote leaves a bit to be desired in #1. It looks and acts clunky. I do a lot of searching for references online, and it's not always straightforward to import into EndNote. I'm always having to manually enter the DOI and manually save a PDF copy of each paper. Also, EndNote costs money, and I would like to take my reference database with me when I leave NRL, so I've been looking for cheap alternatives.

Enter Zotero. It's a firefox plugin developed at George Mason University, and it accomplishes #1 almost perfectly. When I find a paper I want to add online, all I have to do is click an icon and it downloads all the information (including DOI) and in most cases also a copy of the PDF. I'm already searching for references in my browser, so it makes perfect sense to manage my references right there in my browser. Zotero does organization and search much better than EndNote. It allows for tags as well as directories, so you can organize everything the way you want to. And Zotero allows you to search text in PDFs! Unfortunately Zotero is not as great with #2. It has a buggy Word plugin, and their citation style settings have errors in them that can't be edited. Also, EndNote did not export DOI numbers or all the PDFs I had downloaded, so I basically have to go through the entire database in Zotero and manually save in the PDFs. However, it turns out it's much quicker just to look up the paper again online and import it directly into Zotero than to edit the existing entry.

I'm toying with the idea of using Zotero for reference management, and then when I write I'll export to EndNote so I can use the great EndNote plugin in Word, but that sounds like way to much work for what it's worth.