19 November 2013

zotero and reference management

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Why I use Zotero

Update 2014-01-02 to explain how I use zotero-autoexport.

I was recently asked why I use Zotero and I thought Id expand on those comments more coherently. There are many reference-management programs (compared here) and I don’t intend to compare them all, but will simply describe my experience with a few programs and why I think Zotero is the best option for collaborative reference management.

I have three primary objectives for using a reference management program:

  1. Citing references when writing papers
  2. Collecting, organizing and searching references
  3. Sharing articles with colleagues

Most programs accomplish the first. I used Endnote for years (including my dissertation) and if you’re working with Microsoft Word, it’s probably still the best option.1 Endnote frustrated me for two reasons. One, adding references was a pain (this has probably improved since I last used it) and the collaborative aspect was terrible. Even emailing a Word document between collaborators with Endnote citation tags almost always ruined the references, requiring re-formatting.

I recently discovered an awesome plugin called zotero-autoexport that, as the name suggests, automatically exports your entire library or selected collections, in whatever format you want! (If you use this, you should ‘Donate’ ((I did!) as it’s a great tool and the developer appreciates the donations.) If you select Bibtex you can a ‘.bib’ file that you can open with JabRef, and more importantly, use with LaTex/Biblatex for writing citations. One inconvenience is the standard zotero citekey is long and unwieldly. From this blog I got the tip on how to change this.

  • Open your translator’s directory through Zotero Preferences. Open the Advanced pane. Click on “Show Data Directory.” This will take you to a “zotero” folder. The “zotero” folder will contain a “translators” folder.
  • There should be (with Zotero Standalone 4.0.17 at least) one called “Bibtex-RobinTan.js”. Open this and read the comment details at the top. If you want a standard bibtex “author-year” key, on ln 17 change set var citeKeyFormat = "%au%yr";. Save.
  • Open the Preferences for zotero-autoexport and select your modified “Bibtex-RobinTan.js” as the export format. Run. Open the exported bibtex file and it should have all your references in bibtex format with your preferred citekey!

My personal workflow is to convince collaborators to use Zotero and have them save references to a Group library (note that this didn’t work at first but the package author quickly fixed the bug. He got a donation from me!). I set up Zotero autoexport to export this library to a Dropbox directory. Every time I work on a paper, I copy the relevant auto-exported collection into the directory with the .tex manuscript file and use then I can use Biblatex for citations. I actually prefer manually updating the .bib file associated with a given manuscript as I’ve recently started to use git for version control of my manuscripts, and this prevents odd problems. The only bug I see to this is that co-authors depend on me to export the .bib file…but in theory they could do it themselves (as long as they export from Zotero) and next time I export we’d end up with the same file.

Onto the second point; we’re all overwhelmed by the literature. The ability to quickly collect and organize references format has become critical. These days we need software that can not only handle traditional journal articles, but pre-prints and blog posts. I started using Mendeley for this reason. When I last used it a year ago, Mendeley was probably the best at this. It has a beautiful and easy-to-use interface, and very functional citation functionality. The initial buy-in is cheap (2GB free storage!) but here’s the big catch. Shared team plans start at $49/month (and that’s the education rate!!!), only allowing you 5 collaborators per group!!! Come on guys, this is outrageous. Admittedly, they do allow unlimited number of groups and space, so you could just spawn groups, but in my academic future, I can’t see spending $588 a year just to share references with colleagues and students, which brings me to point (3).

In my wild west dreams of running my own lab with busy students and collaborators across the world, I want to be able to share useful articles and references. When writing papers, I don’t want to run into compatability problems, but to use the same reference database. Instead of searching through email for papers, I want to be able to go to my reference manager and find the relevant article, including a copy of the PDF and any notes. Enter Zotero.

Zotero does everything I’ve mentioned above, though maybe not quite as well as the other programs. Similar to Mendeley, it’s free to download and available on all platforms (go linux!). It really excels at downloading bibliography information and PDFs with a single-click from your web browswer. Zotero doesn’t have a built-in PDF viewer, but I actually prefer using an external program for opening and annotating files so this isn’t a problem.

But here’s the big plus for Zotero: you can have any number of shared libraries with any number of members. I currently have 4 shared libraries with 2-12 collaborators each…at no extra cost. We can all add papers to the library, and manage references without emailing back and forth. And this will expand to however many projects and collaborators I can handle! Yay!

When your library expands beyond the free 300MB, you can pay Zotero for extra storage. I pay $20/year for 2GB (almost 2,000 PDFs) and will probably step up the $60 for 6GB soon (a mere $5 per month). I think is quite reasonable for the service as you also get a decent web interface which means you can access your articles from anywhere, but if you want cheaper here’s information on how to sync your library using Dropbox.

For what it’s worth, Zotero also open-source. There are many useful plug-ins, which can make working with latex or LyX easier (hint: time to ditch Word!). Finally, though I’m actually not opposed to this on any principle, Zotero isn’t owned by Elsevier as is Mendeley.

So to conclude, I use Zotero because

  • Low buy-in - easy to to get collaborators to sign up
  • Sustainability - the cost of maintaining shared libraries with collaborators is manageable on a postdoc budget
  • Ease of use - web-import functionality is great. now if I only I had time to read all those papers. but I can search them!
  • Open source - yadda yadda yadda

  1. Yes, as you can probably guess from this statement, I gave up on Word in favor of latex (or Google Docs if I really need WYSIWYG) and think you should to if you perform statistical analyses and write papers (which means you if you’re reading this and you’re a scientist), but that’s for another day.

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