I’ve grown increasingly frustrated with EndNote, its awkward interface and buggy Word integration. I’ve looked at a few alternate solutions: Mendeley, Papers, CiteULike. I ended up settling for Zotero, which I now love.
I don’t think it makes any sense for a citation management software to use ask you to use its own internal search engine. There’s already a ton of excellent search resources: Google Scholar, PubMed, Scopus. The right time, in my opinion, to enter a citation into a database is right after you’ve read the abstract and decided it was relevant. That way your citation database can also act as a reading stack. Since you browse for papers in a web browser, it only makes sense that citation software should be tightly integrated with a web browser.
Zotero is a well integrated Firefox plugin that allows you to add references as you are browsing the internet. It works on Windows, Mac and Linux (Ubuntu is shown above). It works on multiple sites: Google Scholar, Wikipedia, PubMed, Nature, Neuron, J Neurosci/phys, Amazon, etc. When you see a referenced article that you like, you click on a button in the address bar and it adds it to your list of references (quite similar to how one manages bookmarks). It parses the information available on the site and formats it appropriately (it reads authorship information, title, journal, abstract if available, etc.). You can add notes to a reference, attach a pdf (or have it do it for you automagically), link articles together, put stuff in folders, add tags, etc.
Perhaps its most useful feature is automatic synchronization between computers. I often think about research ideas on my way home and do a quick search for interesting references on Google Scholar before going to bed. The next day, I can access all the references I found from work and print them up. I encourage you to take two minutes and watch the introductory video on the homepage, it’s very convincing.
xcorr: AI & neuro 
6 responses to “Citation management with Zotero”
[…] is my preferred citation manager; it lives inside of Firefox, and it automatically detects references to papers when you browse a […]
[…] Zotero is a citation manager that I adore. Previously, I lamented that it’s troublesome to sync a Zotero library to a tablet. I’ve just finished a simple app to give you an easy way to view your Zotero library on the go. Kind of like Pocket (formerly read it later) but for papers instead of webpages. […]
[…] trickiest bit is getting the papers in and out of the tablet. As I’ve mentioned before, I’m a big fan of Zotero. Originally, I thought I would access my Zotero library directly on the tablet. There’s an […]
SWEET. I also hadn’t known about the drag/drop pdf ability. I absolutely cannot imagine waiting in line to photocopy a journal article back in the day… And before photocopiers?
For emailing references, if you use webmail (Gmail for example), once you have the refs in your library you can drag and drop them into the body of an email and it’ll create a little bibliography, like so:
1. D. Ferster et K. D Miller, « Neural mechanisms of orientation selectivity in the visual cortex », Annual Review of Neuroscience 23, no. 1 (2000): 441–471.
2. P. Lennie et J. A Movshon, « Coding of color and form in the geniculostriate visual pathway (invited review) », JOSA A 22, no. 10 (2005): 2013–2033.
3. Rajesh P. N. Rao et Dana H. Ballard, « Predictive coding in the visual cortex: a functional interpretation of some extra-classical receptive-field effects », Nat Neurosci 2, no. 1 (janvier 1999): 79-87.
4. D. C Somers, S. B Nelson, et M. Sur, « An emergent model of orientation selectivity in cat visual cortical simple cells », Journal of Neuroscience 15, no. 8 (1995): 5448.
I absolutely love zotero. The best part by far is the ability to add a paper as soon as I get a link to it or see it in a search. The only thing I’d add is an option to quickly email a link, citation, or paper to someone rather than having to click through to the original site.
It also elegantly handles adding non-traditional academic content, e.g. blogposts or tutorials that I might not want to cite, but want to have in the same place as the papers I read.
Finally as with many open source projects, the online documentation and support network is pretty good.