For my work I need to reference a lot of statements, mainly with papers and books in the biological / medical literature. Usually “professionals” use two proprietary software, Reference Manager or EndNote (both owned by Thomson Reuters). But there are a few very interesting free alternatives (see this comparison of reference management software).

I switched from Mendeley to Zotero a few weeks ago and I’m very happy. Here is why …

First, let me say that I was quite happy with Mendeley. There is a nice website, a desktop application, mobile apps (now also for Android) so you can add, edit and consult your references everywhere (even offline, synchronisation needs connectivity of course). Mendeley does what it needs to do: it can capture references from websites (like Pubmed or publishers’) within the browser, you have several options to file and sort your documents, citing papers from a word processor is easy. It’s free to use with some amount of space (here, “free” means it costs nothing) and I even was a Mendeley advisor.

Zotero does all this (minus the advisory program) but I feel it does it better. Zotero is also free and here I mean it’s a free software you can contribute to (the code is on Github). Not that I am able to but the idea of people being able to look at its code and fix or improve it appeals to me. Plus, it is a project of the Roy Rosenzweig Center for History and New Media (RRCHNM) at George Mason University and not one of the major publishers of closed access papers (Elsevier).

By the way, it’s funny to see that EndNote and Reference Manager are owned by a company that organise and summarise content (Thomson Reuters creates a.o. the Journal Citation Reports) and that Elsevier, a company that publishes content, bought Mendeley.

At first look, Zotero desktop interface might look too simple but it’s just plain efficiency, without bells and whistles. Most of the information is available at a glance, from the high-level hierarchy of “collections” (think of drawers) on the left, the main list of references in the middle (think of headers of bristol 3-by-5 index cards) to all the details of the currently selected reference on the right.

Double-click on a reference and you open the publication in PDF if you have it. If you don’t have it, it brings you to the abstract (well, to the page the reference was created from). And Zotero opens the PDF in your PDF reader, it doesn’t try to open it in its own reader with its own convention to store annotations you might add to the paper. Simple. Efficient.

Zotero is born from the browser (Firefox), it uses the same language, it can even just live in your browser. Maybe because of that, I have the feeling it has currently the best capture capabilities on the market. With proprietary software, the last time I used them, everything needed to be done within the software. But doing my bibliographical review outside the web is not my way of working: on the web, you have PubMed, linked to all publishers’ websites, with full-text if available, you have also access to related articles, books, etc. My first scan of the literature always includes a lot of things I don’t want to keep for later on (except to document a systematic literature review). But for the papers I keep, Zotero always managed to correctly capture the metadata, is able to download the PDF in most of publishers websites (where I have or my employer has access) and puts it directly in the collection currently open in Zotero desktop.

I read something interesting, I click on the Zotero icon and the paper sits in my library. How easier can it be?

So, what I like about Zotero is that it does everything very simply and does it with efficiency. And it’s free (as in free speech)!

First illustration: Source Material from Josh DiMauro on Flickr (licence CC-by-nc-nd). Screenshot is mine 🙂

• Computers
• Open Source