Sunday, 9 September 2012

Mendeley and Zotero - let the games begin

A few days ago I sat down to start planning out my teaching sessions and started considering how I would recommend to our students they manage their information - not just by noting down the references of useful sources they find, but practical ways of saving and storing documents in a way that will enable the to find them again. I was reminded of this blog post by Patrick Dunleavy I read last week: 'I was an EndNote refusenik, but now I’m a Mendeley convert' and I decided it was about time I started exploring some online tools.

So, a few weeks ago when I was starting to think atbou Thing 15 I downloaded Zotero Standalone. and then forgot about it. I am not a firefox user, having been converted to Chrome a while back and discovering that using any other browser now seems just very clunky. Nevertheless, I thought I'd give Zotero a go, and see how far I got. Not very far is the answer. Unfortunately while on the university campus I am restricted as to the things I can download, and apparently add-ons into my browser aren't allowed, so I failed in my attempt to download the Zotero Connector. I began to feel the stirrings of frustration. Next I tried to import a document, which didn't work, and directed me to a singularly unhelpful help page. I started to play around with trying to manage pdfs and bibliographies and found myself very confused. At this point I gave up. Sorry Zotero.

I decided to turn to Mendeley and play with a different tool. Downloading Mendeley desktop was straightforward (as was downloading Zotero Standalone, to be fair). But the Mendeley interface seemed more intuitive, and the help far more abundant. It took me no time at all to find the 'watch folders' function, and suddenly all of the pdfs I'd named in a cryptic an inconsistent manner over the last 3 years, and then carefully stored in a selection of random folders, magically appeared in Mendeley - the majority of which with the correct metadata and all with the pdf attached. I was impressed. I then signed-in to Web Mendeley and the sync function meant the records for all my documents were there instantaneously  Impressed again.

It was about now I wanted to download the Web importer for my browser - but I knew I'd run into the same problems downloading it as I had before, so I went home to try this. Having felt a little guilty about being unfair to Zotero, I also downloaded the Zotero Connector to compare. I think the Zotero Connector works better - it'll pick up all of the records on a webpage and import them into Zotero Standalone very quickly. Mendeley Web Importer was more tricky, as you have to allow pop-ups for every separate site, and make sure you're logged in to Web Mendeley, You then get a list of all the records on a page, and select each one for downloading individually (although this was useful - a quick way of sifting through my results and only saving the records for the results I thought were most useful). As far as I can see I'd still need to download and save my pdfs though if I wanted them stored in Mendeley Desktop as well, so perhaps saving the pdf directly to my watched folder would be a better way of importing the information...and side-step pop-blocker issues with the Mendleey Web Importer.

By this time, as you can probably tell, I was sold on Mendeley. Installed at work and at home, with my documents quickly synced across both, and the watched folder option - yep, it's all working for me. The final thing to do was install the MS Word add-on to use Mendeley to create my citations and references in an actual document. This installs straight into the References ribbon in Word, and is straightforward to use. In fact, under the Add-ins tab, the Zotero reference management tools had appeared as well so I had a play with these. I'm not sure there's much to choose between them really. just as, if you have access to Endnote or Refworks, you'd be using those as well in much the same way. And I've never really used this sort of tool in my own work, as I find tinkering with the style to make sure it meets my needs time-consuming and frustrating. So I gave up at this point - these are my own prejudices effecting my judgement.

I suspect, for anyone needing to use a bibliographic reference tool, using either Zotero or Mendeley would be extremely helpful, and possibly more user-friendly than Endnote. Mendeley gets my vote though, just for how incredibly easy (and satisfying) it is to use. And I haven't even started exploring the collaborative/file-sharing functionality that's made Mendeley so successful...


  1. FYI - getting PDFs into Zotero is as easy as dragging them. The import function is for importing bibliographic data like PDF. I've clarified that on the support page the error message sent you to.
    Like Mendeley, Zotero can get bibliographic data for PDFs online:
    though for both programs, the quality of that data varies (e.g. initials instead of full first names of authors, incomplete Journal names, no abstract, etc.). Especially if you want to use the software for citation generation, it is a much better idea to go through the publisher websites.

    1. Cheers Adam - I figured it would be something I'd missed!

  2. Wasn't going to bother much with this task, but having read this I am at least intending to take a look at Mendeley.

  3. I am one of the founders of Docear, which is a new software for organizing, creating, and discovering academic literature. Today, we released version 1.0 of Docear after a ~2 year beta phase. If you are interested in reference management, you might want to have a look at Docear. The three most distinct features of Docear are:

    1. A single-section user-interface that differs significantly from the interfaces you know from Zotero, JabRef, Mendeley, Endnote, ... and that allows a more comprehensive organization of your electronic literature (PDFs) and the annotations you created (i.e highlighted text, comments, and bookmarks).

    2. A 'literature suite concept' that allows you to draft and write your own assignments, papers, theses, books, etc. based on the annotations you previously created.

    3. A research paper recommender system that allows you to discover new academic literature.

    And Docear is free and open source and available for Windows, Mac, and Linux. More information can be found in our Blog, including a detailed explanation of what makes Docear superior to Mendeley, Zotero, etc. (at least in our opinion :-) ).

    If you don't like reading, there is also a 6 minute introduction video on our homepage ;-)

    In case you are using a BibTeX based reference manager such as JabRef (and you don't want to switch to Docear), you might at least be interested in Docear4Word Docear4Word allows you to insert references and bibliographies from BibTeX files to MS-Word documents. Hence, it makes writing papers much easier, since e.g. JabRef has no own MS Word add-on.

    Finally, I would like to point you to a recent Blog post I wrote about what makes an evil reference manager. Maybe the post helps you deciding which reference manager to use (even if it's not Docear).