Bench philosophy: Reference management

Digital Bookshelves
by Steven Buckingham, Labtimes 06/2011

Some of our readers may remember what drafting a manuscript was like before the days of reference managers. Citations had to be put in by hand, double check made against the bibliography and this was done every time a piece of text was added or taken out. Boring, time-consuming and error-prone. “But we were happy in them days.” Really?

These days, reference managers (RM) do much more than put in bibliographies. So what should you look for in a reference manager? And what options are there to choose from?

Actually, we are spoilt for choice and reference managers differ in how much of your research life they want to take over – I mean, help with, sorry. Some are web-based, while others are good old-fashioned pre-cloud desktop applications. Others are proud of being just glorified index cards, while others try to integrate not only with manuscript drafting but also with other aspects of knowledge management, such as note-taking. Some are intended for just private use, whereas others centre on social bookmarking. And the great thing is you don’t even have to pay for many of them.

Let’s look at the desktop-based applications first. Now, I admit that reference managers are rapidly retreating from the desktop. After all, mobility is the watchword today. Why put a database on your PC when it is already in the cloud? But keeping their ground on our hard drives are the commercial giants, EndNote ( and ReferenceManager ( Here, we see the classic overall functional RM design: connect with bibliography database for searching, pull down the ones you want onto your PC, insert them direct into your document as you write. These are the main steps that probably account for 90% or more of your interaction with this programme.

Be adventurous and creative

Braver souls might venture to try some of the more sophisticated tricks it can offer. For example, you can use EndNote to manage your figure legends and the placing of your figures in-line in the manuscript. EndNote will also try to find full-text papers based on the bibliographic data you feed it, and allows annotation and full search of PDFs. But EndNote refuses to be left behind the flight into the web – a licence automatically entitles you to an account with EndNoteWeb.

Thomson-Reuter’s reference management products rely on their solid reputation as no-nonsense, trustworthy stay-in-the-background applications. So much so, that if you look at the ReferenceManager website, you might get the (wrong) impression that this app is somewhat lacking in energy: the “latest features” section points out the ability to spell check and to “move between references with new, previous and next buttons.”

For Mac users, a prime contender in the desktop class is Bookends. In keeping with the Mac claims to ease of use, Bookends is particularly good for attaching arbitrary files to references, viewing PDFs within the programme and previewing formatted references. And then there is Sente (, which has just about all the extras I can think of – note-taking and highlighting in PDFs, search by ISBN or DOI, hierarchical tags. Another popular reference manager running on Mac and iPad is, of course, Papers (

Taken over by Biblioscape

We all like managers that take over our entire life, right? So you might like Biblioscape ( by CG Information. While RMs are not exactly competing to see who can be the simplest, Biblioscape is a classic example of a reference manager with ambitions to take over your entire world (in a helpful way, of course). Apart from the usual searching, managing and inserting of references, this programme also allows you to take notes and organise thoughts using a feature they call “charts” (which look a bit like mindmaps with extras), as well as some other novel features. It considers itself to be not just an RM but a fully comprehensive knowledge manager. You have to pay for all this, of course.

OK, so perhaps you don’t go for all the bells and whistles – may-be you just want a reference manager that just, well, manages references. Then JabRef ( is for you: an excellent interface to Bibtex databases (the simplest and most robust form there is) that will help you find references, attach files, such as PDFs and so on. No write-and-cite, though. And you certainly can’t beat the price, as it is freeware.

There are good reasons why the shift to web-based RM software has been embraced almost universally. Mobility is the obvious: have you ever regretted building up a massive database in a proprietary format, only to find yourself locked out when you moved to a lab that used different software?

Awfully slow

But there is a downside. First, no matter how fast your connection, web-based services can be just slow enough to be irritating. And the awkward software that links the database to your word processor can be pretty cranky. Of course, that big favourite with major academic institutions, RefWorks (, is completely web-based. But did you know that if you are a member of a University, your institutional access is for life? So, even after you get fired for spending too much time trying out bibliographic software, you will retain your access to RefWorks for ever.

There are also some very exciting RMs that are web-based but enhanced with an optional desktop app. The one that has taken the academic world somewhat by storm over the past few years is Mendeley ( If you approach Mendeley primarily through the desktop application, you have something that is a bit like a cross between EndNote and Adobe Acrobat. References are easily imported from major databases using a browser bookmarklet, and can be sorted in the old-fashioned way using folders or tags. Entries are closely linked to your local folder of PDFs, and its integrated PDF viewer allows you to annotate and highlight your PDFs.

In keeping with another recent trend in RMs, Mendeley is able to scan PDFs and automatically extract bibliographic information from them. And it does a pretty good job of it, getting it right more than 90% of the time. And when it does get this a bit wrong, it detects that something might be amiss and prompts you to check it, which it will help you do by offering to search Google scholar using the extracted title. It will also automatically monitor folders for new PDFs, so if you download a paper to that folder, Mendeley will automatically scan the PDF, pull out the metadata and add it to your library. What is more, it will rename PDFs with meaningful names based on authors or title – no more folders stuffed with unhelpfully-named files like “nrn10056.pdf”!

Social bookmarking

If you approach Mendeley in its web form, you will see a classic example of the growth of RMs into the social bookmarking world. The Mendeley design is basically “Facebook for researchers”. The idea, of course, is that you can post references to papers and share comments, which is great if your collaborators are hundreds of miles away, or if you just don’t like talking to them. It does raise the question of whether serious, productive, academic discussion can really be practical using “comment” and “like” but, nonetheless, is a convenient way to bring papers to your collaborators’ attention. And as you might expect, Mendeley provides a plug-in to the main word processors (i.e. Word and OpenOffice/LibraOffice).

Of course, Mendeley was not by any means the first of the social bookmarking sites. Here, we must give pride of place to Connotea – a member of the Nature Publishing network group. Connotea (, like its closely related Cite-U-Like (, is designed to provide a place to store a bibliography online. However, they are really aimed at making it easier to share links and find related references; other than a basic export option, they offer little of the more advanced reference management features.

Transferring information

But that is not really a problem because Cite-U-Like, Mendeley and Zotero (more of that later) all get on so well that transferring information between them is trivial. So much so, that you can set up your accounts so that anything you add to Cite-U-Like is automatically forwarded to your Mendeley account.

Zotero ( is quite different from many of the other solutions we have talked about. Although it is “only” a Firefox plug-in (there are ways of getting it to work with other browsers), it can pack quite a punch. It will detect when you are on a page, in which it can recognise bibliographic data, such as journal web sites, and will put up a little icon in the browser address bar. Click on the browser and it will download the citation. And if you have set up the options just right, it will also do its best at downloading any linked PDFs.

There is one majorly exciting current trend in the way RMs are developing that tell us how we will be managing our references tomorrow. We all know about the close connection between your reference collection and our manuscripts. But there is a third player in the production team: the study notes. Two software solutions come to mind. The first, Sciplore (, is not really a reference manager in the EndNote sense of the word (there are no facilities for inserting references into a manuscript) but it does integrate your PDF collection with mind mapping. It is built upon the free mind mapping programme, FreeMind, and extends its functionality so that branches in the mind map can link directly to PDFs. More than that, if you bookmark your PDFs, these bookmarks can be imported as a branch into SciPlore.

No storage limit

But if you really want to see how note-taking and reference management can be integrated with citation insertion, go take a look at qiqqa ( In addition to the usual RM capabilities (citation formatting, document organising and annotations), qiqqa automatically extracts bookmarks and annotations you have put into your PDFs to create a new, summary document. Qiqqa is integrated with its own mind-mapping module and the authors also claim that qiqqa will suggest documents in your library as you type. Documents can be stored and shared online and – get this – there is no storage limit, in contrast to Zotero and some other RMs. The only let-down with qiqqa is that it does not download citations from the web as easily as I would hope. Still, qiqqa is certainly more feature rich than many of its competitors and won’t cost you a penny.

Last Changed: 10.11.2012