Mendeley Reference Manager

Cite this article as:
Leighton, S. Mendeley Reference Manager, Don't Forget the Bubbles, 2013. Available at:

Formatting references is a nightmare – is Mendeley a useful tool?

The problem

Imagine the following scenario…

After weeks of reading through the relevant literature, highlighting the key points and scribbling notes and plans on wads of paper, you are now ready to sit down at your desk to start typing your latest meta-analysis for submission to the Lancet. However, the Lancet has a strict referencing policy. They want proper formatting and won't accept poorly organised references.

You don't want a repeat of the painful experience you had referencing your last manuscript. It was not fun spending hours manually inputting the references, only to realise that their order had changed, the formatting was wrong and then having to start all over.

You've heard of reference managers – they used to have EndNote on the PCs at uni. However, it seemed pretty unintuitive and, besides, you don't want to have to spend over £100 to buy a copy.

Mendeley may be helpful…

At the heart of the Mendeley suite is the reference manager programme. There are versions available for Mac, Windows and your favourite flavours of Linux. Once you install it, you will be prompted to create a free account at which gives you access to cloud storage.

Now you can start uploading the papers you reference into the Mendeley program. This can be done manually or, better still, automatically via the pdf if you have it or via a simple web-browser extension to scrape the reference from the online journal or sites like PubMed and Medline. Because Mendeley is also an online research community, most of the journal articles you want to reference will already be on Mendeley's crowd-sourced research catalogue so, in theory but not always in practice, will be properly formatted and error free. You can tag each reference and put them into different folders to organise them and make them easy to search through.

The Mendeley desktop client (on Ubuntu Linux)

There is an excellent plugin for your word processor of choice – Microsoft Word and the free open source LibreOffice are both supported. This give you the ability to insert a reference by clicking and searching by paper title, author or tag. You can choose the style of referencing from a drop down menu – i.e Vancouver, Harvard etc – and it all changes automatically. Mendeley will keep all the numbers in order for you if you insert or cut and paste text and dynamically update your bibliography.

If you have access to the pdf files they will also be uploaded and catalogued in your personal portable research cloud. This can be accessed anywhere via a web interface or apps for iPhone, iPad and Android via your Mendeley account. They can also be annotated and highlighted with these additions again saved to your cloud. This is an admirable step towards being paperless, although, it may be a copyright concern.

You can also use the community aspect of Mendeley to aid in research collaboration. Create your profile include a brief biography of your research, upload your papers and Mendeley serves as a sort of LinkedIn professional social network for researchers.

Criticisms of the product

While the product is free, it was recently purchased by the Elsevier publishing group for ~$100 million. I am worried that Mendeley moving from an open-source startup founded by PhD students looking for a solution to a common problem, to part of a multinational profit driven company will result in a loosening of its principles.

Despite the takeover, Mendeley says they will stay open source. This has allowed for the free but unofficial Android app to be developed. Time will tell…

It is a concern that you are required and encouraged to create a social media style account. While this may be useful for professional networking, your personal information is open to abuse for advertising and market research.

As hinted above, the formatting of the references is not always perfect. Also, it would be simpler to just have a word processor extension that searched from an online database of references. It is a bit 'clunky' having to first upload references to the desktop or web client before you can then import the reference to your document.

However, given the above issues, Mendeley is a useful product which I would recommend as long as you remember there is no such thing as a free lunch…

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Sam is a junior doctor training in Glasgow, Scotland. Passionate about improving technology in healthcare. Blogs about both. Director and medical apps developer at Polwarth Limited.

Author: Sam Leighton Sam is a junior doctor training in Glasgow, Scotland. Passionate about improving technology in healthcare. Blogs about both. Director and medical apps developer at Polwarth Limited.