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How To Get Organized With Reference Managers for Science—Mendeley

A stack of books with a pair of glasses on top and library shelves in the background to represent the reference manager Mendeley

Are you currently thinking about or actually writing your thesis, latest grant proposal, or your next game-changing paper?

If so, you’ll know how overwhelming it can sometimes be to simply start writing.

For me, one of the most daunting aspects of the writing process is keeping up with the latest publications and organizing the relevant papers, mainly because of the sheer wealth of available literature.

Can you relate? If so, you’ve come to the right place.

In this post, we are going to cover Mendeley, one of the most established reference managers among scientists.

What Is Mendeley?

In the first 6 months of my undergraduate degree, I painstakingly referenced all of my assignments manually, until a kind postdoc took pity on me and introduced me to the world of reference managers, specifically to EndNote.

A year or so later, as a student on a budget and on a quest to find free software, I trialed Mendeley. I haven’t looked back.

Founded by three PhD students and named after the biologist Gregor Mendel and chemist Dmitri Mendeleyev, [1] Mendeley is a free reference manager program that can be downloaded at www.mendeley.com.

Like all reference managers, Mendeley allows you to generate and organize a library of key publications, and, importantly, it allows you to seamlessly insert citations as you write.

It also generates a bibliography in the specific style you require. Mendeley has many very useful features in common with other reference managers (e.g., subfolder organization, PDF annotation, and highlighting), but it also has some unique tools—let’s discuss these in more detail.

Cite as You Write

Plugins for Microsoft Word

If you use Microsoft Word, Mendeley offers the Cite plugin, which allows you to easily insert citations and bibliographies as you write without having to leave your document.

When you’ve been deciding where to submit a paper, you’ll probably have noticed that many journals have different referencing style guidelines.

Being able to switch styles at the click of a mouse is a huge time and stress saver! Mendeley Cite works with the following: Microsoft Word 2016 and above, Microsoft Online, Microsoft Office 365, and the Microsoft Word app for iPad.

Compatibility with LaTeX

If you use the typesetting software LaTeX, Mendeley has great functionality with BibTeX files. You can have all of your citations in one Mendeley library and each time you update your Mendeley library the corresponding .bibtex files are also updated.

This means that the next time you LaTeX your manuscript or thesis document, Mendeley reaches in and pulls up the latest version of the .bibtex file.

I haven’t used this feature myself, mostly because I’m intimidated by LaTeX, but I’ve heard from others that it is quite impressive.

Build Your Mendeley Library

One of the issues I encountered when I used EndNote was that I often lost track of my references because of the nature of online searches.

You know how it goes: I would start reading one paper from which I would find a host of other interesting papers to look up, then I’d also come across some interesting paper titles or work from academics I had cited before.

That would set me off on a clicking frenzy and I would end up with endless open tabs on my web browser and dozens of downloaded PDFs in the ever-expanding but rarely explored “Interesting Papers” folder.

More often than not, I would end up in a situation where all of those interesting PDFs would languish without a corresponding citation entry in EndNote.

Luckily, Mendeley has a couple of really useful tools to help you overcome this.

Watched Folders

The first of these tools is the watched folders feature. With this feature, you can assign specific “watched folders” and any PDF you download to these folders will automatically be added to your Mendeley library.

This saves time and means that your library is effortlessly maintained and that you won’t lose that one vital paper that may hold the key to the final conclusions in your manuscript!

Web Importer

The second important feature, and definitely my favorite, is the Mendeley Web Importer.

This is a browser extension that detects article identifiers on a web page and automatically retrieves metadata and PDF full texts (where available) for you to add to your library.

This can be done with a simple click of your mouse. The Mendeley Web Importer is supported on Google Chrome, Mozilla Firefox, Apple Safari, and Microsoft Edge.

Now when I succumb to frenzied literature searches, I am safe in the knowledge that as long as I save PDFs in a watched folder or use the Web Importer, when I’m ready to write I can automatically and seamlessly start inserting citations into my manuscript.

Moreover, if there are any issues with imported or saved PDFs, Mendeley will bring this to my attention. I obviously can’t speak for everyone, but these two features feel much more efficient and intuitive to me than having to export a citation every time I download a paper.

As the Mendeley team claim, these features allow us to “spend less time navigating and more time building [our] knowledge base”.

Access your Library Anywhere

Mendeley allows you to access your library anywhere so you can now continue your research wherever and whenever you want.

“How”, you ask? Automatic real-time cloud syncing to Mendeley servers means you can access your library from any computer with internet access using the desktop application or any internet browser.

This allows you to keep your library up to date, and read and write where you want, and, most importantly for me, you don’t have to worry about losing your entire Mendeley library if your computer dies a terrible and unexpected death.

Mendeley offers 2GB of free cloud space but, be warned, this can be easily exhausted if you have an extensive library.

If being able to access your library from any computer is particularly important to you, there are monthly paid options to upgrade to 5GB, 10GB, and unlimited storage space.

Collaborate

In today’s research landscape, collaboration is key. Mendeley now facilitates this by allowing you to share papers with collaborators and colleagues by creating shared folders containing notes and annotations, as well as papers.

The contents of these folders are accessible to group members, allowing everyone to share opinions, as well as interesting articles you may not have found yet.

Keep Your Thoughts in One Place

The Mendeley Reference Manager also allows you to easily highlight and annotate PDFs using Mendeley’s annotation tools.

I find these features really useful because they allow me to capture my thoughts in one place instead of across different Microsoft Word documents or in different physical notebooks.

These features allow you to:

  1. Create sticky notes on the PDFs you are reading to record your thoughts.
  2. Highlight key sections of text so you can more easily find them later. You can also use different colors to color code and differentiate your highlights. And let’s face it, everyone loves a highlighter, even if it’s an electronic one.
  3. Work on multiple PDFs at once and easily switch between them as you annotate using Mendeley’s multi-tab format.
  4. Pick up where you left off because Mendeley remembers the furthest point you reached in a PDF and opens your PDFs in the same location on all devices.

Mendeley Is Great, but It Isn’t Perfect

While it’s great, Mendeley does have some issues. A major one for biologists is the difficulty in italicizing within a citation.

Microsoft Word users can work around this issue in the Mendeley Reference manager by inserting HTML tags around the text within the citation that needs to be italicized (e.g., <i>Escherichia coli</i>).

The workaround is a bit more complicated for BibTeX/LaTeX users but there are a couple of options.*

The reference manager can be slow to open, maybe because it is checking the “watched folder”, but once open, it usually runs smoothly.

There is one exception, though: if I have my Microsoft Word document in full-screen mode on my MacBook Pro, the Mendeley in-text citation tool won’t open, meaning that I can’t insert a citation.

Although annoying, the solution is to manually stretch the Word page to fit the whole screen. Also, the range of citation styles isn’t great, but you can make your own or adjust a pre-existing style.

None of these issues has stopped me from using Mendeley, but they might be more important to some people.

Another important factor to note is that Mendeley was purchased by the academic publisher Elsevier in 2013. This sale upset some members of the scientific community, with some people suggesting that Mendeley’s buy-out by Elsevier was problematic for Mendeley’s open sharing model.

What do you think? This may or may not be an important issue for you. Whatever your stance, I urge you to find a reference manager that works for you; it really will save you time! You can check out an overview of the main reference managers here.

Mendeley was my first introduction to the world of reference managers and I hope the features we’ve discussed in this post have enlightened you about the wonders of this software.

If you’re keen to start organizing your papers, then you should head over to the Bitesize Bio Managing the Scientific Literature Hub.

*If you’re wondering, Word users can insert html tags (<i>Species name</i>) within their Mendeley citation, while BibTeX/LaTeX users need to turn off a setting (Tools > Options > BibTeX > turn off “Escape LaTeX special characters”) and then use \textit{Species name} as you would within text.

References

  1. Henning V. (2008) How our name evolved from B-movie monster to Mendeley. Mendeley Blog. https://blog.mendeley.com/2008/04/23/how-our-name-evolved-from-b-movie-monster-to-mendeley/ (accessed October 29, 2021).

Originally published April 29, 2013. Reviewed and updated January 2022.

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4 Comments

  1. Matthias on April 30, 2013 at 12:37 pm

    quite interesting is that all the big publishers are starting to invest/get into the Reference managment “business”.

    So – important fact for this:
    Mendeley was recently bought by Elsevier.
    Due to that there is also a “Mendelete” movement. 🙂 – quite a good article about that:
    http://enjoythedisruption.com/post/47527556151/my-thoughts-on-mendeley-elsevier-why-i-left-to-start
    Or a bit more rough (complaining that elsevier gets the data of scientists and intitutions):

    But Elsevier is not the only one:
    Springer bought mekentos – better known for papers.

    Thomas Reuters is behind EndNote,
    ProQuest behind RefWorks,
    Readcube already partners with Nature and Wiley& Sons,

    So the point in that is not that its bad software – i used mendeley for some time: whom do you want to know about your work? As open access starts to spread you can clearly see by my points above that the big publishers are doing some moves.

    So to complete my list (feel free to add):
    Others hat should be on the list when you search for your favourite reference/literature reader or manager are Utopia Documents (well – its a reader not a manager), Docear, Jabref and Zotero (which is my weapon of choice).

    • 5 to 16 chars on May 3, 2013 at 7:00 am

      Thanks for this post, Matthias. I was not aware that so many of the other programs were backed by publishers. (I use Jabref, so I’m in the clear.)

      I also think this article is oddly-timed to write about Mendeley without mentioning the uproar over the recent buy-out by Elsevier. I think you’ve touched on good points with this comment. As a scientist, open-source is extremely important, not only for ideology, but also full-disclosure of what the program does.

    • Nick Oswald on May 22, 2013 at 10:04 am

      Thanks Matthias – thanks for this — we had this article scheduled for a long time in advance, which is why there was no mention of the buy-out.

      You raise a very pertinent point though..thank you. We’ll put together an article on the buy-outs, and what they mean for users, in the near future.

  2. Kurt Lager on April 30, 2013 at 5:23 am

    It’s good to be able to keep local copies of PDF:s, but I would never do it for articles which I have full access to online. I only do it for articles which I have scanned paper copies of. It’s more important to also be able to attach other types of files to a reference, e.g a text file or a figure cut out from the article and attached as an image. Today many articles also contain extensive supplementary information in various file formats.

    It’s also important where references are imported from. If you import the same reference from different sites e.g. PubMed, the publisher, Google Scholar etc there are usually always some differences, some might miss some information e.g. DOI number or abstract or the format is different, therefore it’s usually best to try and import as many references as possible from the same source, and the most comprehensive source is PubMed.

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