Comparison: EndNote and Mendeley

There are so many types of reference software out there that it's sometimes difficult to make an informed decision about which software fits your needs best. In this research tip, we explore two populair options: EndNote (Clarivate) and Mendeley (Elsevier).


What is reference software?

You use reference software to gather, edit, organise, save, and share references. It also allows you to easily cite while you're writing, so you don't have to do that at the end of your writing process.

Reference software can be helpful when you (plan to) publish a lot of papers, when you're collaborating with other researchers, or if you want to keep an overview of all the sources that interest you.



All Ghent University students and researchers have a licence for EndNote. (If/When you leave Ghent University, you won't have access anymore.) This means you have to open the desktop version of EndNote via Athena. To access your online library, you need to make a (free) personal account and open a browser in Athena.

You can import references from a browser opened in Athena. This way you have access to the sources and your browser is linked to your EndNote library.

For Mendeley, you need to make a (free) account and download and install the software. You install Mendeley Desktop locally and can only open it on that particular device. You can use your online library on every device. You will still have access to your library if/when you leave Ghent University.

You need to operate within the UGentNet to import references. If you're working from home, you need to set up a VPN connection and open a local browser. (Browsers in Athena have access to the sources you need, but won't be able to connect to your Mendeley Desktop).

Verdict: EndNote via Athena (every device with internet) ; Mendeley locally and with VPN connection (Mendeley Desktop on one device only).


Importing references

If you work with EndNote and want to import references, you need to open a browser via Athena, go to the library catalogue > databases > choose your database. After importing all your references, you can import PDFs of the full article in bulk, as well as add PDFs manually.

Mendeley requires you to set up a VPN connection. Now you can go to the publisher's page immediately. You can import the reference and the PDF (if one is available) at the same time. You need to install the Web Importer for this (Open Mendeley Desktop > Tools > Install Web Importer). You can add PDFs manually but can't upload PDFs in bulk after the fact and the maximum of PDFs for a free account is 3.000 PDFs.

Verdict: EndNote allows uploading PDFs in bulk ; Mendeley let's you import reference and PDF at the same time.


Editing and sorting references

Updating references automatically and manually is possible in both programs, as well as finding and deleting duplicates, and exporting your references. You can also easily sync your online and desktop library.

EndNote allows for Groups, Smart Groups, and Groups Sets. This means you can structure your (Smart) Groups into Group Sets and that you can upload references automatically into a Smart Group based on a search query (e.g. all publications by the author Zhang after 2010 with "yellow dwarf virus" in the title).

In Mendeley, you don't have Smart Groups, but you can make folders with multiple sublevels (instead of the one in EndNote). This means more control over your folder system.

Verdict: EndNote lets you sort references automatically into Smart Groups ; Mendeley enables a more elegant folder system.


Cite While You Write features

You can use cite while you're writing (in Word) with both EndNote and Mendeley. For EndNote, you open your paper in Word via Athena. For Mendeley, you need to install the MS Word Plugin (Open Mendeley Desktop > Tool > MS Word Plugin). Both let you adjust the citation style in Word, and edit the (content of) the references in EndNote or Mendeley itself.

If you use EndNote, the list of references cited will automatically appear at the bottom of your document. With Mendeley, you need to insert it manually. This can be done wherever you want.

If you use the document preparation system LaTeX, you can use both EndNote and Mendeley. However, there are fewer steps  involved when you use Mendeley.

Verdict: Mendeley lets you choose where the reference list goes.


More info

Want to compare other reference software? This wikipedia page provides a nice overview.

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Last modified Oct. 27, 2022, 10:23 a.m.