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How to Get Organized With Reference Managers for Science—EndNote

Posted in: Taming the Literature
Image of a filing cabinet with open drawers and lots of coloured files to represent the reference manager EndNote

If you’ve had the chance to catch up with the Bitesize Bio Managing the Scientific Literature Hub, you may have seen our article discussing how you can use the Mendeley Reference Manager to stay organized.

In this article, we’re focusing on what might be the best-known reference manager—EndNoteTM.

What is EndNote?

EndNote was my first introduction to the world of reference managers during my undergraduate degree, and I loved it!

Originally founded by Thomas Reuters but now owned by ClarivateTM Analytics, EndNote is a reference manager that is often available for free through universities.

If this is the case at your institution, you should definitely take advantage of it!

However, if your university doesn’t offer EndNote or if, like me, you like to have it on your own personal computer, you can invest in a personal license.


If you already have a personal license for EndNote X9 (or earlier), you can upgrade to EndNote 20 for a one-off fee of £102/$139.

Alternatively, a full license can cost as much as £252/$341, or £114/$154 with a student discount.

Clarivate Analytics also offers special pricing for group licenses for lab groups of institutions, so that may be a good option depending on your circumstances.

Top 5 Features of EndNote

Like other reference managers, EndNote allows you to

  • manually or automatically organize your papers into specific groups;
  • easily insert citations as you write;
  • generate bibliographies from a choice of over 7000 referencing styles;
  • annotate PDFs; and
  • share reference libraries with collaborators.

In addition to these features, EndNote also offers a list of other very useful tools; let’s discuss these in more detail.

1. Cite While You Write

For many of us, EndNote is mainly used to insert citations into documents and create perfectly formatted bibliographies.

Like Mendeley and Zotero, EndNote also offers a plugin that allows you to use the Cite While You Write feature in Microsoft® Word.

This feature allows you to seamlessly insert hyperlinked in-text citations and bibliographies while you write—just remember to have the EndNote library you are using open in the background.

With this feature, there’s no need for you to switch between programs or documents.

This is important for me because it allows me to write without losing my train of thought or that ever-important momentum!

Another useful aspect of the Cite While You Write feature is the ability to switch between and even customize different citation styles.

This is super useful if you need to submit your manuscript to different journals, which, just to make life easy for us, often have different referencing style guidelines.

2. Stay Organized With Smart Groups

EndNote makes it simple to add new references and PDFs by searching databases such as PubMed and Web of Science directly from the reference manager program.

Alternatively, EndNote also allows you to directly import PDFs you have already downloaded onto your computer.

You can do this by simply selecting the folders you wish to import, or by dragging and dropping directly into EndNote.

Moreover, you can automatically organize your papers into subgroups using the Smart Group tool.

With this, you can easily create rules to categorize your papers into specific groups and subgroups using your chosen criteria.

For example, you might want to organize papers by a particular author or topic; Smart Groups lets you do this.

These Smart Groups are automatically updated when you add new PDFs that match the criteria. If you later decide to remove a reference from a group, the reference will remain in your library, so you won’t need to find it again at a later date.

3. Avoid Duplicate References

If you’ve ever accidentally duplicated references, you know how much of a mess it can make of your in-text citations and bibliography.

EndNote now helps to prevent this by using DOIs and/or PMCIDs to remove duplicate references, leaving you with one less thing to worry about. Always a bonus!

4. Make More Informed Journal Submission Decisions with Manuscript Matcher

You’ve done the science and written it all up.

Now comes the task of finding the ideal journal in which to publish your hard work. EndNote X9, EndNote 20, and EndNote Online now utilize Web of Science to suggest top candidates for your manuscript using the journal Manuscript Matcher feature.

Using sophisticated clustering algorithms, Manuscript Matcher analyzes millions of citation connections to find relevant links to your work.

You can then use this tool to decide which journals you want to submit your manuscript to.

Although I haven’t used this feature myself, I have to say it sounds very interesting!

We’d love to hear your experiences of using this feature. Thumbs up or thumbs down?

5. Sync with EndNote Online

If you have EndNote X8 and above, you can take advantage of the free cloud synchronizing features offered with EndNote Online.

This feature gives you access to your reference library across desktop, web, and iPad. In addition, EndNote Online also offers unlimited storage space for full texts and file attachments, and you can have an unlimited number of references.

If you’ve read our latest article on using Mendeley, then you may know that I was, until recently, a devoted member of Team Mendeley.

Despite this, I think EndNote is also a good reference manager with its own unique features.

In my opinion, it has two main disadvantages:

  1. it isn’t free; and
  2. there are different versions of EndNote with different features depending on the version you have access to.

Nonetheless, if you’re new to the world of reference managers, I would encourage you to try a few out until you find the one that works for you.

You might need to have a play around but you’re sure to find a reference manager that suits your needs.

Look out for the next post in this series in which we focus on a lesser-known reference manager—ReadCube Papers.

For more tips on keeping track of the scientific literature, head over to the Bitesize Bio Managing the Scientific Literature Hub.

Please share any useful EndNote tips in the comments below. If this article has been helpful, then please share it with your social networks.

Originally published May 20, 2013. Reviewed and updated December 2021.

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  1. Kurt Lager on May 22, 2013 at 5:15 am

    In a time when everything is stored online on the net, it’s ironic that so many still keep local copies of PDF:s. It people make notes in the electronic PDF copy I might understand it, but otherwise you just occupy storage place and disks are not safe storage places.

  2. joanbarau on May 21, 2013 at 9:30 am

    Well, since it appears that Mendeley will be left out of the post series, I’ll try to make justice to it here:

    Its free so far and works on MACOS & PC.
    It provides some free storage space on the web.
    It has other sharing-team features that I never used.
    It lets you open the referenced PDF internally and adding comments and highlighting, or deciding to open the PDF externally using whatever you use to view/edit PDFs.

    It allows you to set up a “watch folder” and an “organized folder”: pretty much a system of folders in which you save all your “%321-&%76jhgd.PDF” in the first folder and Mendeley automatically upload this reference in your library while updating title/author/journal with info in the web, AND creates a copy of this file in the second folder renaming it to, for example “2013_JohnWho_Journal_PaperTitle”.

    In my opinion this last feature is THE best thing about a reference manager. It helps you stay organized with the actual PDF files and it will be a killer once they implement the option of creating subfolders matching your customized libraries (you will be able to subdivide by project/paper/subject).

    Finally, it also has the same type of WORD plugin for “cite while you write” feature and it provides hundreds of reference formatting options according to each journal requirements. For the more advanced users, reference output formatting is also customizable once you learn to edit the information files for each reference type.

    I’ve tested EndNote, Zotero, Reading Cube and Papers, but the “Watch Folder/organizing PDF thing” was the feature of Mendeley that really got me.

    Hope you guys appreciate!

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