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How to get Organized With Reference Managers for Science – EndNote

An open drawer of a wooden filing cabinet containing papers and documents to represent the reference manager Endnote

Last week we discussed Papers, which is a well-known reference manager used by many academics. Today I am focusing on what might be the most well-known reference manager – EndNote.

Thomson Reuters’ EndNote is often available free through Universities. And if you have this opportunity, you should definitely take advantage of it!  If you want EndNote on your own personal computer, you may have to invest in a personal license, which can cost as much as £159/$250, although student discounts and discounts through Universities are offered.

Like Papers, EndNote allows you to organise your papers manually or automatically through Smart groups using criteria you choose.  Smart groups will also update automatically whenever you add new PDFs that match the criteria.

A great feature of EndNote is the ability to directly import PDFs that are already on your computer. Importing PDFs is accomplished simply by selecting the folders you wish to import, or by dragging and dropping directly into EndNote.

Adding new references and PDFs is also simple as you can search databases such as PubMed and Web of Science directly from EndNote. Setting up EndNote to search these online databases using your University’s subscriptions is a little more complicated than other software however.  You will need to input an OpenURL address and an authentication address, and these can be a little difficult to find.

For many, the main use of EndNote is for inserting citations into documents and creating bibliographies. EndNote automatically installs a Plug-in for Microsoft Word, which is incredibly easy to use – just remember to have the EndNote library you are using open.

Cloud syncing is supported and you can Sync your references with EndNote Web. However, if you want to sync your PDF files as well, you will need to have a subscription to EndNote Web with advanced features, which gives you 5 GB of storage. The good news is that with your purchase of EndNote X6 you automatically get a free 2-year subscription to the advanced features.

Apps for the iPad and the iPhone are available for those that want to have access to their library from anywhere, and EndNote for iPad can sync directly to DropBox.

Come back next for the final post in this series in which I will focus on, in my opinion, a more quirky reference manager – Zotero.

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


  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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