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Citation Managers

Library Basics

  • When opening EndNote for the first time, you will need to create a new library. (File --> New)
  • You can rename it if you want, and then save it to your hard drive.
  • Don't save active EndNote libraries to a server or cloud-based storage, as they could corrupt over time. This includes OneDrive and iCloud, so make sure your libraries are not syncing to either service.
  • You can have as many libraries as you'd like, but if you plan to use EndNote online, you can only sync one desktop library to your online account.
  • You can customize the way your library looks. Under Edit --> Preferences, you can change the font size under Display Fonts. Change which fields are shown in the library (author, title, rating, etc.) under Display Fields.
  • Need a backed up copy of your library? Create a compressed library (File--> Compress library). Compressed libraries (with the file extension .enlx) can be stored anywhere, including in the cloud.

Adding References

There are 4 ways to add references to your EndNote library:


  • Select New Reference under the References tab, choose Reference Type (i.e. article, book) and type in the relevant info 

Search within EndNote

  • You can search some databases from directly within EndNote, and then add either everything you find or just selected references into your library. Click on the database you want to search under Online Search, and enter your search terms. This is best for simple searches, like when you have a PubMed ID. 

Export from databases

  • Many databases allow you to export an EndNote or RIS file into EndNote
  • For example, in PubMed, go to Send to and select Citation Manager
  • Trying to add a book to your EndNote library? You can export reference information directly from PittCat

Import a text file

  • You can also import a text file, by selecting File -> Import
  • Select the appropriate import option (ex. EndNote import for EndNote files)

Organizing References

You can organize your EndNote library using groups. To create a group, go to Groups --> Create Group. Name it, and then drag and drop references into it.

There are other types of groups:

Smart Group

  • EndNote can file references for you. Go to Groups --> Create Smart Group
  • Select the parameters for your group - what do you want in it? Articles by a certain author or on a certain subject? You can use Boolean operators (AND, OR, NOT) if needed.
  • EndNote will file all the references currently in your library that meet the criteria, as well as any future references you add

Combination Group

  • Create a group made from other groups. Go to Groups --> Create From Groups
  • Use Boolean operators to decide which articles from other groups should be in your new group

You can also create a Group Set, and file groups themselves by dragging and dropping

image showing groups and group sets in an EndNote library

Adding PDFs

When you add references, you're just getting the citation information. However, you can also attach PDFs and then annotate them inside EndNote.


  • Highlight the reference and drag and drop the PDF into it. Alternatively, in EN20 and 21, click 'Attach File' in the right side pane and you will be prompted to browse for the file. (In EN x9, click on the paperclip icon, also in the right side pane.)

Have EndNote do the work

  • Select the reference(s) you're looking for, and then select References --> Find Full Text. EndNote will search for all freely available full text and attach PDFs it finds. You can ask EndNote to also search for articles Pitt subscribes to, which will bring back way more PDFs. To do that you need to add some information to your preferences; the instructions are located here: Full Text Set Up 
  • Note: EndNote won't find everything, but it will save you a lot of work
  • Use this Find Full Text Tutorial to guide you through these steps

Have a PDF (or folder of PDFs...) and just want to quickly import it into EndNote as a reference?

  • File --> Import, then select file or folder
  • Browse for your file/folder
  • Select PDF as your import option (if you have a Mac, make sure you click on the options button to do this)
  • Double check your reference - if it is a scanned copy or doesn't have a DOI, it will not import properly

Annotating PDFs

You can annotate PDFs in EndNote. Highlight any reference that has an attached PDF, and then click on PDF in the right pane. From there, click the icon that is a box with an arrow coming out of it. (If you hover over the icon, it says 'Open the reference in a new window.' Once your article pops up, click the text bubble icon to access highlighting and underlining tools.

EN21 allows you to annotate PDFs


Finding retracted articles in your library

Sometimes articles may be retracted, corrected, or otherwise flagged after publication. Like the citation manager Zotero, EndNote 20 and 21 have an integration with Retraction Watch. That means you'll be notified if an article in your library has been retracted. In EndNote you will see a folder on the left side (under 'All References') that says Retractions. Any retracted articles will be put there (and will stay in all references as well). EndNote will also notify you if you cite a retracted article using Cite While You Write.

Note that to see retracted articles you will need to have one library synced with EndNote Online; you will then see retractions in all of your libraries, regardless of their sync status.