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EndNote Desktop: PDFs

A guide to EndNote Desktop X9

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PDFs Overview

EndNote Desktop provides a number of features to work with PDFs:

  • Attach the full-text PDF of an article to a reference.
  • Read, add notes, and highlight PDFs.
  • Find and attach PDFs for article references.
  • Automatically import PDFs from a designated folder on your device every time Desktop is opened.
  • Create a reference from an imported PDF.

Find Full Text Feature

EndNote Desktop allows users to find full text articles from their library.  There are four options to do this: 1) Web of Science Full Text Links, 2) DOI (Digital Object Identifier), 3) PubMed Linkout (US National Library of Medicine), and 4) OpenURL.. SIU users may only use the first three options because EndNote is not compatible with the Alma link resolver at this time.  You may enable the first three options in EndNote to use those:

Step 1 - Open EndNote

Step 2 - Go to the Edit Menu, click on Preferences

Step 3 - Click the Find Full Text Link

Step 4 - Check the boxes next to the first three options

Find Full Text Options

Import PDFs

You can import PDFs into your EndNote Desktop library. EndNote will create a reference from the PDF, but often it wil not be complete.

Step 1: From the File menu choose Import and then select File.

Step 2: Click on the Choose button to select the file to import from your device.

Step 3: In the Import Option field, select PDF.

Step 4: Click Import.

Step 5: A new reference for the PDF will appear in your Imported References folder. Double click on the reference to edit it.

Read and Annotate PDFs

You can use EndNote Desktop to read and annotate PDFs.

Read PDFs:

1. Select a reference in the Reference List Panel.

2. Click on the PDF viewer button in  the Tabs panel to preview attached PDFs or click the "Open PDF" button to open the PDF in a larger window.

Highlight PDFs:

1. Select the text to be highlighted and then click on the highlight button in the toolbar of the PDF window. 

2. Be sure to click the PDF Save Icon   when you're finished.

Annotate PDFs (add a Sticky Note):

Step 1: Select the area of the PDF to add the note.

Step 2: Click the Sticky Note button in the toolbar and then click the section of the PDF where you want to add the note.

Step 3: Click the Sticky Note button again to unselect it. (Otherwise, you’ll continue to add notes to the PDF.)

Step 4. Double click the Sticky Note icon you just added to the body of the PDF and add your comments in the text box that pops up.

Step 4.Click the PDF Save Icon   and click the X in the upper right-hand corner of the Sticky Note window when you're finished adding comments.

Step 5. To delete a Sticky Note, right-click over it and select Delete Annotation.

Attach PDFs

It's very simple to attach a PDF to a reference in your library.

Step 1: Double click on the desire reference.

Step 2: Click the paper clip icon at the top of the screen.



Step 3: Select the PDF from your device and click the Open button.

Step 4: You're done! The PDF will open in the EndNote Desktop PDF reader.

Step 5: Make sure to save when you exit the reference editor.

PDF Preferences

To begin using the PDF functions of EndNote Desktop set your PDF handling preferences.

Step 1: Click the Edit menu, choose Preferences, and click on PDF Handling in the Preferences pop-up window.

Step 2: In the section of the pop-up window labelled "PDF Auto Renaming Options", choose the desired naming convention for PDFs. The naming convention is used when PDFs are imported into Desktop either with the Find Full Text or the PDF Auto Import feature.

Step 3: Enable automatic PDF importing from a folder on your computer by checking the Enable automatic importing box and clicking Select folder to choose the folder from which to automatically import PDFs into EndNote Desktop every time you open it. You can also create a new folder on your device when the Select folder dialog appears.

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