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Working with PDFs in EndNote

Import PDF(s)

EndNote can import and create records from PDF files. EndNote can also import PDFs from sub-folders, and is able to create a group set for the imported files.

To import PDFs into your EndNote library:

  1. Select File> Import
  2. At the Import File text box, click on Choose, to select a PDF
  3. At the Import Option text box, select PDF from the drop-down menu, then Import
  4. Your selected file will be imported with PDF file attached to the reference

  • With EndNote X7 and later versions, you can leave the Duplicates option set to Import All because EndNote will try to identify existing records in the library that match the PDF. If it identifies a match, it will attach the PDF to the existing record instead of creating a new record.

Note: If your imported PDF has a DOI: it will import with quite a few of the fields filled in.
        If your PDF does not have a DOI: it will create a blank record with the title of the reference the name of the PDF.

Import PDFs as a group set

To import PDFs into your EndNote library as a group set:

  1. Select File> Import
  2. Choose the folder that contains subfolders of PDFs
  3. Tick the boxes for Include files in subfolders and Create a Group Set for this import
  4. Click Import

Find full-text PDFs

EndNote has the ability to search for full-text PDFs of journal articles that have already been added to your EndNote library.

  1. Highlight the reference(s) you'd like EndNote to find the full-text
  2. Go to References menu > Find Full Text > Find Full Text or click on the Find Full Text icon

3. You may be prompted to sign in to Deakin Single Sign On. Enter your Deakin credentials and click Login. Then click Continue

4. When EndNote completes the search, you will see how many full text articles were retrieved on the left side of the window. The retrieved PDFs will be attached to their respective reference and can be viewed in the Attached PDFs tab.

Note: There are some important limitations to bear in mind when using EndNote's Find Full Text feature.

  1. EndNote is unlikely to retrieve all PDF files.
    • In many cases, you will be required to download the PDF separately and manually attach it to the reference in your EndNote library.
  2. The search process takes quite some time and freezes the program, so we suggest only selecting up to 10 references at a time.
  3. Articles in the ScienceDirect database, published by Elsevier, cannot reliably be identified using Find Full Text.
    • This is a known issue, and is awaiting for a fix from EndNote's developer, Clarivate. PDF files from ScienceDirect therefore need to be manually downloaded and attached to references in your EndNote library.

Manually attach a PDF

To manually attach full-text PDFs to references in your EndNote library:

  1. Download the PDF file and save it on your computer
  2. In EndNote double click the reference in the central window/list to open the Summary panel
  3. Click on the PDF section
  4. Click on Attach PDF and select the PDF file you want to attach from your computer
  5. Click Open

PDF viewer

To open PDF files in a full window view:

  1. Double click the reference in the Endnote library
  2. Change the Summary panel to PDF
  3. Click on Open PDF icon

Note: EndNote will automatically open the first PDF attached to a reference when you select the PDF viewer panel.

You can annotate PDF files attached to the reference by adding highlighting, sticky notes, and other features. These annotations are also searchable in EndNote.

Mac users:

  • Users may encounter problems with the EndNote PDF viewer.
    • Clarivate advises that this can affect users on any of the Mojave, High Sierra, or Sierra operating systems. Clarivate recommends annotating PDFs in an external PDF application or using the free EndNote for iPad app.

PDF auto renaming

EndNote has a feature that will rename PDFs automatically as you import them into EndNote

  1. Select Edit menu > Preferences (Endnote20 menu > Preferences on Mac)
  2. Select PDF Handling
  3. In PDF Auto Renaming Options select the naming format you want or customise your own format
  4. Click OK

PDF auto import folder

You can nominate in EndNote a particular folder where you like to download your PDFs. When you nominate a folder, EndNote will monitor this folder, and automatically import new PDFs added to this folder into your EndNote library whenever you open your library.

  1. Select Edit > preferences (Endnote20 menu > Preferences on Mac)
  2. Select PDF Handling
  3. Under PDF Auto Import Folder tick the box next to Enable automatic importing
  4. Select the folder you want to be scanned regularly
  5. Click OK

Note: EndNote creates a folder called imported within your nominated folder and automatically moves all the PDFs that it has already scanned into this folder. This ensures that EndNote won't scan the same PDFs again.

Find full-text PDFs with Endnote Click browser add-on

Endnote Click is a free browser plug-in that helps you to download references and full-text PDFs to your Endnote library. Watch a video about how to get set up..

Endnote20 in action