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EndNote 20: Importing and managing PDF files, EndNote Click

Guide published on 10th February 2022

PDFs and EndNote, including EndNote Click

PDF copies of full-text articles can be included in your EndNote library, attached to the relevant records. This can happen in a number of ways, which are detailed in the tabs below:

  1. You have imported a record or number of records from a database search and wish to attach the full text PDF to the EndNote record. If you don't have the PDF of the article already, see Find full text in this guide'. If you do have the article see 'Attaching a PDF file', below.
  2. You already have some PDF's, or a folder containing a collection of pdf articles, and want to import them into your library. See 'Import a PDF file' OR 'Import a folder of PDF's'.
  3. You have manually created a record in your library and then wish to attach the PDF to it. See 'Attaching a PDF file'.
  4. EndNote Click is a browser extension for Chrome, Firefox, Edge and Opera that you can use to locate article PDFs to then export to your EndNote library. A basic record is simultaneously created. EndNote Click can be activated from the Tools menu if it doesn't automatically install. In either case you will need to set EndNote Click to recognise Monash University Library journal subscriptions. Further information is in the Clarivate EndNote Click guide.

Importing and managing PDF files

First of all obtain and save the required PDF file to a temporary location that is easy to find - somewhere like the Desktop is fine.

There are two methods of attaching a PDF to a record in your library.

Method 1.

  1. Select the relevant record
  2. In the Summary panel click + Attach file 
  3. Navigate to and select the relevant file

If you use this method leave selected the option ' Copy this file to the default file attachment folder and create a relative link'

Method 2.

  1. Arrange your windows so that you can see both your EndNote library and the downloaded PDF file
  2. Drag the unopened PDF onto the relevant record in the EndNote reference list.

A paper clip next to the entry will indicate that the record has an attachment. The PDF will be accessible in the right hand panel.

EndNote has created a copy of the PDF file within the associated .Data folder of your EndNote library. It is for this reason that it is important when backing up your library that you create either a compressed library or make sure that you back up both your .enl file and the related .Data folder.

PDF documents can be imported into EndNote. If the reference is already in your library the PDF will be attached to that reference, if not, then a new reference will be created and the PDF attached to it.

If the PDF file contains a DOI (Digital Object Identifier) within the metadata of the file or on the first two pages of the document, the information is sent to CrossRef and PubMed which send back the bibliographic information when it is found, and it is imported into your EndNote library.  EndNote must have internet access during the import process. If the PDF does not have a DOI, the document will still be imported but an entry will need to be created from the information on the document (view the tab Create an entry from an imported PDF). Note: Entries cannot be created from scanned copies of pdf documents.

  1. Open your EndNote library
  2. Go to File and select Import
  3. Choose File
  4. Click  the Choose...  button and navigate to, and select, the required file. 
  5. Set Import Option to PDF , and Duplicates to Import All
  6. Click Import 
  7. The reference is placed in a temporary group called 'Imported References'.        

Any EndNote entries that are created using this method should be checked for accuracy and completeness. It may be necessary to edit entries where there are errors.

Digital Object Identifier

A DOI (digital object identifier) is a unique alphanumeric code for persistent identification of an electronic item on the Internet.

A DOI name may look something like this  

  • doi: 10.1111/jan.12128
  • doi: 10.1016/j.jamcollsurg.2011.09.026
  • http://dx.doi.org/10.1111/j.1530-0277.2011.01717.x
  • doi: S0034-71672012000500020

Not all articles are allocated with a DOI, although they are becoming more common.  The DOI may be listed on the front page of an article, or within the database record. 

If you have a DOI and want to see the matching citation (or the full-text if you have access), use a DOI resolver, or try pasting the DOI into a Google search.

PDF documents can be imported into EndNote. If the reference is already in your library the PDF will be attached to that reference, it not, then a new reference will be created and the PDF attached to it.

For any PDF files that contain a DOI (Digital Object Identifier) within the metadata of the file or on the first two pages of the document, the information is sent to CrossRef and PubMed who send back the bibliographic information, when it is found, and imports it into your EndNote library.  EndNote must have internet access during the import process. Any PDF's that do not have a DOI, the document will still be imported but an entry will need to be created from the information on the document (view the tab above for help on creating an entry). Note: Entries cannot be created from scanned copies of pdf documents.

  1. Open your EndNote library
  2. Go to File and select Import
  3. Choose Folder
  4. Click the Choose button and navigate to, and select the required folder. If you have selected a folder that contains subfolders check the 'Include files in sub-folders' box to include these files in the import. If you wish to create a group set in EndNote from these sub-folders tick the option to 'Create a group set for this import'.
  5. Set the Import Option to PDF
  6. The Duplicates dropdown menu gives you three options relating to the management of duplicates. Choose your preference from here.
  7. Click Import.
  8. The references are placed in a temporary group called 'Imported References'.         

Any EndNote entries that are created using this method should be checked for accuracy and and completeness. It may be necessary to edit entries where there are errors.

Digital Object Identifier

A DOI (digital object identifier) is a unique alphanumeric code for persistent identification of an electronic item on the Internet.

A DOI name may look something like this  

  • doi: 10.1111/jan.12128
  • doi: 10.1016/j.jamcollsurg.2011.09.026
  • http://dx.doi.org/10.1111/j.1530-0277.2011.01717.x
  • doi: S0034-71672012000500020

Not all articles are allocated with a DOI, although they are becoming more common.  The DOI may be listed on the front page of an article, or within the database record. 

If you have a DOI and want to see the matching citation (or the full-text if you have access), use a DOI resolver, or try pasting the DOI into a Google search.

  1. Select Import from the File menu
  2. Navigate yourself to the file or folder required
  3. In the box that appears select 'PDF file or Folder' from the Import Option. If you have subfolders set up you may choose the option of 'PDF Folder as a Group Set instead'
  4. Click Import

You can set your preferences in EndNote to enable automatic importing of PDF's from a designated folder on your computer. The auto import folder will check for new PDF's when a library is opened. Whilst you are working in your library EndNote will also scan for newly added files every 10 minutes. Any new files will be imported automatically and renamed, if you have set a renaming preference.

  1. Select Edit  
  2. Select Preferences  (On a Mac Preferences is found under the 'EndNote 20' menu option)
  3. Select PDF handling
  4. In 'PDF Auto Import Folder', select 'Enable automatic importing'
  5. Click 'Select Folder' button, navigate to, and then select the required folder
  6. Click OK.

 Any EndNote entries that are created from the auto import folder should be checked for accuracy and and completeness. It may be necessary to edit entries where there are errors.

When a PDF is imported and there is no entry created in your EndNote library the 'Find reference updates' function may assist in creating a new entry.

  1. Click on the empty entry to display the PDF document, and using information in the document, complete the Author, Title and Year fields in the reference template
  2. From References on the menu bar, select the 'Find Reference Updates' . EndNote will search for the reference and if information found, return with a box containing that information.
  3. Select 'Update All Fields' OR 'Update Empty Fields'
  4. Click 'Save Updates'

Your reference will then be populated with all of the missing information.

Important note: Not all references will be found by EndNote. There may be some that will require all of the details to be added manually.

Many PDF files have meaningless file names. EndNote allows you to automatically rename the PDF's that you import into your library to a more meaningful name.

  1. Select Edit
  2. Select Preferences
  3. Choose PDF Handling
  4. Select the option that best suits your needs.
  5. Click OK.      

EndNote's built in PDF viewer allows you to:

  • highlight text with a highlighter
  • add comments in a 'sticky note'
  • search the text in the PDF document as well as any added comments.
  1. In the right panel click PDF to open the default viewer.
  2. For the full screen view, click the 'Open this PDF' icon on the right hand side of the toolbar. 
  3. Click the 'Markup/annotation' icon (next to the Search icon) for the options.   

Copyright notice

Downloading records into your library from a database is usually quick and easy. Finding the full text of associated articles is also possible, but to ensure you comply with copyright law and database license requirements, be aware of the following issues:

  • You must ensure you adhere to copyright regulations related to ‘fair dealing’ when uploading and attaching full text documents to your Endnote library. For example, in general only one article per journal issue or 10% of a book can be attached. Further information on ‘fair dealing’ is available from the University copyright site or your Faculty Copyright officer.
  • While it may be acceptable to share your EndNote Library of references with others, it may breach Copyright Regulations or Database Licence Agreements to share any of the full text material downloaded from Monash databases.
  • It is possible that some articles may be “Open Access”, that is, the publishers have made them freely available to the public. But to be safe, and avoid any breach of regulation, we recommend you do not share ANY full-text material from your library. Those with access to your Library references have the option of looking up and getting access to the full text themselves if they are authorised to have such access and this will avoid any potential breach of Licence Agreement.
  • For the same reasons, material downloaded under Monash licencing agreements will need to be deleted from your data folders when you leave Monash.