EndNote

EndNote is a reference management software that can be used on Windows and Macintosh computers. It allows you to create a collection of bibliographic records and files to use for your research and writing.

Set your PDF handling preferences

EndNote allows you to set up preferences for handling PDF files in your library.

You can choose to set either one or both preferences. They don’t have to be set at the same time. These functions work best for resources that have a DOI (Digital Object Identifier). If the article doesn’t have a DOI, EndNote will still import it, but you'll need to do a bit more work to get the record populated.

 

Set up PDF Auto Renaming

PDFs that are imported from Databases and Google Scholar often have file names that bear no relation to the article, e.g. Content Server(2).pdf or download.pdf. You can tell EndNote to rename the copies that you attach to your records so that they are identifiable.

  1. Open EndNote.
  2. Open the Edit menu in the toolbar and select Preferences (Windows users).
    Go to the EndNote tab and select Preferences (Mac users).
  3. In the Preferences menu, select PDF Handling.
  4. Select the PDF Auto Renaming Option that suits you.
    • Don’t rename = The file attachment will have whatever random name it was downloaded with.
    • Author + Year + Title = The lead author’s surname, the year of publication and as much of the title as will fit within the character limit for the file name.
    • Author + Title = The lead author’s surname and as much of the title as will fit within the character limit for the file name.
    • Author + Year = The lead author’s surname and the year of publication
    • Title = The title – up to 46 characters.
    • Custom = you can choose up to 3 EndNote record fields to include in the file name.
  5. Click Apply, then OK (Windows users).
    Click Save (Mac users)

 

Set up a PDF Auto Import Folder

You can create a folder and set EndNote to automatically create a record and attach the file for any PDF you add to that folder. If it has a DOI, it will also populate the record with the reference details. This folder needs to be fairly close to the surface, e.g. Documents\EndNote\Articles for library. If the full name of the pdf including the file path is more than 248 characters long (including spaces) the pdf will not open.

  1. Start by creating an empty folder with a short name that makes sense to you when you see it.
  2. Open EndNote.
  3. Open the Edit menu in the toolbar and select Preferences (Windows users).
    Go to the EndNote tab and select Preferences (Mac users).
  4. Select PDF Handling.
  5. Tick the box for Enable automatic importing
  6. Click Select folder and navigate to the new folder you created.
  7. Click on it to add its file path to the box. This tells EndNote to use that folder for automatically importing PDFs.
  8. Click Apply, then OK (Windows users).
    Click Save (Mac users)

Use PDF handling to automatically import PDFs

Once you've set your file naming preferences and created your auto import folder, you can add PDF files to that folder for EndNote to import automatically. Like Find Full Text, this function works best with articles with a DOI.

Use your PDF Auto Import Folder

  1. Search for articles in Library Search or the databases.
  2. Download the PDF files you want and save them to the new Auto Import folder you created.
  3. Open EndNote and it should automatically start to import the articles. (If EndNote is already open, but the articles are not importing, close EndNote and re-open it to start the process.)
    • EndNote creates an Imported folder inside the Auto Import folder and moves the articles into it as it adds them to your library.
    • At the same time, a list of these imported references will appear in your EndNote library.
    • If there is a DOI, the details of the article will populate the fields and you’ll have a full reference with PDF attached and renamed.
  4. Double-check the details for the fields that display in the reference. Sometimes the automatically populated records have missing data, or data entered in the wrong field.
  5. Edit as needed.
  6. Save the record and close it.

 

The file is attached, but the record is empty:

Articles that don’t have a DOI will have a title that appears as the name of the PDF in pointy brackets, e.g. <document.pdf>. For these, there is a little more work to do.

  1. Highlight the reference in the library panel on the left to open the record in the reference panel on the right.
  2. Open the PDF using the drop down menu for the file in the Summary tab.
  3. Go to the Edit tab to open the record for editing.
  4. Copy the author and title information from the PDF to those fields of the record. Save and close the reference.
  5. Open the References menu and click Find Reference Updates.
    If EndNote can find the details, it will populate the reference as it did for the article with the DOI.
  6. If it was successful, double check the fields that display in the reference.
  7. Edit as needed.
  8. Save and close the completed record.

 

There’s still no record:

If EndNote can’t automatically populate the record for you, you’ll have to add the details in manually.

  1. Open the reference again.
  2. Type in the missing data, or copy and paste details from the PDF into the fields of the record.
  3. Save your changes.
  4. Close the PDF.

 

NOTES:

  • Every file you attach to EndNote (either manually or with the automatic import) is then put into the My EndNote Library.Data folder. If you delete this .Data folder or move it to a different location from the library, EndNote won’t be able to find the file to open it. It’s best to leave this folder alone.
  • If you are manually renaming files, use only letters and numbers for the file names. Sometimes other characters, e.g. hyphens and underscores can cause problems with PDFs in EndNote

Attaching files to EndNote records (video)

This video is for EndNote 20

Manually import PDFs from a folder to EndNote

You can manually import PDF files to create records in your EndNote library. If they have a (Digital Object Identifier) DOI, the record should be automatically populated with the field data for the reference. If there is no DOI, you will need to manually enter the data yourself. Many PDFs will allow you to copy and paste text, so if you have the PDF open in a separate window, you can try that.

Import a single PDF file

  1. Open your EndNote Library
  2. Open the File menu and choose Import.
  3. Select File from the submenu. An Import File window will open.
    • For Import File, click Choose and navigate to the PDF you want to use.
    • For Import Option, select PDF.
    • For Duplicates, choose one the three options:
      • Import All: This will import the file even if it's a duplicate.
      • Discard Duplicates: This will exclude duplicate files.
      • Import into Duplicates Library: This imports duplicate files into a duplicate EndNote library.
    • For Text Translation, choose No Translation.
  4. Click Import. The file will be attached to a record which will appear in the Imported References group of your EndNote library.
  5. Check the fields of the reference to see that the data has been correctly added.
  6. Edit where necessary and save the changes.

 

Import a folder of PDF files

  1. Open your EndNote Library
  2. Open the File menu and choose Import.
  3. Select Folder from the submenu. An Import Folder window will open.
    • For Import Folder, click Choose and navigate to the PDF you want to use. Click Open.
      • Tick Include files in subfolders if the folder you have selected has subfolders of PDFs you also want to import.
      • Tick Create a Group Set for this import if you want EndNote to create a Group Set with the same name as the folder.
    • For Import Option, select PDF.
    • For Duplicates, choose one the three options:
      • Import All: This will import the file even if it's a duplicate.
      • Discard Duplicates: This will exclude duplicate files.
      • Import into Duplicates Library: This imports duplicate files into a duplicate EndNote library.
    • For Text Translation, choose No Translation.
  4. Click Import. Each file will be attached to a record which will appear in the Imported References group of your EndNote library.
  5. Check the fields of the reference to see that the data has been correctly added.
  6. Edit where necessary and save the changes.

Use the Find Full Text option to attach files

The Find Full Text function will only work with articles available from certain large online electronic journal collections. The EndNote software has to be individually coded for each of these databases, so not all articles that are available online will be retrieved by the Find Full Text function. If you highlight some references and select Find Full Text, EndNote will try to locate a PDF of the article. Normally only journal articles can be retrieved in full text. If EndNote is able to find the PDF, it will download it and attach it to the reference as a File Attachment. The PDF will be stored in the DATA folder associated with your EndNote library.

 

Configure the Find Full Text settings in your EndNote library:

  1. Open EndNote
  2. Open the Edit menu and select Preferences.
  3. Click Find Full Text in the left hand menu of the Preferences window. You will see a range of tools that can be used to retrieve full text. Make sure that DOI and Open URL are ticked. You will only need the others of you use those databases.
  4. Open URL helps when you are using Library Search to find and export records to your library. Replace the existing text in the OpenURL Path box with:
    https://cqu-primo.hosted.exlibrisgroup.com/openurl/61CQU/61CQU_SP
  5. If you are working on a campus computer, skip to Step 7.
  6. If you are working off campus, or using your own device, add the following to the URL box under Authenticate with:
    http://ezproxy.cqu.edu.au/login?url=
  7. Click Apply.
  8. Click OK.

 

Begin using Find Full Text:

It is best to work with small batches of 5 to 10 references. If you search for too many at a time EndNote slows down and the Find Full Text function looks like it’s not working.

  1. Highlight a small batch of the references in your library that you want EndNote to search for.
  2. Open the References menu, go to Find Full text and then select Find Full Text from the submenu.
  3. If you are working off campus, you will be asked to authenticate with your CQUniversity staff username / student number and password.
  4. Click on Continue to begin the search.
  5. Repeat steps 1 to 4 as needed for small batches of the remaining references you wish to search for the full text of.

A Find Full Text group set is located at the bottom of the Groups Pane (left-hand side of the library window). In this group set you can see auto-groups which allow you to monitor progress of the search.

If EndNote is unable to download the full text of the article, it may be able to find a URL link and insert it into the URL field of the reference. It may be possible to download the PDF using this link and attach it to the reference yourself.

EndNote browser extension for accessing PDFs

File attachment plugin

EndNote Click opens in a new window, formerly known as Kopernio, is the official browser extension for EndNote. It's a plugin that allows you to access PDFs in our subscription databases as well as Open Access content.

This plugin works with Chrome, Firefox and Opera.

You need to set up an account for EndNote Click. If you use EndNote Online, you can use that account for this.

Manually attach files to records in your library

What you export from databases to EndNote are item records containing citation details and sometimes the abstract and other notes. Files need to be attached separately.

Only PDF files will display as attachments with the paperclip icon in EndNote, but a number of other formats can also be attached.

  • PDF files, Word documents, PowerPoint presentations, spread-sheets, audio files, video files and others like this go into File attachment field.
  • Photos, diagrams and tables go into the Figure attachment field so you can insert them into your document as Figures. See Create a Figure record and attach a table or image file for instructions.

 

There are 3 ways to attach files to individual references.

1. Attach a file to a record in the Summary tab

  1. Save a copy of the file to your computer.
  2. Select the reference in the main panel of your EndNote library to open the Summary/Edit panel on the right.
  3. Click the + Attach File button on the Summary tab and navigate to the file you need.
  4. Highlight the file and click Open. You’ll see the file attached just above the Attach File button.

 

2. Attach a file to a record in the Edit tab

  1. Save a copy of the file to your computer.
  2. Select the reference in the main panel of your EndNote library to open the Summary/Edit panel on the right.
  3. Go to the Edit tab and scroll down to the File Attachments field.
  4. Click the + Attach File button in the File Attachments field and navigate to the file you need.
  5. Select the file and click Open. You’ll see the file in the File Attachment field.

 

3. Drag and drop a file onto a reference in the main library panel

  1. Save a copy of the file to your computer.
  2. Select the reference in the main panel of your EndNote library to open the Summary/Edit panel on the right.
  3. Drag and drop the file onto the Summary/ Edit panel of the highlighted reference.