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EndNote

Guide for EndNote citation management users

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on your success and new opportunities

 

 

  1. Back up your current EndNote library in multiple formats.

  2. Learn more about your options to downsize, update, or use an alternative citation management program.

  3. Take action! Make a choice about your citation management.

if you are a RefWorks user, go here and follow the instructions.

Step One: Backing up EndNote

We recommend periodic backup in at least 3 methods.

1. Sync online backup

If you haven't already, Go to your Settings/Preferences and Enable Sync. Then Sync your library

2. Compressed Library

If your library is large, make a compressed library and save it on an external drive. PC Menu below, MAC menu to the right

EndNote PC File Menu with Compressed Library option selected     MACMac EndNote Menu with Compressed Library option highlighted

You will be able to select the details about the library, such as whether to include file attachments, selected references, or the entire library. Both PC and Mac options will look the same.

Compressed Library Detail

Click next. The final step is to navigate to the place you want to save the new file. We suggest putting it on a USB or other external drive. it's also a good idea to rename the file so that the date of backup is included.

3. Citations only export format (.RIS)

The previous library backup methods are for use with a version of EndNote. You should create at least one file type that can be opened by other citation managers. The plus is that you'll have a quick way to make sure you don't have to recreate your work in collecting references and citations. The down side is that this will not bring in your file attachments.RIS export is a quick method.

  • Go to the File menu and select Export
  • The default name is your Library Name. You may want to rename the file to something that will include the backup date.
  • You have three options: "Save file as Type", "Output Style" and a check box option to only export "Selected References" (highlighted items)  instead of the whole library. See images below.
  • For RIS export, select "Text only" as the file type and "RefMan (RIS) Export" as the Output style.
  • Make sure you'll remember where you save the file.
  • One the file is saved, if the file extension is .txt, rename the file so the extension at the end is .ris
  • Save the .ris file. The icon will usually change once you've done this.

Now you all major citation managers should be able to import your references.

EndNote PC menu for ExportingEndNote export options

Is there a way to export both my citations and attached PDFs to another citation manager?

Zotero and Mendeley both provide directions to import EndNote citations with PDFs; however, users report varying levels of success. See the Transferring section for the instructions. Make sure you backup and keep an extra copy of the Endnote Library before attempting. In general, this process works best if you are importing to a new, empty citation management library, as the relative file locations in Endnote must stay the same. Having references and files already in the new library can cause pathway errors.

Step Two: What are my options?

I've been using Endnote 21 and I want to keep using EndNote.

Your options:

  • Keep an unlimited access account: While you still have UGA SSO access, download the new EndNote 2025 as soon as UGA makes it available. We expect to have EndNote 2025 available for free download the week of April 28.
    • Downloading the new program should restart your clock on unlimited access; although, we won't know the amount of time that will be provided. Typically, EndNote gives three years from the program download.
    • What happens when I run out of time on my free unlimited online access and storage space?
      • You can purchase a new EndNote license wherever you are OR
      • You can downsize to the EndNote Basic free account with 5G of storage.
  • Downsize to a free, Basic Account.
    • Before choosing to downsize, run a Sync and look at the Sync Status Report. It will let you know how much space you are using. Most people are well below the 5G limit and should be fine with the Basic account, but it's good to check. Look for the attachments section:
    • Snippet from a Sync Status showing the amount of storage space used for attachments
    • Go to this EndNote Basic Log In page.
    • Check to see if your existing EndNote account and library will automatically transfer here by using the same log in credentials as on your EndNote 21 Online account.
      • If you are successful, Sync the account, and update your email to one that you will continue to have access to.
      • If you are not successful, create a new account with an email you will continue to have access to.
        • Transfer your EndNote Library to the new account (up to 5 GB) See Instructions next section.

I've been using EndNote and I want to move to another citation management program.

  • Check out our comparison charts box!
  • Take action! Decide which service you would like to move to.
    • We will provide instructions to assist you in moving to Mendeley and Zotero. See the Transferring boxes.

I've already been using an EndNote Basic Account

  • There is nothing that you need to do to remain in it, but you should make sure that the email associated with the account is one that you can still access.

I've been using another service.

  • Your separation from UGA has no effect. You'll remain under whatever program or subscription that you currently have.

Transferring from EndNote to Zotero

Trying to keep your PDFs with your citations? 
You'll need to export in XML format. The following instructions are from Zotero's Knowledge Base
In EndNote:
  • Look at your Sync Status report so you'll know how much space your citations take up. The free version of Zotero only has 300MB
  • If you need more space, you'll need to either use a free version, or try linking Zotero to an online storage, such as DropBox or Google Drive. If you are going to try linking Zotero to online storage, you should stop and do that first. See next section.
  • Convert any figures to file attachments.
  • The export format for this is XML.
  1. If you wish to export a subset of your EndNote library, select the entries you wish to export.
  2. Go to the File menu → Export. A dialog box will pop up asking you where to save the export file.
  3. Navigate to your EndNote data directory (typically, My Documents\endnote.Data). This directory contains a 'PDF' folder, but you should be sure to select the data directory rather than any subfolder.
    • This is important! Zotero will look for file attachments in a directory relative to the location of the exported XML file. If you save this file in the wrong spot, file attachments won't be included when you import into Zotero.
  4. For “Save as type:”, choose “XML”.
  5. If you only want to export a subset of your library, check the “Export Selected References” box. Otherwise, make sure it is unchecked.
  6. Click “Save”.
  7. Close EndNote.
In Zotero
  • Ideally you will move to a new, empty Zotero Library.
  • If you are not importing into an empty library, Zotero highly recommends making a backup of your Zotero data directory. This can avoid frustration if you do not like the way your library has transferred. In that event, simply restore your library from the backup.
  • You should also temporarily disable automatic sync in Zotero's Sync preferences. After you have imported your library and checked to be sure you are satisfied with the imported data, you can re-enable automatic sync.

1. Click “Import…” in the File menu. 

2. A dialog box will appear asking you to select the file to import. 

3. Navigate to the location where you exported your EndNote library (if you followed the above instructions, this should be My Documents\endnote.Data) and select the .xml file. 

4. Click Open.

  • If Zotero encounters any fields in the EndNote XML data that it does not support (e.g., custom fields, author address, author affiliation), it will add these data to a note attached to the imported item. These notes will be tagged with “_EndnoteXML import”. If the import adds many of these notes, Zotero's performance can be negatively impacted.
  • About notes:
    • Review each of these notes to determine if the data needs to be retained and delete any unnecessary notes. 
    • Check these notes to determine if any data can be migrated to Zotero fields 
    • You can quickly display all of the notes generated during import by clicking on the “_EndnoteXML import” tag in the tag selector in the lower-left corner of the Zotero window. 
    • If you don't want to go through each note, you can quickly delete all by selecting the tag in the tag selector, clicking in the items list and typing Cmd+A (Mac) or Ctrl+A (Windows/Linux) to select all matching items, and then right-clicking on a selected item and choosing “Move Items to Trash…”.

Getting addtional Zotero storage space

  • The easiest way is to simply buy Zotero space. You can get 2G for $20/year, 6 GB, $60/year, and Unlimited, $120/year.
  • If you are already paying for Dropbox or Google Drive space, you may want to attempt to use a special add in called Zotfile, or use the following instructions to bypass Zotero's base directories and store your files there.

These instructions come from the Washington State University Libraries, and we've even included their team's advice note, because it seems very helpful.

WSU Note: I actually highly recommend using Zotero's own storage (I pay $20/year for 2 gigs which isn't much money - it simplifies things considerably and also helps support Zotero). That said, if you really want to use your own cloud storage, this is one way to do this, but you can also use the ZotFile application for PDFs, or save PDF or other files to cloud services individually. Also, note that this is all about saving attachment files to cloud storage and establishing links to your Zotero record. Do NOT store your entire Zotero directory on cloud storage - that will corrupt your files and make a big mess.

If you have Dropbox/Google Drive/etc. Saved as a Drive on Your Computer

  1. Create a folder in your computer’s Dropbox/GDrive/OneDrive drive to store your Zotero PDFs, i.e. ZoteroFilesinDropbox. Make sure it is properly synced with Dropbox/GDrive/etc. online.
  2. In Zotero, go to Zotero Preferences -> Advanced -> Files and Folders. Here you will change your Zotero file storage Base Directory by using the Choose… option to go to the folder you just set up.
  3. Now any PDF files you download as attachments to a Zotero record will be automatically saved in this synced folder, which will store the files online in your cloud storage app.
    • Note: This is a *relational* link – if you change the file structure in any way, the link between the saved file in Dropbox/GDrive/etc. and your Zotero record will be lost.
  4. Once you have created a Zotero record and separately uploaded your PDF to your cloud storage option, make sure you are working with the correct record in Zotero for your article. Open your Dropbox/GDrive/etc. online and open the PDF so it is readable on-screen, with a .PDF extension. Attach your link to its Zotero record  using either the paperclip option in Zotero‘s toolbar (Attach Link to URI) or by right-clicking on the Zotero item, selecting Add Attachment, and then selecting Attach Link to URI. You will be prompted to paste in the file URL and add a title. Zotero will not be able to extract the correct title using Rename File from Parent Metadata, but you can change it later manually.
    • Note: If you use Google Drive, once you open the PDF in Drive you will have to click on the pop-out option in the upper right of the page to get a unique URL (it will not have a PDF extension, but it will work).
  5. Sync your Zotero library so the article’s item record on your library on Zotero.org is updated as well to include the cloud storage file links.
  6. Now from this computer, or your library on Zotero.org, or any other computer that is synced to it, you will be able to open the PDF from the Zotero record if you are logged in to your Dropbox/etc. account (if you aren’t, you will be prompted to log in). Note: If you are opening it from your Zotero application on your desktop/laptop, the file will just open as an online PDF once you click on the link. If you are accessing it online from Zotero.org, you will have to click on the Attachment Details link at the bottom of the article item record and then you will see the Dropbox/GDrive/etc. link.
  7. Using these settings, any saved webpage screenshots will continue to be saved in your regular Zotero folder, not on Dropbox/GDrive/etc., and the screenshots will be saved on and directly accessible from your library on Zotero.org.
  8. Any PDF files previously saved to your regular Zotero folder will still be there, and will continue to be saved on, and directly accessible from, your library on Zotero.org.
  9. If you don’t want ALL your article PDFs (or other attachment files) to be saved to your Dropbox/GDrive/etc., you can keep your default Zotero preferences and save individual items to Dropbox/etc., manually as needed. To do this, move/upload the PDF file you want to access via Dropbox/etc. to Dropbox/etc. manually, then follow the directions starting at #4.

This is also the option you can use to save non-PDF files including audio or video files to your cloud storage, however you may not be able to open the file in your cloud service if it doesn't include the ability to play it, although you will be able to download it.

Note: the Link to File option allows you to link a Zotero record to a file saved on your desktop that is not in your Zotero directory – this can be good for large files you do not want to upload online. You can also use this with a Dropbox/GDrive desktop drive etc. so that the file is accessible online and connected to your laptop’s Zotero library record, but it will not be directly linked to the online Zotero.org record for the item.

Transferring from EndNote to Mendeley

To import RIS citations
  • Make sure you completed in EndNote the instructions from Step One, #3: Citations only export.
  • Make sure you remember the file location.
  • Open Mendeley.
  • Click Add new, select Import library, then choose the file-type RIS (*.ris)
 
Trying to keep your PDFs with your citations? 
You'll need to export in XML format. The following instructions are modified from the Renssalaer Polytechnic Institute Libraries.
  • Open EndNote, click File, then Export (Choose "Export Selected References" to export selected items).

  • Set the output file as "XML" (from the drop-down list next to "Save as type".)

  • Save the export file to your computer.

In Mendeley

  • Log in to Mendeley

  • Click Add new, then Import library, then choose EndNote XML (*.xml).

  • Select the EndNote file you have saved earlier, then click Open to import your EndNote references or the whole library to Mendeley.
  • Press Sync in Mendeley Desktop to save the changes in the cloud.

     

Transfer from Endnote to EndNote Basic

You only need to follow the directions here if you did not have a successful automatic transfer of your account. See the box, "Step Two: What are my options?" > Downsize to a free, Basic Account. An automatic transfer will bring in all your references, groups, group sets and attachments.

  • Log in
  • Go to the grey toolbar and hover over My References > Collect
  • Select Import References

The EndNote Basic Toolbar

Import References options

  • Select RefMan RIS from the Import Option pull-down menu
  • The "To" pull-down menu lists any available groups for organization, and let's you make a new group.
  • Go to File and Browse to the file location
  • Click ok

This method will not bring in the PDF attachments