How do I import a Mendeley library into Zotero?

Zotero can directly import a Mendeley database, but due to changes by Mendeley’s parent company Elsevier, you’ll first need to install an old version of Mendeley Desktop. Later versions of Mendeley Desktop began encrypting the local database, preventing you from getting your own data out of the app.

You must sync all data and files in your current version of Mendeley before downgrading. If you don’t want to sync your data to Elsevier’s servers, your only option is to use one of the available export formats, such as BibTeX, to transfer your data to Zotero. Exporting includes basic item details but omits your folder structure, various metadata fields (date added, favorite, and others), and PDF annotations.

To perform a full import, follow these steps:

  1. Make sure you’ve synced all data and files in your current version of Mendeley. Syncing data alone isn’t enough, since Mendeley sync doesn’t make any information about attached files available unless you actually sync the files themselves.
  2. If using Mendeley Desktop, make a backup of your Mendeley database.
  3. Close Mendeley Desktop
  4. Download and install Mendeley Desktop 1.18 using the links below.
  5. Open Mendeley Desktop 1.18 and perform a fresh sync to pull down your Mendeley data from the Elsevier servers. (If Mendeley doesn't open, you may need to go to your Mendeley data directory and move the file ending with @www.mendeley.com.sqlite out of the way.)
  6. Verify that all your data and files are available locally. If some files are unavailable, it may help to add all items in the library to a folder and restart Mendeley Desktop.
  7. Install the Zotero Beta, which is currently required to import highlights and notes into Zotero’s new PDF reader and iOS app.
  8. Start the import in Zotero by going to File → “Import…” and choosing the “Mendeley” option.

Mendeley 1.18 installers

Known Issues

In addition to the database encryption discussed below, there are a few other issues to be aware of when importing from Mendeley.

  • To import PDF highlight and note annotations, you currently must import using the Zotero Beta, which adds support for annotations. If you’ve previously imported from Mendeley using Zotero’s importer, you can repeat the process with the beta to bring in your highlights and notes.
  • It’s not possible to directly import group libraries. To import items in group libraries, simply copy the group items to a collection in your Mendeley library before importing. You can then create a Zotero group and drag imported collections or items to that group.
  • Mendeley allows any field to be added to any type. When importing into Zotero, if a field isn’t valid for a given item type, the field is placed into the Extra field. When possible, those will be used automatically in citations (e.g., Original Date), and future versions of Zotero will automatically convert those to any real fields that become available.
  • When using the Zotero word processor plugins, document citations created with Mendeley won’t currently be linked to imported citations in your Zotero database. Zotero’s word processor plugins can, however, read Mendeley citations and their embedded metadata, so you can continue using the same documents with Zotero.

Troubleshooting

Make sure you’re running the latest version of Zotero available via Help → “Check for Updates…”.

If you’re running the latest version and something doesn’t come through how you expect or you run into any trouble, let us know in the Zotero Forums.

Mendeley Database Encryption

Starting in Mendeley Desktop 1.19, Elsevier began encrypting the local Mendeley database, making it unreadable by Zotero and other standard database tools. Elsevier made this change a few months after Zotero publicly announced work on an importer, despite having long touted the openness of its database format as a guarantee against lock-in and explaining in its documentation that the database could be accessed using standard tools. Until recently, Mendeley Desktop imported data from Zotero’s own open database, as it had since 2009.

The Mendeley 1.19 release notes claimed that the encryption was for “improved security” on shared machines, yet applications rarely encrypt their local data files, as file protections are generally handled by the operating system with account permissions and full-disk encryption, and anyone using the same operating system account or an admin account can already install a keylogger to capture passwords. Elsevier later stated that the change was required by new European privacy regulations — a bizarre claim, given that those regulations are designed to give people control over their data and guarantee data portability, not the opposite — and continued to assert, falsely, that full local export was still possible, while repeatedly dismissing reports of the change as “#fakenews”.

Direct access to the Mendeley database is the only local way to export the full contents of one’s own research. The export formats supported by Mendeley don’t contain folders, various metadata fields (date added, favorite, and others), or PDF annotations. Mendeley offers a web-based API, but it only contains uploaded data, so relying on it would mean that anyone wanting to export their own data would first need to upload all their data and files to Elsevier’s servers. The API is under Elsevier’s control and can be changed or discontinued at any time.

Since making this change, Elsevier has released its replacement for Mendeley Desktop, Mendeley Reference Manager, which is essentially a wrapper around the website and doesn’t contain a real local database at all.

kb/mendeley_import.txt · Last modified: 2021/03/29 14:49 by dstillman