Differences

This shows you the differences between two versions of the page.

--- kb:mendeley_import [2019/02/28 21:10] – [The Import Process] Update Mendeley data directory link dstillman
+++ kb:mendeley_import [2022/12/27 16:40] (current) – [Using Mendeley Citations] dstillman
@@ Line 1: / Line 1: @@
 ====== How do I import a Mendeley library into Zotero? ======
-Zotero includes support for directly importing a Mendeley database into Zotero via File → “Import…”, but due to recent changes by Elsevier, the company that produces the Mendeley software, some extra steps may be required.
+Zotero can directly import all data, including the full folder structure, from an online Mendeley library.
-===== Mendeley Database Encryption =====
+To import your Mendeley library, follow these steps:
-Mendeley 1.19 and later have begun encrypting the local 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 [[https://service.elsevier.com/app/answers/detail/a_id/22098/kw/database/supporthub/mendeley/|erroneously continuing to state]] in its documentation that the database can be accessed using standard tools. At the same time, Mendeley continues to import data from Zotero’s own open database, as it has since 2009.
+  - Make sure that all data and files have been synced to Mendeley servers.
+    * If you use **Mendeley Desktop**, check your sync settings to make sure that data and files are being synced, and confirm that you can open PDFs in your online Mendeley library.
+    * If you use **Mendeley Reference Manager**, your data and files are already all online.
+  - Make sure you're running at least Zotero 6, which contains the latest version of the importer as well as a [[/blog/zotero-6|new PDF reader]] that can display PDF annotations imported from Mendeley.
+  - Go to File → Import within Zotero and choose the "Mendeley Reference Manager (online import)" option.
-The [[https://www.mendeley.com/release-notes/v1_19|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 [[https://twitter.com/mendeley_com/status/1006915998841221120|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 [[https://twitter.com/mendeley_com/status/1006919608471818240|repeatedly]] [[https://twitter.com/MendeleySupport/status/1006920802120470528|dismissing]] reports of the change as "#fakenews".
+You'll be asked to log in to Mendeley to allow Zotero to perform the import. Your Mendeley password is never seen or stored.
-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.
+===== Alternative Method ======
-===== Known Issues =====
+If for some reason you're not able to perform a direct online import, it's possible to import from a local Mendeley database by installing an old version of Mendeley Desktop from before Mendeley began [[#mendeley_database_encryption|encrypting]] the local database. See the [[mendeley_local_import|local import instructions]] for more information.
-In addition to the database encryption discussed above, there are a few other issues to be aware of when importing from Mendeley.
+===== Using Mendeley Citations =====
-  * Mendeley stores PDF annotations and highlights in its database rather than storing them in the file where they would be accessible to other PDF readers, so Zotero extracts annotations to a note stored under the item, with links back to the original page. Highlights are not imported. To embed annotations and highlights into the PDF files themselves so they can be imported into Zotero, you have a couple options:
+Zotero's Word and LibreOffice plugins can read citations created by Mendeley Desktop and automatically relink them to imported Mendeley items in your Zotero library, so you can continue using the same documents with Zotero.
-    - Mendeley provides an option to generate a PDF with annotations and highlights added back to the file. Prior to Mendeley 1.19.3, that option could only be run for one file at a time; in 1.19.3, it can be run for multiple files but doesn’t include highlights. In our testing, exported PDFs also don’t always contain the text of annotations. But if you’re able to satisfactorily export annotations and/or highlights, you could use that option for one or more files and then replace the imported files in Zotero (right-click on the item and choose “Show File”) with the annotated versions.
-    - You can also try using the third-party [[https://github.com/cycomanic/Menextract2pdf|Menextract2pdf]] script to write annotations and highlights back to the PDFs in Mendeley before importing into Zotero. See the [[#preserving_mendeley_annotations_and_highlights|instructions below]].
-  * 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.
-===== The Import Process =====
+Prior to Zotero 6.0.19 (released in December 2022), Zotero could read and use Mendeley citations, but they wouldn't be linked to imported items in your Zotero library. If you imported your Mendeley library using Zotero 6.0.18 or earlier, you'll need to repeat the import process once using Zotero 6.0.19 or later — just select "Relink Mendeley Desktop citations" when starting the importer. (If you've already imported citations using 6.0.19 or later, this option will no longer appear.)
-** If you have a Mendeley version older than 1.18:**
+Citations created with Mendeley Cite are not readable by Zotero.
-Upgrade to Mendeley 1.18 using the [[#Mendeley 1.18 installers|links below]] and then start the import in Zotero by going to File → “Import…” and choosing the “Mendeley” option.
+===== Known Issues =====
-** If you have Mendeley 1.18 and haven’t yet upgraded to Mendeley 1.19 or later:**
+There are a few issues to be aware of when importing from Mendeley.
-Start the import in Zotero by going to File → “Import…” and choosing the “Mendeley” option.
+  * If your Mendeley account requires institutional credentials to log in, you may need to create a separate Mendeley account and connect it to the institutional account, and then use the personal account to log in. See [[https://service.elsevier.com/app/answers/detail/a_id/33535/supporthub/mendeley/p/16075/|How do I use institutional (Shibboleth) credentials with Mendeley?]] on the Mendeley support site for more information.
+  * It’s not possible to directly import group libraries. To import items in group libraries, 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.
-** If you’ve already upgraded to 1.19 and have an automatic backup of your Mendeley SQLite database in the Mendeley data directory:**
+  * 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.
-Locate your [[https://service.elsevier.com/app/answers/detail/a_id/18153/|Mendeley data directory]] and look for a backupSlot1 (or higher) folder. If you see a database in the form %%<email>@www.mendeley.com.sqlite%% within one of the backup directories, copy it into the data directory one level up. Then start the import in Zotero by going to File → “Import…”, choosing the “Mendeley” option, and selecting that database.
-If the backupSlot//N// folder contains an .sqlite filename with a long string of random characters, the backup has already been overwritten by the encrypted database. Check another backupSlot folder or use one of the methods below.
-** If you’ve already upgraded to 1.19 and have a recent backup of your Mendeley SQLite database:**
-Start the import in Zotero by going to File → “Import…”. If you haven’t moved your backup files back into the Mendeley data directory, use the file option to select the %%<email>@www.mendeley.com.sqlite%% or online.sqlite database in your backup directory.
-** If you’ve already upgraded to 1.19 and are not able to import from a recent backup of your Mendeley SQLite database:**
-It's possible to recreate an unencrypted database by syncing from an older version of Mendeley Desktop. However, this requires syncing all data and files to Elsevier's servers before downgrading. Even syncing data alone isn't sufficient: Mendeley sync doesn't make any information about attached files available unless you actually sync the files themselves.
-If you don't want to sync any 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. As discussed above, you'll lose your folder structure and some other data.
-If you're syncing your library data but don't want to sync files, you'll need to manually relink files in Mendeley after downgrading or in Zotero after importing.
-(Note that at Zotero we strongly believe you should be fully in control of your own research data, and we don't think you should have to make these choices, but these are the available options given the design decisions Elsevier has made.)
-If you're comfortable syncing your data to Elsevier, or have already done so, here are the steps:
-  - Make sure you've synced all data and — if you want to avoid reassociating files manually — files to Elsevier's servers.
-  - Move your database out of the [[https://service.elsevier.com/app/answers/detail/a_id/18153/|Mendeley data directory]] to a temporary location.
-  - Download Mendeley 1.18.
-  - Perform a fresh sync to pull down your Mendeley data from the Elsevier servers.
-  - Start the import in Zotero by going to File → “Import…” and choosing the “Mendeley” option.
-==== Mendeley 1.18 installers ====
-<html>
-<ul>
-<li><a href="https://desktop-download.mendeley.com/download/Mendeley-Desktop-1.18-win32.exe">Mendeley Desktop 1.18 for Windows</a></li>
-<li><a href="https://desktop-download.mendeley.com/download/Mendeley-Desktop-1.18-OSX-Universal.dmg">Mendeley Desktop 1.18 for macOS</a></li>
-<li><a href="https://desktop-download.mendeley.com/download/apt/pool/main/m/mendeleydesktop/mendeleydesktop_1.18-stable_i386.deb">Mendeley Desktop 1.18 for Ubuntu (32-bit)</a></li>
-<li><a href="https://desktop-download.mendeley.com/download/apt/pool/main/m/mendeleydesktop/mendeleydesktop_1.18-stable_amd64.deb">Mendeley Desktop 1.18 for Ubuntu (64-bit)</a></li>
-<li><a href="https://desktop-download.mendeley.com/download/linux/mendeleydesktop-1.18-linux-i486.tar.bz2">Mendeley Desktop 1.18 for Linux (32-bit)</a></li>
-<li><a href="https://desktop-download.mendeley.com/download/linux/mendeleydesktop-1.18-linux-x86_64.tar.bz2">Mendeley Desktop 1.18 for Linux (64-bit)</a></li>
-</ul>
-</html>
 ===== Troubleshooting =====
-Make sure you're running the latest version of Zotero available via Help → "Check for Updates…".
+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 [[https://forums.zotero.org/|Zotero Forums]].
+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 [[https://forums.zotero.org/|Zotero Forums]].
-===== Preserving Mendeley Annotations and Highlights =====
+===== Mendeley Database Encryption =====
-As [[#known_issues|noted above]], Mendeley stores PDF annotations and highlights in its own database rather than in the PDF itself where they would be accessible to other PDF readers, and while Zotero will extract annotations to child notes with links back to the PDF, embedded annotations and highlights will not be imported.
+The importer described above imports data directly from an online Mendeley library, which requires all data and files to be uploaded to Elsevier servers in order to be imported into Zotero.
-To use the third-party [[https://github.com/cycomanic/Menextract2pdf|menextract2pdf]] script to save annotations and highlights back to all of the PDFs in your library before importing into Zotero, follow these steps:
+Zotero originally announced work on a fully local importer in early 2018, but a few months later, Elsevier began encrypting the local Mendeley database, making it unreadable by Zotero and other standard database tools. This change came despite Mendeley having long touted the openness of their database format as a guarantee against lock-in and explaining in documentation that the database could be accessed using standard tools. Mendeley Desktop itself had imported data from Zotero’s own open database since 2009.
-==== macOS or Linux ====
+The [[https://www.mendeley.com/release-notes/v1_19|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 someone using the same operating system account or an admin account can already install a keylogger to capture passwords. Mendeley later [[https://twitter.com/mendeley_com/status/1006915998841221120|switched to claiming]] 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 [[https://twitter.com/mendeley_com/status/1006919608471818240|repeatedly]] [[https://twitter.com/MendeleySupport/status/1006920802120470528|dismissing]] reports of the change as “#fakenews”.
-  - Close Mendeley
+Direct access to the Mendeley database is the only fully 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. While Mendeley offers a web-based API, it contains only uploaded data, so relying on it means that anyone wanting to export their own data first needs to upload all their data and files to Elsevier’s servers. The API is under Elsevier’s control and can be [[https://service.elsevier.com/app/answers/detail/a_id/31598/supporthub/mendeley/p/16075/|changed]] or [[https://blog.mendeley.com/2021/03/11/mendeley-refocusing-announcement-mobile-app-retirement/|discontinued]] at any time.
-  - Make a backup of your [[https://service.elsevier.com/app/answers/detail/a_id/22098/kw/database/supporthub/mendeley/|Mendeley data directory]], including the ''Downloaded'' folder that holds your PDF files (and other locations on your computer where you have PDF files you wish to save Mendeley annotations to)
-  - Download and unzip the menextract2pdf script from [[https://github.com/cycomanic/Menextract2pdf/archive/master.zip|here]]
-  - Open Terminal, navigate to the unzipped Menextract2pdf folder, and run the following command (filling in the correct file paths):
-    * <code>menextract2pdf_overwrite.sh "/Path/To/Mendeley/Data Folder/" "/Path/To/Mendeley/PDF/Folder/"</code>
-  - For example, on macOS, if you have your Mendeley database in the [[https://service.elsevier.com/app/answers/detail/a_id/22098/kw/database/supporthub/mendeley/|default location]] and your PDFs stored in Mendeley's "Downloaded" folder, you would enter:
-    * <code>menextract2pdf_overwrite.sh "/Users/"Your Name"/Library/Application Support/Mendeley Desktop" "/Users/"Your Name"/Library/Application Support/Mendeley Desktop/Downloaded/"</code>
-==== Windows ====
+Since making this change, Elsevier has replaced Mendeley Desktop with Mendeley Reference Manager, which is essentially a wrapper around the website and doesn’t contain a real local database at all.
-  - Install [[https://www.python.org/downloads/|Python]]
-  - Close Mendeley
-  - Make a backup of your [[https://service.elsevier.com/app/answers/detail/a_id/22098/kw/database/supporthub/mendeley/|Mendeley data directory]], including the ''Downloaded'' folder that holds your PDF files (and other locations on your computer where you have PDF files you wish to save Mendeley annotations to)
-  - Download and unzip the menextract2pdf script from [[https://github.com/cycomanic/Menextract2pdf/archive/master.zip|here]]
-  - Open Command Prompt, navigate to the unzipped Menextract2pdf folder, and run the following command (filling in the correct file paths):
-    * <code>menextract2pdf_overwrite.bat "C:\Path\To\Mendeley\Data Folder\" "C:\Path\To\Mendeley\PDF\Folder\"</code>
-  - For example, if you have your Mendeley database in the [[https://service.elsevier.com/app/answers/detail/a_id/22098/kw/database/supporthub/mendeley/|default location]] and your PDFs stored in Mendeley's "Downloaded" folder, you would enter:
-    * <code>menextract2pdf_overwrite.bat "%LOCALAPPDATA%\Mendeley Ltd.\Mendeley Desktop\" "%LOCALAPPDATA%\Mendeley Ltd.\Mendeley Desktop\Downloaded\"</code>
 {{tag>kb entry}}