Migrate Mendeley folders into JabRef subgroups

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Hi everybody,
I am moving from Mendeley to JabRef. So far I’ve imported my database through BibTeX database, but I would like to keep the folder structure from Mendeley. Is there any tool that would help me with?

The best way so far would be to export into bibtex files for every folder, but I have close to 100 folders in my hierarchy and I would avoid that if there is any possibility to do it otherwise. I’ve already searched for it, but have not found any solution. To be honest, I’ve found very few instructions how to migrate from Mendeley.

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I have been looking for instructions to successfully migrate from Mendeley to JabRef. I tested a few options, and found one good one that I want to share in hope that it can be refined and become helpful for others. I would hope that it could make it on to the main page of JabRef at some time.

The challenge of migrating from Mendeley to JabRef are the different ways of addressing:

  • Collections
  • PDF-annotations
  • PDF note

If you are not using these in your Mendeley database, then a simple “Mendeley Export” and “JabRef Import” would work perfectly :slight_smile:

Why are these fields important?

  • The “collections” are perfect for organizing references, e.g. make one collection for each paper you write or each topic that you investigate, and drag in each of the PDFs related to that paper. What is stored is only a shortcut!
  • If you have PDF-annotations, then Mendeley gives the option of exporing PDFs with annotations. The challenge is that these annotations are not stored as custom PDF annotations, but are rather embedded into the PDF text.
  • Mendeleys PDF note, is a text field outside the PDF where you can write general notes related to a paper.

To migrate the Mendeley collections and have the Mendeleys PDF annotations/notes stored as PDF annotations, I had success with using Menotexport:

Migration from Mendeley to JabRef via Menotexport v1.5.1

  • supports collections, PDF-annotations (and Mendeleys PDF note as an in-document note):
  1. From Mendeley: If you run Mendeley v1.19 or newer, the database is encrypted. Then synchronize your full database, including PDFs to their could. Next, install Mendeley v1.18. Upon starting Mendeley v1.18 and synchronizing, an uncrypted version of the database is downloaded.
  2. Install Menotexport v1.5.1, select “Export PDF” to have PDF annotations and -notes stored in the proper format, and select “Export bib” to export the database that will include the “collections”.
  3. Open the bib-file in a text editor. Replace the field “folder =” by “group =”, and add a list of all the “collections” at the end of the file. (Open the file from JabRef and add a few layers of collections to get an example of the format written into the bib-file.)
  4. Enjoy JabRef with your old collections and PDF-annotations :slight_smile:

Alternative approach: Migration from Mendeley v1.19 via Zotero to JabRef

  • stores Mendeleys PDF note as a field in the bib-file
  • the collection-structure is captured, and might be exported to JabRef by use of the Better BibTeX plugin
  • all PDFs are stored in separate folders
  • does not address PDF-annotations