A blog by Rob J Hyndman 

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Switching from JabRef to Mendeley

Published on 20 September 2011

Mende­ley has a lot more facil­i­ties than JabRef, and I’ve rec­om­mended that every­one in my research group switch to Mende­ley. How­ever, if you’ve been using JabRef for a while then you won’t want to lose all your pdf links and other infor­ma­tion stored in JabRef. Here are a cou­ple of ideas to make the con­ver­sion simpler.

Mende­ley will allow a bib file to be imported, but will drop any infor­ma­tion it doesn’t know how to deal with. There­fore you need to edit the bib file in order to pre­pare it for import­ing in Mendeley.


If you have used non-​​standard fields to store some infor­ma­tion and you want to retain it, change the field to annote. For exam­ple, I have a lot of printed papers in my fil­ing cab­i­net which are all num­bered. In the bib file, I use the field fileno so I can quickly find a hard copy of a paper. e.g., fileno={456} tells me that the paper is #456 in my fil­ing cab­i­net. (These days I store pdfs instead, but older papers are in hard copy.) To keep this infor­ma­tion in Mende­ley, I did a global search and replace chang­ing
fileno = {
annote = {File:
Then when Mende­ley imports the bib file, these papers will have a note giv­ing the file number.

PDF links

A more com­pli­cated issue is that the JabRef syn­tax for link­ing pdf files is dif­fer­ent from that used in Mende­ley. In the bib file pro­duced by JabRef, you will find lines such as

file = {deSilEtAl2009_EM.pdf:deSilEtAl2009_EM.pdf:PDF},

This refers to a file deSilEtAl2009_EM.pdf stored in a direc­tory some­where on your hard disk. The direc­tory that JabRef uses to store the files is recorded else­where. To retain these links, you need to add in the direc­tory infor­ma­tion and remove the dupli­cated filename.

First do the fol­low­ing replace­ment. Change
file = {
file = {:C$\backslash$:/rob/PDFs/
where the replace­ment text refers to the direc­tory con­tain­ing your pdfs. Here, my direc­tory is c:\rob\PDFs. The drive infor­ma­tion c:\ needs to be changed to :C$\backslash$: and the direc­tory path should have back slashes changed to for­ward slashes.

Sec­ond, use a regex replace­ment to remove dupli­cate file names.  I’m using Notepad++ to edit my bib file and I used the fol­low­ing search and replace (with reg­u­lar expres­sion checked):
Put in the search box : [A-Za-z0-9_.-]*:([A-Za-z0-9_.-]*.pdf)
and in the replace box: \1

That should do it. Now import the bib file into Mende­ley and hope­fully the anno­ta­tions and pdf link­ages will be preserved.

I sug­gest that you first cre­ate a small bib file with only one or two papers to check that it works before import­ing a large bib file con­tain­ing all your papers.

I have not con­sid­ered how to con­vert JabRef groups of papers to Mende­ley fold­ers as I never used JabRef groups.

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10 Comments  comments 
  • http://mendeley.com/profiles/william-gunn Mr. Gunn

    This is great, Rob, thanks! Minds if we add these tips to the wiki?

    • http://robjhyndman.com Rob J Hyndman

      No prob­lems. But it would be nice if at least a cou­ple of peo­ple check that it works for them as well.

  • http://www.gfreeman.co.uk GF

    Any thoughts on Zotero? It’s really very advanced now, and doesn’t require Fire­fox any more.

  • Pierre

    I see more and more peo­ple using Mende­ley in my team. It really seems pow­er­ful and their vision is quite appeal­ing, but the closed source soft­ware + cloud based stor­age makes me feel uneasy. How do you feel about this ?

    (I’ll prob­a­bly stick to my old fash­ioned desk­top based kBib­Tex for a cou­ple of months at least…)

    • http://robjhyndman.com Rob J Hyndman

      I love cloud stor­age (with local sync­ing) as it pro­vides an auto­matic backup.

      I’m also not fussed using closed source soft­ware pro­vided it is good. I love my iPhone which is closed source but works bril­liantly, but I hate MS-​​Word which is closed source but awful. The impor­tant issue is not who has access to the source but whether the soft­ware is any good.

  • Jacob Pog­son

    I’ve been using Papers for Mac and iOS or some years now and have found it use­ful for my own work and  stud­ies. Not so much writ­ing, but keep­ing track of all the things I’ve read and should read in my field. 

    Now Mende­ley has an iOS app, I think I’ll try it again.

  • DGal­lagher

    A few issues I found with mov­ing to Mende­ley from JabRef. Inclu­sion of braces around cap­i­tal let­ters such as acronyms in titles, the use of dou­ble braces around title field by Mende­ley and abil­ity to use stan­dard IEEE LaTeX abbre­vi­a­tions. I would also like the abil­ity to open remote doc­u­ments by DOI inter­nal to Mendeley.

  • Vitaly

    Thanks, Rob. It worked for me with one small change… If a file name con­tain “_​” like in “Smith_1987_keyword.pdf”, then in the .bib file, it should be replaced with “_​” before import­ing to Mende­ley (“Smith_1987_keyword.pdf”). Oth­er­wise it does not find the file.

  • Chen­ming Zhang

    The only thing through is that mende­ley is not com­pletely free (not a soft­ware with GPL lisence)