Wednesday, November 25, 2009

Zotero AND JabRef: how to make both work for you

So yesterday I posted about how I switched over to JabRef reference software, mainly because it allows relative links, but also because it easily lets you see and edit the BibTex entry, which as a LaTeX user, is very helpful. There are two things JabRef does not really do that Zotero does that I find really useful:

1) Zotero can easily capture reference information from a variety of website formats, even if no Bibtex or RIS entry is provided

2) You can drop a pdf directly into Zotero, index it, and then retrieve the reference information automatically, assuming the article is online somewhere

If the article's webpage has a BibTex or RIS entry available for download, you can simply download this and import it into your JabRef database, but I have noticed some journals still do not offer this service (shame on them!)

So this morning I have been happily using Zotero to collect reference information I find online and to auto-generate some entries based off some PDFs I already had. Once I am done, I can export to a RIS file and then import that RIS file to my current JabRef database. My BibTex keys are automatically generated on import, so I simply select the new entries, go to Tools -> Scan Database -> Sync Files and any new PDFs I obtained during the day will be linked to their entry in JabRef.

I keep my Main.bib file that is my current JabRef database inside my folder with all my reference PDFs. At the end of the day, I can simply commit the whole folder to subversion. Everything is not only backed up, but when I checked out the folder on my Windows machine, all my PDF links will work perfectly and I won't have to tweak my database one bit!

I used to hesitate putting all my PDFs in svn, but our school server is pretty huge and the 1 GB or so of PDFs that I have now does not even make a dent. Plus, after hearing from a friend how he lost his whole PDF database and had to go download or even scan (yikes!) all his references again, I decided backing up all my articles in svn was not only OK, but necessary!


  1. Thanks Monica.
    I just started using both JabRef and Zotero.
    Did you tried the Sciplore, you were talking about in your previous post, in message area.
    I was thinking about trying it out.
    Anyway your this post has made me on use both, otherwise I was going to ditch one of them. Thanks

  2. Thanks a lot, I have been wondering about Zotero forever now and your blog helped... The best advantage is the online backup I think.. Even thinking about losing my library makes me want to faint!

  3. Nice take -will probably adopt this approach. Thanks for the write-up; I love learning how others get their research organized (being information scientist that's what I geek out on).

  4. By the way, check out It's an slight deviation of Freemind focused on researchers.

  5. thanks for the hint. now I'm happy :-)