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JabRef vs Zotero with Word Processor

January 8, 2008

I have talked about JabRef and Zotero here several times, especially the latter. However, it’s JabRef which I use for my work. Zotero is quite handy to collection the references but its file format is not a native BibTex file that I can use directly with LaTeX. The BibTeX file exported by Zotero still has some bug (see many discussions on this topic in Zotero’s forum). Therefore, I have disabled its ability to download RIS/Refer files, and use it mostly for general topics (including physics).

Recently, when I wrote the report in MS Word (sometimes I still use that), I thought, why not try Zotero’s Word plugin to insert the citations (or Writer, if you prefer)? Well, I only tried for 10+ min and went back to my old way since I had a deadline.

Today, I finally had time to check Zotero’s plugin and JabRef’s customer export filter. The short answer is that JabRef works better for me but Zotero has its own advantages. First, let me show you my old way of putting references in a Word or OOo Writer document, and then outline each method.

The basic in-text citation I used is similar to the basic one for Chicago Manual of Style (CMS) or APA (American Psychological Association) style, but is adopted from the bibtex key: 1st Author’s last name + year of publication, e.g. Einstein1905. In this way, it’s just like writing it in LaTeX file without the \cite command. The style for bibliographies in the end usually follows the style for Physical Review journals. Before this report, I manually typed them or copied them into text from the pdf file produced by LaTeX + BibTeX. Even with the copied text, I still needed to apply the style (bold or italic font) manually. That’s tedious if you have many bibliography entries to modify.

Here are improved methods to make inserting citations easier in MS Word or OOo Writer.

Method 1: Zotero’s plugin

  1. Go to Add-on (in Word) Click at (insert citation) to choose which one to insert (single or multiple entries). Click at “Show Editor” can let you edit the in-text citation format before putting it into the document.
  2. Click at to generate a bibliography of all items you just cited.


If using JabRef’s database, first select entries you’d cite and save them into another database (.bib). Open it in any editor and remove the header (two lines starting with #) and the comment lines in the bottom. Then import them into Zotero, which will be placed in a new folder automatically.

I got some problem when I tried to edit the bibliography to remove unwanted information (e.g url) appearing in the bibliography. An error message showed up, saying “Run-time error ’91’: Object variable or with block variable not set”. Consulted in Zotero forum but still couldn’t know what the problem was (very persistent).

I gave up and then went to try JabRef. Later (after installing the latest version 1.0.2 and its plugin — released today!), mysteriously I no longer encountered these problems. For instance, when I switched to a different style (Natural Journal), the unwanted url information disappeared, which didn’t come back even after I switched back to CMS. πŸ˜•

Anyway, without this run-time error, Zotero does work very efficiently in Word (supposedly OOo Writer too). You may need to manually edit the bibliography information for some entries if the citation is exported from BibTeX format. The good thing is that it can automatically react according to the changes of the style and adding/removing the bibliography entries (need to click to update the references). However, Zotero still cannot now can compress the in-text citation numbers, e.g. 1–3, which is a piece of cake for like what LaTeX + BibTeX (with the natbib package) do.

For people who mostly use word processor for writing, Zotero is your best tool, especially that it’s now more mature than the previous versions.

(see also Zotero Extension for MS Word and OpenOffice and New Screencast of Zotero plugin for Word)

[03/17/2009] Update: Ever since, Zotero has improved quite a lot.Β  Check out this recent post, “Try out New Features in Zotero 1.5 Beta“.

Method 2: JabRef custom export filter

  1. Write the BibTeX key as the in-text citation manually or copy it from JabRef (right click at an entry and select “Copy BibTeX key (I wish there’s a hot key for this)
  2. Export the selected bibliography entries into a RTF file using your custom export filter. Copy the whole bibliography into the right place of your document.


The first thing is to create the custom export filter following the bibliography style you prefer. I used the example based on Organization Science’s style from here and tweaked the style close to the one for Reviews of Modern Physics. To add a new export filter:

  • Unzip all the files in some directory
  • In JabRef/Options/Manage custom exports, add a new one by giving the export name, the file position (the main file, xxx.layout), and the file extension (.rtf)

Tweaking the style takes some trials since I don’t know the markup language used here, but it’s not difficult when you have an example to start with. JabRef provides some commands to replace TeX-specified characters, e.g. {\a} or {\”{o}}, with their HTML or XML presentations (still has some bug when exporting to RTF).

Once the custom export filter is set up, using JabRef with any word processor is very convenient, as long as you use author + year for the in-text citation format. It’s good for people who use LaTeX and BibTeX mostly for their works but occasionally need to work on any word processor.

Wait, JabRef can do more. πŸ˜‰

Method 3: JabRef default export filter

Another easy way is to export your JabRef database (or selected entries) into MS Word 2007 (XML) format. Then use the built-in citation tool in Word. For OOo Writer users, check out this help docuement. I didn’t go through this method, so I’m not sure if there’s a bug or not.

Anyway, JabRef is a nice tool, not just for the LaTeX + BibTeX users. πŸ™‚

(see also JabRef HTML Export Filter)

Related Articles:

PS: MS Office Word Team posted this article on their blog, “Bibliography & Citation 1011“. Even though the bibliography tool in Word 2007 has been improved πŸ™„ , it is still not a good tool to manage your bibliographies (“Manage Sources” under Reference ribbon). Choose either JabRef or Zotero instead.

16 Comments leave one →
  1. Kurt permalink
    May 21, 2008 8:33 pm

    Have you tried the BibTex4Word add-in for Microsoft Word? It works with JabRef databases.

  2. May 22, 2008 7:12 am

    I haven’t had time to try it yest. 😳

  3. Mathieu permalink
    March 3, 2009 8:02 pm

    I haven’t tried it yet, but found it on the same search that drove me here: there’s a OOo plugin for JabRef to directly (and dynamically) connect the 2 software, like EndNote can be connected to Word (I guess, again, not tested).

    (by the way, created by the main JabRef developer)

    Could well be the best solution for word processors…

    • March 3, 2009 10:38 pm

      Hi, Mathieu, thanks for the info. πŸ™‚ That seems to be a good way. I’ll check later.

  4. Bruce permalink
    March 15, 2009 5:24 am

    The bottom line is that if you are happy using LaTeX to write your documents, then a BibTeX-oriented application like JabRef is probably your solution.

    If, OTOH, you live in a world of web applications or traditional word-processors, or if you’re someone in the humanities an dsome areas of the social sciences, then Zotero has significant advantages. One of them is its use of CSL (which, full disclosure, I designed) to configure styling. The format is powerful but compact, and language-agnostic. In part because of that, there are many, many more styles available (now, over a thousand).

    While it’s true Zotero doesn’t yet collapse citation numbers, that is supported in CSL, so I expect it to be added at some point.

    • March 15, 2009 7:33 am

      Bruce, I agree with you. This is why I recommend both Zotero and JabRef in my blog and at school. Both have their own advantages. JabRef is more specific for working with LaTeX/BibTeX, while Zotero seems to be more versatile. Especially for people who use EndNote with MS Word, they should try Zotero.

  5. Rick permalink
    March 17, 2009 3:02 am

    Zotero collapses my citation numbers just fine. I tend to use it with Writer, but the CSL interpreter is the same & I am surprised that MS Word would be any different. Perhaps you tried citation styles that do not have collapsing? Try out e.g. the Scripta Mater. style to see how this all should work.

    • March 17, 2009 7:45 pm

      Rick, I just tried Zotero with APS citation style in MS Word and it did collapse the citation numbers. That’s great! It’s been a long time since my last try on this feature, and apparently Zotero has been improved quite a lot. I updated my post above. Thanks for the comment.

  6. erik permalink
    March 28, 2010 7:32 am

    RE: Copy BibTeX key (I wish there’s a hot key for this)

    actually there is one. its ctrl + shift + K

  7. Tuxy permalink
    June 5, 2010 10:37 pm

    Sadly, to this day fetching metadata from PDFf documents with Zotero is broken on Linux, this alone makes Zotero near useless for me. JabRef on the other hand works perfectly it can even update metadata, XMP at that, jabRef is the best free referencing tools I have tried so far.

    • Rick permalink
      June 18, 2010 8:02 am

      I fetch metadata from PDFs on linux in Zotero all the time. Why do you think it is broken?

      • June 18, 2010 8:09 am

        I don’t know what you meant. I didn’t try this in Zotero. I use JabRef for research papers instead.

      • Rick permalink
        June 18, 2010 11:21 pm

        I was replying to Tuxy’s June 5 post, that claims that fetching PDF metadata in Zotero on Linux is somehow broken. I don’t think that it is.


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