The killer feature that a reference management tool must have: be portable in plain text

June 22nd, 2009 by jose

Frankly, there are too many reference managers today.1note2007 This  is counterproductive because we all need to spend time checking the newcomers, just in case there’s a new feature that we were missing.

Most reference managers graft themselves to word or to openOffice. For example, Mendeley, and zotero both use internal reference functionality in word. In doing so, they use features that are available only on those editors. I think this is a big error for at least 3 reasons:

  1. I draft my papers on a text editor or oneNote. This has a lot of advantages for me. But I would not be able to use say Mendeley or Zotero on oneNote; and I do want to keep references on my notetaking tool. Using a text editor has a lot of nice advantages over a word processor too, if you know how to use it.
  2. It’s a lot faster to massage your reference the way you like it. It takes several clicks on zotero to get an Author (year, p. XX) reference. In endNote, it’d be a few keystrokes.
  3. There are bottlenecks in our digital lives that are plain text. For example, emails, forum posts, and google docs are cases of writing that may need reference management but are ill-served by most current offerings. I want to copy-paste chunks of scientific writing and still carry my references; there’s life outside word processors, and quite a lot of it!

So what reference managers work ok on plain text. Well, here is the surprise: as far as I know, only bibTeX and endnote. This is surprising because they are the oldest. One would have thought that newcomers would have taken advantage of what these older tools learned.

Lurking in the Zotero forums, I saw people asking for support of this exact feature. But it seems that it’s never going to happen. It would take a lot of reengineering, and all users that are happy with the current solution (and have amassed a large body of authored docs) would complain.

so, where does this leave me? I need to either comply and write everything in word to take advantage of Mendeley and Zotero, or stick to oneNote, but use endNote references. Of course I could also do everything on a text editor and use bibTeX, but right now, it’s more trouble than it’s worth.

Does anyone know a good solution for my setting?

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23 Responses to “The killer feature that a reference management tool must have: be portable in plain text”

  1. BruceNo Gravatar Says:

    This isn’t a straightforward problem to solve, but Zotero has a new “RTF scan” feature that supports this sort of authoring. You might try that and push on them to fix issues as they come up.

    Pandoc has a simple markdown extension for encoding citations; am hoping to see Zotero adopt support for that as well.

  2. Peter SmithNo Gravatar Says:


    The new RTF Scan feature will go along way towards what you want.

    Using text markers such as (Lave, 1991) to insert references, and {{Bibliography}} to insert a bibliography.

    Alas, at the moment it only works with RTF files, but I think the developers are on track for a plain text version.


  3. CBNo Gravatar Says:

    I use Zotero to store my refs, but write in LaTeX/Bibtex. What I do is make a Zotero collection for a given piece of research or writing, and export Bibtex from it. I run this quickly through Bibtool (, which I have set up to create bibtex keys in my own desired format. This way whilst writing I can add citations in plain text without having to refer to zotero.

    It’s hardly a perfect system. It’s a bit clunky to have to run my exports through bibtool every time, and LaTeX/Bibtex is a UI horror. But it gets the job done, without ever having to pollute myself with Word.

  4. DanNo Gravatar Says:

    Using BibTeX doesn’t mean you have to write out everything longhand in a text editor. There are tons of BibTeX managers out there–GUI front-ends to the underlying text file. I personally use JabRef but there are many others. Also, Google Scholar’s “export to BibTeX” feature means that I can copy and paste the reference right into JabRef (there is a BibTeX code input panel in JabRef that allows you to type in BibTeX source if you want).

  5. VincentNo Gravatar Says:

    I just looked at the Jabref help file, and it seems to be quite easy to create custom export filters. I’m sure it would take about 15 minutes to make one that gives you an “Author (Year, p.XX)” filter. With it, you would simply need to right click on the reference and select “Export to clipboard”.

    I have been concerned with interoperability and backward compatibility recently, and, after much thought, I have decided to move to a text-only system.

    I use dropbox to sync 2 files on all my computers: one for the main library, and one for the references that need to be merged to the main library. Whenever I want to add a reference, I use google scholar’s great function to retrieve the bibtex reference, and I import to the main library using Jabref if it is installed on the computer I’m working on.

    The great thing about Jabref is that it auto-generates bibtex keys according to a template I gave it. This ensures that my keys are consistent in the main library.

    When I’m not at home or on a computer that doesn’t have Jabref installed, I paste the google-generated bibtex ref into the second text file. It is then synced via Dropbox, and I just import it using Jabref later on when I have a chance.

    My database is a text file which needs minimal care, works on mac/win/linux, the keys are consistent, and I can copy the references to clipboard in pretty much any format I can think of with just one click. Plus, I know I,ll be able to read the .bib files in 10 years.

  6. RebeccaNo Gravatar Says:

    I personally would be happy if they could integrate with OneNote the way they do with Word.

    That having been said, Zotero allows you to create a bibliography on a single item to your clipboard – 2 clicks and I can essentially copy and paste the reference into whatever I am writing in. I’ve been doing that as I go along with OneNote. It’s imperfect, but the fact that I rarely have to do data entry with Zotero makes it far better than EndNote in my book.

  7. Green Grads » Green Grads Grab #10 Says:

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  8. ParisNo Gravatar Says:

    Bookends for the Mac will scan plain text. It can even try to unscan a plain text file with already formated references.

  9. VictorNo Gravatar Says:

    Hi Jose,

    good point. We have something like this on the Mendeley roadmap, in order to support more text editors on Mac… I’ll look into it!


  10. Kris Says:

    To expand on the BibTex GUIs available, I have been using BibDesk ( on the mac for years and it handles all of the basics. I’ve always wanted to keep it quick and simple with reference managers and most of the bloat in the popular ones is what drives me away.

    It is super fast to add a reference from Google Scholar by copying and dragging the BibTex information (which you can turn on in Google Scholar Prefs) and you can even add a script to autoadd by ISBN.

    I just add to BibDesk from Papers, Google Scholar, or ISBN and save the .bib file in the same dir as my writings, import into LyX, and write on!

  11. joseNo Gravatar Says:

    , ,
    When I said “doing everything in a text editor” I would use jabref of course.

    , Smith.
    rtf scan sounds promising, but it solves a different problem. You still have to format the references yourself (e.g., type say 3 lastnames off the top of your head), and hope the scanner picks them. Not ideal. Using a reference manager would be easier, select a row in a database, and press a shortcut (although some make it particularly cumbersome; Zotero, I’m looking at you). The problem is that it destroys flow to have to alt-tab to a different window. The ideal situation is to start typing something that the editor knows is a reference, and then get tab completion. JabRef support this on emacs, vim, winEdt and LyX, but it’s hard to configure.

    : looking forward to see what you have in mind

  12. BruceNo Gravatar Says:

    The ideal situation is to start typing something that the editor knows is a reference, and then get tab completion.
    I agree, though you seem to be shifting goal posts a bit. This sort of feature is much harder to support, particularly if you need it to work in different applications.

    JabRef support this on emacs, vim, winEdt and LyX, but it’s hard to configure.

    There’s the rub. It’s also likely only tied to LaTeX authoring?

  13. darioNo Gravatar Says:

    BibDesk has an autocompletion functionality that a variety of editors can access. TeXShop, for example, has built-in support for BibDesk autocompletions, you can fill in/complete a reference in a document linked to a .bib file using the F5 key. There are scripts that allow to fetch BibDesk autocompletions in applications such as Word, TextEdit, LyX, Pages.
    If this is not enough, e.g. if your editor cannot directly link to BibDesk (for instance BBEdit or TextWrangler), autocompletion is also available via system-wide OS X services that can be called from any application.

  14. JasonNo Gravatar Says:

    RefWorks supports citations and bibliographies in several file formats – Word for Windows/Mac, OpenOffice (.odt), rtf, html, and plain text. You can manually type citation placeholders into such documents (on- or offline), or you can use a feature called One-Line/Cite View to insert them. Then RefWorks can format the paper to create the bibliography in your chosen output style. You can also cite using the Write-N-Cite add-in (though only with Word).

    Full disclosure – I work for RefWorks-COS as a trainer. Just wanted to share the option.

  15. CJNo Gravatar Says:

    Have you tried Mendeley? I use it all the time, it organises all your pdfs, is a bibliography manager, sorts out all the meta-data and also hosts a researcher network where you can collaborate with other researchers.

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  17. joseNo Gravatar Says:

    bibDesk does have the feature. Still, I’m not a mac person, so I’d like to know if there’s anything similar for windows/linux, apart from jabRef.

  18. DanielNo Gravatar Says: combines note taking, reference management and collaboration in one platform. And when you’re done with structuring your project, you can export it to as .doc or .rtf.

  19. Martin V.No Gravatar Says:

    bibTeX and endnote are still the best for plain text. Newcomers failed to make any signigicant upgrades from these tools. But why?

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  22. Wez Charlton Says:

    I use a combination of JabRef to manage the BibTeX database and then use the BibTex4Word macros to insert the references from within Word.

    BibTeX4Word is available from

    This seems to work fairly well for Word, while maintaining the database in BibTeX format for future use

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