Reference management programs compared

February 20th, 2009 by jose

The Max Planck institute of biochemistry has put together a nice review of bibliographic programs. They seem to think that refworks has an edge, and that makes me curious enough to try it.

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14 Responses to “Reference management programs compared”

  1. JöranNo Gravatar Says:

    only one star for JabRef’s output functionality is not really appropriate, in my opinion. if you combine JabRef with e.g. BibTex4Word (and Miktex) you can have virtually any citation style as output you want.

  2. jeffNo Gravatar Says:

    Also, putting Zotero’s input at only two stars is shocking. The only reason I still use Firefox, ever, is because it is so darned easy to add references to Zotero. If there were a single four star rating for input, it should go to Zotero.

    Also: PC only. As a Mac user, I know of some different players that would make for a different chart, obviously.

  3. darioNo Gravatar Says:

    I am quite surprised to see online reference managers (Connotea, Bibsonomy) mixed with purely offline reference managers (EndNote). And I second Jeff, this list is strongly PC+Windows+Office biased.

  4. Says:

    Take a look at, I found it recently in the comments to other post in this blog and hoping that soon it would be my choice for reference management (it’s still in beta for the moment but developers are very responsive to users’ feedback).
    Input gets to a new level, since it can automatically extract metadata from the PDF files that you already have, and adding new items to your database requires no additional actions (you just save a PDF to your drive).
    For the rest it’s going to have the same functionality as EndNote plus online shared groups in a CiteULike style.
    It goes for Mac too.

  5. parezcoydigoNo Gravatar Says:

    Not to pile on, but I’d like to see Mac managers up there too. I use Bookends, which had a bit of a learning curve but which I now like. It plays well with the various research database and writing tools I like to use. It also has a nice built-in sync feature for keeping two computers running up-to-date databases. There’s also Sente, which is well regarded.

    I used Zotero for a while, but I didn’t like having to use Firefox, or having to have a browser open to use it. It is very good, though, at grabbing citations off the web. That functionality is definitely 4-star. Being tied to the browser, however, was not 4-star for me.

  6. kdNo Gravatar Says:

    I think that the methodology biases the findings. Also there are errors, for example, Zotero’s collections do allow for multilevel folders. There’s a failure to give extra points for open source.

    parezcodygigo: I’ve found that for functions that are closely coupled to the web (as reference management is), a web browser is the ideal place to have your tools.

    My problem right now is I’ve been using zotero heavily for a couple of years now (even built some text mining tools on top of it), but my new research group are big on endnote, which is going to have me testing the zotero -> endnote interoperability to the limits.

  7. parezcoydigoNo Gravatar Says:


    Well, Bookends has a built-in browser for when it is necessary, as well as a means for searching directly in one’s university library catalogue. To each our their own, but I prefer not to be tied to/tied in-to Firefox whenever I want to work with my reference manager. But, I’m a distractible fellow, and an open browser is an endless temptation to the great internet mind and time suck for me. It simply works better for me to separate my research activities from my web browser.

  8. Mike N.No Gravatar Says:

    I’ll give another vote for Bookends. I used EndNote for a few years and it was fine, but Bookends definitely has more features. I also tried Zotero briefly but found it more cumbersome than Bookends.

    I would also recommend people try Sente (also Mac only). That was a close second choice for me.

  9. EmmaNo Gravatar Says:

    I’m not a Mac user … so some of the Mac suggestions aren’t of that much interest to me.

    I am, however, interested in kd’s attempts to link Zotero & EndNote. I use both – we have EndNote round the campus, but I don’t have it off campus – so tend to use Zotero (running in a portable version of Firefox, as I use a number of different computers) as a temporary store. Sometimes, though, it works better than others, and I’m never quite sure what I do differently!
    (The only drawback to that is that I generally start browsing from a PC based browser, & then want to save something so have to switch to the portable version.

  10. Februari internet tips via tweets « Dee’tjes: over internet, zoeken en bibliotheken Says:

    [...] Reference management programs compared: The Max Planck institute of biochemistry has put together a nice review . [...]

  11. Matt Says:

    Comparison of Reference Management Software on Wikipedia seems to do a much better job.

  12. kdNo Gravatar Says:

    Looking at endnote/zotero interopearability, a bit further as, it looks to me like the easiest way is to collect references in zotero then to export to RIS and then import to endnote if you need to use endnote at all. Leave all file attachemnt/storage etc to zotero where integration is relatively painless.

    One thing that zotero does which endnote doesn’t do, and means that I really can’t use endnote is it doesn’t store when I added a reference into my database. I rely on this to remind me of what I was doing at the time.

    If you need to import from an endnote file with embedded links to files in it, try to make sure you only have absolute links to the file, not relative ones because when you make the files relative, the links get stored as some ridiculous propietary url scheme that is hard to translate back to the correct format that zotero requires for import of links from RIS [ correct because it's based on an open source standard, not on a scheme that Thompson pulled out of their hat, then added spurious newlines to ;) ] I’ll be writing a script to fix links in endnote generated RIS some time soonish – from a programming point of view it looks easy enough once the stupider bits of the proprietary format are dealt with.

    Anyhow, I think that once I showed the boss the ease with which zotero can link one reference to another, store notes and generally organise things in a coherent way, we’ll all be using zotero before too long.

  13. Mr. GunnNo Gravatar Says:

    Sorry to come in late on this post, Jose. There’s also a good comparison of reference managers at Nature Network, and I wrote a post about my experiences with reference managers here.

    KD – If you’d like an all-in-one solution, you should try Mendeley. It will automatically import and extract info from PDFs as well as store articles you bookmark from the browser. No mucking about with .ris files, which I’ve certainly done my share of.

    I’m now working for Mendeley, so if you’ve got any questions about upcoming plans, comments about needed features, or just complaints in general, I can make sure the responsible people see them.

    Well, thanks for letting me intrude. You should do your own comparison sometime, I’d love to see it!

  14. Compare Bibliographic Management « cwilliams11 Says:

    [...] August 7, 2009 at 10:34 am · Filed under Uncategorized The Max Planck Institute of Biochemistry offers up a comparison of bibliographic management systems (via Academic Productivity). [...]

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