Reference Manager Overview

This chart gives a feature overview of some popular reference managers. It is also available as PDF. Feature lists are are just a starting point, usability, available support and cost are other important considerations. The information on this chart is collected to the best of my knowledge, please contact me if you have suggestions for improvement.

Version History

15 March 2009: Initial version.

18 April 2009: I’ve updated the chart and added 2collab, the “Read” category, sharing of PDF files and the Mendeley bookmarklet and fulltext search.

15 July 2009: I’ve updated the chart to indicate that Mendeley and labmeeting have integrated PDF viewers, and that 2collab can search Scopus.

20 July 2009: I’ve added the offline version of RefWorks for Windows, EndNote OpenOffice plugin and fulltext search in several tools.

22 February 2010: Many small changes, including a few more categories. Added Citavi and dropped 2collab, LabMeeting and Connotea.

6 August 2010: Added Mendeley API and iPhone app, EndNote X4 features.

19 September 2010: Moved chart to PLoS Blogs, made it a static page with new short URL, added PDF download option and added Creative Commons license.

60 Responses to Reference Manager Overview

  1. AJ Cann says:

    Background colours are a bit dark Martin, making the labels difficult to read.

  2. Martin Fenner says:

    I changed the file from .jpg to .png. And the next version might have lighter colors.

  3. SAm says:

    Thanks, this is useful. I agree the figure-ground contrast needs work.
    Zotero outputs bibtex, does that qualify it for a colored “LaTex” box, or you meaning something else?

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  5. AJ Cann says:

    Thanks, that’s better but I still struggle to read the first two.

  6. Martin Fenner says:

    Sam, almost all reference managers export in the BibTex format, I mean something more in this chart. JabRef is one of several reference managers built around BibTex. Mendeley is also doing a little bit more than export, as it can automatically sync one or more BibTex files with its library. I’m not a LaTex user, so I would appreciate feedback in this area.

  7. amarois says:

    Thanks Martin for this update.

    I worked a few months ago with 2 PhD for a little training course on Mendeley. They heavily use LaTeX, and what they said is that the software is very useful for their personal workflow. The bibtex files synced is not perfect, but the job is done.

    Personally, I think that Mendeley could do more with the shared pdf : the notes and highlighting are not shared between two users (it is not embedded into the files).

  8. PatrickD says:

    Hi some remarks:
    - Zotero can support LaTeX writing with copy and paste process.
    - With the next Version (now in public beta) Citavi supports PDF read functions.
    - Maybe it would be useful to add the compared versionnumbers of the tools.
    In total very nice work will use it has a handout in my next citation management workshop.

    Thanks Martin

    Patrick

  9. Martin Fenner says:

    Patrick, thank you for your comments. Adding the version number that was tested is a very good idea, will go into the next update. Most reference managers do copy and paste of formatted references (e.g. OpenOffice/Refworks), but that is not the same as having a plugin. And please use the chart in your workshops. For the next update I might do a version of the chart for presentations with 5 slides Search/Share/Store/Read/Write.

  10. PatrickD says:

    I don’t mean copy and paste I mean real drag and drop with the mouse (see http://www.bibliothek2null.de/2009/01/12/tip-zotero-und-bibsonomy-zusammen-nutzen/ (in german) ) but you are right having a plugin in definitely different.

  11. Martin Fenner says:

    Patrick, thank you for the clarification. Is there a good blog post/resource that looks at LaTex/BibTex integration with the tools listed above (Mendeley, CiteULike, Papers, etc.) in more detail? If not, I invite an experienced LaTex/BibTex user to write a guest blog post about this.

  12. Grant says:

    Is there a reason BibDesk is left out? (Just interested.)

    One way to resolve the colour issue, might be to have the column label text in the colour, with a white (or light grey) background?

  13. Martin Fenner says:

    I thought that it would be good if the overview chart is only one page (so that it is really an overview). This means a natural limit in the number of features and reference managers I can list. This is obviously an arbitrary decision, but I don’t think there are good numbers of what are the eight most popular reference managers.

    Your suggestion regarding the column labels is a good one, I will do that in the next update.

  14. Lucas D says:

    Perhaps under “Store” you could include a category for storing/syncing with WebDAV servers. Zotero, for instance, allows one to store all one’s attachments/pdfs in one’s own WebDav server. Mendeley, on the other hand, requires buying space for anything over 500 MB personal files.

  15. Martin Fenner says:

    Lucas, what would be the advantage of using a WebDav server over storing the files in the web version of the reference manager? Do you want to use the library with multiple users, or would you use WebDav for Backup?

  16. PatrickD says:

    Hi some more thought.
    1) I know the problems with the number of the programms, but maybe a database soultion that can generate a pdf would be the best one. (I know this is a little to much work ;-) ) because I realy miss Sente. Even if it not as well known as papers. It is maybe the most advanced citation management programm for the mac that has a real mac usebility.

    2) Is it possible to provide the souce. (or is it crated in a graphic programm?) This makes it possible to generate your own view and add or leave out a tool that you don ‘t need in your context eg. if the institutuion don’t offer a refworks account.

  17. Martin Fenner says:

    Patrick, the current version of the overview chart is done with Numbers (a spreadsheet for Mac users). I can certainly provide that chart as either Excel or Google Docs document, so that users can generate their own views, e.g. with the applications available at a particular instiution.

    A database solution would also be nice, but that require a lot of work. For version 3.0 of the chart I would consider starting individual pages for each reference manager, listing a feature overview from the chart, a little summary, and useful links. At this stage I would need help maintaining the information.

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  19. Kerim Friedman says:

    Also surprised not to see Sente listed. IMHO it is the best choice out there for Mac (and now iPad) users.

  20. Jen D says:

    Hi Martin – This looks fabulous. I’m writing to ask permission to adapt your idea and chart for law users (per the creative commons license posted). How would you like me to attribute your work? And, per your comment above, I would love to have your excel file as a starting point! Thanks!

  21. Martin Fenner says:

    Jen, please feel to reuse the chart. Please link to this page (http://bit.ly/refman). The next chart update (including a spreadsheet version) should happen later this month.

  22. Adele van der Merwe says:

    Thank you for this information. I need to do a comparative study (more details required for the report) regarding Zotero, Mendeley, EndNote and Refworks and this is going to safe hours of work. One question: are there any other open source reference management systems that one should take note of?

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  26. Patrick Hilt says:

    Hi Martin, thanks for the overview.
    To my understanding, Citavi should get the first and the third “Read”. Citavi puts all PDFs in one folder. Since you access them from inside the programme, you do not need to search the files from outside of Citavi – does that qualify for “File organizer”? Also the second and third “Write”, since Citavi supports LaTeX and OpenOffice.

  27. Lucas says:

    Hi Martin,

    I just happened to come across this page again, and I see that you responded to my post. Sorry for the delay in getting back to you.

    My point was that the option to use one’s own WebDAV server can, in some cases, allow one to save money. Let me explain: Zotero offers 100 MB of space for free, and then you have to pay for more space. Mendeley offers, I think, 500 MB of space free, and then you have to pay for more. However, Zotero uniquely offers the alternative of using any other WebDAV server for storage. In my case, I already have free, virtually unlimited WebDAV storage through my university, so I can set Zotero up to store my entire library through that service. Since the size of my library is currently a little more than 500 MB, this means that I can use Zotero for free, whereas to use Mendeley I would have to pay for extra storage. (Also, Mendeley somewhat annoyingly displays a permanent warning/advertisement about the need to buy more space once one’s library nears the limit.)

    Hope that helps clarify, and thanks again for this great post.

    Best,

    Lucas

  28. Lucas,

    Thanks for the update. What you say makes perfect sense.

  29. Patrick,

    the Citavi part of the chart indeed needs an update, as it received a major update at the end of last year.

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  32. Laurent Castellucci says:

    Martin,
    Stumbled across your blog (and this) while trying to research reference management options for my organization and it’s a godsend.

    I am curious about something though. We currently use Reference Manager and I see no mention of it anywhere (although you do mention EndNotes a lot.) Is there some reason it isn’t widely used? As far as I can tell, the one feature it has which explains why it is used here is that it allows for a central database on a network that all the users can access. It seems everyone else approximates this with a web interface.

    That functionality (collaborative reference library) is pretty crucial, and I suspect the fear on this end is that legal issues would prevent us from storing pdfs on an outside server.

    I would LOVE to get away from Reference Manager, as I find it seems to cause as many problems as it solves. (It looks like Citavi team, should it come out soon, would offer something like this.)

    As you know the field far better than I, am I correct in thinking that this is something only RefMan provides currently? Is there some reason it’s not among the managers you discuss on this site?

    (Yes, I realize I have just wandered in here and most rudely asked to pick your brain, but I promise I am doing the supplemental reading to try and catch up.)

  33. Martin Fenner says:

    Laurent,

    this overview always needs updating, and Reference Manager is a program that I should add. A central reference database is an important feature, and the different tools have a slightly different approach to this.

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  36. I think the new version of Papers (2.0) has some sharing capabilities but I haven’t updated yet because I’m still trying to figure out one system to use. My filing is such a disaster right now between Endnote references collected over the past decade and PDFs in papers but only 1/3-1/2 with appropriate metadata. I’m reluctant to switch now just to have to switch again later if the business model fails or one loses and stops being updated.

  37. Carly Hylton says:

    @LucasD, @Martin Fenner
    It was my understanding that you could NOT sync a central WebDAV with Zotero…
    Are you syncing with DropBox and DropDAV? This is the only way I know about going about this.
    The reason I ask is that my lab would like to be able to sync with our server so that we might be able to centrally organize our libraries, however, using DropBox and DropDAV seems like the only way to do this, and then we would need to keep all of our libraries on a central hard drive!
    Any info you might be able to provide would be greatly appreciated!
    Loved the graph!

  38. Martin Fenner says:

    Carly, if you have Zotero 2.x you can create an account at Zotero.org to sync your liberaries.

  39. Carly Hylton says:

    @LucasD @Martin Fenner
    Right, gotcha.
    Moreover, LucasD writes:
    “However, Zotero uniquely offers the alternative of using any other WebDAV server for storage. In my case, I already have free, virtually unlimited WebDAV storage through my university, so I can set Zotero up to store my entire library through that service. Since the size of my library is currently a little more than 500 MB, this means that I can use Zotero for free”
    This, specifically, is what we have been trying to implement without success…

  40. Martin Fenner says:

    Carly, I can’t recommend specifics about on WebDAV storage for Zotero, but having an account at Zotero.org is the preferred solution unless you know what you are doing with WebDav. The rates that Zotero.org is charging beyond the free 100 Mb look reasonable to me.

  41. Sean says:

    Thats a great list.. thanks for sharing it! I’ve never used Zotero but will certainly give it a look. Increasingly, I prefer to have everything I use accessible from the cloud (mine, or others), so Zotero sounds interesting.

  42. Andrea says:

    This has been an excellent resource to use in library workshops. Any chance you’re planning an update soon?

  43. Martin Fenner says:

    Andrea, an update is long overdue. I’m still in transition to my new job at PLoS, but I plan to update this overview ion the summer.

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  46. James Welsh says:

    I was wondering if anyone knows how references and citations integrate through to layout and publishing software such as Indesign? Our experience is the citations are not compatible with layout software. I am looking for a solution that helps the researchers include accurate citations from published documents as well as the web in their Word documents and its citation management features; but then I need that document to be compatible with the footnote, biblography and indexing features of Indesign.

  47. Martin Fenner says:

    James, you can always fall back to inserting citations as plain text, and most reference managers support this copy/paste. Don’t ever use the citation management features of Microsoft Word, they are too basic for most needs.

  48. adam.smith says:

    Most citation managers also have a button to remove the links/codes they insert in the Word document. In Zotero and Mendeley it’s called “Remove Field Codes”

  49. James Welsh says:

    Thanks gentlemen:
    Stupid questions:
    After the codes are removed are the citations left in the manuscript?
    Does the RMS place the citations in Word footnotes automatically?
    Do editors need to have the RMS in order to edit the documents?

  50. Martin Fenner says:

    James, removing the codes leaves the citations in the manuscript, and they are then just text like everything else. I wouldn’t use Microsoft Word footnotes, as this makes things more complicated.

  51. I would be interested if storage devices and apps change nowadays. Is there a movement to cloud services or still local for Data?

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  55. Patty says:

    Thanks Martin for your excellent overview, it saved me a ton of work! However, looking into this on request (preparation for a move away from RefMan) I also came accross BiBus. Is there a reason (other than space limitations) why you didn’t include BiBus?

  56. James Welsh says:

    EndNote now has a version for iPad. It also has the “EndNote Web” version. I belive it does work with citations embedded in pdf’s and on websites.

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  58. Joeran says:

    In case you will update your list, I would be very glad if you could also include our reference manager Docear http://www.docear.org/2013/10/17/docear-1-0-stable-a-new-video-new-manual-new-homepage-new-details-page/
    Docear is open source, available for Windows, Linux, and Mac OS, and offers a very unique user interface. In addition, Docear allows not only organizing PDFs and references but also drafting your own papers, books, etc.

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