Which one is the best reference management software?

Update 2013-10-14: For a more serious analysis read What makes a bad reference manager?
Update 2013-11-11: For some statistical data read On the popularity of reference managers, and their rise and fall
Update 2014-01-15: For a detailed review, read Comprehensive Comparison of Reference Managers: Mendeley vs. Zotero vs. Docear

<irony>Have you ever wondered what the best reference management software is? Well, today I found the answer on RefWorks’ web site: The best reference manager is RefWorks! Look at the picture below. It might be a little bit confusing but we did the math: Refworks is best and beats EndNote, EndNote Web, Reference Manager, Zotero, and Mendeley in virtually all categories.

Comparison of reference management software - Refworks is the best reference manager

Source: RefWorks

But hey, wait. There is another review of reference managers that I found on Mendeley’s website. This time Mendeley is the winner over EndNote, Zotero, Papers, and also over RefWorks. Look at the picture – it proves that Mendeley is best!

reference management comparison - best reference manager

Source: Mendeley

Oh, stop, wait! Qiqqa is best! Here, look at the chart that I found on their website and  learn that Qiqqa has many many features which EndNote, Zotero and Mendeley don’t have.

Reference Management Tools Compared - Qiqqa is the best reference manager

Source: Qiqqa

Oh no, I am sorry, I was wrong again. It’s colwiz which is the best reference management software (guess, where I found the following chart). Colwiz is far more superior than Mendeley, Endnote, Zotero, and even than the social networks Researchgate and Academia. Look at all the features Colwiz offers, and the others don’t:

Comparison of Tools for Reference Management - ColWiz is best reference manager

Source: Colwiz

Oh no, another one. This time Flow from ProQuest is the clear winner… [added on 2014-07-29]

Source: ProQuest

Unfortunately, Docear wasn’t included in any of the reviews. So, I did a comparison and guess what: Docear is the very best reference management tool! Look at the table. It shows that Docear offers so much more features than all the other tools.

Best reference manager: Docear

Source: Docear


I wonder if there is a single researcher out there who really believes in the charts that are available on the tools’ web pages. Do you? If yes, I think we will have to add the review table I made myself to our homepage :-). btw. did I miss some charts? Are there more reference managers out there that have feature comparison charts on their websites?


32 comments to Which one is the best reference management software?

  • Marc

    *lol*, i always knew docear is best

  • JzJ

    For me your chart with a single row:
    – Mind Maps
    would be the game changer and make Docear the winner. :-)

  • Well, for me, JabRef is the best actually 😉 But you should know this one…

  • James Smith

    One feature row missing. Has the product made it past beta testing.

    Not going to trust my research stream to something that isn’t version >= 1.0.

    Best of luck, it looks like this will be a great product.

    • Hi James,

      yes that’s a good point, indeed. And it does not favor Docear ;-). Anyway, I would like to point out that Docear, even not being declared as 1.0 stable yet, works very well for the vast majority of our users. And since Beta 3, there has not been a single user who lost any data (or at least nobody told us of it). In addition, if you activate Docear’s free backup function, you will have a backup of all revisions of all your mind maps.


  • Andres

    There are as many truths as person are… Everyone says the better one is the one he sells (also if he doesn’t believe it), he develops (for as a child, you know all the good parts) and as user (you get used to, and it was fight to find it, to learn it, and would be a great fight to change, so better stick to it).
    Every one sees the things which are relevant for him – I see in Docear the mind mapping as perfect for my visual structuring of ideas, and I don’t care about formats, if I anyway do that in LaTeX.
    So, perspectives, I guess nearly all are good, have their own pros and cons (standard info to share with other apps is quite important for me, but is it really priority for any user if the “closed” system works in his own workflow?)

    I can say nothing, except to all developers – try to make your stuff compatible with the others (not necessary, as said, but in my very personal opinion the community would gain) :)

  • syedaftab

    i think qiqqa is the best

    • And is there also a reason why you think that qiqqa is best? (have you tried all the other tools?)

      • Vijay

        Hey Dorean,

        Freeplane with a reference manager is a brilliant idea. Joining the two worlds of tagging and sorting of sorts?!

        In terms of qiqqa what I feel has been done very well is in their reference sniffer tool. Many times after the title extraction the required metafile of the papers is not found, whether in qiqqa, Docear or Mendeley. Inadvertently or purposefully they put a browser within the reference adding/sniffing window wherein you can browse to that paper and import the metafile within that same window. So this is quite fast especially when importing references of many PDF’s where it can be done in line, even if some metafile extractions are not possible!

        I must say however that 8/10 times Docear does pick up the metafile when the title is correct, so thats fantastic! Also there is Mindmp with that so.!



  • Joel

    Haha, nice one. I have also always found it intriguing that we have so many reference managers that all are the best! Each one throwing convincing green check marks in my face and proliferating at a rate reminiscent of that of Linux distros (imagine this chart http://futurist.se/gldt/wp-content/uploads/12.10/gldt1210.svg, but for reference managers ten years from now. And with more check marks and only straight lines)

    I love the idea of Docear, great initiative! I’m also happy to see that you are recommending PDF-XChange, it’s my favorite PDF viewer and editor, but is not getting the attention it deserves. Six month ago and I would have switched over to Docear in an instance, but right now I have this idea that I learn better if I write all my notes and annotations by hand, so I’m trying to make something happen in OneNote… I am using XMind sometimes though, so maybe I will try to work Docear into my rotation instead. In any case, good luck! I’m looking forward to see what happens with your project.

  • Linda t

    Dear Joeran,

    After having seen some tutorials of refworks, mendeley and docear, I am interested in using Docear, maybe because I am more of a graphic person.
    However I there is a feature that it is as important to me, which is: if I need to change the citation manager, (refworks, mendeley, colwiz, etc.), can I do so?

    Thank you very much in advance for your kind reply.

  • Linda t

    Dear Joeran,

    thank you for your prompt response. I am sorry for the confusion.
    I reformulate my question.
    Lets assume that I install Docear and that I specifically create a folder for the pdf’s (i.e. “Phd Linda”).
    Then, lets assume that I need to use Mendeley instead of Docear. Can I have my references imported in Mendeley? And more in general, can I do this with any other reference manager?

    Kind regards,

    • Docear is storing it’s reference database as BibTeX file. Almost all reference managers (e.g. Mendeley) can import this data. What cannot be imported by other reference managers is the structure you give to the papers in your mind maps.

  • Alan

    Hi Joeran,

    I was wondering if you could share your impressions about Sotero. I started using Endnote and got tired of it. I switched to Sotero and wrote my dissertation with it. I am now a junior professor and happy with Sotero still. However, cine I am now planing on working more extensively with others, collaboration will become more important both across Mac-PC platforms and with others, in the production of collaborative papers.

    Sotero uses the cloud to synchronize, leaving copies of my library in my desktop or device, and has limits in the size an attached file can have for it to be synchronized. For example, if I have a whole book in my desktop Sente, the reference gets synchronized but a message appears alerting me that this particular file is too large.

    You can share libraries and export it to Endnote or other formats. Still I have to decide what I am going to recommend for the group to use, and would appreciate your thoughts.


  • Francis

    That was your response? Either SoSciSo is joking and JabRef is terrible or I’d expect some retort…
    This article is interesting but seriously lacking. You have features shown but could you include some UI slides to show how the user experience is enhanced over other sites? I’d like an interactive list where I can drop down functionality and see how the sites compare? Otherwise apples/oranges. :)

  • Harry

    But which one works with EverNote?

  • Jean

    Surprised you didn’t include ReadCube in this. They’ve got probably the best UI across all of these tools plus a pretty stacked deck of features. It’s also free. I’d be worth throwing in the mix for sure. I gave up both EndNote and Papers for it!

    • There are many other interesting reference managers of which ReadCube certainly is one (others are e.g. Qiqqa or ColWiz). However, we just had not the time to include these tools in the review. Btw. I believe that ReadCube also uses a proprietary format for PDF annotations, which kind of locks you in (but I am not sure, please correct me if I am wrong)

  • Krishnakumar

    Hallo Joeran,

    Thank you for nice post. Your comparison of database software is very useful. I have a question, will Docear allow for intranet sync? I mean if a small research group wants to have a common database network in intranet would it be possible?

    Thank you very much in advance,

    Best regards,
    Dr. Krishnakumar

  • Hi Joeran – it’s Jimme from Qiqqa. I love the irony in the comparison charts. Nice one pulling them all down and putting them together. One of the banes of our life here at Qiqqa HQ is the number of people always telling us to add a new tick next to the competing products in our matrix. So I thought I might play pass-the-parcel on that front… :-)

    Qiqqa most certainly does support mindmaps! It has since the beginning and has always been core to the product (I am quite a visual processing kind of guy myself). You can see them in action here: https://www.youtube.com/watch?v=5QF-4DNGSHk#t=9m01s

    That said, I do love the mindmaps in Docear too and how you guys leveraged Freeplane.

    Keep it awesome!

    • hi Jimme, thank you for pointing out the mind-mapping functionality – i adjusted the table. However, as far as I see, mind-maps in Qiqqa are only intended for brainstorming, not for organizing PDFs – is that correct?

  • Jones

    A feature I’m missing from a lot of these is Endnote’s cite while you write… And since I’m using a mac especially one that works with available text processing applications. Even when it is implemented as in Endnote – if you use M$Word or Pages – it does not really do the trick: it will only allow insertoins like (Author name, Year) and not Author name(Year). I really don’t get it. The ability to cite without leaving your writing application and the ability to cite with the right format should be central to any of these programs…

  • This is brilliant. Nice work Joeran!

    re your question on organising PDFs with a mind map. You can save a brain storm and reopen it with PDFs and the connections you’re drawing between them (and open those PDFs from the brainstorm). You can’t yet do things like the Docear integration of Freeplane allows you to do such as collapse node trees, change node colours, font, etc.

  • May

    Hi Joeran!
    How about the feature of tagging each pdf file and get a grouping of documents according to these tags. It’s a useful feature that helps with the process of creating categories. I don’t believe it exists in Docear, right ?
    Please correct me if I’m mistaken.

  • Sebastian

    Concerning the ability to add papers while searching the web, the simplicity in organizing them, to work at the same paper with your lab and the easy way to download them to my library i tried loads of different reference managers. In the end I only was convinced by paperpile.com which won them all.

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