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]

Reference Manager Comparison

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?


Joeran Beel

Please visit https://isg.beel.org/people/joeran-beel/ for more details about me.


Sara · 24th May 2022 at 08:23

Refworks and its add-in for Works are the shittiest program you could ever use. Had countless problems with it and it never works as it should. Use something else!

Zane · 27th February 2018 at 03:05

I don’t understand how Docear could be the best when it is built with Java. Running the latest Java Runtime Library which is required by Docear on Windows 10 takes away 30% of my CPU power, while Zotero uses only 0.3% when it’s open. The efficiency is very low even though the functionality is great.

Tursun Wali · 11th September 2016 at 04:31

Docear Experts and Fans alike,
I am Tursun, I am in Malaysia, I am writing my PhD thesis. previously use MS WORD, now want to try Docear. After few videos, I believe that it can good care of citations and formatting of the citations.
My university has a thesis template, we have to follow it.
Is the anyway that when Docear exports to MS WORD, it exports based on my university template? Otherwise, It seems that I have to manually format it to comply University thesis format.

Christopher J Poor · 9th March 2016 at 11:43

DocFetcher is similar to Foxtrot but is free and open source.

Chistopher J Poor · 8th March 2016 at 15:59

Hi Steven,
I know about the stress and frustrations of writing a PhD. I have just started on my second one. I hope it is still going OK. I am afraid I only just came across your post on Docear’s forum.
I am also using Scrivener, although I only just started. I would be interested to hear about your experiences using it. I looked at many citation managers after deciding to ditch Endnote because of their proprietary format, high cost and charging for new releases. I settled on Zotero https://www.zotero.org/ because it is open source, free and compares favourably in many ways with most of the others. Its best feature is probably the robust ability to gather metadata from various sites: Google Scholar, Amazon, Worldcat etc. It also accepts DOIs and ISBNs for the creation of entries (you can copy and paste these from pdfs that have text layers).
Zotero works best as a Firefox plugin but also works well as a standalone app which is also compatible with Chrome and Safari. It integrates very nicely with Word and LibreOffice (even with LaTex).

If you use Zotero standalone or Zotero for Firefox you will be able to download the Mac plugin for Word from this page: https://www.zotero.org/support/word_processor_plugin_installation
Here is a youtube demo of how to cite in Word with Zotero: https://www.youtube.com/watch?v=RuRF8zxkxIo#!
One thing you might also like is the ability to drag and drop any number of pdfs from Finder into the central pane of Zotero and then right click on them to have the meta-data extracted and make a parent reference item.

If you want to you can make a “collection” in Zotero for each folder you have your pdfs in and drag them into there. I do not do this, though. I use Zotero’s collection to organize my references and their attached pdfs according to writing projects.
One thing I realized after starting to use Scrivener and dragging a couple of hundred pdfs into it is that I really should probably be doing it one at a time as I cite them and according to whether I have notes and annotations that can be added to Scrivener. This way I will be able to more easily organise the few dozen references I need rather than having an extra hundred or so I don’t.
Zotero has a great add-on to extract annotations from pdfs and it is now also integrated with Scrivener via a plugin for Zotero: http://zotplus.github.io/zotero-better-bibtex/index.html

I have also been frustrated with Spotlight not finding my files and have been using the trial version of Foxtrot http://www.foxtrot.ch/buy/index.html which works brilliantly.
I have also used Docear, but mainly for creating an outline in the mind map. Of course Scrivener is great for this also. I actually export my Zotero collection (subset) for use in Docear and can arrange the references on the mind map to get an idea of the outline. The pdfs can be inserted and Docear also extracts their annotations.
Zotero also has a good plugin to extract annotations: https://addons.mozilla.org/en-US/firefox/addon/zotfile/?src=api

As far as updating the references to more recent articles, I haven’t got any experiences with Bibliography managers that to this (apparently Docear’s suggestion help – see below, but I don’t know from my experience). What I do in this situation is search Google scholar for the article I have, look at the “cited by” link at the bottom of that entry, and then restrict the results to the latest ones (far left of Google results page).

I do have most of my pdfs that I downloaded organised in folders on my Mac. I can then find them by subject in Finder. However, lately I have been letting Zotero handle the downloads for most of them and only storing copies of especially important references in my folders. Zotero keeps the pdfs in a database which you can sync with Dropbox. You can also sync the references themselves on Zotero’s server for free (a good backup).
Zotero allows you to search very conveniently through the pdfs it stores, including the text within (as long as the pdfs have a text layer – or if you have OCRd them with something like pdfpen.)

Now to your questions:

1: I don’t know if any citation manager can pull out the references already formatted by another one in Word. I’m pretty sure this would have to be a Find and Replace labour intensive process. It would be a matter of searching for the “(“ at the beginning of a citation, copy the author’s name, and then going to “insert citation” and paste. This would then give you the citation in Zotero’s cite box. Enter and it’s inserted. Delete the old citation.

2: The cite codes you would insert in Scrivener include the author’s name. Also, the citation process brings up the author, year and title when you enter the author or any word in the title.

3: As I said, I don’t think it is necessarily desirable to try to keep the folder structure from Finder. That is one way you have the articles organized, and you can organise them differently in Zotero. Typically you would import all the pdfs you want into “My Library” and then you would organise them (actually symlinks) into “collections” according to what you are writing. You can also store “smart collections” which are saved searches that are updated as you add new items.

The second part of this question is something that I dealt with for some years while writing my first PhD thesis. My old Uni also had limited access to databases and I relied on a) Google scholar pdfs and b) The California Bay Area public library system. The San Francisco Public Library is free to join for anyone living in the area and has access to JStor. You might find similar possibilities where you are. Ask you librarian. You could also try openpdf, the Open Library, CORE connecting repositories, BASE Bielefeld Academic Search Engine; Copac National; Zetoc; Microsoft Academic Search; iSEEK – Education; ERIC – Education Resources; The Virtual Learning Resources Center; The Universal Digital Library; and Community Texts. If you have trouble finding the urls for these let me know.

4: Zotero will find and insert references into its database based on the DOI or ISBN you give it. I have found this to work well. As far as I know Zotero does not point you to similar references. As I said above, the only way I have experience with this is doing it myself on the web. However, according to this page: http://bundlr.com/clips/52de0fde35419b00150007af Docear recommender system for research papers is similar to that of Mendeley. All papers that Docear recommends are available for free in full-text, though sometimes the linked URLs are dead.
I believe that Zotero will extract the meta data correctly for your pdfs most of the time. As I said, it will do this for many pdf selected at once. This requires an internet connection and will be resource intensive. Particularly if there is another app accessing the internet from you computer (in my case it is probably Crashplan cloud backup – a good, reasonably priced service) the process may take more than several minutes for a couple of dozen files. Again, for finding files on your drive, try Foxtrot.

You could have Zotero on as many Macs as you like, also PCs and Linux (for no cost). The citations will sync with Zotero’s server and the pdfs you can sync through Dropbox.

Hope this has been of some help.

Contact me if I can provide any further info,

Steven · 22nd November 2015 at 20:19

I’m in the final stages of writing my PhD and I realised from writing the first chapters that I desperately need a citation manager (DOH!) Joerdan, first off, thanks for the 2 posts I read, this one and the one comparing Zotero with Menedely and of course Docear. Of course I have spent an entire weekend trying to figure out which citation manager will do for me and have tried Mendeley and Bookends (I heard a lot of -ve stuff on Endnotes back at uni) and got very frustrated when I tried Mendeley and many of the books I have in PDF are seen as journal papers and give me completely random citation information. Bookends on the other hand doesn’t even find a bunch of the papers even if those papers have DOI info in them! I was quite depressed because I am starting an new chapter and I don’t want to spend a month at the end of my PhD sorting through my references and apart from trying to figure out from where I pulled out the references, I have to then do the tedious and horrible job of formatting all them to one standard format that I still haven’t figured out, given that I am doing an interdisciplinary Phd between anthropology, geography and environmental science! You can also imagine the very eclectic reference library of PDFs I already have – a 23Gb folder with 91 folders in it and I don’t know how many sub-folders within quite a few of those folders. Sorting through them is already difficult as it is but let’s not go there and make things simple. for this post.

I will tell you what my needs are and hopefully you can just point me to what you think is the right citation manager for me because I can’t continue to “waste” time trying to compare citation libraries when the deadline for my the next chapter is looming up!

Some background here might be useful for you – I am using SCRIVENER to write my thesis, and yes, I am a visual person and I use mind maps both on the Mac – I use Mindjet at the moment and manually on a white board and on my window panes! So a citation manager that can handle mind mapping would be useful.

Secondly I had written most of my chapters 2 – 3 years ago and then for personal reasons (I was diagnosed with an “invisible” learning disability half way through my PhD, which threw me off my game and I had to take a long time-out from the PhD. So now I find myself having to update my references and some of my work. So I already have Word files with individual chapters with in-text references and citations such as (Reed 2010; Healey 2006: 25; Goldman 2000) and in some of these chapters I already have a reference section compiled at the end of the chapter, though not necessarily all in the same format. BUT for most of my chapters I need to update my references to more recent articles etc. So I thought that Mendeley could help with this, since you can find similar papers and you can then sort by date to find more recent articles. The fact that I would need to put the folders and subfolders manually (and 91 folders is no joke, besides the subfolders) is I think untenable.

SO there are already 2 questions here: 1) Is there a citation manager that can pull out those reference sections from my Word files that I already have and format them into the right format, including the in-text citations and references? And 2) compatibility with SCRIVENER is a must, and if possible, even if there will be BIBtext or whatever the codes are called embedded in the text of the chapter, I would need to see the actual citation, because many times I go back to the same author several times while writing a chapter and would need to cross-reference. Not knowing from where I got the reference or citation is not really an option for me.

3) I don’t think that there is an easy and fast way of importing all my references into a citation manager keeping the original folder structure as the folders on my Mac’s HDD, and if there is, please do tell! The important thing here, is that if I have citations that I have used or am thinking of using but are quite old, I would want to quickly find more up-to-date research, i.e. articles, books, whatever that have the latest research on the topic I’m writing about. the hiccup is that I am not writing from within an actual university, and the university I am attached to at the moment does not have a particularly good e-libarary that I can use and worse than that, being interdisciplinary in a university that does not have an anthropology department, for example (I followed my 1st supervisor to the uni where he moved to), means that I can’t find anything within their library and am relying on open source stuff or at least what the Internet sends my way – Elvisir, for example, provides abstracts, so I can at least access those and if the paper is a must read, I will somehow find a way to get it (from friends at my old uni etc.).

So Q.4) would be if there is a citation manager similar to Mendeley that would point me to updated references.

The easiest thing to do till now is to create a sub-folder in my Chapter folder named References and copy all the papers I use or refer to in the chapter – I could then upload those in my citation manager (whichever it will be) and go from there. The problem is trying to find papers from my large reference folder / sub-folders – I am finding out that the spotlight or search functions from the finder of the folder does not work very well – I have tried putting searches for articles I KNOW I have in one of the sub-folders and it just doesn’t find it! That is very frustrating, so if there is some simple way of putting all my PDFs into a citation manager that can then accurately find the proper reference tags (unlike Mendeley and Bookends), that would be swell. In fact, Mendeley even screwed up the name of the first book I imported into it – it changed the name and even when i deleted it from the database and put it back in, it just continued showing me the wrong name and authors – it pulled out some DOI and just stuck with that and even when I changed the ISBN to the one on the eBook (as a PDF), it just wouldn’t find it online for me through the ISBN.

Of course, the last important factor is that I am a MAC user. I need to be able to work between a Mac Mini with Yosemite and an iMac 27 with Snow Leopard, though that is not a massive issue. I might need this compatibility since I use Dropbox – all my PhD work including the Reference library are on Dropbox, so if I can use a citation manager that stays on Dropbox and I can open it on both the Mac Mini and the iMac with their different OS X versions, that would be great!

Any thoughts before I go completely insane here? If you tell me that DocEar does all of that, I’ll gladly go for it. also note that I have never used citation managers in the past, but I now realise that I do need one if I am too finish my thesis on time and not waste a lot of time at the end fretting going through the manuscript checking references and formatting etc.

Thanks and apologies for the VERY LONG post!

Fred · 9th August 2015 at 10:38

You have missed readcube’s chart https://www.readcube.com/compare

Sebastian · 2nd April 2015 at 06:48

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.

May · 25th March 2015 at 11:07

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.

James Phillips [Qiqqa] · 4th December 2014 at 13:53

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.

Jones · 24th September 2014 at 21:30

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…

Jimme · 10th September 2014 at 00:08

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!

    Joeran [Docear] · 11th September 2014 at 15:45

    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?

Krishnakumar · 4th August 2014 at 10:42

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

Jean · 9th June 2014 at 21:55

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!

    Joeran [Docear] · 10th June 2014 at 09:38

    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)

Harry · 28th March 2014 at 14:36

But which one works with EverNote?

Francis · 26th March 2014 at 17:41

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. 🙂

Alan · 25th March 2014 at 21:33

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.


Linda t · 27th January 2014 at 18:20

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,

    Joeran [Docear] · 28th January 2014 at 08:38

    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.

Linda t · 27th January 2014 at 17:27

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.

Joel · 18th December 2013 at 00:11

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.

syedaftab · 26th November 2013 at 16:03

i think qiqqa is the best

    Joeran [Docear] · 26th November 2013 at 16:14

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

      Vijay · 18th December 2013 at 21:42

      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.!



Andres · 18th October 2013 at 03:01

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) 🙂

James Smith · 22nd September 2013 at 22:13

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.

    Joeran [Docear] · 23rd September 2013 at 08:12

    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.


SoSciSo · 30th August 2013 at 11:45

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

JzJ · 28th August 2013 at 08:41

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

Marc · 28th August 2013 at 08:36

*lol*, i always knew docear is best

Comprehensive Comparison of Reference Managers: Mendeley vs. Zotero vs. Docear | Prof Dr Joeran Beel · 23rd March 2018 at 12:52

[…] In this Blog-post, we compare Zotero, Mendeley, and Docear and we hope that the comparison helps you to decide which of the reference managers is best for you. Of course, there are many other reference managers. Hopefully, we can include them in the comparison some day, but for now we only have time to compare the three. We really tried to do a fair comparison, based on a list of criteria that we consider important for reference management software. Of course, the criteria are subjectively selected, as are all criteria by all reviewers, and you might not agree with all of them. However, even if you disagree with our evaluation, you might find at least some new and interesting aspects as to evaluate reference management tools. You are very welcome to share your constructive criticism in the comments, as well as links to other reviews. In addition, it should be obvious that we – the developers of Docear – are somewhat biased. However, this comparison is most certainly more objective than those that Mendeley and other reference managers did ;-). […]

نرم افزارهای مدیریت منابع | کتابدار 2.0 · 23rd September 2015 at 13:28

[…] https://ISG.beel.org/blog/2013/08/27/off-topic-which-one-is-the-best-reference-management-software-tool/ […]

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