I am a little surprised that Zotero has not received any votes yet, in this discussion. I believe that Zotero is way more user-friendly than Endnote, while offering same functionalities (and more, in some cases). Plus, it is FREE ,which is something to consider even if EndNote is free for you right now, through your institution. Once you graduate / change jobs, EndNote will no longer be free, and the costs keep growing. Like many software vendors, Thomson Reuters (EndNote's owner) is very good at using new versions as a way to make its users pay again. And again. Zotero, on the other hand, is open source, so you never have to pay (unless you choose to store all of your files in the cloud -- then you pay for storage).

There are many ways to compare these programs. Here are a couple of links to good comparison tables. But ultimately, you have to make your own decision, based on how long you are planning to use the software, how much material you plan to handle (300 references? 3,000? 20,000?), how you prefer to store, handle, name, index, annotate etc. your large PDF files (full-text books, theses, long articles), what field of studies you are in, etc. etc.

http://libguides.mit.edu/content.php?pid=55486&sid=427307

http://en.wikipedia.org/wiki/Comparison_of_reference_management_software

http://blogs.plos.org/mfenner/reference-manager-overview/

endnote is compatible with Nvivo, if you do some qualitative analysis, might be interesting..

Thanks for your suggestions. I've started writing with EndNote, as it seems best for Windows.

I did my whole thesis with LaTeX/Bibtex (using BibDesk, which is also compatible with Word). This makes the whole document look fantastic and it's so much easier to typeset equations, etc., but it does have an initial learning curve, and it isn't the best for collaborating with non-LaTeX-literate people.

I am a little surprised that Zotero has not received any votes yet, in this discussion. I believe that Zotero is way more user-friendly than Endnote, while offering same functionalities (and more, in some cases). Plus, it is FREE ,which is something to consider even if EndNote is free for you right now, through your institution. Once you graduate / change jobs, EndNote will no longer be free, and the costs keep growing. Like many software vendors, Thomson Reuters (EndNote's owner) is very good at using new versions as a way to make its users pay again. And again. Zotero, on the other hand, is open source, so you never have to pay (unless you choose to store all of your files in the cloud -- then you pay for storage).

There are many ways to compare these programs. Here are a couple of links to good comparison tables. But ultimately, you have to make your own decision, based on how long you are planning to use the software, how much material you plan to handle (300 references? 3,000? 20,000?), how you prefer to store, handle, name, index, annotate etc. your large PDF files (full-text books, theses, long articles), what field of studies you are in, etc. etc.

http://libguides.mit.edu/content.php?pid=55486&sid=427307

http://en.wikipedia.org/wiki/Comparison_of_reference_management_software

http://blogs.plos.org/mfenner/reference-manager-overview/

I prefer mendeley...

There is also qiqqa

http://www.qiqqa.com/73951

I think EndNote is the best ... simple to use but gives you the ability to customize it to your specific needs

Hi all,

I would suggest trying qiqqa, which is a free tool and will help a lot in writing a dissertation.

We have recently discussed using qiqqa for research management in a discussion on Research Gate. It is a wonderful tool which has a lot of added features compared to zotero and endnote.. I have no doubts many of you will get hooked after trying it..

the discussion thread can be followed at:

https://www.researchgate.net/post/How_to_manage_research_sources?

regards, raza

@ Alexey: I agree and i was a hard core Zotero user until i found out about qiqqa last week and am switching over because of the many more capabilities it has. I would suggest to try qiqqa.. it can help organize and also analyze your references with autotags and starts making some sense out of a huge number of references..

regards, raza

The way Qiqqa (http://www.qiqqa.com/70557) makes sense of your references is by organising and prioritising them, finding links through a text analysis and clustering, pointing out what you have not read yet, and allowing full library and text searching and annotation.

I used Zotero for years and recently switched to Mendeley. It is fairly easy to set up across computers if you set the watch-folder to your dropbox. However the function that made me switch from zotero to mendeley is that mendeley can automatically organize and rename all pdf files on your computer, which ended up being a life-saver for me, as I had pdfs in many different individual project folders. Mendeley automatically organized them all into a central, searchable database.

Just an FYI - when professors are commenting on references make sure the program you use will allow them to do this.. my students were using Zotero as it was recommended by another instructor. When one of them incorrectly formatted their references, in the editing mode in Word, I attempted to correct the format so the student could see how it should have been done. My correction deleted all of their references.. no fun

Hello, I am one of the founders of Docear, which is a new software for organizing, creating, and discovering academic literature. Today, we released version 1.0 of Docear after a ~2 year beta phase. If you are interested in reference management, you might want to have a look at Docear. The three most distinct features of Docear are:

1. A single-section user-interface that differs significantly from the interfaces you know from Zotero, JabRef, Mendeley, Endnote, ... and that allows a more comprehensive organization of your electronic literature (PDFs) and the annotations you created (i.e highlighted text, comments, and bookmarks).

2. A 'literature suite concept' that allows you to draft and write your own assignments, papers, theses, books, etc. based on the annotations you previously created.

3. A research paper recommender system that allows you to discover new academic literature.

And Docear is free and open source and available for Windows, Mac, and Linux. More information can be found in our Blog, including a detailed explanation of what makes Docear superior to Mendeley, Zotero, etc. (at least in our opinion :-) ). If you don't like reading, there is also a 6 minute introduction video on our homepage http://www.docear.org ;-)

In case you are using a BibTeX based reference manager such as JabRef (and you don't want to switch to Docear), you might at least be interested in Docear4Word http://www.docear.org/software/add-ons/docear4word/overview/. Docear4Word allows you to insert references and bibliographies from BibTeX files to MS-Word documents. Hence, it makes writing papers much easier, since e.g. JabRef has no own MS Word add-on.

Finally, I would like to point you to a recent Blog post I wrote about what makes an evil reference manager. Maybe the post helps you deciding which reference manager to use (even if it's not Docear). http://www.docear.org/2013/10/14/what-makes-a-really-really-bad-reference-manager/

Hi Luis, we are developing for several years now, and we will do anything we can do continue our development. As such, I would say, chances are pretty good that Docear is sustainable :-)

if you are interested in a comparison of Mendeley and Zotero (and Docear), also with regard to sustainability, our new in-depth review might be interesting http://www.docear.org/2014/01/15/comprehensive-comparison-of-reference-managers-mendeley-vs-zotero-vs-docear/

Zotero is the best

@Abu: If you ask the wrong question, people's answers will not help you. The question you should ask is "Qiqqa, EndNote, Mendeley, or Zotero- which one is best for writing a dissertation?

Mendeley ! ! Several things to point out : 1) It is very easy to build your own library. Just drag your previous PDFs or any links to the Mendeley and it automatically get the citations for you. 2) Once you install "Importer", you can download whatever articles you find interesting online and save immediately to your library. 3) It is almost free (up to 2 Gb storage for you library).

I would approach it from a different angle.. instead of asking what which one we think is best why not find out which one your committee likes.. I am suggesting this because some of my students use zotero.  Its a pain as far as I am concerned when I try to edit their citations or reference list. For example, I tried to edit a reference to show the student how it should have been written, only to have the whole reference list disappear.  I am sure there's probably someway to fix/set it so that this doesn't happen, but as I don't use zotero I don't know how that would be done. So, I would check to see what your committee members like or don't like.

I use and like Qiqqa, but the high prices will make me find another software. In qiqqa site is possible to compare functions of Qiqqa, Zotero, Endnote and Mendeley. See http://www.qiqqa.com/About/Compare 

The basic version of Qiqqa is adequate for all but working in large research groups, and is free. http://www.qiqqa.com/70557

Dear Abu

Also see some notes on the implementation of Mendeley references into a LaTeX document, which might help to save frustration for a few new researchers:

Step-by-Step Procedure to include Mendeley References into LaTeX Journal Articles, Conference Papers, Thesis, Dissertations and Research Proposals

https://www.researchgate.net/publication/283831577_Step-by-Step_Procedure_to_include_Mendeley_References_into_LaTeX_Journal_Articles_Conference_Papers_Thesis_Dissertations_and_Research_Proposals

Technical Report Step-by-Step Procedure to Cite References from Mendeley and ...

For me, I suggest Zotero, 

Although my university offers EndNote for free, but I found that Zotero has several advantages than EndNote:

On the other hand, I found EndNote has some advantages over Zotero:

I also tried Mendeley, I found it similar to Zotero as open source and free, while its interface is alike EndNote, but the main benefit of it is that it indexes all the references in my computer, and give therm clear name. Another advantage that it enables markup on references, with its own tools. 

Hi everyone,

Really, all options described are good. But, I have been used the Qiqqa and I guess amazing. So, one more option for try!

Best wishes

:).. will try it surely.. thanks..

I can tell you: any of them would be a good RM, even i've worked with Zotero, Docear and Mendeley, any. The best way to know is... try and mistake. Some are good for ones and not for others... It depends on how do you work with. You can try with Zotero (the best one if you read some comments) and complement with Docear (an off the record RM). 

Let me suggest a link...  

Please, after your exercise, let us know about your experience... 

Thanks and good dissertation!

http://www.docear.org/2013/08/27/off-topic-which-one-is-the-best-reference-management-software-tool/

My favourite reference manager is Mendeley. I was using End Note while doing a PhD, and it might be that back then End Note was not as improved. However, Mendeley is free, looks great, is simple to start using, and is user friendly. It's not just a manager, it organizes your references, checks duplicates, and helps you explore more literature based on your library. It's worth trying.

hi all,

i have been using endnote during my phd studies but now am currently looking at other alternatives.

did some research on the net and a lot of peers suggest zotero.

i will be trying zotero and hopefully can give some feedback after.

cheers.

If anyone uses EndNote or Mendeley for PDF files management, migration to Zotero may be a serious problem because Zotero does not support links to PDF when importing references. It means, if you save your library in exportable format (with paths to PDF files) and try to import it to Zotero, Zotero will copy all PDF attachments into its own folder (it may be time- and disc space-consuming for library with >1000 PDFs) and any connection with initial files will be lost.

P.S. Migration from EndNote to Mendeley hasn't such a problem.

Yes the above information is correct. I also have similar findings.

Can you please suggest a reference manager tool for WPS writer?

ENdnote support it, but I have 'invalid citation or the parameter is incorrect' message when I cite a reference. I cannot fix that problem... I am looking for a new reference manager tool to support WPS writer.

It also depends on whether you are using mac or windows and Microsoft word or Mac pages or other writing apps. 

Qiqqa is also a good competitor in the list of tools.

Mendeley vs. Zotero vs. Docear vs. qiqqa

I've been using Mendeley and there's a lot of things I like about it, but I am now going to change to endnote because Mendeley becomes incredibly slow once you get over about 30-40 references in a paper/chapter.  It can take 1-2 minutes just to insert a citation.  When I try to edit citations, it freezes.  I've been trying to get a response from Mendeley support for months now - the best they can do is suggest reinstalling (doesn't work).  So, sadly, goodbye to Mendeley. 

I also agree with Claire's statement. I've been using Mendeley for my undergraduate studies and I still like the user friendliness of it. Basic reason for me to switch to EndNote was the unformatted citations, which is not available in Mendeley.

It may not make a noticeable difference in small documents, but in a large document (such as a PhD thesis) formatted citations slows down word processing to a great extent or may even freeze.

Both Mendeley and EndNote have almost all relevant bibliography styles for Journals, but I find it is bit more easy in EndNote to customize styles as well.

If the the institution offers EndNote for free (at least during your studies) you can use it and export your library along with all PDFs without much of a trouble to Mendeley.

I have experienced a LOT of problems with Zotero, particularly with the last version 5.0. This program slows my PC and many times freezes it. It is a nightmare to use it. Mendely does not slows my PC. The other problem I found with Zotero is that there is not a direct way to export references from Scopus. You have to first save references to some compatible format and then go to Zotero standalone and import them. With Mendeley, you can exporte them directly.  There are other advanteges with Mendeley that have been already mentioned in other responses. I am now uninstalling Zotero and migrating to Mendeley.   

I use EndNote, extremely easy to use.

I do not use any, but I notices that my students expecially endnot and to a lesser extend zotero and I get a big number of reference lists that are just wrong, especially when there is more than one author. I assume that this is more a probloem of data entry than the software packages, but what I want to say is that it is very tempting to have such automated processes, but at the same time students miss to learn basic academic generic skills.

I wonder if there is anyone (or organization) which has stress-tested the various options in a consistent way. The feature differences seem pretty minor when half of your citations suddenly lose their PDF links. This happened to me yesterday and I have spent probably 6 hours trying various recovery options, documenting what I did, and posting various questions to Mendeley. No answers to any of them. I'm not looking forward to manually reconnecting nearly 400 references.

Testing links anyone?

I prefer Zotero.

1. The functionality is similar to the other platforms.

2. It is free.

3. There is an excellent add-on for use with Chrome.

4. The integration with Word is excellent.

5. I am able to back-up and access all of my saved works from the Zotero account.

Overall, very pleased with Zotero.

Thanks Jon - you motivated me to install Zotero. I was able to import a *.ris export I did when Mendeley was briefly working, and it found all the files, except where I had more than one, as when a reference also has supplemental material.

I'm not sure which I'll keep, because I was able to delete everything in Mendeley and restore it from the *.ris file. Now I have two working reference managers, but trying to use both at once as a long-term test doesn't seem like a good idea right now.

Hi Steve (James S. Ryan),

I was successful in exporting the *.ris format from Mendeley and importing into Zotero. I have also been saving pdf files as associated files with citation information and it looks like all of my pdf files were maintained.

This is not an easy question to answer as it depends on individual preference. I wrote my dissertation using Endnote 6, and I had a blast with it. Except for a few configuration issues, it worked like magic. During my research, I toyed briefly with Mendeley but considering the pressures of the research, it didn't make sense to spend time learning a new application. I have no doubt the others (Mendely, Zotero) have unique advantages. The key, I believe, is to find one that works for you and go with it. Once you find what works, move on..until it no longer works. No application is perfect.

I tried both Mendeley and Endnote and could say that Endnote worked out better for me. Hope this helps. There are a bunch of plus and minuses for both of them, as others already mentioned.

Zotero is the best

Mendeley

Have a look at F1000Workspace.com

After my Postdoc I went to work there to build this tool- so I am not completely neutral ;)

But just to give you an overview: - plugins for Word and Google Docs

- search PubMed and Google Docs from inside Word or Google Docs (only PubMed)

- Easy to share references with colleagues

- article suggestions based on your save articles (only for 30 days in the free version)

- unlimited references (stored in the cloud)

- Android and iOS app

- article suggestions based on your save articles (only for 30 days in the free version)

- great costumer service

I hope it helps

Joao

EndNote is better than the others

Google Scholar is better.

Endnote is paid, and I've just found out that Mendeley is administrated by Elsevier...Since I still prefer fully supporting freeware I go for Zotero in this one.

Following

Mendeley is best.......

I have always had issues with Mendeley due to its lapses in collating references and other errors in functionality. I would, therefore, go for Zotero.

Aside Zotero, however, you can always cross-check whatever results the software gives you by copying the citation and pasting in Google Scholar which also provides commendable results in relation to the main reference section.

Zotero

I have used Mendeley for some years, but recently with the new update it became very disappointing and somewhat annoying. The problem is missing papers. I am now thinking for alternatives.

Although I'm happy with Zotero, I am a bit worried about its future on iOS and its integration with Safari on MacOS in particular. I randomly saw a reference to "Papers" which I'd tried years ago. It has continued in development, and has been bought a few times, it appears. Now ReadCube is the (somewhat) linear follow on. Looks interesting although I suspect I'll stick w Zotero...

https://www.readcube.com

I am using the old version of mendeley. It very nice and also free of cost.

i recommend Zotero. its free and easy to use.

Zotero is my choice. Its simple to use

I highly recommend Zotero. It is free, open source, and very powerful. Additionally, you can have virtually unlimited cloud storage if you set it up following this tutorial:

Method Tutorial: The Best Reference Manager Setup (Zotero + ZotFile...

I recommend Zotero too since its free, open-source, and easy to use.

zotero is open source and free

Zotero is best to use for bibliography or references in the dissertation.

is desktop app for windows 7 for zotero available? If it is there please send the link.

Dr. Suhail Anjum Abdur Raheem Sayyed

This is the link to download zotero for windows

https://www.zotero.org/download/client/dl?channel=release&platform=win32&version=5.0.58

Zotero System Requirements

macOS 10.9-10.14 1)

Windows 7 or later

Linux

Thank you Respected Dr. Sabry Abdallah sir

Has anyone used Zotero for a PhD or other large piece of work? I prefer it to Endnote but I'm worried it might not cope with a large number of references in a big document

Clare Burgon I use Zotero for all my work. Used it for my thesis with no problems!

Nicolas Farina great to know - thanks Nick!

Zotero and Mandeley both are great options. Both are free of cost. Endnote is the most popular these days though and it is not free by the way. All three are my favorites.

You can used any Zotero and Mandeley both are good. Zotero is bit easy but still vote for endnote web as it facilitates you to open your library anywhere

Does anyone know how a document with references added with Zotero responds when someone without Zotero edits the in text references and then sends back to you? I'm using Zotero for my dissertation but my advisor doesn't use any reference managing software. Does the document retain the Zotero magic even when someone without Zotero saves it? I could see a situation in which just because they saved it, it unlinks all the citations, and then if they make changes that are to be reflected in the references, I will have to re-add every reference.

I am used to use Mendeley in any of my article project. It is little bit heavier software comparing to Zotero because we can open pdf source directly on Mendeley desktop when we have the PDF file on our PC while Zotero can't. However, we can choose whether to use bodynote or footnote to cites experts' theories in Zotero, while Mendeley only can use bodynote. Therefore, either to use Zotero or Mendeley really depends on our needs.

Mendely and Zotero both free And good for the writing..

As a career-long decision I recommend to choose Zotero as your academic library managing tool. It's open source, free with a commitment to stay free forever (Mendeley is owned by Elsevier), and it is possible to have unlimited synced storage for free. Check my blog post to see how to set it up

https://ikashnitsky.github.io/2019/zotero/

I used Mendeley as it is free and easy. Most, I love its practicability.

Endnote kann ich nichts zu sagen.

Mendeley hat mich enttäuscht. Wenn man bereits auf dem Rechner gespeicherte PDF importiert geht das zwar schnell, produziert aber so krass viele Fehler, dass es für mich komplett unbrauchbar ist. Eine Kollegin schwört trotzdem darauf, aber verwendet immer nur das Browser-Plugin zum importieren. Ich habe keine grosse Lust, 250 Artikel nochmal online zu suchen nur deswegen.

Zotero liest dieselben Files langsamer aber mit guter Qualität ein. Dieselbe Stichprobe von Files scheint soweit fehlerfrei bezüglich Autoren, Titel, Jahr, usw.

Zotero's damn good. Most of the very few files it didn't recognize fully are PDF without text recognition. As soon as you do this afterwards and ask Zotero for metadata again, it works fine.

Mendeley remains on my PC for now as a warning example. Just in case someone asks me and doesn't want to believe how bad it is ;)

I recommend Zotero. It is easy to work with.

It will depend on cost/affordability, familiarity and ease of learning. I personally use EndNote but for one who cannot afford to pay for EndNote, Zotero would be ideal

I used EndNote and Mendeley. In my view, Mendeley is better than EndNote. I do not have any information about the third software Zotero.

In my view, EndNote is the best references management software. Once you get used to it, you get addicted to it!