Dear Isanka,

We can not say that what is the best. Both have distinct features. However, I use End Note in my works, because, it helps to manage all the references including books. 

Best Wishes

I prefer Zotero, but Mendeley is a close second.

Here are a few links that should help you to make a final choice:

https://www.mendeley.com/compare-mendeley

http://libguides.wustl.edu/choose

http://guides.lib.unc.edu/comparecitationmanagers

http://www.researchgate.net/post/Which_software_is_better_EndNote_X5_or_Mendeley

Hi Isanka,

I have no close experience of Mendeley, but I would always prefer EndNote above Zotero because I found it so much easier to edit individual entries and create bibliographies (and it also allowed me to import a substantial Allegro bibliography of several thousand entries, which I could not achieve in Zotero). The link to Word in EndNote also works very well and makes keeping track of your references very easy indeed. However, it is probably a good idea to have a look at the links Artur provided as they might give you a more comprehensive consideration than my humble opinion here.

Good luck with your eventual choice,

Jörn

I was working with Zotero. But I recomend you to use Endnote. 

But, and that is a key point...  It is not easy to say what is "the best"... You have to keep in mind your particular needs.

If you want "community sourced reference database", then zotero has interesting support. I do not know how well this is supported in the others.

An other point to think of is Mendeley is free but for EndNote you have to pay. The latest version of EndNote is X7. Honestly, I prefer EndNote, but if you want to share with others, Mendeley is more adapted. If you want more options and group sharing, you will have to pay a subscription for Mendeley. The comparative graphic linked above will give you different option.

Hi Ishanka,

 I have been using both EndNote and Mendeley and prefer of using Endnote over Mendeley though the EndNote is not a free referencing source. Simply agreeing with Nadia and Jorn. Eventually it based on your particular needs.

Best of luck with your studies!!!

Eranthi

Dear Ishanka,

Mendeley provides the user with 2 GB of free web storage space

It is good and is free but requires registration.

Mendeley Desktop runs on Windows, Mac and Linux:

Some characteristics:

Automatic extraction of metadata from PDF papers.

Back-up and synchronization across multiple computers and with a private online account (I combine with Dropbox)

PDF viewer with sticky notes, text highlighting and full-screen reading.

Full-text search across papers.

Citations and bibliographies in Microsoft Word, OpenOffice.org, and LibreOffice.

Import of documents and research papers from external websites (e.g., PubMed, Google Scholar, Arxiv) via browser bookmarklet.

BibTeX export/file sync.

Private groups to collaboratively tag and annotate research papers.

Public groups to share reading lists.

Ishanka Weerasekara now can you summarize all these comments about which is better? regarding all these answers.

thank you

Hi Beleed, 

They have different 'good's and 'bad's. After been using both of them,I prefer Endnote over Mendeley. :-) Thanks for the comment.

https://thesiswhisperer.com/2013/08/21/endnote-vs-well-everything-else/

https://thesiswhisperer.com/2013/08/21/endnote-vs-well-everything-else/

I found this post since I was looking for a good alternative for EndNote. Over the past year, EndNote is not working very well for Mac users. When Microsoft Office 2016 was released, Thomson Reuters could not handle this update, and Mac users were forced to keep using Word 2011. It took them almost a year to get this issue fixed. A few weeks later, a new update for Mac (macOS Sierra) was available and again, Thomson Reuters failed to make EndNote compatible with this new update. The most shameful however is, if I understand it correctly, is that the new version of Endnote, X8, is compatible with macOS Sierra. It almost looks like Thomson Reuters is forcing users to pay large amount of money to upgrade their software.

Despite I agree with Roy, EndNote still has few competitors, and Mendeley is not among them. I would recommend trying Bookends.

Has any of them the ability to create diagrams like Mind Maps using our annotations and highlights on bags of pdfs? Or even using tags we may use instead of folders?

I tried http://www.docear.org/ but it seems like too hard to use... And, for instance, in the first use I could not "minimize" de annotations from PDFs I had attached to a mind map. That is, the mind map got ugly and full of information. =\

Do you know any better software to manage annotations? Maybe End*Note* can do this?

Any solution to organize ideas mainly related to our annotations and tags considering a large number of pdfs? Or considering starting from 1 pdf and going to a larger number.

Many thanks!

@Henry Heberle, maybe you are looking for something like this:

• http://www.vosviewer.com/
• http://nailsproject.net/
• https://www.qcamap.org/

Hi,

Mendeley, Endnote, RefWorks,  Zotero  - it does not matter what the color of the cat is, as long as she catches mice.

Choose one that suits your requirements. If Mendeley does your job, it makes no sense to waste time, power and the means of migration.

If not, then do the analysis and comparison and choose the one best suited to your needs and opportunities. All systems have their advantages and disadvantages.

Greetings.

Mendely

1- Simple with the built in PDF reader to highlight and add notes.

2- Has extensions for browsers (integration with chrome)

3- Has desktop application

4- Has cloud storage & ability to connect dropbox

5- FREE

6- Plugin to Integrate with word

7- Watched folders (you can specify folders on your PC, Mendely will automatically add PDFs you save to these folders).

8- Integration with Zetero.

I've mostly used EndNote, but currently, it is not really compatible with Mac OS High Sierra (or Sierra, I believe). It runs, but excruciatingly slowly. If you do use it on an up-to-date Mac, don't use the "link to PDF" feature; I'm told the new PDF handling in Mac OS is causing the lag, so if you skip this, it might just work ok. In the meantime, EndNote is taking a LONG time (Sierra came out over a year ago, I think) to fix the issue, so I'm going to give Mendeley another try and might go back to EndNote when it's time to format. I understand Zotero is also good. I should mention the social network aspect of Mendeley doesn't interest me at all. For me a reference manager is for managing references and citations, and I also use it as a catalogue.

Also, the only time I seriously tried Mendeley previously, the "watched folders" feature was a disaster for me. It constantly imported things wrongly from PDFs and created duplicates. I'd be very wary about using it.

UPDATE: After importing my >7000-reference library into Mendeley, I'm not impressed. Its navigation is glitchy. In EndNote, you can type the first few letters of the Author's name (or item's title - whatever you have library sorted by) and it'll jump to select that item. That doesn't work in Mendeley - at least not the version I have on the OS I have.

Zotero, on the other hand, looks pretty good so far. None of the extremely slow functionality of EndNote. It's very fast with linked PDFs, too, so whatever problem EndNote has with Mac's current PDF handling, it's EndNote-specific - Zotero has no such issues. It is (VERY!) slow to load initially, but once it does, it completes operations very quickly. My only real complaint about it is that it's a lot harder to customise reference & citation styles - allows a high level of precision and control, using CSL, but that's not friendly to a non-expert user. There are libraries of styles online, though.

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- great to collaborate

- 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

I have been using Mendeley for quite a while and have found it good, until recently when I have been getting glitches, and no customer service response. Thinking of moving to Endnote provided the migration is not too hard.

EndNote is still the gold standard of bibliographic software.

useful question and good answers

All answers are useful to me.

Thank you all.

Mendeley old version is good. But new updated version is crashing.

I used Endnote before, very good and easy to use the software, work like charm in keeping the track of your references in word file itself in the Endnote, but it crashes time to time, then I Switched to Mendeley, work smooth, efficient for me, can search and download references within the software, and super easy to use with OS High Sierra and OS Mojave.

There is also another free reference manager known as Zotero

Thanks for useful suggestions

Mendeley is quite good and easy to use. Recently i have downloaded Zotero but I need some practice to work on this so can,t say anything about Zotero right now.

Mendeley has easy learning loop but for long run and serious kind of work Endnote is the best though with difficult learning loop but once you are come over nothing is like this:)

After years of using many citation management software I would limit the compitition between Zotero and Mendeley. Actually I prefer Mendeley for its usability, userfriendly interface and supporting tools that allow importing files and publications from anywhere, reading and annotating them from inside Mendeley and building collaborative research groups. In my opinion it is a complete research platform.

I prefer Mendeley as it is free and simple

I agree that Mendeley is simple, free, also offers free storage space, allows the group network, has an integrated PDF viewer.

And when you use it with your institutional email, they give you a superior storage space and more possibilities to generate groups.

On the other hand, it is easily integrated into Word and open acess text processors.

Mendeley is free and wonderful tool once you know how to use it.I would recommend it.no doubt

Do you know if Mendeley works already with MacOS Mojave? just in case, I don't want to have same problems I had with HighSierra. Thanks a lot.

i have used endnote in my previous research papers with a little much ease than i tried with zotero and mendley. So far, Endnote is reasonably handy. Expensive though, its worth the ride. Give yourself a free trial of Endnote for a month. Thank me later.

An update on my earlier response:

1. EndNote remains unusably slow on Mac. It seems version X9 hasn't fixed the issue. Clarivariate claims it's due to Mac OS's "new" PDF-handling methods, but I think that's nonsense. I compressed my 7000-ref library without any PDF attachments and re-imported it, and it was still hopelessly slow to even jump to references. The problem has persisted over multiple OS releases and more than 2 years. As far as I'm concerned EndNote no longer supports Mac OS, regardless of what they might claim.

2. Zotero isn't perfect. It does get pretty slow to find references, once libraries and numbers of citations get to a certain size. The main problem I have is that it doesn't have a way to completely turn off cite-while-you-write. You can speed it up by turning off the auto-refresh, but it's nowhere near as good as EndNote used to be, where you could just add temporary citations until you were ready to format your bibliography & citations when done. Still, at the moment, it's the less frustrating option, & works faster than Mendeley on Mac (although seems to randomly lag in calling up the insert citation box, that seems to be more because of my slow hard drive than the software).

3. The inability to encode your own citation styles or edit existing styles is a big problem for most users with Zotero. I find the available styles tend to have glitches in them & editing it pretty tough going. Also, formatting citations & bibliography gets slow without excessively long documents.

I saw someone on EndNote forum recommend Bookends. I don't have time to try it, and it's not free (but way cheaper than EndNote), but something to consider, especially if you can get your institution to pay for it!

In my opinion, Mendeley is more comfortable and simpler.

I found that EndNote slowed down my work as my references increased. I am learning to use Mendeley now and i like it so far. Mendeley being free is also a considerable bonus

Each one has advantages and disadvantages. But I moved from Endnote to Mendeley because:

• The most important tool of Mendeley is Sync. If you use different computers at home or work, Sync makes it easy to get up and go and have your references on your home computer, work computer or mobile device.
• Also you can use Mendeley web importer to download citations and organize them easily in your library.
• Another important point is that Mendeley is free.

I think its a matter of choice, both require downloading the full text before referencing but I think endnote is more flexible to mendeley.

I am using the old version of mendeley. it is easy and free.

Endnote no good at all,very slow am getting used with the mendeley, seems to be good.

I switched to Zotero from Endnote, then to Mendeley when it was just released. Over the years, the desktop version of Mendeley doesn't change too much in terms of interface and functions. But the stability has been improved significantly. I feel more comfortable to use Mendeley to manage your own paper library. However, when it comes to citation management, I think Endnote is still better. It has a larger citation style library. In most cases, you just need to download the citation style and then use it. On the other hand, you often need to customise your style in Mendeley.

I would say End note is better than Mendeley. In Endnote, one can simply export the references in the master list to Endnote (when offline). For Mendeley, you cannot do this, though you have options of searching directly when online. And as we know, sometimes a book you read maynot be available online. Otherwise for beginners, Mendeley is easier and for free.

Definitely Mendeley is an obvious choice .

I was almost to ask same question then found new answers here. I am using Endnote since 2012 and now want to choose either upgrade subscription or switch to

Endnote is still powerful, can sync different PCs, i think up to 3, with ipad version as well. Reading directly impeoved a lot with ability to highlight and sync the highlights as well, a feature i was looking for when i first used it long time ago.

Only is that Mendely is free and most of my students are using it. These two softwares do not recognize each other and if you use one then all your team should use in order to be able to share your writings. Difficult to choose still.

I really don't like EndNote. I use Mendely these days and Love it.

after a while I used Mendely, I found a terrible feature. Mendely is awful in grouping papers. It just keep papers in its folder but I want them in my folders!! so I changed my mind and got back to EndNote. This is my advise: If you want to be professional with your papers, use EndNote, otherwise you can use simpler software like Mendely.

I've used Endnote for a long time and always have been happy with it. It's easy to use and has all it needs to have your literature collected and sorted and easy to use in Microsoft work. I can definitely recommend it, but have to admit that I don't have any experiences with Mendeley. An advantage of Endnote might be that it's easy to work with others as many researchers already use it.

EndNot is the best choice .

Mendeley

mendeley.

I think mendeley is easy and better than EndNot

MENDELEY IS PRESENTLY NON-FUNCTIONAL with MOJAVE. So if you are a MAC user you CANNOT use MENDELEY. They have absolutely no idea of when or even if this will ever be fixed.

The main advantage of Mendeley is that it's free, provides social network.

I have used both and I think there are not important differences. But I rather use Mendeley, its free!

Men

Endnote.

I like mendeley because it's free and easy to use.non experience with endnote

Academics should reject Mendeley and its parent company Elsevier:

https://medium.com/the-nature-of-food/academics-should-ditch-elsevier-and-mendeley-heres-how-153f1a8bf5f4

As an alternative, I highly recommend Zotero. It is free, open source, and very powerful. I used to use Mendeley and do not miss it at all.

Additionally, you can have virtually unlimited cloud storage if you set it up using the following tutorial:

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

I used to recommend Endnote, but I now recommend Mendeley. I was using Endnote X8 and then upgraded to X9, currently running MacOS 10.13.6 on a Late 2013 MacBook Pro, and Endnote has been SLOW as a dog on my Mac. For some reason it's still a 32-bit program (why is that?). So I recently I moved my 2,200+ item database with many PDFs to Mendeley in under 10 minutes and the only thing I do not like is that my "Research Notes" and "Notes" got merged, however, the performance of Mendeley is MUCH FASTER than EndNote. EndNote development apparently is Windows focused and MacOS is just an afterthought for them, since the Mac performance issues have been widely reported over the past two years and there is no fix in sight. So now I use Mendeley desktop for the Mac which is a contemporary 64-bit program with a cleaner interface, and much faster performance all around. While it does not have as many features as Endnote, and I lost all of my "collections" (but easily re-created since everything is keyword), I now am happier using Mendeley as it fits my need for a fast and snappy bibliographic database and citation manager.

Can you use both at once? My Mendeley crashed and I lost all my refs. I gave up on it, uninstalled and installed EndNote. However, now I have reinstalled Mendeley (as well), and see all my refs have returned! BUT, when I download new refs, they go automatically and only to EndNote. Any advice? Thanks in advance!

Jennie Blicher-Hansen from my limited investigation of the issue, it's tricky to manage two separate bibliographic systems since each has it's own database and it's own web synchronization system. Endnote is certainly the most feature-rich and robust option, and if you are on Windows performance will be acceptable. No matter the system, a periodic export in .ris or .bib format will provide you a backup in the event of a disaster. This, in addition to the web sync options, provides an extra level of security. While I miss the extensive set of fields that Endnote provides, the dog-slow performance under MacOS was making it unusable for me, so I switched to Mendeley. Fortunately all of my note in the notes field came across perfectly. If Endnote fixes the MacOS performance problems, I might go back to it.

Thank you very much for a helpful answer : - ) I am on MacOS too, so perhaps I should stick with Mendeley. Thank you !

I still use ENDNOTE with its robust features though on windows. Endnote X7 works well on my mac

I am more familiar with Endnote, but i found that as the references / bibliography got numerous, inserting new citations became very, very slow. I now use Mendeley and it seems to be the same, but still slightly better than Endnote. So, for me, the major attraction is that Mendeley is free, which is a huge plus.

I would highly recommend using Mendeley because of three major features which are not the case for Endnote:

- Can be used on Linux Systems

- Citation manager plugin available for open source office software Libre Office (Endnote plugin only for Microsoft Word)

- Citation style language (CSL) can be easily modified to your needs (Less of a "Black-Box" compared to Endnote)

Stability wise I did not experience any difference between the two.

I used EndNote for my dissertation proposal. It can be a "bear." Complex, needed to call Helpdesk all the time as it's not intuitive at all. Kept crashing when adding a pdf. Saw a really respected researcher physician who highly recommended Mendeley. It looked much easier to use, but pros and cons to everything as one person pointed out.

I find all very useful. They all have pros and Cons. Mendeley is great with the inbuilt Reader and it is free and easy to you. The only reason I prefer Endnote because of its link to the web of Science. In the past I have used the Microsoft built in feature for this, though a little cumbersome still got the job done. Verdict use the one that works for you.

Salam.

By default, each time you add a citation in WORD by EndNote it updates all the citations and maybe the bibliography and because of this as the references / bibliography gets numerous, inserting new citations becomes very, very slow.

The solution is that you should uncheck a choice that makes the EndNote update frequently. When you finished the citation you can update the numbers and citations manually at once.

Mendeley... Works seamlessly across desktop, web and mobile. The article suggestion based on your library is also good.

I never ever recommend Endnote. This reference software just wastes your time, I'd highly recommend Mendeley. If anyone needs any help with Mendeley, let me know. I'll be happy to help with it

Each of Endnote, Mendeley, and Zotero has pros and cons, there is no "best" in this app category. The bottom line: Each has a different set of features, and it depends on which of those features are important to you (there are several articles on line doing feature by feature comparisons so no need to go on about that). Recently Mendeley encrypted their database in order to make the export of the data to other systems more difficult, which is really not user-friendly. I decided to move my database to Zotero which has a lot going for it in terms of being open source, syncing between multiple instances and the web, it works really well for me. While Mendeley does have the best PDF reader and offers a really nice iOS app and I really liked using it, in the end, I found that the way Zotero manages notes and attachments and syncs with their web server and the interface in general works for me. The Endnote web interface is terrible, and the slow performance on the Mac made me migrate to Mendeley, however, I was curious to see how easily I could convert to Zotero without loss of essential data and I was able to do it in a matter of a couple of hours. Now I'm a happy Zotero user, in the end, the overall feature set works for me, and the day to day use of it is smoother in terms of the app on my Mac and I only occasionally use it via the web. It's interesting that each of these three has a different economic model: Zotero is open source and free (unless you want additional storage on their server); Mendeley is free but not open source and provide by a publisher; Endnote is a product you pay for. Three very different business models, which is most compatible with academia? Only time will tell.

David Tames I agree with you. Fortunately, Mendeley gives unlimited space to some universities including the one I'm working on. I think there should be other reference manager apps too that are better than Mendeley and Zotero but as you said all of them has got its own economic model and we should see which one is more suitable for us. I heard that citavi is one of the best ref manager but you need to buy it

Kourosh Esfandiar I bit the bullet and decided go with Zorero and pay the monthly storage fee out of my own pocket because: 1. I prefer the Zotero feature set as a whole after using Endnote and Mendeley; 2. I like supporting an open source academically focused project; 3. Mendeley's recent move to an encrypted database and their disingenuous explanation for the change rubbed by fur the wrong way. There have been numerous postings here and there about it, including this one: https://news.ycombinator.com/item?id=17607917

David Tames thanks for the reply, I'll have a look at the link

Sometime ago, i had to learn a reference manager. I had heard of endnotes, so tried to know more about it. Learnt that it was a paid software and then I found mendeley. Tried it, it was free and easy. Four years later, I am still using mendeley. Its sufficient for me. So until I find that it not enough, I will keep using it.

I know it has limited space, but that's sufficient if you download only bibliography details into the database and not full text. Its at least the case for me.

I found EndNote very easy and useful. I highly recommend the EndNote software program.

I prefer to use mendeley,so far is the only one that I tried.useful and easy.free

after comparing endnote & mendeley, it is much easier using mendeley & it is free!!!

I have used numerous versions of Endnote for about 15+ years and have not had any issues with it. It has served as a fantastic resource/database for finding literature in my "files" and as a reference manager when writing articles and reports. I particularly like being able to create custom citation formats when needed.

However, it should be noted that I have not used the other software packages for comparison.

I have used both Mendeley and EndNote and have faced with a lot of errors when using the latter. One of the problems was with syncing it with Microsoft Word. When you install its add-on for MS Word, there is no guarantee that it will appear in the MS Word. Another problem was updating the references of a file that was created on another device by a colleague.

Mendeley, on the other hand, has been working very well for me. It is pretty light and user friendly. It can recognize all the details of references on your web browser and add them to your library. You can easily download and use the styles you do not have in your database.

Overall, I would recommend using Mendeley, rather than EndNote.

I've always used EndNote in academia but now I am working in another sector which doesn't traditionally use this kind of software and has no budget for it. I've setup a free Mendeley account online which has been great to use but I can't see a way of editing the format of citations when I import them to word to create a reference list/bibliography? For example, it imports the author and 'et al' but I want all authors. I also want the year of publish in brackets. I've contacted the support team and they can't give me an answer as they've said all their citations are taken from a Zotero repository? Is this just an issue with the free web version? I'm really missing Endnote as I knew how to edit citation formats in that!

Amanda, I have experienced the same kind of issue but have managed to edit entries in Word by very careful use of the arrow keys (the four up-down-left-right keys bottom right on my Mac keyborad) to enter the citation in text, position the cursor, and then edit it. Mendeley asks if I want to do this to which I reply yes. It meets my current needs and hope this may work for you too.

My big concern with Zotero is precisley the free aspect. Many, but many, free companies could not take the buisness over time and kills the product. It has to be some monetary aspect involved if not it is not releiable in the long run. Other aspect is the lack of Ipad app since many of my reading is done there

Used Endnote but now shifted to Mendeley

Arun K Das I've previously used the paid version of Endnote but now only have access to the online free version of Mendeley. It seems relatively straightforward but the main problem I'm having is the format the references are in when you export from Mendeley into word to create a reference list. In Endnote I could modify the format to match the style of the journal I was submitting to, but I can't see how to do this with Mendeley. I contacted their support service but was told that their database stems from Zotero so they couldn't help me.Do you have any tips?

Dear @ Amanda Seims . I will be happy to help you. Go to word file -click References tab-then select style- there will a drop down menu-type the name of the journal- then see the rightside -one install button is there. install it. and use.

if you have any problem, then mail me ([email protected]). or please see this video

here is the link-https://www.youtube.com/watch?v=IOr86xtMuHs&t=236s

hope this will help.

Thank-you Arun K Das . I'll try that.

@ Amanda.

still if you have problem, install "team viewer" . then give me code, i can show you in your computer even sitting faraway here.

Amanda Seims Hi Amanda,

you can either select pre formated styles from the dropdown as Arun Kr Das pointed out. See this Mendeley intro guide on page 10 for details

(https://desktop-download.mendeley.com/download/Getting_Started_Guide.pdf)

I think reading this quick intro really helps to get you familiar with the software and use it to its full potential (i.e. automated file import and file organizer etc...)

If you can't find a citation style that fits your needs you can always write your own with CSL (Citation style language). Mendeley provides detailed infos on how to do that. They even provide a easy to use CSL editor:

https://www.mendeley.com/guides/csl-editor

All citation styles currently available for Mendeley can be found on Github:

https://github.com/citation-style-language/styles