Zotero vs Endnote 4: the battle is on!

This guest post is by Gabriel Oguda, who is studying for an MPhil in Health Promotion at the University of Bergen in Norway. Gabriel follows me on Twitter and told me that Zotero recently saved him from an epic thesis fail. I asked him to share his story …

I must begin by saying I am a very conservative person. Give me a lower version of SPSS and I will not upgrade unless it breaks down or loses my files.

Yet that is what happened last week when the EndNote X4 library I had laboriously assembled failed to turn up – two days before the final submission of my class assignment.

“Why not shift to Zotero?” a classmate suggested as I painfully hurried to reconstruct the library. I remember receiving a brief orientation on Zotero on the first week of my new course, but quickly forgot to follow up as I settled in. As I write this, I have just submitted my assignment with all the sources, properly referenced. So what did the magic? Here is my experience with both EndNote X4 and Zotero.


The University of Bergen pre-subscribes all students to EndNote X4, for free. You enjoy the freedom of referencing using EndNote X4 up until your graduation. When the systems stop recognizing you as a student, you have to buy the program online if you have to continue using it. Zotero is free for all. As long as you have the Mozilla Firefox browser, your library is secure. What’s more, you can access your library offline so you need not to worry about Internet connection. If you are the student who works with limited funds, Zotero is the program for you.


When EndNote introduced EndNote X4 compatible with Word 2011 for Mac, I had to contact the university IT department to configure it for me. Part of the reason why I lost my previous library is due to the complexities encountered with working back and forth to harmonize the settings before and after the upgrades. Moreover, the whole EndNote bundle can only be downloaded from the university IT website which often requires the help of a technician because it involves numerous steps that are too tedious for a student willing to stock a library limited with time. Zotero is readily available on their website and can be downloaded easily.

Importing references

Working on research proposals and theses can be time consuming. Students often want to utilize every drop of time available. Importing references has never been easier using Zotero. To use the words of one of my tutors, “…you can just google a reference, click a button and have all the pertinent info saved in the appropriate fields. It is so time-saving!” EndNote X4 also has this feature but it’s limited to specific sites with peer-reviewed articles like ISI Web of Knowledge, but even then you have to register on the website for you to enjoy this feature.


I still wonder why I was stuck to EndNote X4 despite all the hassles I had to go through. Zotero, one of my classmates observes “offers you a nice overview of your references with an easy drag & drop system, allows you to create folders and to attach documents, comments, tags etc., which some of the other free systems don’t.” If you are the student who likes keeping track of the references you have used, take notes and make comments within a reference library, then Zotero is the program for you.

Referencing village

From the term “global village”, “referencing village” is my new slang that denotes the interaction of all manner of referencing approaches on one platform. Everyday I learn something new. Today I have been informed that on top of Windows and Mac, students using Linux as their preferred operating system can also access Zotero. The admin at Zotero are not stopping at this, either. They have just launched a new application dubbed “Zotero Everywhere”.

 Zotero Everywhere, according to their site will have two main components: a standalone desktop version of Zotero with full integration into a variety of web browsers and a radically expanded application programming interface (API) to provide web and mobile access to Zotero libraries. As a student from a developing country, I couldn’t ask for more from a referencing program.

So that’s my story, fellow student struggling with #phdemotions. As we continue struggling in this world of academia, let’s remember David Brent’s words that “a problem shared is halved.” Let the sharing continue unabated.

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47 thoughts on “Zotero vs Endnote 4: the battle is on!

  1. Kylie says:

    Great post – thanks!
    I’ve recently decided to use Endnote web for my PhD journey because I want a portable system that can cope with my being in multiple locations (without necessarily having access to a laptop). Does anyone know of any obvious limitations of using cloud based reference systems like this? For example, the thought that came to mind while reading this post is will they upgrade Endnote web in such a way that limits the library of I have built in its current version?

    • Avram Lyon says:

      Unless you are confident that you will always have access to the internet when working, you may want to look into running Zotero and Firefox from a USB drive — you could also install Zotero Standalone on a USB drive. It obviously depends on where you’re going, but I very frequently work in places where internet access is not available– Zotero (and other desktop software) gives you access to all your bibliographic data even in no-internet archives, libraries, etc.

      • Mark says:

        But Zotero supports syncing! The USB drive solution is a workaround that dates from the time that Zotero didn’t synchronize. The most recent versions of Zotero can simply synchronize your library so that you have access to your references from any PC, all of the time — either via a web interface or via a Zotero client.

        I have four different work places. On all of them, Zotero automatically synchronizes any change I make anywhere. So my whole library is always available wherever I work. This is much better than Endnote Web, which I found to have a clunky web interface and no good word processor integration unless you pay.

      • Avram Lyon says:

        @Mark: Note that Kylie said: “I want a portable system that can cope with my being in multiple locations (without necessarily having access to a laptop).”

        Zotero can’t yet serve this group without using Zotero Standalone on a USB drive, although a full-fledged web interface (that is, on par feature-wise with the desktop client) is hopefully coming soon.

  2. Awuor Ponge says:

    Just installed ZOTERO in my machine…thanks to Gabriel Oguda’s indication. I’m going through the Tutorials and will soon be up and running and will be able to make comments appropriately after testing how efficient the system is in managing referencing…Once more, thanks to Gabriel… and to ZOTERO for making this software available online at no cost…That is the essence of promoting and facilitating effective scholarship.

    Keep it up!

  3. Avram Lyon says:

    Note that some components of Zotero Everywhere are already available for testing by interested users who’d like to get away from Firefox. See http://www.zotero.org/support/standalone.

    Also, I’d encourage you to set aside your conservatism for a moment and install Zotero 2.1rc3 (a release candidate of the new 2.1 version, soon to be a final release), since it brings a lot of nice new functionality and is, I believe, more stable and more reliable than the older 2.0.9 release.

    And glad to hear that Zotero saved you!

    • Gabriel Oguda says:

      Sure, Avram. I am still interacting with it. Thanks for your insights. You have made Zotero a must-have program! One-Stop Shop.

      • Barbara Lynch-Johnson says:

        Hello Gabriel,
        I’m in my first semester studying for a Masters in Library and Information Science at the University of Pittsburgh in Pennsylvania. I’ve been away from the classroom for a number of years, so this technology is new to me. However, I’m determined to be proficient with this!

      • Mr. Gunn says:

        You can see a comparison of various programs at http://bit.ly/refman I would say Mendeley, in comparison, is browser and operating system independent, so you can access your papers wherever you are. It’s also really easy to use and there’s a getting started tutorial right in the app, if you’d like to give it a try. http://mendeley.com

    • Asa Johannesen says:

      I use Mendeley. Best thing since sliced bread – if you’re in the sciences, that is. My philosopher boyfriend finds that most of his articles don’t have doi’s and really poor metadata, so he ends up inputting a lot of stuff manually into Mendeley. Not really Mendeley’s fault, though.

  4. Ben Leong says:

    I love using Zotero – mainly because the Firefox browser (and the hundred-odd tabs I have open at any moment) is where I discover new references, so it’s also where I want to bookmark them.

    The automatic import isn’t perfect, but I don’t think anything else is doing a better job at the moment. Every publisher seems to format their metadata a bit differently, so it’s always worth doing a quick check to make sure that all the relevant bibliographic info made it into the reference library. I particularly like the option to import multiple references at once. From a Google Scholar search, for example, click the import button in the address bar – then select any or all of the references from that page, to auto-import whatever is relevant.

    I use tags a lot (in Delicious and Zotero) for sorting information. For academic articles I often find a lot at once, and read them later. Tagging new articles with “unread” means you can easily find them later, and remove that tag once you’ve read it.

    I also attach stored copies of all my references to the Zotero items. That way I can use the Zotero navigation pane to find whatever item I’m looking for (via tag, keyword, author, title etc) and open it directly from the browser.

    It also means that when I’m logged in to the Zotero website, I can access PDFs of everything in my reference library… when moving to a new work desktop computer, I installed Firefox & Zotero, and then downloaded a local copy of everything in the library. Given all the time that goes into finding, tagging and sorting references, I like having lots of redundant backups available 🙂

  5. Avram Lyon says:

    The automatic import isn’t perfect, but I don’t think anything else is doing a better job at the moment. Every publisher seems to format their metadata a bit differently, so it’s always worth doing a quick check to make sure that all the relevant bibliographic info made it into the reference library.

    The quality of automatic imports is, as you note, very much dependent on how publishers provide metadata. But if you run into any specific issues, please post them to the forums (or here, or on Twitter) and I’ll look into them; the translators that enable import from various sites are written and maintained by a bunch of volunteers, and we can often tweak them to fix the data issues you’re seeing.

  6. Anonymous says:

    Well done Oguda, am checking the Zotero program now and its quiet interesting. Guess will try it and see for my self.

  7. Erin Hoffer says:

    Sounds fascinating. But what supports the team building Zotero? Is it open source? Is it a start-up hoping to sell subscriptions or advertising? Or be bought by Google? Just wondering how the team will be able to keep up with customer needs for support and new features.

    • Sebastian says:

      Zotero is open source. It’s run out of the Center for History and New Media at George Mason University, a public university in the US state of Virginia.
      Development is funded partly by grants, partly (at least in the medium run) by revenue from the Corporation for Digital Scholarship
      a non-profit corporation, whose board is made up of various academics and who runs Zotero’s for-pay storage system (you can sync your data with Zotero for free, but have to pay if you also want to sync large amounts – >100MB – of file attachments such as article pdfs.)
      Finally, it being open source, some components of Zotero are written and maintained by volunteers – mostly academics – such as the citation style language
      Many useful plugins
      as well as most translators (that would be Avram above) and citation styles

      See also here

      • Avram Lyon says:

        Zotero is an open-source project based at the Center for History and New Media at George Mason University in Virginia. The main project funding so far has come from a series of grants to get the project going and work on specific areas. Grants have covered each of the stages in the development of Zotero’s groups, syncing, and other major areas of functionality. While I don’t know about the project’s next funding targets, it is safe to say that the project is not interested in selling subscriptions or advertising, and certainly not in acquisition. With the introduction of paid online storage (beyond 100MB), the team formed the Corporation for Digital Scholarship, a not-for-profit headed by a number of academics who volunteer to run it, to segregate that operation from CHNM and GMU. While Zotero storage, the only form of subscription-based service offered, does cost more than the Amazon storage that backs it, the difference is used to help cover other server and overhead costs, but is not, as far as I know, intended to support the core development effort. New features are being added by the core team, and the community of interested users has seen a lot of activity in recent months, with a volunteer contributor producing the citation engine that powers Zotero 2.1’s bibliographies (and those of Mendeley), the same contributor producing a new multilingual version that’s coming soon, a number of plugins, a wide range of site translators, and many citation styles.

      • Avram Lyon says:

        And thanks to a very active user community, support requests on the Zotero forums, on Twitter, and even on unrelated blogs, are answered at least as quickly as those of the commercial, proprietary products on the market.

        Sorry if this sounds like a naked advertisement– but I am just a very active user, and think most people would do well to explore what Zotero can offer. And a big part of that is the freedom to shape it to your personal research needs.

        [in two parts because a longer post wouldn’t show up. This repeats much of what Sebastian has said, but I thought I’d post anyway, since I’d drafted it.]

  8. J. Melinn says:

    Sorry to hear of your recent X4 upgrade experience and subsequent problems. Each university has its own method for distributing site-wide installers and some go more smoothly than others. We will reach out to the University of Bergen to see if there’s anything we can do to help avoid these problems in the future.

    I think you’ve pointed out a few ways that EndNote could improve, and we appreciate your feedback on those. But there are also some things here that I think we already do pretty well. Google Scholar, for example, can be easily configured to send reference information directly to EndNote. There are a few different types of groups that you can use to organize your library of references. (There’s even an automatically created group that tells you which things you’ve cited in a paper.) I don’t want to just list off features here, get in touch if you want more information. @EndNoteNews is available or I’m pretty easy to find.

    As with all reference management packages, EndNote solves a lot of problems, but not all of them, and there is always room for improvement. We welcome your feedback.

    • Gabriel Oguda says:

      Dear Melinn, thanks for taking time to clarify and inform about EndNote. I am happy to hear that you are working to make referencing less tedious. Let us continue sharing experiences. Its the only way to clear grey areas and demystify otherwise complex packages students use in their daily interactions on the corridors of academia. Humbled that you took time to respond. Appreciated.

  9. Nik says:

    If you’re interested in software to get the most out of your academic/research PDFs, and make your PHD easier, take a look atQiqqa (http://www.qiqqa.com).

    Started by a PHD student to overcome limitations found in the other software currently available.

  10. Julia says:

    I have been using Zotero for about three or four years now. When I started, I used to keep the database on a USB, but don’t now. Instead I have hooked it up with Dropbox so it syncs to my Dropbox cloud. (Just drop the SQLITE library into your Dropbox folder) In addition I have it marked for my ground level backup system to pick up too. However it is very robust. I love for several reasons.
    Its simple to add things, and you can store the actual digital objects to which you are referring with the reference (PDF’s, soundfiles, web snapshots, pretty much anything. Their website snapshots by the way are the whole page, not just the bit you can see as with a screenshot.) You can cluster these with notes you make under the one reference in Zotero, so it makes a searchable, retrievable library of all the stuff you’ve collected, not just a citation and abstract. If you tag well this makes finding things which refer to the same topic or theme and then re-reading them, a snap. And if you look carefully on their tips pages you can see that you can almost use “reports” which include your notes, to build an outline for a document you might be writing.
    Second the quick adding of citations through one click ‘translators’ in the address bar, is a big bonus. The RMIT library call number always comes out wrong if you use the RMIT translator, so that is a bit of a bug, but I have contacted them about it and apparently it involves some field they can’t move.
    My absolutely favourite bit of Zotero however is their support. Particularly in my early days of using it I screwed it up in most imaginable ways as I was being a bit experimental. In every case they got back to me within about a day and a half with a solution. The Zotero forums are really comprehensive, so use them first but those George Mason guys never sleep. Also Zotero has built into it a good automated error collecting and reporting system so you don’t have to pretend to be an open source nerd to report problems.
    Now if someone can come up with a good way to link Scrivener with Zotero, I’ll be in writing seventh heaven.

    • Sebastian says:

      “(Just drop the SQLITE library into your Dropbox folder) ”
      uhm – no, don’t do that. Every time someone comes to the Zotero forum with a (more or less) hopelessly corrupted library, the first question is “do you sync Zotero with dropbox” and the answer is usually yes.
      Dropbox is not a suitable tool for syncing databases.
      Beyond Zotero’s own storage system (a little pricey, but with some extra perks such as online accessibility and group sharing of files) you can use WebDav storage that is as cheap as Dropbox for syncing (it is, in fact, possible to set up webDav on dropbox), if you’re on a mac or linux machine you can use a sym link of the storage folder (i.e. the one with all the files but not the sqlite) to dropbox, but if you care about your data, don’t put your sqlite into drobox – being careless once could irretrievably damage your database.

      • Julia says:

        Thanks for the warning. I can see what you mean if you try to sync two ways. Fortunately I don’t use Dropbox as a sync so much as a cloud backup – but there again it wasn’t designed for that either.
        However I am interested in your webDav solution and I suspect others reading this are also. Can you go though ‘how to’ at a bit more of a ‘for dummies’ level so I can understand the answer? I found this site http://www.webdav.org/ but it looks a bit old. Their “recent news” isn’t.
        Also looking again at Zotero storage. How do you figure out how big your library is, and what files to include in the estimate? Think mine comes in at under 1GB but like to be sure. $20 per year sounds affordable now the AU$ has parity!

      • Sebastian says:

        Julia – the size of your library for sync purposes is about the size of your storage folder (i.e. the folder named “storage” in the zotero data folder
        if you have a lot of snapshots in there, it’s actually a little smaller I believe, because they’re compressed online, but not 100% sure about that.

        For webdav – depending on your level of technical expertise, see e.g. here
        or here

        there are other webdav services than jungledisk such as icloud that are often recommended, that would work the same way as described in the first link.

        But if you want a hassle-free solution and can afford the Zotero storage rates, that’s probably the way to go for you & you’d help to sustain Zotero.

      • Julia says:

        Have now put my money where my mouth is and signed up for attached file storage as well as syncing data with Zotero, and moved the database out of Dropbox. This has made Dropbox behave better with the rest of my stuff.
        My library was bigger than I thought so its taking a while to sync properly and I have had some sync errors, but none that broke the process. It just looked cross for a bit but went on syncing after restarts. Not finished yet. I think the other Firefox message I am getting from time to time – on unresponsive scripts – might be interfering, which means I should shut something down, a tab maybe (or like Ben, @ March 17, 2011 at 5:47 pm, a hundred or so tabs) but I’ll report that over at Zotero Forums.
        Its a shame you don’t get a PhD for having a fabulous bibliographic library because I’m sure that’s where a good deal of my scholarly effort has gone.

    • Avram Lyon says:

      Second the quick adding of citations through one click ‘translators’ in the address bar, is a big bonus. The RMIT library call number always comes out wrong if you use the RMIT translator, so that is a bit of a bug, but I have contacted them about it and apparently it involves some field they can’t move.

      This is a common issue, essentially because our translators tend to save the canonical or recommended call number, while library’s own call number for the item is sometimes missed. I ran into this (and the same library response) at UCLA in my own work, and I hope that we’ll have this fixed in a coming release of the underlying MARC translator.

      • Julia says:

        Avram Lyon, Slavic Literature and Zotero person: Well that’s just amazing as I understand it was a knotty problem. Zotero will purr like a Rolls Royce!
        Rest of Thesis Whisperer audience: See. I told you they were responsive!

        • ingermewburn says:

          Yes – I have been watching this discussion unfold with quiet pleasure 🙂
          It is just this kind of collaborative knowledge sharing I was hoping for when I started the whisperer…

  11. Lucy says:

    I’ve just downloaded Zotero and look forward to playing with it. I gave up on Endnote long ago and have been manually storing references and notes in a massive Word doc, which is not ideal. Thanks for introducing me to what sounds like a strong endnote alternative.

  12. PoorPuer says:

    I’ve been using Zotero for 2 years now, and it is getting better and better. You may want to check out Mendeley as well, though until it becomes fully compatible with Zotero, I am not using it. There is also Wizfolio, but that one is not free, and even it were, I’d still stick to Zotero.

    But whatever you decide on, stay away from Endnote. It is evil. Their product is bad, their customer support is bad, their new product releases may or may not be backward compatible, but you will be charged an arm and a leg not just for the initial product purchase, but for new version as well. I’d stay away from them even if they were free, to save yourself lots of headache. On top of all that, they are a corporate bully — they tried to sue Zotero (unsuccessfully), to kill their competition, not through making a better product, but through manipulating the IP law (and we all know how often it is abused). EndNote should be apologizing let and right, and offering their customer rebates… not that I have any strong opinions. 😉

  13. Gavin Koh says:

    I’ve been using Zotero for 4 years now and it’s caused me no end of trouble. It is fine if your document has up to around 50 references, but once you hit 100 references (my PhD thesis has about 600 now) Zotero slows to a crawl and the simple act of adding a single reference to a document can lock Word for >5 minutes. You can’t even have more than one Word document open at the same time, because the simple act of switching documents is enough to confuse Zotero so it doesn’t know which document it is updating. The trouble is, you try Zotero out for a spin and it looks good, but the problems don’t show up until you are committed to it and it is too late to change.

  14. adam.smith says:

    @Gavin – sorry you’re having a bad experience, but that’s not the norm with Zotero. I know of several dissertations (including my own) and at least a couple of books that have been referenced entirely with Zotero without these issues.
    @Nik – wait, don’t you use csl and citeproc-js for citations, just like Zotero? Why would we expect that to be much faster?

  15. Anonymous says:

    To me, the only problem with Endnote is that it does not run on linux. Otherwise I would definetely stay with it. Zotero seems cool, with lots of colors, with some drag and drop, but really I think Endnote is far better. I’ve never had any problem with Endnote and it has always been extremely easy to use (although no drag and drop ok, I know drag and drop is supercool).

    Problems with zotero :
    – I tried it some years ago, and after one month I realized that some papers could not be imported. Just impossible. When I imported a list of papers from web of science, a small fraction would never be imported. So I went back to Endnote. Now I have to switch to linux, because windows is a deep crap, so I am back with zotero.
    – Endnote has the possility to insert non formatted references and then format them all at once when the document is finished. Zotero wants to format everything everytime you insert a reference, which, as someone pointed out just above, can take a very long time when you have many references. Yes, there is the rtfscan thing in zotero. But it does not do anything with me (I get exactly the same file in output) and also works only with RTF files. (hence the name). Also for this reason, it is impossible to copy one reference and paste it in the same document. Which is extremely annoying in some cases. I really don’t understand why this does not exist in zotero when it is known that the most used reference managers use that system. (and please don’t tell me why it is impossible in zotero, my point is “why zotero was not made in a way that this does work ?”)
    – I have 1500 refs in my library, which I don’t consider too much. But Zotero freezes during 15 seconds everytime I open it. So I lose a bit more time than what I save with the ” drag and drop feature”.
    – About the support, yes many people can answer your questions on the forums. But I don’t know how it is with endnote, because I never had to ask anything to the customer support, eventhough I have been using endnote longer than zotero.

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