Zotero, an Endnote alternative

I wasn’t planning to make this a software weblog, but I’ll make an exception for Zotero because I think fellow researchers will find it an interesting tool. Zotero [ˌzɔˈtɛɹoʊ] is a free piece of software that lives in your browser, helping you to ‘collect, manage and cite your research sources’ in all sorts of beautiful ways. It bills itself as The Next-Generation Research Tool, and in this post I’ll try to explain why I think that’s true. The background to this posting is that I made the move from Endnote to Zotero two months ago — and I have never since considered going back.

It all started when I upgraded from Endnote 7 to Endnote X to get Unicode support.1 Endnote X included Endnote Web, a web-based implementation that looked interesting. I had some difficulty getting the two to work together, and when I finally did, there were drawbacks that made me look out for an alternative. A Google search led me to Zotero, which was a breeze to install. I could simply import my Endnote library and started a testdrive. Within minutes I was totally hooked. The Zotero interface offered everything I had been missing in Endnote and then some. What makes Zotero so good?

Seamless integration with online research

First of all, Zotero answers the needs of researchers in the digital age. The rise of online repositories like JSTOR, ProQuest, SpringerLink, and Google Scholar has caused a shift in our research habits; we spend more time browsing virtual libraries, and less time hanging around in physical ones.2 Zotero seamlessly integrates with this online experience by automating the wearisome labour of saving references and by offering many ways to manage and enrich the data thus collected. All from within the web browser.3

Get ZoteroWith Zotero, adding a reference from an online repository to your database takes exactly one click. If an abstract is available (as in such repositories as SpringerLink and CSA), it will be saved with the record; if you have fulltext access to the repository, Zotero will moreover save a local copy of the PDF. But Zotero doesn’t just grab references from repositories; it can also save a snapshot of any web page and make it available for citation. This comes in handy when you want to make sure you have a copy of the page for future reference. Web pages saved in this way can be viewed offline, and Zotero even lets you annotate these snapshots just as you would do on paper. Unlike your paper scribbles, all of your Zotero annotations and notes are searchable.

Reference management, the intuitive way

Secondly, Zotero is a fully fledged reference manager with an intuitive interface. For those of you using Endnote —as I did until two months ago— this combination may sound otherworldly. Basically, Zotero takes that huge flat list of references that stares you in the face when you start up Endnote and transforms it into a neat, manageable and searchable personal library. No more trying to get your mind around the intricacies of Showing and Hiding references in Endnote — instead, use collections, tags and saveable searches to take control of your library.

Zotero enables you to organize references into collections. References can be in more than one collection and collections can have subcollections. References can be related to each other so that you can easily link reviews or chapters of a book to the book itself.4 Advanced search capabilities enable you to do fulltext searches in your library or in portions of it (yes, it can index your PDFs too!). Searches can be saved; if saved, they are dynamically updated so that any new items fitting the search criteria are found too. Zotero also brings the power of tagging to your reference database, enabling fine-grained categorization as well as easy category intersection. And of course, Zotero can import and export citations in all major formats, making it perfectly easy to switch back to Endnote, or more to the point, to share citations with colleagues.

Word processor integration

Insert and edit citations and bibliographiesNot only is Zotero a great reference manager, it integrates with your favourite word processor too. It supports both Microsoft Word and OpenOffice/NeoOffice through plugins (here’s how), adding a bunch of buttons to your word processor which help you insert and edit citations and bibliographies. In a preference window you can specify the citation style you want to use. The most commonly used styles are already available, and the list of supported styles continues to grow. XML-savy users can add and distribute their own citation styles.

Another thing worth mentioning is that Zotero will run on Mac and Linux just as fine as on Windows. This is because Zotero is built on the Firefox extension framework. (One implication of this is that Zotero will only run on Firefox 2 and not, for example, on Internet Explorer. If you do not already use Firefox, this is as good a reason as any to switch.) While we’re at it, some of you may also like to know that under the hood, Zotero uses the sqlite database engine. If you are not sure what that means, the most important thing to remember is that Zotero is based on open source technologies which, by their very nature, will continue to be freely available in the future (unlike proprietary software, the development and maintenance of which is driven by monetary interests).

That’s just the start of it

In this post I have focused on those features of Zotero that made me decide to switch. But I have not nearly exhausted everything it does. Some things I find particularly cool are the fact that it can export to HTML with embedded COinS metadata, allowing other Zotero users to surf by and capture the references (more info); its ability to generate reports, consisting of a list of selected references together with tags and notes you added (example); the option to visualize your references on a timeline (screenshots); and the possibility to build a bibliography simply by dragging and dropping references from Zotero into any text edit box (which is how I usually cite on The Ideophone).

If you want to give Zotero a try (remember it’s free!), here are some useful resources:

  • A review of Zotero by Scott McLemee at Inside Higher Education
  • Zotero.org, the page from where you can install Zotero and find detailed instructions for use
  • Documentation, including nice introductory screencasts
  • The Zotero forums, a place where helpful people hang around to answer your questions
  • A podcast on Zotero presented by Chris Strauber, Reference & Web Services Librarian at Wofford College

Thanks for reading — comments welcome!


  1. Some Unicode support been in place since v. 8 on, though without RTL abilities. []
  2. We all like to stress how we still appreciate the feel of paper in our hands, and the smell of books in a well-stocked library. The point here is merely that as more and more of these offline sources become available for online searching, our research habits (though not necessarily our reading habits) are bound to be affected by this. []
  3. Endnote, the mammoth of reference management, has a radically different approach. As a standalone application, it isolates the reference database from where the action is. This is perfectly understandable from a traditional perspective (don’t forget Endnote is a pre-web application), but I would argue that it is seriously out of sync with today’s reality, adding unneccesary complexity to things we don’t want to waste our time on.
    Yes, I know Endnote boasts the ability to search for references from within the application. But seriously, how many of us routinely go to ‘Tools > Connect’, select a repository, search, wait while references are being retrieved (in the process some four dialog windows have opened on top of each other), then select those that seem interesting on the basis of author, year, or title (if you want more information, you have to doubleclick a reference, opening a fifth window), and finally copy them to Endnote? Of course, Endnote can import RIS files from the web — but Zotero does that too, and does it better. []
  4. Right now, there is only one type of relation. In the future, a more complete set of relations will be added, e.g. ‘cites X’ (and its reverse ‘is cited by X’), ‘is a chapter of X’, ‘reviews X’ (more info). []

32 thoughts on “Zotero, an Endnote alternative”

  1. Thanks for this post, Mark. It’s got some really useful information. I think that Zotero would be extremely helpful for doctoral candidates or people who write for a limited range of publications that accept the available styles. I think, however, that Endnote is still likely to be better than Zotero for people who write for a range of journals which each have their own idiosyncratic little features. From what I can gather (not having used Zotero), being able to either simply download or set up a style for each journal and not have to worry about checking the referencing formatting is possibly the only feature where Endnote currently outperforms Zotero.

    Do you happen to know if you can import your Zotero library back into Endnote if you need to be able to use a style that Zotero doesn’t offer?

  2. From what I can gather (not having used Zotero), being able to either simply download or set up a style for each journal and not have to worry about checking the referencing formatting is possibly the only feature where Endnote currently outperforms Zotero.

    I agree. Compared to Endnote, Zotero is light on citation styles currently. I expect this to change while Zotero builds up a userbase and a community (people will start contributing styles).

    In the meantime, it is perfectly possible to import a selection of references into Endnote for the purposes of using a certain style. I just tried it and it is a very straighforward process: Select the references in Zotero, rightclick and export to RIS; then go to Endnote, choose File>Import, browse to the file and click OK (don’t forget to specify Refman RIS under ‘Import option’; Endnote doesn’t autodetect the format even if you feed it a perfectly valid .ris file).

    Update (2009)
    As I expected back in 2008, the number of styles has grown swiftly. As of 2010, Zotero supports literally thousands of styles and even can import EndNote .ens styles.

  3. Thanks, Mark, for reviewing this piece of software. Looks interesting.

    I too, have given up using Endnote, in part because its proprietary, and because I have become a dedicated user of LaTeX. As a result, I have moved over to BibDesk, which is free, open source, and works well with LaTeX. However, it’s not nearly as nice as Endnote when it comes to extracting citations from online sources. This makes me wonder if it is possible to use Zotero as a way to grab citations and import them into BibDesk.

  4. I use Zotero to grab citations for my BibTeX files, and it works well so far. I can’t compare it to Endnote, because I never used it. My only complaint is that Zotero seems to be a resource hog, so it can make Firefox run slowly. I’ve solved that by exporting my files to BibTeX and deleting them from Zotero.

  5. Tulugaq, Lev — I gather both of you use LateX. Last I checked (one year ago), the Unicode support was problematic and very hack-like, and that was the reason for me to steer away from it — though with considerable regret, for I am a great fan of structural (as opposed to presentational) markup. Has it gotten easier? Or do both of you happen to work on languages ith ASCII-compatible orthographies?

    Tulugaq says:
    My only complaint is that Zotero seems to be a resource hog, so it can make Firefox run slowly.

    I’ve not experienced this myself; it may have to do with the size of the database, or perhaps it’s a memory issue. In any case, I have heard that Zotero 2.0 will be faster and more reliable since there are a lot of improvements to the underlying architecture in Firefox 3.

  6. Oh, definitely not ASCII-compatible. I use Unicode all the time in LaTeX, but then, I’m usually using XeLaTeX, which uses Unicode natively, rather than regular LaTeX. You just input the text in Unicode directly – no cumbersome shortcuts. At the beginning of the document, you have to specify some font information, but from then on, you just type in Unicode and compile the document. I’d be happy to share my XeLaTeX template with you if you’d like to see how I do it. I’m no LaTeX expert – far from it! – but if it’d help, I’m game.

    In Zotero, so far it hasn’t mattered that much to me whether it’s Unicode-compliant or not (to be quite honest, I didn’t even check before trying it out). That’s because most of the sources I’d be searching for (Eskimo-Aleut linguistics) wouldn’t have their bib record entered in Unicode anyway. Most of the time when I find bibliographic info in or about Iñupiaq, for example, whoever typed it up just omitted all diacritics and typed it up as if the orthography were English. The letter ġ would just be typed as g, for example. So whether it’s Unicode or not, I still have to go in and replace with the proper Iñupiaq letters where necessary.

  7. Interesting point, Mark. No, as far as I know, LaTeX does not handle Unicode well, as Tulugaq says. But, like you, I haven’t looked into the matter for about a year, so things may have changed. So far it hasn’t been a serious issue for me, because of the particular languages I am working with. Of course, regardless of the language-specific particulars, there are always Unicode issues related to digital archiving best practice.

    I am interested to hear that XeLaTeX handles Unicode nicely — I’ll need to look into that.

  8. Seems interesting. I’ve been looking for an alternative to Endnote as this is one of the last reasons I still use Windows. However, a common scenario would be that I receive a Word document with embedded Endnote citations. Opening in OpenOffice has the effect of stripping them out. I note that OOo3 does not remove them, which is an improvement, but it still removes the Endnote Field codes. Zotero does not seem to provide a solution to this problem. Still, I will take a closer look at Zotero and perhaps there will be a solution in the future.

  9. Karl, as you probably know, the problem there is really with Endnote, since its proprietary format makes it extremely difficult to devise a working converter (and if you try to make Endnote more interoperable, you get sued).
    However, the fact that so many of us are running into this same issue provides some reason for hope. Nothing is impossible in the open source development model, given enough motivated people.

  10. Hello. I am looking for a software to assist me in my research work. I use Mac OS Snow Leopard, and Pages as my word processing software. I used to do bibliography and search information online manually, but found that Pages is compatible with EndNote X2 with reference and pull down menu. I am still learning to use EndNote as I t’m typing this. Was wondering whether I should rather invest my time learning Zotero instead? Is Zotero compatible with Pages? I guess I could get used of using Firefox instead of Safari as long as Zotero automatized what I manually do.

  11. Hi there. Unfortunately, Apple has made the choice to support only EndNote in Pages. They haven’t even made the interface extensible as, for example, MS Word and Open Office, so there is nothing Zotero can do to support Pages (background info here). Zotero does have the RTF scan feature which enables you to automate the citation process to some extent, but that’s about as far it goes without Apple opening up its interface. I wish it was different, for in my experience 10 minutes of investing your time in Zotero is equal to a couple of hours in EndNote.
    Please do contact Apple and ask them to make Pages more open so that their customers have free choice over the citation manager they wish to use. If enough people ask for it they’ll certainly consider improving Pages, especially because it should not be too difficult for them to support open standards.

  12. Hi Mark.

    This forum has been much help in guiding me to choose the right software which works for me and my machine! Thanks for your recent input as well. I could just dive into any software like EndNote because it is compatible with macintosh’s Pages but one first look at EndNote X2 I knew that I should browse a bit more. It is complicated and not user friendly. The pdf guide total up to 750 pages! It’s either it is very detailed or simply long winded. A good software should make it easy for user to learn and use.

    I have downloaded Zotero and gave it a a go yesterday. It’s quite simply and certainly friendlier than EndNote. And can’t believe it’s free! Although Zotero does not work with Pages it is able to create bibliography in RTF format which can than be copied into pages so far without any errors. I mean for something which is open sourced that is good enough. I am still figuring out how to copy multiple citations from different folders in Zotero at once into a single RTF. I had to go to different folders separately yesterday. Is there a way to do that?

    My earlier research has also pointed me to a software called Bookends which is made for macintosh platform. I appreciate comments from those who are familiar with Bookends.



  13. Kal, you can either click on ‘My Library’ and select the references that you want to include in a bibliography (‘My Library’ always displays all sources), or you can make a separate folder (Zotero calls these ‘collections’) which contains all of the items you want to cite so that you don’t have to navigate the different folders.

  14. What you need is a running EndNote version. If you don’t have access to EndNote, I’d be willing to help with the conversion. You could send me the .enl file so that I can try to export the references in a format that can be imported by Zotero.

  15. Mark, thanks for the offer. I found a workaround so I won’t bother you with converting the .enl file for me. I pasted text from the .htm into WizFolio and used that to export as .ris for import into Zotero.

    Thanks again,

  16. hi dear more experienced users,

    would it make sense to switch from EN web to Z in a paper already including >50 refs? or is it not worth the effort? (due to annoyances with logging into EN)

    thanks for replies.

    best, h

  17. Well, since EN en EN Web use a proprietary database format (i.e. your citations are locked in) there is no way to convert the citations in your document automatically to the Zotero format.

    However, if you can export at least your library to Zotero, then converting the citations in the document manually is still doable by hand. Save flattened copy of the document, get your refs in Zotero, and go through the citations one by one, inserting them anew from your Zotero library using the word processor plugin. It should not take more than 30 minutes of focused work.

  18. I think, however, that Endnote is still likely to be better than Zotero for people who write for a range of journals

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