Zotero vs. EndNote

The “automatically attach associated PDFs and other files when saving items” setting actually works with Zotero-compatible publisher sites (i.e. ScienceDirect), not Zotero-compatible databases – it really needs a name change!

I’m a bit saddened that even on a “Hacker” blog, the issue of openness isn’t addressed at all. With Endnote you’re saving your data in a proprietary format. Citation styles that you create are subject to a ridiculous EULA that Thompson Reuter is fully willing to enforce with lawsuits. Endnote’s output filters are notoriously bad – the RIS export doesn’t conform to any published standards _and_ is inconsistent between versions.
Also, Zotero, by virtue of being open, is suitable in various ways for plugins, data-mining via API or via direct access to the database etc. – see the list of already existing plugins for an example and the API options haven’t even existed for a long time.

Also, yes, for advanced users inserting citations may be faster with Endnote, but it’s also quite difficult to style them properly. Getting something like (cf. Smith 1776 for the original work; Meyer 2001 provides an overview) is a big hassle in Endnote. If you then want to turn this into Chicago style – you’ll have to manually create a footnote and cut and paste the citation into the footnote – it’s one click with Zotero/csl.

Since csl 1.0 the ability to get precise output for citation styles for Zotero (and other software using csl such as Mendeley and Papers 2) is far superior – issues like precise disambiguation routines, page-range collapsing rules, various forms of name-ordering for names with particles like “von” “de” etc. – are just some of the features that are far ahead of Endnote (and given the limited nature of Endnote’s style language will likely never be achieved).

Thanks for pointing us to some of the databases that work well with this feature of Zotero’s. I should have said that I’m not involved in a lot of database-based research at the moment, and so haven’t tested it exhaustively in even the databases that I would use most regularly in my own research. Anecdotal evidence isn’t bad, as long as one makes it plain that it is, in fact, anecdotal.

And for the record, Zotero grabbed the PDF for me from JSTOR and Sciencedirect. It doesn’t appear to work with EBSCO databases (such as our library’s version of MLA International) or Literature Online.

You bring up a good point about the openness of the two platforms. I didn’t want to go into this discussion in the article because while openness is important, it’s not going to be foremost in many users minds. (Not that it shouldn’t be!) Most people just want to find the tool that works for them.

Once you’re up to speed with EndNote ninja-ery, it’s not that hard to style your example: {cf. Smith, 1776 #33for the original work; Meyer, 2001 #133provides an overview}. Granted, that’s not pretty, but learning how the prefixes and suffixes work isn’t any harder than the page numbers. And most citations in my experience aren’t as difficult as that.

You do make a good point about the relative ease of moving to Chicago style in Zotero. EndNote doesn’t handle that shift very well.

Thanks for the comments! You’re obviously well aware of the issues that suggest why Zotero is such a robust and important resource.

Crap. Why am I hand-typing my works cited again? I’ve got to get my hands on this.

Thanks for the face-off. I posted a question about citation managers in last Wednesday’s open thread so this is very, very helpful. As disclosure, right now I’m using Bookends but this convinced me to take another look at EndNote.

The search for the perfect citation manager continues!

ps. I, too, hate the little pop up window.

that depends – as I say above, in possibility, csl (i.e. Zotero – but not just) citation styles _can_ produce better output than Endnote, but that’s only fully realized for a few styles. I’m pretty sure that APA by now is better in csl, as are the various Chicago and Turabian styles.
MLA is likely a judgment call, with some flaws for either.
People on the Zotero forum make a strong (and afaik successful) effort to follow up on every report of mistakes in a citation style, but since the format has been around for less than 5 years and has only been used heavily for the last 3 many of the less frequently used styles have not seen the type of vetting that many endnote style (maybe?) have.

I don’t know that the perfect citation manager exists. One could certainly spend a lot of time weighing all of the options. From my limited investigation of the field (which is limited more by what it could be than in comparison with my peers), all of the tools I’ve seen do what they are supposed to do. Each has strengths and quirks that you will wish it didn’t have. The best solution, in my opinion, is to make a decision to adopt one framework and then move forward and get your writing/work done. And when making that decision, Zotero and EndNote are to good options given how many people use them.

And that pop-up window is the worst.

@sebastiank At least for APA csl is still lacking. It doesn’t include the requirement for multiple (more than 8) authors. (EndNote does.)

With my original comment I was trying to point out that I think the formatting is another area of comparison that’s essential. Personally, I’d guess most people don’t care how that happens, and just that the styles are right.

@Brian I wouldn’t call it community driven, but there is definitely a place to discuss and report issues with EndNote content: http://bit.ly/jzwZf0

Also, am I missing something with Disqus? Seems like I can only reply to the first comment in a thread.

@Jen As far as Disqus goes, I think we’ve just hit the maximum for nesting conversations. Since we’re four-deep, we can’t reply to replies any more.

And thank you for providing the link to the EndNote Styles, Filter, and Connections forum.

@Brian Was I just the one who pulled the thread into intricate style detail arguments? Oh no, I was! I’ll try to stay away from there. Problem is, those are the types of things I hear about that really do determine which application is most useful in particular disciplines.

Being a Mac user, I have used EndNote for years (when everyone else was using Ref Manager). I wouldn’t want to try to format a bib without it. I liked some earlier versions more than I like the current iteration. The online search feature is great, but in the latest version I have the interface melds the search into your library, or shows you only one OR the other – I end up opening a dummy library so that I can see the search and my current library in two separate windows, and know which is which.

Microsoft Word integration is pretty good. Formatting the output style can be kind of arcane and annoying, but once you have it, the style can be saved and you don’t have to do it again. When I’ve had difficulty with fidelity of the output, it can usually be traced to a formatting issue.

Haven’t tried Zotero. I would love it if Papers (pdf library software) would incorporate a bibliographic add-on. That would be cool.

One interesting opportunity to make sure that citation styles really follow the style guides is automatic testing. For CSL, the basic infrastructure is already in place, although the (unfunded) CSL project currently lacks the resources to put real work into this approach:

http://xbiblio-devel.2463403.n2.nabble.com/Infrastructure-for-style-level-testing-td6248958.html

I still prefer Biblioscape. Though pricey, the advanced versions included fabulous note- and task-management tools absent from the two products you review.

You’re certainly right that using a citation manager is far better than not using one at all. And both of these tools is very useful.

I wanted to have the win-lose framework (although I tried to put emphasis on the win rather than the lose) because there are clear differences between the tools, and I don’t think we should be chary of calling a spade a spade. If identifying strengths helps lead to better application development, all the better for all involved!

I’d be interested to see what your syllabus looks like for that workshop. We teach the two apps separately (60 minutes for Zotero, 90 for EndNote). I’ve thought about a combined one, but it seems like it would confuse more than educate. I’m assuming your experience proves otherwise, however.

For me the intractable problem is how to write: where do the citations go?

I have a similar “vs.” list between Zotero and Bookends. I love Zotero, but its plugins only allow it to interact with Libre and Word–and I don’t particularly like writing in Libre and Word–and its RTF scan feature is not yet well-developed enough to make it useful for writing articles and books.

…and those licenses do not include home use for students and faculty – i.e. students still have to pay (though reduced rate) if they want to install on their private laptops…

I’m realizing now that I hadn’t responded to all of your questions. When importing PDFs into EndNote, I grabbed a handful of random journal articles I had and imported them. None of them imported with the metadata. It’s admittedly an imperfect test and certainly constrained by my own field of study.

As for EndNote Web’s capture, I like the fact that it works across all modern browsers (something that Zotero is now starting to do as well). But I find that it doesn’t capture metadata from as many sites as Zotero and that it is much slower.

I know what you’re saying about the way EndNote handles online search, crankycat. I too find it distracting that those search results are (by default) added to one’s library automatically. I’ve become used to it and have strategies for dealing with this. But I find that I add most of my sources from databases or by hand, rather than built-in search, so this doesn’t matter as much.

I’ll certainly agree with you about how wonderfully easy it is to share citations with others using Zotero. In fact, that functionality forms the backbone of my Annotated Zotero Group Bibliography Assignment.

I have run a few precise comparisons between Endnote and Zotero to see how well they handle the requirements for a range of styles (APA, MLA, Chicago, etc.). Looking at examples of the same work, styled in various ways, between the two shows that for some references neither gets it quite right! A bit of tweaking and adjusting is necessary to conform with the level of precision that may or may not be required (by a dissertation gatekeeper for example!). I find Endnote to be much easier to work with in adjusting individual reference types in each style.

Zotero has full support for titles and all data in pretty much any language– I use it for four languages and three scripts on a regular basis. There’s a lot of very interesting work going on to support the language-specific name formatting and so forth in the citation styles, so Zotero probably has the most advanced support in that area. The other incredibly revolutionary development is the multilingual project (http://www.zotero.org/blog/new-release-multilingual-zotero-with-duplicates-detection/), spearheaded by Frank Bennett at Nagoya University in Japan, which offers the possibility of maintaining metadata on items and authors in several languages or scripts (including transliterations) at once. The full project description is at http://gsl-nagoya-u.net/http/pub/zotero-multilingual-overview.html .

I’m not too familiar with EndNote, but Zotero supports Unicode (see also http://www.zotero.org/support/supported_languages ), so it can handle pretty much anything.

Also, Zotero/CSL has extensive support for automatic localization of citations and bibliographies, including localization of terms (e.g. quotation marks), date formats and grammar options ( http://citationstyles.org/downloads/specification.html#locale ).

Finally, Frank Bennett, a Zotero user, has created “Multilingual Zotero”, which allows transliterations and translations of bibliographic data to be stored and cited. With a bit of luck, these features will find their way into mainstream Zotero in the near future. See http://www.zotero.org/support/supported_languages#multilingual_zotero

Thanks, that helps. I’m not sure what I can say about the PDF importing, other than to reiterate that it does rely on the DOI. Usually I’m seeing much better results than what you got, but that very well may have to do with the discipline.

Regarding capture, it’s always a work in progress. That link I shared to the forum for styles and filters would also apply for capture issues.

Really good and balanced round up of the two applications.

I have been using zotero since I discovered it a few years ago. It impressed me so much that I never picked up endnote again, despite having only just bought a license for it. The main thing that drew me to it was how much easier it was to collect sources online. To me, this is the most time consuming part of the ref management process, so second shaved off each new source adds up to a lot of time. Also, the easier the process, the more likely you are to keep your library up to date. It sounds like endnote has improved since I last used it, but if it’s not surpassed zotero on this criteria, I’m not ready to give it another try!

I think it’s worth mentioning that neither of the tools is exactly user friendly for making changes to citation formats. But you can do it in each, and once you learn how, it’s not that hard.

There’s a lot to like about Zotero, and I share the widely felt affection for its openness; but customizability can be the deciding factor in some contexts where record exchange isn’t needed. Custom reference types (not just citation formats/styles) are crucial for certain use cases. When I last considered migrating a personal research database of 13,000+ hand-entered records out of EndNote into Zotero, lack of custom reference types in the latter sadly killed the idea, so I remain an EndNote user. This may have changed, but at the time Zotero development seemed resolutely guided by a principle that all references must be potentially shareable as is. That’s fine for a large subset of prospective use cases, but the constraints it imposes on customization don’t fit well with databases representing a wider range of unusual media (in my case, mostly ephemera ranging from stereo views to postcards to phonograph cylinders to movie posters to a dozen others), each type of which has a distinct set of physical and intellectual attributes best represented by dedicated data elements/fields. I prefer Zotero in concept, but EndNote (despite its frustrations) lets me do what I need to do. YMMV!

Thanks for speaking more clearly to the need for customization than I was able to in the post.

For some of our undergraduate students with major senior projects, a citation manager can ease a lot of stress and help them keep organized. If they learn to use the tool earlier on, they can bring discipline and organization to their research over time, similar to the idea of building a portfolio of their written work. Depends on the major(s) and the individual proclivities of the students.

If you’re looking for solid research PDF management software, check out Qiqqa (http://www.qiqqa.com). It’s Windows only right now, but offers very similar features to what’s discussed here, including syncing, as well as some unique features not found elsewhere.

If you work with a lot of PDFs, you’ll love it. It’s OCR and search is particularly strong.

It’s also free.

(Ok yes, I am a developer on it, but take a look – you might find it to be just what you’re looking for )

Thanks for mentioning Qippa, another new one to me. I’ll have to scare up some access to a Windows box to give it a try.

That’s great Brian – just give me a shout if you have any queries at all. Its got an interesting roadmap ahead of it, and we love shaping it with feedback from those that use this kind of software all day long.

An issue of scale is certainly important. When teaching EndNote I’ve often commented to people that one’s libraries can contain thousands of citations, but that I personally can’t imagine mine ever getting that way. That is of course due to my area of study, and others have much larger resource sets. I don’t have any experience using Zotero with this number. I wonder if I can draw any Zoterons into answering this via Twitter…

Zotero does suffer more from super large libraries, though it has been improving steadily. I know of people working with libraries of about 20k items without issues, but I would doubt that 50k+ would work well – the effect, of course, would be slow-down, likely at some point unbearably so.

Nice post Brian, neat to see how much of a conversation this has kicked off. When you get down to it I think their is a lot of this that has to do with the way the tools we use become embedded in our actual research processes. That is, how the stages of our work become deeply interwoven into the tools that we use. Several of the things you highlight as features strike me as ways that using Endnote has actually played an important role in structuring the way you think about and engage in research. Frankly, I think any good explanation of how each of us use tools is going to do this.

When I was working on my undergraduate thesis my adviser insisted that I should learn to use Endnote. So he showed me how he used it. He would use Z39.50 to pull records for books and articles and organize them in his library. He would then key in how he actually wanted to cite them in the extra field. When it came time to cite something he would look it up and copy over the citation. He was a super stickler about these kind of things and there was just simply no way that an Endnote style could be written to get the citations to work in the slight variant of the Chicago Manual of Style which he used.

It was impossible for me to get into using Endnote. Frankly, the interface never really made sense to me. The idea of getting information via Z39.50 was very strange and the notion of keeping all of these individual Endnote libraries was beyond me. When I tried to graft it onto how I was trying to do my research it just wouldn’t take.

When I started working on Zotero the whole iTunes-like thing ended up being the part of the system that completely made sense to me. Now six months out from working on the project I can say that I am still using Zotero whenever I am doing significant writing. In my case, I tend to create folders for each project I am taking on and then keep Zotero in Firefox running in an adjacent window at which point I then use the drag and drop to cite feature to add in-text citations. I then manage the references in a given paper inside Zotero’s folder structure, so I just drag out the entirety of a folder to create the bibliography. In my case, I tend to switch editing my writing between google docs, word, and open office and I am just uninterested in dealing with the kind of field code trickiness that comes from dealing with any of the add-ons for word processors. With the windows right next to eachother there is no trade off time. I just grab drag and drop or use the keyboard short cut to get the intext citation.

At this point, the 3300 items in my Zotero library are really so deeply interwoven into my own ways of thinking and doing writing and research that it is hard for me to imagine ever changing to another tool. I think it is fair to say the many of the design decisions embodied in Zotero have become a part of how I engage in research and writing.

I think Openness isn’t on users minds because reviewers don’t bring it to their attention. But apart from the philosophy of it, there are some very practical consequences, such as data migration. Moving from EndNote has been a pain for me but moving between Zotero and Mendeley and BibTex is very easy. Moreover, the EndNote lawsuit is never from my mind when I discourage people from using it. I do not want to support a company that will put its business before my rights.

Another thing to note is the appalling practice of EndNote to provide an upgrade every year at pretty much full price that is so incremental that it often just fixes bugs or adds features that should have always been there. Also, I haven’t used EndNote since version X1 but I always found the interface and search functionality abysmal.

Awesome. I did not even think there was a market for this kind of thing, much less someone eager to write a script for it. Will certainly check it out.

I like Zotero but resently i use websendsms.com i can write my notes and share them with my friends, also I send sms in my country and other countries.