Choosing reference management software: Endnote, Zotero, Mendeley?

skaertus

I am starting a book with academic purposes, and I intend to choose a reference manager to handle the citations. The citations are in footnotes (which is kind of tricky for a reference management software) and very specific (the most common citation styles will not cut it).

This is expected to be some sort of long term engagement, since the book may have to be updated from time to time. So, I need a reference manager that keeps being updated over time, and that may fulfill my needs over the years.

As the book is expected to have more than 1,000 citations, the software must be fast, respond fast, and not be buggy.

Also, I plan to use Windows (or OS X) and Microsoft Word. Sometimes I may use the iPad or even the iPhone to type some text (I know I probably will not be able to insert citations in these devices, but at least I do not want to lose the citations I have already inserted). I am definitely not using Linux, and probably not using LibreOffice.org or any other word processor for the task.

My main contenders so far are Endnote, Zotero and Mendeley. I am not considering other reference managers because I think these three are the most popular. My concern here is that I do not want to start using a reference manager that may be discontinued within the next 5 years because it had poor sales or because the company behind it is facing financial difficulties.

I have a copy of Endnote X7 and I may well upgrade it to Endnote X8 if it is worth it. Endnote seems to be solid, but development seems to be slow. I did not see much progress in Endnote in the last few years. I used Endnote for my PhD thesis and it was very slow in updating using the cite-while-you-write feature. In addition, some references got messed up when I accidentally replaced the library for an older version (it relies on the number of the reference instead of the name of author). Endnote was also poor to get references from Google Scholar. On the plus side, it was quite easy to customize styles in Endnote. Now Endnote is not under Thomson Reuters anymore, but under a company called Clarivate Analytics (some sort of spin-off). I do not know what this will represent for future development of Endnote, though.

I have also used Zotero, and it seems to be a good alternative, but I did not use it extensively. The Word plug-in seems very nice. It even insert citations directly in footnotes, so I do not have to insert the footnote and then the citation (which is the case with Endnote and Mendeley). However, I do not know about its speed and whether it is possible to convert the formatted citations to fields to make it faster if necessary. Development seems to be not so fast either (although not so sluggish as Endnote). One of my concerns is that it is run by a university and not a private company. Will it have funds to compete with the big guys in the future? Or will it be swallowed?

I have also used Mendeley. Mendeley started as being a poor alternative, but I am impressed at its development. The interface seems very good, and even better than the contenders. The Word plug-in seems very nice at this point, and it was even able to convert Zotero references into Mendeley references. The Mendeley website is also more visited than Zotero and Endnote websites, according to Alexa (these are #2 and #3 respectively). Mendeley was purchased by Elsevier, and it may be good having a rich parent to support it. But is it fast and flexible?

Now, which one should I go with? Or should I choose another one? I want a reference manager that is good, fast and straightforward, and that is updated at a fast pace and does not fall behind the others or get discontinued. And, if possible, that allows me to convert the citations to another format so I can use it with another reference manager if I need it to.

Thanks a lot.

adamsmith

I mean -- obviously people here are not going to be impartial.
Zotero being run by a university/a non profit is an advantage and should be the opposite of a cause for concern. They just have to break even and don't have to monetize you (or your data) -- and my understanding is that the finances are quite solid. My (personal and anecdotal) sense is that Mendeley is going to enter a rough phase. Since being bought by Elsevier, they have lost a lot of talent, including most (all?) of the senior developers as well as both founders and have just outsourced their customer support to the Philipines. It's also the most awkward working with footnotes.
Zotero is also typically relatively fast with development and has just slowed down a good bit for the last ~2 years as developers re-wrote large parts of the software for the upcoming version 5. The expectation is certainly that things will speed up again once 5.0 is released

Here are some of the areas where you'll run into problems with Zotero:
1) I do think you will lose your citations (or rather their connection to Zotero) when using any currently available product for writing on iOS, so that might be a problem.
With Papership, there is a pretty nice iOS app, though and there's significant work underway on the website.

2) Zotero's Word integration is currently slow in large documents and there is no way to convert Zotero citations into somethign static to speed this up. I would generally recommend, authoring book manuscripts in chapter anyway, though (I think Word will struggle with 1000s of footnotes anyway), so that might be less of an issue. It's also something that Zotero is working on, though I won't promise an ETA.

I don't know Endnote quite as well, but have always found it rather clunky compared to Zotero.

adomasven

2) Zotero's Word integration is currently slow in large documents and there is no way to convert Zotero citations into somethign static to speed this up. I would generally recommend, authoring book manuscripts in chapter anyway, though (I think Word will struggle with 1000s of footnotes anyway), so that might be less of an issue. It's also something that Zotero is working on, though I won't promise an ETA.

The ETA for this is some few months, hopefully. If nothing critical comes up I'll begin working on this shortly.

bwiernik

Regarding iOS, I believe you can safely use the Word app (fields remain intact), but obviously, you can't use any Zotero functionality.

I switched to Zotero from Endnote several years ago. My experience has been that Zotero handles large libraries better than Endnote (though both can get slowed down with very large, 100,000+ item libraries). Zotero's sharing features are also far superior (this was the major reason I switched), and the Word plugin is easier to use in my opinion. Also, by using the open CSL citation style language project, Zotero has a wider range of styles immediately available for formatting. Most importantly, it is dramatically easier to import items into Zotero than Endnote (or, frankly, any other citation manager).

Gurdas_Sandhu

(@adamsmith If OP starts with Zotero, and later decided to switch to Mendeley, will Mendeley pull the Zotero references and maintain the connections in the Word file?)

If yes, then starting with Zotero is your safest bet. You will probably like Zotero and never need to switch, but if you did need to switch, then Mendeley is an easy option.

Since this is for a book, note that Zotero cannot:
1. Have multiple bibliographies in one document - this is solved if you are writing each chapter separately, which is recommended in any case.
2. Create a single bibliography with categories for type of reference such as books, journals or levels by chapter.

adamsmith

@bwiernik

My experience has been that Zotero handles very large libraries better than Zotero.

Clearly a typo, but the direction matters here and not clear to me -- who handles very large libraries better?

adamsmith

@gurdas -- I don't believe Mendeley is able to maintain the connection to a Zotero-created Word file, no. It does sync the references, though.

bwiernik

@adamsmith Thanks. Fixed that. Zotero handles large libraries smoother than Endnote

Gurdas_Sandhu

@bwiernik third time's a charm .. :)

bwiernik

I swear my phone must be autocorrecting "Endnote" to "Zotero"

mark

I've used Zotero to write a PhD with a 500+ item bibliography. Beyond 200+ citations in a single document, any Word processor will start to slow down, so writing by chapter and merging later is generally a good idea. Zotero coped perfectly well. I love its Word interface and how easy it is to build a library (I've switched to Zotero from EndNote, and also tried Mendeley, but Zotero is the one that best caters to my needs). Zotero handles citations in footnotes well.

skaertus

I am using Zotero and I am starting to run on problems due to the number of citations. Lots of citations slow down the document and there is absolutely no way I can turn them into code fields like I did in Endnote. Although the timeframe for this functionality to be added was estimated to be a few months, I see no signs of it yet.

Now I regret not using Endnote from the beginning. I am thinking of switching to Endnote. I know I will have a lot of work to do, but it may be worth it.

Is there another solution? One that does not involve breaking the work into smaller chapters, as I feel this would not be really productive in my case?

adamsmith

Although the timeframe for this functionality to be added was estimated to be a few months, I see no signs of it yet.

Not sure what type of signs you expect -- a feature is either present or not and I'd say we're definitely still within "a few" months -- but the code is essentially in place:
https://github.com/zotero/zotero/pull/1242

adomasven

Is there another solution? One that does not involve breaking the work into smaller chapters, as I feel this would not be really productive in my case?

Changing to an author-date format (like APA) might help as those are slightly less stressful on the word and citation processor. You can switch back to your intended citation style before submission.

skaertus

Thanks, adamsmith, I had not yet seen this one. Although this is not exactly the "temporary citations" of Endnote, this seems to solve my problem, as it speeds up the citation process. It seems to be a major update, at least for me. I would only like to know when it is expected to make it to the final version. The last updates seem to be in June.

skaertus

Thanks adomasven, I will try that. My field of study still requires all citations to be made in footnotes (and those citation styles are really hard to configure; although the one I use is pretty much good, it is actually still not perfect).

bwiernik

The recommendation is to write your paper using an author date style, then change the Document Preferences to a footnote style before submission. This will save some time during the writing process because Author date styles are somewhat faster.

skaertus

Thanks, bwiernik.

One thing I noticed is that when I insert a footnote citation, Zotero inserts the footnote and the citation automatically. I could not find this kind of functionality with other reference managers (although I could be wrong). With both Endnote and Mendeley, I have to first insert the footnote and then the citation; it is a two-step process.

Will I have any issues if I use the in-text author-date citations and then convert them to footnotes?

LiborA

Will I have any issues if I use the in-text author-date citations and then convert them to footnotes?

There are usually no problems.

bwiernik

Zotero is designed to easily switch between the two formats. You should be fine. I would recommend Annual Reviews Author Date as a Style to use. When you switch to footnotes, it might take a few minutes with a lot of references, but just let it run until completion.

skaertus

I've been waiting with patience for the feature to be implemented. And nothing yet. Now that I have over 500 footnotes, it is becoming impossible for Zotero to insert a citation without some serious slowdowns. Very frustrating indeed.

I am thinking of switching to Endnote, as I cannot wait indefinitely for the feature to be implemented in Zotero. It will probably take me a long time, since I will have to insert every citation again, and there are hundreds of them. I did not think I would ever say this, but I regret now that I chose to do this in Zotero instead of Endnote.

Any recommendation?

noksagt

Any recommendation?

You were advised to switch from a footnote style to an endnote author-date stye to improve performance while you're still editing/authoring the document. Given that you're still referring to the number of footnotes, I'm not sure if you've adopted the recommendations you've received already?

LiborA

Last version of Zotero has feature for disabling of update document. Did you use it?

bwiernik

That delayed updates feature is currently in the beta release of Zotero.

In my experience, Endnote also slows down dramatically with that many references, and it is much less user friendly in most other areas of the program.

skaertus

LiborA, I could not find this feature. Where is it?

skaertus

bwiernik, Endnote also slows down a lot. This is not because of Endnote or Zotero. It's because all the references are updated all at once.

But Endnote has a feature which allows the use of unformatted citations (instead of Cite-While-You-Write). I was not aware what was the purpose of this. But then it became very useful, because it allows the insertion of the codes instead of the citation itself. You can convert them in formatted citations, and vice-versa, anytime. It is very handy and makes inserting citations very fast.

Unfortunately, Zotero does not provide this kind of funcionality, which I found really, really useful.

I can understand the feature is in the beta release. And of course these features may take some time to develop. It is not the developer's fault. However, I have to use them right now. I cannot wait until all the issues are sorted out, which may take a week or six months.

And Endnote, with all its downsides, has this very useful feature, which, to my knowledge, is not replicated in Zotero.

bwiernik

As has been said a few times above, this feature has been added to Zotero and is currently available in the beta release for testing https://www.zotero.org/support/dev_builds#zotero_50_beta

skaertus

bwiernik, thanks. But is this only in the beta version?

DWL-SDCA

@skaertus The slowness issue has mostly been addressed in the _very stable_ beta version of Zotero. (I've been using beta versions for a year or more and continue to be without major problems related to newness.) I'll eventually move from the beta path to the standard release but I've been satisfied with using the beta releases in our live production environment. It is always a good idea to keep saving incremental backup versions of your documents.

bwiernik

The delay updates feature is part of a major overhaul to the word processor integration code to increase the speed. It's currently released in the beta version for testing by users. Given the size of the changes to the word processor code, it's likely to be in beta for a few weeks before being released to the main version of Zotero (a bit longer than normal).