Choosing reference management software

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 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.

I think if you are posting this to an Endnote forum, you will get “EndNote” as the answer.  I do think the current software provider intends to continue development based on my contact with them.  If you post this same to Mendeley or Zotero’s equivalent forums, you will get a different answer, I am sure!  

I don’t see any of them going away anytime soon.  I like EndNote and have used it for >20 yrs.  I don’t find it that slow, I turn off some of the bells and whistles though.  I can always turn them on at the end, if I want URL links to bibliography, for example, but find it slows down large document updates.  I have overcome the record number issues.   

Having said all that.  I suspect that over time, some new product taking advantage of new hardware may appear, requiring software conversion.  A good new provider (or new product from a preexisting provider) will also include the tools to expedite the transfer though!  Backward compatibility is wonderful, but eventually Developers may need to just start over.  (I will probably retire before then though!)

I’ve also used Endnote for nearly 15 years so I’m not sure I’m going to give an impartial response. But I have tried to switch from Endnote a couple of times and keep coming back to it. It’s not the best for PDF management and reading and its definitely slow to get new features. But I find Endnote’s CWYW rock solid for my needs. For me Zotero was the only real alternative but I found it more difficult to insert and edit citations. I don’t find it slow but I only have about 800 references in my current library. I guess I’m just too invested in Endnote to switch these days.

The only other thing I would say is that Readcube has purchased the app Papers which was well regarded. They are planning to release a brand new reference manager later in the year that combines the 2 apps. So if you can wait it might be worth seeing what they deliver before you make up your mind.

I’m also a long-time user of Endnote and concur with what the others have said. On a different note, Endnote’s speed in inserting and updating citations in the bibliography is affected not only by your computer’s OS but the speed of the processors and amount of RAM. My old 64-bit computer which had an Intel i7 processor with 1.60-2.80 GHz and 8 GB memory carried on for four academic book publications.

Besides checking your hardware, you should also check with your editor about production requirements for submitting your book. Often production has different criteria which will impact the workflow and formatting of the book. So check on what the requirement is for treating footnotes, bibliography, TOC, tables and figures (if applicable). For example, will the book chapters be submitted as separate files or as an aggregate single file? Will the bibliography, TOC, tables and figures need to be formatted as individual files? What file format should figures be submitted as (e.g. bitmap, PNG, etc.). And, since you’re using footnotes, how does production want them to be formatted (e.g., at the bottom of the page or gathered together on a separate page)?

Another thing is if you anticipate working with a colleague at some point you may wish to check what reference software he/she is using as you will need to be able to integrate that material into yours.

Knowing as much as you can about the submission format before starting will prevent a lot of headaches at the backend when you need to meet the book’s deadline.

When I was trying to reach a conclusion, I evaluated Zoter, Mendeley, and Endnote. 

Many of my initial impressions were the same as yours, and between seeing how many other faculty were using Endnote, I decided to pay the high price tag and use it. I’ve come to regret that decision. 

I now frequent the forums hoping to address a major flaw with Endnote: the find full text feature is completely broken for me. I’ve been troubleshooting the problem for days with the campus librarians and nobody can give an explanation other than perhaps the APIs have changed. But this is a total guess because Endnote doesn’t provide any kind of feedback on what’s happening behind the scenes: you push a button and pray that it works. 

For me, not providing the user with feedback - especially when there is an error - is a major flaw in software usability and design. There are other little quirks about the software as well. I’ve come to the conclusion that Endnote is not being invested in by the owner and it’s stagnant, I suspect it’s the result of capturing enough of the market. 

The find full text feature was a major deciding factor to use the software, so without it, the playing field compared to Zotero and Mendeley changes considerably.

In regards to Zotero, when I was in graduate school, many of my cohorts used it because it was free. There were a lot of workshops hosted at the campus libraries about how to be better with it, and there is extensive documentation on the library websites. 

During that time, Mendeley was also popular – I think mostly for the group sharing ability which I don’t think Zotero supported at the time – but I personally found Mendeley clunky to use. 

As of this week, due to the problems with Endnote, I’ve been reevaluating my decisions and giving another look at Zotero and Mendeley. 

I have to say that I am really impressed with Mendeley, and here’s a short list why:

  • It has fantastic citation searching. Attach a random PDF and it will do a full text search against it’s database and fill out all of the article metadata. It really leaves Endnote in the dust on this. 

  • The UI for Mendeley is very clean and polished. In comparison, Endnote looks like it was ported from Windows 95: it’s ugly and out of date. I prefer the layout of Mendeley showing the list of articles, metadata, and the article PDF so I can mark up notes. I understand if someone has been using Endnote for 10+ years and is adverse to learning a new layout, but I’m not invested in that way. 

  • The duplicate merging is superior on Mendeley compared to Endnote. For example, I have two duplicates on Endnote that it can’t reconcile. One doesn’t have the metadata but it has the PDF, the other has the PDF but not the metadata, and they both share the same article title. Endnote cannot detect this duplicate and it won’t allow me to merge them. OTOH, Mendeley easily detected the duplicate article and allowed me to merge them.

  • Finding “more like this” is another fantastic feature of Mendeley and junk in Endnote. Because Mendeley keeps a database of the articles, you can do a “more like this” search and find relevant articles that other people are using… which has a really nice feature and returns great results. The best I’ve found with Endnote is some junk catalog search, which for me only returned book titles and I couldn’t figure out how to tweak it to actually search journal articles.

  • Endnote x8 crashes constantly on my Mac. I keep everything updated on my computer and work in the technical fields. Endnote will just randomly crash if you ask it to do too much. Then whatever task you’ve had going at the time is dumped and you have to start over. It’s pretty obnoxious. There are lots of complaints about it in the forums, but the company doesn’t seemed bothered by it. Mendeley and Zotero haven’t crashed on me yet. 

My recommendation, after my own personal and anecdotal experiences, is with Mendeley. Endnote isn’t the only game in town anymore, but they haven’t gotten the memo.