Reference Management Software: Mendeley, Endnote, Zotero, Papers?

[Peter Shull]

Hi All,

I'm curious to know your experience and thoughts on reference management software. I have been using Mendeley for the last 2 years but have not tried any other systems. If you have a minute, please reply with:

1) Name of management software you are currently using (or software you are knowledgeable about)

2) Pros of that software

3) Cons of that software

Thanks,
Pete

[Pietro Garofalo]

Re: Reference Management Software: Mendeley, Endnote, Zotero, Papers?

This is an interesting topic, I am happy to answer.

1) The software I currently use is Zotero plugin for Firefox.

2) The main advantage is related to its plug in functionality and the "one click" working. There may be others like this now, but since the time in which Zotero started I did not stop working with it. As a consequence, more computers can share the same Zotero database within your user account. You can save local versions of the papers, easily copy the information to your clipboard.

3) The cons is probably related to its nature as plugin: not everybody was excited to hear that it was a plugin and moreover its microsoft word plugin also requires a separate installation for the integration with documents, so not completely easy going for some people

[Ed Schrank]

Re: Reference Management Software: Mendeley, Endnote, Zotero, Papers?

Zotero all the way. I have been using Zotero for many years. (note for Pietro: get the stand alone version, it is fantastic and frees you from the browser).
Pros: too many to list all, but here are a few:
As a faculty member, great for working with students. I can create and share folders with students. Collaboration is a breeze.
Search features. Again awesome. I can find any entry in seconds. No more digging through the file cabinet!
I can attach the pdf right to the entry. Again, no file cabinet issues.
The database is with me on every machine I sit down at as it syncs my database to the cloud and keeps everything up to date from home to work
Cons:
Have to double check entries, as depending on your source, errors can creep in (example: Journal title abbreviations, sometimes wrong, but easily fixed). Drives my students nuts.
Constant updates to keep current. This is good and bad. Errors keep getting fixed since it is open source, but if you don't keep up to date, you will find it stops working. The fix: get the latest update. Pretty automated, so not a big deal, but gets irritating.

[Brian Schulz]

Re: Reference Management Software: Mendeley, Endnote, Zotero, Papers?

Pete,

Good topic- I hope this thread helps lots of people out. Here's my input:

1) Zotero. Despite the availability of the standalone version I'm sticking with the FireFox plugin because it's easy to find and import references. I also always have FireFox open, so that's one less program to open.

2) Everyone seems to have covered this well, but here's two more pros: 1) It's free 2) You can install it yourself (the FireFox plugin at least) even in restrictive computing environments (admin access not needed). This seems like a small point, but it can be critical. A friend of mine once waited three months or so for someone from IT to install his copy of EndNote for him. He gave up waiting and we installed EndNote in less than 5 minutes and had him up and running.

3) My only con is that it is difficult to edit Zotero reference styles. I could easily create reference style for any specific journal using EndNote, but you've got to edit the CSL code to do this in Zotero. It's not too hard to find a similar style and edit it to fit your needs, but this is soon becoming a moot point as more and more styles are posted to the style repository (https://www.zotero.org/styles/) and on journal webpages.

If you want a thorough comparison of the capabilities and compatibilities of current reference management software, Wikipedia has a pretty good comparison article- http://en.wikipedia.org/wiki/Compari...ement_software

[Gary Christopher]

Re: Reference Management Software: Mendeley, Endnote, Zotero, Papers?

I use EndNote exclusively. I started using it when I was working on my MS thesis in 2000 and have stayed with it, through my doctoral dissertation and several presentations, not to mention a forced transition from WordPerfect to Word. The only thing I don't like about it is that it doesn't fully and accurately format in APA style - I have to make some manual changes. If I have to use any other citation style, and EndNote doesn't do it perfectly, I'm up a tree, because I'm pretty much all about APA (even if they can't make up their minds what they want). I'm also experiencing difficulties with the Cite-While-You-Write function of EndNote X5 and Word 2010. Haven't figured that one out yet - one day...

Gary Christopher
Associate Professor
William Penn University
Oskaloosa, Iowa
christopherg@wmpenn.edu

[Samuel Hamner]

Re: Reference Management Software: Mendeley, Endnote, Zotero, Papers?

Hi Pete,

I've used Endnote throughout grad school, and now I am currently using Mendeley. Endnote is expensive if you don't have a license (and it is impossible to edit documents later if you don't have the license anymore). I also found Endnote to be clunky, although I did like how it integrated well with MS Word (though that may not be as important if you use Latex), and you could easily search PubMed within Endnote.

Now I am using Mendeley, which is free. It has a nice stand alone application for Windows (not sure about the Mac side, although the website says it works with Mac and Bibtex). I like how you can build a library which is connected to the PDF files stored on your computer. If you have a large collection of PDFs, it can take a bit of work to get everything organized at first. Once its setup, you can easily search your library and open the reference within the app. It's also great for collaborating with groups; you can share references, articles and libraries. Mendeley also integrates well with MS Word, and it was easy for me to change the references formatting for different journals. Here's Mendeley's comparison: http://www.mendeley.com/compare-mendeley/

[Elizabeth Russell Esposito]

Re: Reference Management Software: Mendeley, Endnote, Zotero, Papers?

Hi Pete,

Thanks for starting this topic.

I have used EndNote and RefWorks. The only issue I had with RefWorks at the time I was using it was that it needed an internet connection, which was not always available to me. I now use EndNote and have not tried it without internet. Both have a large number of reference styles and a simple user interface for using new styles. EndNote integrates well with Microsoft Word; the only bugs I have found are that it will not work correctly when Track Changes is on. Multiple EndNote libraries can be stored and shared within your lab but the issue previously mentioned of double entries does create some problems. The search capabilities have been great and I have found it a nice way to catalog, group and store references.

--
Elizabeth Russell, PhD

[alaam2005]

Re: Reference Management Software: Mendeley, Endnote, Zotero, Papers?

Hi all,
Thanks for sharing your ideas, and great to know about these tools especially Zotero and endnote. Just lately I needed a software to do indexing, so I'm using the windows browser for searching in the papers and some electronic books. This is done by installing iFilter from adobe and need some tweeks on windows to change how windows look inside the PDF documents and to rebuilt indexing.
Two days ago, a classmate told me about a software called Readcube which is free and it's great for researchers because it can index all your papers and books (if they're readable) and recommend you papers. Also, it connect directly to your university proxy so you download papers directly. It connect to PubMed, Google scholar and Microsoft academic. It has a recent design too. For Mac and PC.

[Peter Shull]

Hi everyone,

I'm thinking of changing reference management software and am curious to know your experience and thoughts (asked this question 8 years ago, but there is likely new and relevant info now). If you have a minute, please reply with:

1) Name of reference management software you are currently using (or software you are knowledgeable about)

2) Pros of that software

3) Cons of that software

Thanks,
Pete

[Ajit Chaudhari]

Hi Pete,

1) I've used all of the big ones over the years for articles and grant proposals over the years (RefWorks, EndNote, Mendeley, Zotero), and I'm currently using Zotero.
2) Pros are the ones that everyone mentioned, plus a big one for me is that Group Libraries work really well for collaborative docs. Like a team writing a grant proposal together. This was extremely painful in EndNote (we figured out stable workarounds but they were painful, happy to explain our workarounds to anyone who needs that info). Importing refs into Zotero using the Chrome Extension is really easy.
3) A few big cons that we can manage:

• if you've got a big doc with lots of refs it gets really slow, so you have to turn off Auto-Refresh. Current R01 proposal has ~230 refs and is 14 pages. It takes several minutes to update all the numbered citations and the reference list.
• if you import references from something other than Pubmed, you don't get the Pubmed ID's and Pubmed Central ID's, which NIH requires in the reference list. So we have to be very careful to always import from Pubmed. Or if we didn't originally, import again and merge records.
• If you have more than one library in Zotero (which you will if you have a personal library plus a Group Library) you have to be really careful to always pick your citations from the correct, same library. Otherwise you will end up with duplicate refs in your list and mal-numbered citations. I really wish Zotero allowed you to choose which library you want to use for a document, and then it only shows you refs in that library.

Thanks,
Ajit

[Peter Shull]

Hi Ajit!

Thanks for these helpful thoughts. It sounds like Zotero is a promising option to try moving forward.

Pete

[Justin Wager]

Hi Pete,

Good idea reviving this from years ago. I'm using Zotero and have since 2009. The pros and cons from early posts here have not changed. In fact, I was reading through this without even realizing it was 8 years old. Ajit raises some good points. Some other thoughts:

Pros:

• Papership, the mobile app, works surprisingly well with Zotero for accessing papers on the go.
• Zotfile (the plugin) adds some other nice functionality like custom file renaming conventions and adding the most recent file from the Downloads folder

Cons:

• Once you get to a large enough library, you will run out of free storage space on Zotero's servers and either need to 1) use a WebDAV server or 2) pay for additional storage. I tried using Box cloud storage for awhile but it didn't play nice with Zotero. Once you are out of storage, you can still store references, but the full-texts will not save to the server and therefore won't be accessible on other devices
• Doesn't work well with track changes in Word, but I suspect few ref managers will. Just need to turn off, edit citation, turn back on

[Peter Shull]

Hi Justin,

Thanks for your thoughts! Sounds like another vote for Zotero.

Best,
Pete