Thursday, January 09, 2014

Citation Manager Death Match

A useful discussion has started around which citation managers a bunny might use.  Two important free citation managers are Mendeley and Zotero.  There is video from Portland State

Eli is invested in EndNote, which has the huge disadvantage that costs $$.  Many, Martin Vermeer, for example is invested into BibTeX/LaTeX which although free, has a significant learning curve, so it looks like these two are the best free choices.  Several libraries have nice tables about picking a citation manager.  Eli really likes the one from the University of Washington

If you need to ...Use: Why:
… work from multiple computers or locations. Zotero
Zotero saves your citation library to your local computer, but syncs with multiple computers so you can work from home, work, or school.
RefWorks is web-based which means that you can access it from anywhere you have an Internet connection.
… work without an Internet connection. Zotero
EndNote desktop
Zotero, Mendeley desktop and EndNote store your citation libraries locally on your computer.
… archive web pages and import citations from sites such as Amazon and Flickr. Zotero
Zotero and Mendeley allow you to easily save snapshots of web pages and annotate them within your citation library. It is a great tool for scraping citation information from web-based publications and some commercial and social networking sites.
… work on a group project or share my citations with others. Zotero
Both RefWorks and Zotero allow you to share your citations through shared folders. With Zotero, you can give individuals or groups permissions to add and edit the citations in the shared folder. With RefWorks, you can also set up a shared group account for collaborating on group projects. 
… work on a mobile device Mendeley
Mendeley offers a mobile app for iPhones and iPads; Zotero has several 3rd-party mobile apps available.

RefWorks and EndnoteBasic offer mobile-optimized sites that work with any web-connected phone or PDA.

and here is the comparison of properties (bunnies may have to hit CNTL/Apple - to shrink this to fit the screen or just go to the University of Washington Library site)

EndNote Desktop Mendeley RefWorks Zotero
Web based? No, this is a desktop product. Can transfer library to EndNote Web Yes. Also available as Mendeley Desktop, which can sync with online account. Yes Yes, lives in browser (Firefox plugin, or Internet Explorer, Chrome and Safari through Zotero Standalone). Can sync with online account but web library not editable
Must be online? No No Yes No
Mobile capability Native app for iPad, currently costs $$. Native app for iPhone and iPad, or check yourMendeley library on your mobile device's web browser. No app, but mobile-optimized site 3rd-party apps available (, or check your Zotero collection on your mobile device's web browser.
Cost $$. Available for purchase at the University Bookstore at a discounted rate (UW students, faculty, and staff only). Free Free to UW users (Libraries pays the subscription costs) Free
Word-processor compatibility MS Office, Open Office, iWork Pages MS Word, Open Office, LaTeX MS Word with Write-N-Cite, any other word processing program using One Line/Cite View option MS Word, Open Office, Google Docs
Import from databases Direct export from specific databases Yes, with Mendeley Import browser plugin. Direct export from specific databases Yes
Import citation info from web pages No Yes, with Mendeley Import browser plugin. Also archives the page and allows annotations. Yes, with RefGrab-It plugin Yes. Also archives the page and allows annotations
Storage capacity Unlimited local storage Unlimited local storage and data syncing; 1 GB free Mendeley web space (larger plans available for purchase) Default limit is 100MB per user, can be increased to 5GB; limit of 20MB per attachment Unlimited local storage and data syncing; 100MB free Zotero web space (larger plans available for purchase)
Attach associated files (PDFs, etc.) Yes Yes, and can annotate Yes (limited) Yes, with option to attach automatically
Search full text of PDFs Yes Yes No Yes
Create group  or shared libraries No Yes. Costs for private groups (1 3-member private group free). Yes, but other users cannot add more references Yes
Create bibliography w/ different styles Yes Yes Yes Yes
Other features Insert figures and charts using word processor integration Sync library w/multiple computers
Use tags to organize/search
Access for web-connected mobile devices Sync library w/multiple computers
Use tags to organize/search


carrot eater said...

I'm also invested in Endnote, but have eyed Mendeley wondering if the grass is greener. Is it?

I've already paid the money to endnote, so the cost doesn't bother me. upgrading from time to time isn't that expensive, though I suppose any cost may be too much if the same thing is available for free elsewhere.

sorry if this appears twice

Anonymous said...

My daughter (doing PhD) pointed me to Mendeley ... the cross platform sync (including native Linux) with offline capability and web page import has transformed my paper writing. And it's free!

Jonathan Gilligan said...

I've used Mendeley, Zotero, and Endnote extensively.

Zotero is, hands down, the easiest one to use for my work. Your mileage may vary, of course. Mendeley is very good for easily importing journal articles, but it is very cumbersome if you're working with other kinds of documents (white papers, World Bank reports, court decisions, newspaper and magazine articles, etc.) whereas for almost everything I use that's available online, Zotero makes it easy to import an accurate bibliographic record with one click.

I have also found that with a bibliograpic database of many tens of thousands of documents, Mendeley's desktop program becomes very unreliable, so I have given up on that and mostly use the web interface.

On the plus side, Mendeley is well suited to collaborative databases. I belong to two large multidisciplinary research projects that use Mendeley to manage large shared biblio databases. However, big shared databases is a paid option. We're paying about $1000 a year for this service.

Since I use all three (although I rarely use Endnote anymore; only when I'm co-authoring something with someone who uses Endnote), I move stuff around between them all the time, and it's pretty straightforward to do so using the Export/Import RIS format, so people who want to see what works best for them can try them all out and transfer their reference collection between them very easily. Mendeley actually has an option to keep its own database synchronized with a Zotero database, but that has never worked reliably for me.


Beware giving aid and comfort to journals whose editors and editorial minions are loathe to do any editing.

Daniel Wirt said...

Amen to what ICBM Seitz said. Like those several journals in which the deniers and merchants of doubt publish (no need to further identify), when they need to obfuscate about the greenhouse effect and thermodynamics and the real world, for example.

toto said...

Zotero is all kinds of awesome.

HEre's how it works:

1- Download PDF paper that you like, drag and drop it into your Zotero window.
2- Right click, "retrieve metadata from PDF".
3- A full entry is automatically created in your Zotero bibliography, with author, title, journal, volume, et. You may also add notes to the entry, which is massively useful - whenever I import a paper I always add a note summarize the gist and main points.
4- BEst part: your entire library is automatically synced with the Zotero servers - including the PDF's of the papers you downloaded! So to transfer your entire library to any other computer, just install Zotero on it, log in and sync. Bam, your full library AND PDFs are automatically transferred.

I still find it amazing that such a useful resource is available for free.