Saturday, February 27, 2010

Mendeley: My New Favorite Reference Manager

This semester, I'm writing my first grant. My graduate program includes a course called Hypothesis Design and Scientific Writing, in which students work with faculty and peers to prepare an application for an NIH National Research Service Award (NRSA). My grant is coming along, but I still have lots of work to do. My goal is to submit the final product to the NIH sometime this summer. If I'm lucky, they'll decide to fund my proposal, and I'll receive additional support for my dissertation research. (Emory Neuroscience students have about a 60% success rate at getting their NRSAs funded, so I have high hopes!)

This grant has required a lot of background reading. I spend my free time in the lab scouring PubMed for relevant articles that will support my hypothesis. I've therefore been required to come up with a system for keeping track of all these papers. After trying several options, I've found Mendeley to be the most useful.

Mendeley shares features with other research bibliography tools like Papers, Zotero, and Quosa, but in general I find it to be more suited to my needs. The Mendeley Desktop program works "like iTunes for research papers." It keeps track of citation information and allows users to sort their references by category. Mendeley stands out, however, by linking the desktop client to web-based services that make my life much easier.

The Mendeley web importer is absolutely dreamy. If I'm looking at an article on Pubmed or on a journal website, I can use the "Import to Mendeley" bookmarklet in Firefox or Safari to automatically add the citation to my Mendeley database. Doing this prompts the user to enter tags and notes about the article right in the browser, which will be carried over to the desktop client as well. This is similar to Zotero's browser-centric approach to reference management, but I prefer Mendeley's approach. The Mendeley bookmarklet is unobtrusive -- it opens a small pop-up window or a new tab every time I add a reference. When I tried Zotero, I didn't like the way that it generated weird browser panes at the bottom of whatever page I was reading when I added a new reference. Adding tags to a Mendeley citation takes just a few seconds and doesn't interrupt my browsing experience -- I just close the tab/pop-up when I'm done. When I want to pore through my references in more detail, I use Mendeley Desktop, which as a dedicated application feels 'separate' from my browser, and makes it easier for me to focus on the articles. I find the interplay between Mendeley Desktop and the web importer to be just right -- this comes in contrast to Quosa, for example, which tries to integrate web-based search into the reference manager, but feels clunky and awkward. I already know how to use PubMed in my browser; I don't want my citation manager to make me learn a different way to search (even though Quosa's automated searches are pretty nifty).

Mendeley also automatically backs up all of my citation information to the cloud. I can log into my Mendeley account from any computer, and if that computer has Mendeley Desktop installed, I can sync the desktop client to my web account by entering my email address and password. The Mendeley account preserves all of a user's citations, as well as custom user-generated notes and tags. So, I can easily access all of my references and notes from home, even if I originally found all of the articles at lab. This is both convenient and smart -- in addition to making my life easier when I need to take a project home with me, this automatically creates two backups of my reference database: one at home, one in the cloud. If my lab computer dies (unlikely for now, since my PI just bought me a shiny new iMac, but it's always a risk), I won't lose my precious papers.

One aspect of Mendeley that doesn't thrill me is the social networking component. My Mendeley account includes a user profile, and I've been encouraged to add 'contacts' who also use Mendeley. I can see how this might be useful for sharing papers between lab members or collaborators, but I don't find it necessary. When my PI wants to send me a paper or an EndNote library, she can just email me the files. And I have some concerns about security -- sharing Mendeley databases with the wrong person might reveal too much about a sensitive line of research. I favor a more open-source approach to science, but many scientists are terrified of being scooped, and would prefer to guard their lab secrets more stringently. Even so, it's quite possible to use Mendeley's other services without creating a list of contacts. And Mendeley uses personalized account info to do a few nifty tricks, like displaying the most popular papers for Biological Sciences, based on which citations were imported by the most Biological Sciences users on a given day. Users can also add papers to the "My Publications" category in their profile, and track the popularity of their own articles on Mendeley.

The web-based features are my primary reason for preferring Mendeley over other options, but I also like Mendeley Desktop a lot. I can attach a PDF to a Mendeley citation, making it easy to browse full-length articles as well as my notes. The desktop client can open tabs containing multiple PDFs and allows highlighting and Post-It style notes right on the article (although for now, these annotations are not kept in the cloud, so I can't highlight a paper at lab and retrieve the same highlighting when I sync Mendeley Desktop at home). I can sort my citations by title, author, publication date, date added to Mendeley, or by my custom tags. Mendeley is also smart enough to show me articles related to a tag even if I didn't tag them that way -- an article that I tagged "review" will come up when I select the "motor neurons" tag, if it talks a lot about motor neurons, even if I didn't add that tag myself.

Mendeley is compatible with EndNote (select any number of citations in Mendeley, export them as an EndNote XML file, and Cite While You Write to your heart's content) and with several word processing programs (obviating the need for EndNote), although it doesn't yet work with Microsoft Word on Macs. I've had no issue using EndNote as a middleman, however. Mendeley can also import citation information from EndNote, Zotero, CiteULike, and RefWorks, making it easy to transition from another reference management system (have not yet tried this myself, since I haven't been working on this project long enough to generate a huge reference database in another system). It's also free! If you're intrigued but not completely sold, check out some other reviews, or just download it and see for yourself.


  1. Thanks for the great review, Laura! I don't know if you've seen it yet, but in the new release there is a Word plugin for Mac, and the web sync now includes annotations you make using the Desktop PDF reader.

    I see the point about security and privacy, but I think for young investigators the danger is probably greater that you'll not get enough attention than too much, so the ability to have a profile and meet colleagues and potential collaborators in my area of research is actually one of the things I like about it best. The way it is now, nothing except your own publications that you add to your profile are publicly available by default, but the cool thing about the shared collections is that the annotations and notes you make on a PDF are shared among members of the shared group automatically, so it works a bit better than email that way.

    I'm actually working with Mendeley now to set up a network of researchers at Universities to spread the word about the open science movement and new ways of collaborating online. Does that sound like something you'd be interested in?

    Here's my Mendeley profile. Feel free to get in touch about this, or if you have other questions about Mendeley or anything else. Email is fine too.

  2. Thanks for your comment, Mr. Gunn! I hadn't seen the new release yet, so way to go for already implementing the features I wanted to see. :-)

    I'm all about the open science movement, although I'm short on time for extracurricular activities these days. I'll contact you on Mendeley to get more info abut your online collaboration projects.

  3. Sounds good, Laura. I look forward to hearing from you.

  4. I recently started using Mendeley, but I can't figure out how to import the results of a PubMed search all together into Mendeley without stepping through each individual paper. For example, if I run a search on PubMed that produces 100 papers and I go through and select 20 or so for reading later, is there any way to import all 20 at a time? I've tried saving the search results as a .XML file and importing in Mendeley desktop, but that just seems to ignore the file (or to treat the .XML as the document itself, rather than a list of references). Any suggestions?

  5. Hi Antony, I've never tried doing that on Mendeley but you can probably get some tips from Mr. Gunn (the commenter above), who works for them! Good luck.

  6. Pubmed doesn't export in any of the common reference formats for some few reason. Try your search on http:// our searching via Jabref. Integrating search into the client its in the plans.

  7. Thanks! Hubmed looks interesting. I'll see what I can do with it.