The Road To Mendeley

I’m sure Kipling will forgive me for hacking the title of his poem, but I’ve been having a lot of fun recently with Mendeley as part of my ongoing “Free Software for Scientists” blog series.  Although Mendeley is not completely free, it’s certainly free to download and use.  Mendeley has a tiered pricing plan that will give you more storage and sharing options if you find yourself running out of room. 

In a nutshell, Mendeley is a combination desktop and web application that makes it easy for you to collect and share papers with your colleagues.

For a while now I’ve been collecting papers on Pancreatic Cancer and trying out a number of ways to share those papers with others.  I’ve used the delicious bookmarking service, for example, to bookmark papers and share them with others.  I’ve also used My NCBI to create and organize corpora.  But none of these methods were really optimal, since they didn’t really fit my workflows (shown below).  So I decided to give Mendeley a try at the recommendation of a fellow twitterer (William Gunn — @mrgunn).

After signing up for a free account, I downloaded and installed the desktop software.  The desktop application runs on Mac OS X, Linux and Windows.

I then created a new collection to store my articles.  You can add papers that you’ve previously downloaded, or import papers from a variety of journal sites.  You can watch specific directories and have any new files that appear in those directories, automatically added to your collection.  You can create public, private or shared collections.  You can also add tags and notes to the articles that you add.  You can export your collection in BibTeX, RIS, and EndNote XML format.   You can also copy all of the articles in a collection, and paste them into a paper that you’re working on.  You can use a number of different citation styles (they seem to have hundreds of them).

But it’s more than just a tool for dealing with academic papers.  I also subscribe to a number of blogs.  For example, Dr. Nick’s Cancerology blog is a really great source for information on new developments in cancer research, and I often find myself bookmarking some his blog entries, in addition to the papers and articles that he refers to.  Mendeley provides a couple of ways of bookmarking web sites and blogs (more about that below).  And when you bookmark the page, Mendeley saves a copy of the page (just in case the website disappears).

Workflow I – Reading Journal Feeds
I’m a fan of Google Reader.  It’s an RSS reader that allows me to collect the abstracts of all of the latest articles.  In previous blog postings, I’ve mentioned how much of a time saver it is for me and how it allows me to take a look at the latest articles from all of the journals that I’m interested in.  I can also collect journals into RSS “bundles” and share them with others.  Here’s what my workflow is like:

  1. Click on the “Cancer” or “Informatics” journal bundle and view the latest articles.
  2. Click on the “Send To” link at the bottom of the article and select “Mendeley” from the list.
  3. The article is then added to my Mendeley collection.  You can add your paper to a specific collection, by selecting the name of the collection from the list box.  You can also add tags to the article.  In my case, I usually add tags for specific genes mentioned in the article.

Here’s a quick hack to add the “Send To Mendeley” function to Google Reader:

  1. In Google Reader, click on the Settings/Reader settings menu item in the upper right corner of the page.
  2. Click the “Send To” tab (the right most link on the page).
  3. Click the “Create a custom link” at the bottom of the page.
  4. Enter “Mendeley” in the Name field.
  5. Enter “http://www.mendeley.com/import/?url=${url}” in the URL field.
  6. Enter “http://www.plosone.org/images/icon_mendeley_16x16.gif” in the Icon URL field
  7. Save your changes and go back to Google Reader.  Now when you select “Send To” you’ll see “Mendeley” as one of your options.

Workflow II – Getting My NCBI Search Results
I receive a weekly email from My NCBI account with the latest articles on pancreatic cancer.  I usually spend a few minutes every week skimming through the email, and then reading the articles that look most promising.

  1. Click on article title in email message, and view the article on the PubMed site.
  2. Click on the “Import to Mendeley” bookmarklet in my web browser.  This bookmarklet is a snippet of JavaScript available from Mendeley, that takes the current web page adds it to your collection.  It’s rather smart, in that it can detect if you’re on PubMed or a specific Journal and get the appropriate article metadata and add it to your collection.

To install the Mendeley Bookmarklet

  1. Go to Mendeley.com
  2. Click “Install The Web Importer” and follow the instructions on the page.

Wish List
Mendeley is a great application, and for the most part it does what I need it to do.  There are however, a few things that would really be nice to add:

  • Extract gene list from paper, or collection.
  • Extract protein-protein interactions from paper or collection.  You could then pull these interactions into Cytoscape and visualize them based on GO terms.
  • Find “more like this”.  Most of the papers that I collect have PubMed IDs associated with them, so it shouldn’t be too difficult to extract the MeSH terms for the papers in a collection, and create a search for papers with similar MeSH terms.
  • Integrated PubMed search.  I would like to be able to search PubMed without leaving the Mendeley application, and then select certain papers to import.  It would also be nice to be able to save the search.
  • Export in PubMed format.  I often find myself needing to analyze the metadata associated with the papers in a particular collection.  The EndNote XML format doesn’t include MeSH terms and abstracts, let alone a PMID which is necessary to do any additional work.  If I could export it into a slightly less verbose form of the PubMed XML format, this would definitely make it easier to work with.
  • Export PMIDs.  In order to get PubMed metadata about my papers, I need to be able to get a list of PMIDs from my collections.

In this article I’ve merely scratched the surface in terms of the functionality in Mendeley.  They recently added a REST API that allows you to run queries against the Mendeley database.  I’ll blog about that later.  But if you haven’t done so already, signup for an account and give it a try.  It definitely makes organizing and managing your research easier.

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About aspenbio

I write software for scientists. I'm interested in Java/Groovy/Grails, the Semantic Web and Cancer Biology.
This entry was posted in Bioinformatics, Informatics and tagged , , . Bookmark the permalink.

One Response to The Road To Mendeley

  1. Pingback: Social Media for Scientists: It’s all about the sharing | Aspen Biosciences Blog

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