Goodbye Paper, Hello Mendeley

September 07, 2010

I used to have eight 4-inch thick binders containing the many technical papers I refer to. Now I have one. Here's how I did it.

Mendeley lets you create an annotated library from a raw collection of your many papers. Make a single directory, throw in all of your PDFs, and Mendely does the rest. Or at least that's how I used it. From the documentation:

Mendeley Desktop lets you set up your personal research paper database from multiple sources: Extract bibliographic data from PDFs automatically, grab citations and documents off web databases with a single click, and sync with other reference managers.

How did I go from binders full of paper to PDFs? Google of course. I searched for the title of each paper and, if necessary, the author with the most distinctive last name. In most cases my first three hits had a direct link to the publisher site, from which I downloaded the PDF.

Although I was impressed with Mendeley's ease of use, I did hit a couple of gotchas:

  • In my first attempt, I downloaded a batch of PDFs into my system's 'Downloads' directory. Then I deleted them, thinking that Mendeley was making its own copies. It was not. I had to re-download a few PDFs because of that mistake.
  • Apparently, if you download multiple copies of the same PDF, Mendeley will create multiple citations. And simply deleting the underlying PDF won't fix the problem. You'll need to delete the reference to the file as well, it seems. Actually I'm still not sure I have that part figured out yet.
  • Although Mendeley is good at extracting bibliographical citation information, it's not perfect. For example, with some older ACS references that begin somewhere in the middle of a page, nothing meaningful could be extracted for title, author, etc. In those cases, the only solution is manual entry.

After a couple of hours, I had a library of 156 citations, complete with full title and bibliographical citation.

I must say that having access to my library this way is very liberating. I no longer need to worry about whether I filed that paper on fingerprint optimization for substructure search under 'fingerprint' or 'sss'. I just search for keywords, authors, or browse the full library.

Another pleasant surprise: Mendeley makes it easy to find all papers by a given author. I was surprised to find author connections among some of the works I thought I knew pretty well. Now if there were just a way to hook this author information into LinkedIn...

I'm also eyeing the iPhone app for use with my iPad as a more comfortable way to read my papers without having to print them out at all.

I haven't been a user of reference managers in the past, but Mendeley has gotten enough right for me to make the switch.