Mendeley: Scientific Article Organizer for PDFs

Research Tools
Scientific Article



August 15, 2011

For the past 6 months or so I’ve been using Mendeley to organize my PDFs. It’s a program that allows you to organize and maintain your scientific articles. While you might be able to implement your own nomenclature and folder organization for your files, this puts them all together in a single database, and lets you look at all the properties of a file that you would be crazy to include in the filename. It’s like comparing the .mp3 file you never look at and the iTunes library you store it in. I’ve been more or less happy with the product so far, especially because it’s free. When you first add a PDF to the system I think it mines it for details. I’m not sure if it simply picks out the DOI or if it picks up key characteristics like journal name, authors and title. It uses this information to fill out all the information you’d want to know about the article. At times it doesn’t get it quite right, and you can tell it what is correct, and run another search which will usually be the last. I don’t think I’ve used it with any article older than 10 years, so I’m not sure how it would work if I used a really old article that was scanned. The last time I checked they had a voting system for new features. Each registered user is given votes (or vote) and they can use that to vote on a feature that they’d like to see. In addition to organizing PDFs, you can view them and annotate them. I’ve never used to help me organize my references for a paper or report, but every once in a while I’d generate a citation for an article. After 6 months I’ve figured out what I do and don’t like:


  • Let’s me see and search through my files, regardless of actual folder
  • Generates citations for fully defined articles
  • Can auto-rename files
  • Let’s me organize the files in the database into virtual folders


  • I’d like to make smart folders that search for certain words, like iTunes smart playlists
  • I’d like some more flexibility auto-naming files. You have some control over what elements are used, and what order they’re in, but I’d like to set a cutoff number of characters for titles that are unreasonably long
  • It’d be nice to consolidate authors semi-automatically. Some authors publish with slight variations in their initials and it lists them as separate people until I manually edit it. It’d be nice if it was able to recognize that they were mostly similar and offer to merge them
  • It also has an online component that uploads your papers. I can’t find a way to turn this off. I don’t want to back my files up online, and since I’m using the free version, I’ve maxed out my limit and it keeps reminding me of this

There is also an online community, but I’ve never used this component. I think that this is still a young program and will grow into a great piece of software (and hopefully still offer free versions!). As far as organization goes, I think it’s only real alternative is Papers, but I don’t own a Mac or an iPad, so someone will have to tell me how they compare.

I also want to mention that this Thursday, Mendeley is hosting a webinar ‘Mendeley for Engineers’ which will be presented by Mendeley’s Community Liaison, Ricardo Vidal. Ricardo will discuss how Mendeley has benefited his research as a Biological Engineer and provide an introduction to Mendeley. The webinar will be held on Thursday, August 25th at 3pm EDT. Register at