Academics work with a lot of PDF files—journal articles, scanned ILL materials, and, increasingly, historical documents available through archives such as Google Books. After my first few posts here at ProfHacker, I received a number of emails asking me to recommend a good program for organizing, tagging, reading, and (especially) annotating PDF files. Folks want to be able to store all their journal articles together in a single program, make notes on them as they would on paper copies, and search their both their articles and their notes easily.

Such an app sounds fantastic, but I have yet to find it. There are a number of PDF applications for OS X that do one or more of these things, but I’ve found no one application that does all that I wish it would. So this will be a different kind of post. I’ll discuss a few of the alternatives in the Mac app universe, and then open the floor to you. Please use the comments to tell us what program(s) you use to organize and annotate PDFs, what features are most important to you in such a program, or how you manage the digital primary and secondary sources in your work. Widows and Linux users—please chime in as well about how you manage PDFs on other platforms.

The Contenders

Apple’s Preview, which comes preinstalled with OS X, includes rudimentary annotation tools. You can highlight text and add comment boxes on the page. I find these tools very clunky, however, and Preview doesn’t help you organize or store large groups of PDF files.

A better choice for annotating PDFs is the free, open-source Skim. Skim’s tagline is “Stop printing and start skimming,” and the app features more robust annotation tools than Preview. You can highlight text, add notes to pages, add bookmarks to frequented pages, and more. Like Preview, however, Skim doesn’t organize PDFs—users still have to open PDFs individually. Another problem I’ve encountered is that many of Skim’s annotations don’t translate in other programs. If I mark up a text and email to it a friend not using Skim, my notes don’t always show up when he opens the PDF.

There are several Mac apps for organizing PDFs. Evernote allows users to collect and tag PDFs (as well as text files, pictures, saved web pages, and other file types). As an added bonus, it’s free and platform independent, meaning you can use Evernote to access PDFs from Macs, PCs, and most smart phones. Evernote offers very few tools for annotating PDFs. One of ProfHacker’s guest authors, Shawn Miller, will take a more comprehensive look at Evernote next week.

The database application DEVONthink is perhaps the strongest contender, and is the application I’m currently using for this task. Like Evernote, it allows users to collect sets of files—PDFs as well as documents, images, video, web archives, and other file types. I’ve yet to find a file type DEVONthink can’t import. These files can be organized into folders, tagged, and even organized into separate databases—one for each research project, for example. DEVONthink Professional Office (there are three tiers of DEVONthink) even includes the ABBYY OCR engine, so the program can convert scans and non-OCRed PDFs into searchable documents. DEVONthink also builds Preview’s annotation features into its PDF viewer. Those annotation features still aren’t as robust as I’d like, but overall DEVONthink does allow me to organize, tag, and annotate articles or archived primary sources.

I don’t know why I’m not satisfied with DEVONthink, but I use it because it’s the best of the lot, not because I feel it’s a stellar program. Even after two years, the interface still seems unintuitive. It is also very expensive to get all DEVONthink’s features. DEVONthink Professional Office costs over $100, even with the 25% educational discount (the other tiers are progressively cheaper, but each sacrifices some functionality). I’m sure that I don’t use the program to its full potential, however, and I know there are plenty of DEVONthink aficionados out in the ProfHacker community. Please let us know what I’m missing in the comments.

I’d also love to hear from anyone using Mekentosj’s Papers. Papers is aimed at scientists and doctors, and so I’ve not tried it out, but for those in scientific fields it might be the best option. Let me know if that’s true.

What software do you use for organizing and annotating PDFs? Please add your thoughts and recommendations in the comments.

[Creative Commons licensed photo by Flickr user redjar.]