Looking for the perfect note-taking system is hard, but still easier than actually doing work

April 7, 2009 5:42 PM

Which note-taking/organizing software does the best job of integrating PDF files?

I'm looking ahead at 4+ years of doing nothing but research and writing, and I'm realizing that my current notetaking system (read document, forget about it a week later) is not exactly working for me. I'd like to switch to one of those magical programs that organizes your world, but after reading all of the many previous AskMe questions on note-taking systems, I can't figure out which one would work best for me. (Currently looking at: Evernote, TiddlyWiki, WikidPad, Scrivener, NoteBook, VooDooPad.)

I've made a half-hearted attempt to use Zotero in the past, and there are a bunch of things about it that I really like (most notably the ability to save and annotate webpages, which is particularly important to me because part of what I study is Internet culture), but there are also a few things about it that I don't like (not free-standing, impossible to look at multiple things at once).

There's one thing that I would really like to be able to do. Many of my readings are PDFs, and many of those aren't recognized as text (or whatever the technical term is -- I mean that you can't highlight text or search). I would like to be able to annotate these readings directly on the PDF, but also be able to view my notes separately, i.e. as a list. I want to be able to see my notes in context, but also to be able to take a step back and look at the big picture of all of my notes for a single reading and possibly all the notes for a collection of readings.

Does any program actually do this? If not, which of these programs do you think would work best for a social theory academic with lots of PDFs, an extremely bad memory, and a tendency to fail to see the big picture? I'm leaning towards one of the Wikis because the of the ability to interconnect everything, but I'm not sure if they can integrate attached files as well as the non-Wiki programs can. Maybe I need to use two separate programs (e.g. Zotero to manage bibliographic info and websites, VooDooPad to take and organize notes), though being able to kill all my organizational birds with one stone sure would be nice.

posted by pluckemin to computers & internet (7 comments total)

DevonThink, as Steven Berlin Johnson explains. (Also, here.) Mac OS X only.
posted by holgate at 5:47 PM on April 7

Oh, right, forgot to specify -- I'm using a Mac with OS X.

Will look into DevonThink...
posted by pluckemin at 5:53 PM on April 7

Papers seems to be the consensus in my corner of academia. It's OSX only, which isn't a problem for you.
posted by chrisamiller at 6:13 PM on April 7

Post it notes in your book.

I just saved you money.
posted by BobbyDigital at 6:37 PM on April 7

I've heard good things about Skim. OSX only, built with the sole purpose of reading and annotating PDFs. Can't speak on a comparison between the other two options mentioned, but it is significantly cheaper than both.
posted by ConstantineXVI at 6:39 PM on April 7

PS: I've noticed a very strong OSX trend with these tools. Could anyone guess a reason besides OSX's built-in PDF support?
posted by ConstantineXVI at 6:43 PM on April 7

OSX finds a lot of support in academia (outside corporate licensing schemes and acquisitions, etc.). It's also a more pleasant operating system for nonexperts than Windows, and humanities types tend to be nonexperts in such matters.

And there's a very strong personal-organization interest among Mac indie and small-shop developers, for cultural reasons you can no doubt imagine.
posted by waxbanks at 7:04 PM on April 7