How can I keep track of academic papers and my handwritten notes on them?
November 24, 2009 1:28 PM   Subscribe

What is the best hardware/software system for keeping track of a) hundreds of academic papers in PDF form and b) my handwritten notes on these hundreds of papers? Bonus if the answer integrates with some sort of citation management software.

I am in a PhD program that requires me to read and take notes on a large number of papers. I can see myself in four years time simply drowning in printouts. My problem is somewhat similar to this previous question.

I don't like reading while sitting in front of my computer (typing hurts and easy internet access kills my productivity), so I tend to print out PDFs and take notes all over them while reading in cafes, libraries, on planes, etc. (Zotero's note system, for instance, isn't great for me because I don't like reading in my browser and typing notes). An ideal system would allow to me read much as I do, but make my notes--and interesting quotes and passages from what I'm reading--searchable for when I'm writing papers, studying for orals, etc.

The problem at that moment is that I end up with all these papers and notes that aren't easy to archive and can't be searched. I fear I don't have the discipline to properly archive all my actual paper notes, and hope that there's a technological fix out there for me.

I'd like advice on whether my best option is
a) a Tablet PC (with what software?)--one potential problem with this would be bulk and the distracting internet access.
b) an eBook reader that supports annotation (the upcoming IREX one?) with some sort of arching software to upload to.
c) One of those smart pens that records what you write (Previously). If these really work and can be integrated with good archiving/searching software I can see this being helpful for interviews and class notes, too.
d) Scanning notes taken on paper into my computer and archiving them from there. Something that sounds onerous and that I probably wouldn't actually do.
e) some brilliant technological solution that hasn't occurred to me.
f) knuckling down and getting a disciplined paper archiving system.

Could these options--a) in particular--be combined with Atlas TI? I love that QDA programs let me jump to specific tagged passages--and apparently the latest version has good support for PDFs. Or will OneNote--or some Mac program I haven't heard of--do this kind of thing better?

I have fairly atrocious handwriting, so OCR doesn't seem to work that well (in Evernote, for instance). I was impressed by Vista's handwriting support the one time I tried it, however--and I gather it learns from its mistakes.

I've heard Apple has a similar option, and would be willing to switch to using Macs if their handwriting recognition or the various note-taking programs I've heard about (Devonthink, Scrivener, Papers, others?) can be combined with some sort of note-capturing system.

I also take notes in lots of books. Any good ideas for capturing these notes that might fit with one of the above options?
posted by col_pogo to Education (10 answers total) 30 users marked this as a favorite
Best answer: I personally am waiting for the Entourage eDGe, due out next year, which would perfectly fit your option (b):

I've seen people that don't ever *write* anything by hand at all anymore -- they just lug the laptop around and do all note-taking electronically. At first, I thought this was a dumb idea, but considering that everything you put in electronically ends up searchable, and I can type a hell of a lot faster than I can write, maybe it's worth the awkwardness factor.

I personally use Papers to manage my own paper library. It's great in some ways, but kind of clunky in others. Definitely give it a whirl if you haven't yet:
posted by enoent at 1:53 PM on November 24, 2009

This all seems very overkill to me. Here is what I did:

First I got a copy of Acrobat Professional and EndNote.

As soon as I found a PDF to read, I saved it to my harddrive and printed a copy. I embedded the electronic copy directly into the endnote record (so it moved with the library if necessary). I highlighted/took notes on the paper copy. Once I had a small stack of read papers, I opened each pdf and highlighted all the sections that I thought were important. I also typed in important comments (no more than 2 paragraphs total) as a note into the PDF. That's it.

Months later when I needed to cite a paper, I could just do it from memory ("paper x is a great example to cite for y"). If not, I just open the PDF and see all the parts I highlighted.
posted by special-k at 1:58 PM on November 24, 2009 [1 favorite]

Best answer: Everything else you mention just seem like different ways to procrastinate and not read the papers.
posted by special-k at 1:59 PM on November 24, 2009

PPS: I use papers now just for general reading/note taking. It's great to use alongside EndNote.
posted by special-k at 2:00 PM on November 24, 2009

On a mac: scrivener and bookends
posted by Namlit at 3:04 PM on November 24, 2009

Best answer: I tried Papers, RefWorks and Endnote to help organize my PDFs and references. None of them really did it, though I do know PhD students who have used them successfully. Anyway you cut it in a PhD, you're going to be drowning in something, whether it's printouts or the hassle of trying to keep your citation management software up and running.

What is working for me right now is keeping my handwritten notes + annotated printouts of articles into somewhat organized binders, and then naming the corresponding digital files into useful names that I can find easily via a few keywords using Spotlight on my computer (mac). I try to keep the digital files somewhat organized via folders, but I don't particularly sweat it. Spotlight remembers keywords that correspond to frequently opened files, so I can pull up all the papers by one author, in a certain journal, or published in a certain year with relatively little input to try and keep things organized.
posted by beepbeepboopboop at 3:11 PM on November 24, 2009

Best answer: I'll add my voice to the chorus for Papers as a general organizational system, with the caveat that it only solves half your problem -- I can't think of a good way to get an existing trove of notes into digital form without stupid amounts of effort. My method for getting handwritten notes integrated is not great -- I read a paper in hardcopy and make notes, and then I have to remember to go into Papers and jot things down in its internal notes feature, which I don't always do promptly/at all.

The thing that I struggle with most in Papers is that there isn't a good built-in way to tie my notes to the relevant parts of the paper. There are people on the Papers user forums who report adding this in by switching the PDF viewer from Preview to Skim, which allows for that sort of annotation, but I haven't tried it myself.

As for notes on books, and notes that aren't directly attached to papers, my advisor makes me type them all up as I go (he calls it a "down payment" on my dissertation), so I actually started importing them into Papers as though they were articles. That way they're all in the same place as everything else, searchable, etc. You could certainly try scanning notes and do the same thing, but I can't help you much with the OCR side of things.
posted by dorque at 6:52 PM on November 24, 2009

Response by poster: Thanks for all the suggestions. As special-k suggests, sitting and dreaming up new ways to manage my note-taking is a way of procrastinating for me. That said, I think do need a new system.

enoent: the EDGe does look it might meet all my requirements. I'll have to keep an eye out for it.

I'll take a look at Papers and Scrivener, although it's not yet clear to me whether it's worth it for me to switch to a Mac.

dorque: I didn't mean that I wanted to move all my existing handwritten notes to whatever system I find. I'm fairly resigned to not being able to do that.
posted by col_pogo at 7:41 PM on November 24, 2009

Best answer: I'm the guy you fear becoming: I'm at the end of my PhD program and drowning in printouts. I've tried a dozen different systems (read on the screen, print everything out, scan in handwritten notes, etc.) and a dozen different software programs (DEVONthink, Zotero, Papers, Scrivener, EndNote, Mendeley, etc.), and I haven't been completely happy with any of them.

Sadly, I don't have a solution for your problem (still looking for one myself), but I can endorse what special-k said: the search for the perfect system is what my office-mate and I have taken to calling an EPD: an Elaborate Procrastination Device. Rather than working on your dissertation, you decide that today is the day to move 300 PDF files from Yojimbo to DEVONthink. Once everything is organized and tagged and OCR'd, you tell yourself, THEN you'll be able to make some real progress on your research.

After five years in graduate school, I am finally coming to grips with the fact that research is and always will be a messy endeavor, and my piles of physical and electronic files will probably always reflect that.

I can speak to one specific part of your question: ATLAS.ti's PDF support is terrible. PDF files load slowly, it's difficult to navigate from one page to the next, and text highlighting (for applying codes) is buggy. This is the first version of ATLAS.ti that supports PDF files, and it's clear that some kinks still need to be worked out.
posted by lewistate at 8:15 PM on November 24, 2009 [4 favorites]

Response by poster: I ended up buying a Livescribe smart pen and am very happy with the purchase. Now if I can only get OCR training to work, I'm sure all my problems will be solved.
posted by col_pogo at 4:24 PM on January 13, 2010 [1 favorite]

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