Jan 31, 2013 - 4 minute read

Organizing Research Papers

I keep finding myself asking this question way too often

I definitely read that in a paper (or, blog post, quora article) a while back, where was it?

Most often it’s either in one of my moleskine notebooks (seriously, those things are incredible - I keep two), date stamped with some scribble or on Evernote. I don’t get annotations and in-place notes. I like to scribble on the side a fair bit and annotate. While iAnnotate apps work, I can’t save that to Evernote yet, while keeping it editable. While I’m pretty sure Evernote or Dropbox can be adapted to do all of this with some cleverness or discipline, but here’s some of the research I did on how to organize your documents, research papers.

What I want

The ideal research note-taking application would let me do few things:

Keeping Track

Keep track of what I’m reading (goodreads attempts this for books, but I mean across devices).

Synced Annotations and Notes

Editable annotations and notes, I’d like to be able to read papers at the airport on my iPad, make notes in-place and when I reach my home, I can organize into a distilled document.


I think I can do the two I mentioned earlier with kindle to some extent. What Kindle doesn’t give but Evernote does is tagging. I can organize things any way I want with tags.

Cross Platform

I’d like it to run on the iPad, Android, and the browser.. I don’t exactly care much about client applications, they’re nice to have in addition to these.

Bibliography wherever applicable (BibTeX)

I’m lazy, and so are most people, I’d like to get BibTeX format documentation generated for me wherever it makes sense, if I got it off of some researcher or some site. It should let me add these if I just got the PDF and I want to keep track. The use case I’m thinking is, if I’m writing a new paper, I’d like to be able to tag with something, and just get a list of BibTeX annotations to paste for LaTeX to generate in whatever format I want.

Collaboration, Sharing

I don’t research alone, unless it’s the time-honored tradition of searching for cat videos, even that reddit probably has got to be the journal of sorts. Actually, on that note, I ran into this paper on how viewing cute images promotes a careful behavior and narrows attention focus. Believe it or not, I ran into it via Sanjay Ghemawat’s G+ post. There you go, with enough cute pics, you might come up with BigTable.

Back to the topic, I’d like to share with other people what I’m reading and ideally maintain a “burn list” of sorts with colleagues on what papers I’m reading for a particular project. There’s some “discovery” part here that you get for cheap but I can barely get around to reading what I plan on reading.

Importing other sources

PDFs, web pages, not just research articles

Possible tools that “get it”

So far I think Mendeley comes the closest to this grand vision (it didn’t do tracking last time I used it but matters less than others), but there are others, this is by no means comprehensive.

  • Mendeley – good tool, I used it extensively for some research at school, beginning to use it again.

  • Papers – I know some people who swear by it, I think it lacks on some of the other features like collaboration, being cross-platform but it does a damn good job of organizing

  • Evernote – Not all the things I find interesting are research papers, evernote lets me “clip” online articles, I can scan paper docs and have it OCR so I can research it in future.. all that good stuff. I use it a lot for keeping notes anyway.

  • Zotero – I know people who like it, didn’t find it too appealing myself

  • Docear – same thing as Papers, really good at organzing, I haven’t used it but I’ve seen it mentioned

Feel free to suggest new ones in the comments, I’m not trying to be extensive. I think Quora and StackExchange do that fairly well. :)