Thesis document organization strategies


in Geek stuff, Oxford, Writing

A practical question to those who have walked the path of grad school before me: when working on a major research project, how did you take notes on books, articles, and the rest? How did you file those notes? Also, how did you file documents and photocopies that served as sources? All the archivist readers of this blog out there, now is your time to show your colours.

I will be using EndNote for citation purposes, largely to save myself from the need to deal with the formatting of hundreds of distinct footnotes (for substantive asides) and endnotes (for simple citation). While the EndNote program does have faculties for note organization, there are two problems. One is the clunky interface, which does not strike me as useful for much beyond the aforementioned auto-citing. The other is the fact that I can only access EndNote on the departmental terminal server; I do not have a copy of my own, but have to use it on a virtual desktop of Windows Server 2003. That said, acquiring my own copy of the program might prove a necessary expense, both for the thesis and subsequent research projects. I certainly wish I had been using it when I wrote the fish paper.

The first big choice for overall organization seems to be pen and paper versus electronic; though the variety of sources will always make the whole library somewhat hybrid, hopefully with 90% in the dominant medium and a well-sorted 10% in the other. I find taking notes on the computer likely to be overly distracting, though my handwritten notes can be far from elegant. At the same time, my computer files are generally both very well organized and easily searchable. As such, the ideal option might be to write notes by hand, then type and print them. Of course, there are time and financial limitations on that approach. The whole blog constellation is also a good organizational tool for me.

Perhaps most important, did anyone try a system that completely failed to work, and should be avoided? I expect the thesis to eventually involve hundreds of sources. Most of them will be books that I have access to but do not own, and journal articles which I can print or photocopy. I have a big hanging file box to sort such articles, and perhaps photocopied sections from books, but I need to devise a system to coordinate the hundreds of pages of my own notes that this project will ultimately rest upon.

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{ 10 comments… read them below or add one }

R.K. September 28, 2006 at 5:43 am

I thought you have been spending time with Oxford dons?

The proper Oxford filing system seems to be tottering piles of dusty leather books, with teacups balanced atop and miscellaneous papers everywhere. See Merlin from “The Sword in the Stone” for an excellent example.

Lee September 28, 2006 at 12:15 pm

Endnote is vital and I’m glad at least one person took my advice of a year ago to learn how to use it. It’s more useful than you might think. Develop a keywork system and when you have read something, make an entry, and make up your keywords for it. As your thesis takes shape, you will know what keywords are going to be most useful. When you come to write, you can search by keyword and all the sources you’ve read that are relevant to a particular section will come up. For instance, a keyword “US aid to Khmer Rouge” helped me find notes that contained references and figures, so when I wanted to write a paragraph on that, it was easy to find. Writing your own good abstracts can also be helpful in identifying that one article you are looking for amongst the 40-odd you read on x subject.

I personally take all my notes now using my laptop and Word. I don’t really understand how people can still use handwritten notes given the level of citation required in modern academic writing. I found it a godsend. I have a terrible memory, which is a bad failing as an academic, but I can often remember a phrase or a figure that I want to use, but cannot remember where it was. Using Windows’ search facility, I could scan all my Word documents in my Thesis folder for a phrase or keyword. This enabled me to find references for many obscure references that would otherwise have been impossible. Presumably a similar function exists on the Mac.

And if you need a personal copy of Endnote, I’m sure I can help you acquire one.

Milan September 28, 2006 at 4:04 pm


Thanks a lot for the advice. Thankfully, the Mac has significantly better search facilities than Windows XP or 2003 machines. As such, there is even more appeal to keeping notes in electronic form. The biggest problem is the very real danger of distraction when reading something dull and taking notes on a computer. I suppose that is just something that needs to be overcome.

Regarding a personal copy of EndNote – any version compatible with Mac OS X would be very helpful indeed.

Lee September 28, 2006 at 4:45 pm

Well, distraction from boring work is a constant problem that everyone (not just academics) face. One method is to work without internet access, which I find makes for a very productive day. It’s just something to struggle with – the alternative, working with paper notes, just seems impossible.

Ben September 28, 2006 at 8:03 pm

I hand write notes. I can’t sit and read from a book, and be typing two-handed at the same time. Now when I revise things (e.g. for teaching prep) I type up shorter versions of the notes. (Incidentally, I know some friends did something like this for MPhil revision – if you think you might teach it later, it’s probably worth it)

I kept one lever arch file for each of my MPhil papers, another for general notes on democracy and another with original journal print outs in. But I spent most of last year in a real mess filing wise, now I’m no longer organised around my taught courses.

sasha September 28, 2006 at 8:47 pm

I too take hand written notes sometimes, since I find it is simply more efficient for me to write than type while reading. Organizing hand written notes can be a daunting task, which is why I’ve come around to advocating the Paul Tennant method (and he claims it’s what he used for his theses…) of taking notes on index cards and then filing them by topic (another possible use for hanging folders).

In order to get around the problem of having to write bibliographical information on every card, I keep a running master list of sources on my computer (just a simple sequential list) and assign each source a 2 digit code – A1 to Z9 and so forth – which is easy to jot on the top corner of a card.

Computer notes are certainly easier to organize, but I don’t think the difference is enough to justify the time that would be needed to type all of one’s notes. I find that reading through a source and taking notes on cards works quite well, so long as I immediately sort and file the cards (lest doing so become a daunting task in and of itself).

Good luck! I don’t envy you the task of trying to keep this all organized, but you’re certainly up to the task if anyone is.

Milan September 28, 2006 at 8:49 pm


I already use the unique identifier for EndNote entries to mark both original documents and sources relating to them. That makes it really easy to cite them rapidly, while writing.

Lee September 29, 2006 at 1:43 pm

I should say that I don’t take notes while reading, I mark stuff of interest with sticky reusable markets and make notes later. I found it makes for more concise notes – note-taking as you go can encourage too much focus on the details without seeing the bigger picture the author is getting at (depending on how well they write). And I type far, far faster than I write (I can type about 70wpm), so it is not time consuming versus hand-writing notes.

Looking into a copy of Endnote for you, Milan.

Milan September 29, 2006 at 5:48 pm

Looking into a copy of Endnote for you, Milan.

Thanks a lot.

. August 14, 2012 at 10:08 pm

A while ago, I mentioned that I’d moved to using Bookends for my paper-handling and referencing needs. I’ve been really impressed with the software and thought it might be nice to do a review. If you have scrolled down, you will already have seen that this review is a bit of an epic. Reference managers are a niche product to start with, and even if you already use one, the chances are that you will feel this is a deeply nerdy and over-detailed review. However, my impression is that Bookends suffers slightly from being eclipsed by better known and superficially more flashy reference managers, which — as you’ll discover if you read this review — I find a crying shame1. Thus, part of my motivation in writing this is to encourage anyone who is curious about Bookends to give it a proper trial. You might end up loving it.

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