Organizing many, many notes for dissertation

Hello all,

I realize this may not be the correct forum to pose my question, but I'd appreciate any suggestions nonetheless. I'm in the process of writing a dissertation and am swamped by notes, quotes, and other miscellany. I've used two programs, OneNote and MindManager, to take these notes so they are all digital. I'm searching for a way to get a handle on the material, perhaps by creating a quick and dirty database or wiki.

Ideally, I'd like to be able to enter the notes as and index them in terms of the document they came from. However, I'd also like to be able to quickly cross-reference notes for specific terms and to be able to tag them with descriptors like "postmodernity," "novel," "Thomas Pynchon," and so on.

Zotero may well be up to the task, but I worry that the voluminous notes I have on works like _Gravity's Rainbow_ may choke the software. There is also the problem of preserving the structure I've imposed on the notes in MindManager.

Thanks for your time,

PiD
  • Can your mind mapping software export to html?
  • Sybille,

    Yup, it sure can. The export is a bit "ugly," but certainly workable.

    Why?

    Have a great one,

    Paul K.
  • Well, you could view your exported html file in Firefox and use the right-click context menu to enter your notes into Zotero, where they could be tagged, associated with sources, and cross-referenced.

    I don't know that this would suit you, though. It also depends on how you'd like to work with your notes. As far as I know, there is at present no way to export notes alone from Zotero, so it might be complicated to get them into a word processor, for example.

    My understanding is that the database has an upper limit of 10,000 entries, with some slow-down possible starting from 5,000 items:
    http://forums.zotero.org/discussion/815/?Focus=3076#Comment_3076
    I'm not sure how, or whether, length of note would complicate matters.
  • Sybille,

    Thanks for the suggestions.
  • edited September 11, 2007
    My understanding is that the database has an upper limit of 10,000 entries, with some slow-down possible starting from 5,000 items
    Just a clarification: there's no strict upper limit, and even the 5,000 figure is completely arbitrary. It all depends on your hardware. And, of course, we're working to speed things up.
  • re PlatoisDerrida, are you familiar with Nota Bene, the wordprocessor designed for dissertation and academic writing (notabene.com)?
  • Mtolincoln,

    I've looked at Nota Bene. It looks like a great program, but the price tag is a bit prohibitive, especially since the software is two(?) years old now.

    Have you found it to be particularly useful?

    PiD
  • edited September 17, 2007
    I don't know if you're interested in Linux/Unix applications at all, but if so, you might check out Tomboy. Although on the surface it looks like just a sticky-note app, it allows for your notes to be interrelated with wiki-type syntax. That feature reminded me of your thread here. I haven't really used Tomboy myself, though.
    http://www.gnome.org/projects/tomboy/features.html

    If you're going to try Tomboy, you might also try Beagle, a desktop search engine that will allow you to do full-text searches on your Tomboy notes and other documents (including Zotero docs if you tell Beagle to index the Zotero storage folder). Some people don't like Beagle, but I find it a very helpful tool.
    http://beagle-project.org/Main_Page

    It should be possible to install both of these apps in any mainstream Linux distro using the included package manager if they are not included "out of the box" (not that Linux really comes in a box....). =)
  • Sybille,

    Thanks for the suggestion. The Linux/Unix operating systems look incredibly stable and robust. However, I recently invested in a tablet pc and need to run a Windows OS, in my case Vista, to get the full tablet functionality.

    Have a great morning,

    PiD
  • (Offtopic)
    I don't use Tomboy myself, but will point out that it can limp along in Windows:
    http://live.gnome.org/Tomboy/Win32

    I'll also point out that Linux supports the most common hot keys on tablets out-of-the-box with most distros & that you can easily install wacom-tools to enable stylus support. (Though this in no means cancels out any other valid reasons you might not to wish to run Linux--you should just know the fact that it is a tablet isn't necessarily a barrier).

    A somewhat commonly suggested alternative to Tomboy is to actually use a wiki, which you mentioned initially. There are single file versions that use javascript & don't require a server & your citation data is already tied to your browser.
    http://en.wikipedia.org/wiki/Personal_wiki
  • Noksagt,

    Can you suggest a personal wiki?
  • Not really. I keep most of my notes in LaTeX. I do have collaborative notes on MediaWiki+refbase, but that is possibly overweight for a single user (ditto for the many other other Apache+MySQL+PHP/perl/python options).

    TiddlyWiki (and various extensions) is probably the most popular personal wiki software, but I haven't used it much myself.
  • tiddlywiki is very cool: portable and easy to backup and use, but may not scale well for those "many many" notes you're talking about. I'm not up on the current discussion, however, so this may be rubbish. It's easy enough to test, though, if you can put in a few sample notes, load up your TW file and duplicate them a few hundred times, (records are stored as plain text near the end of the file) and start playing, tagging, etc.
  • I just imported only 700 citations from endnote, giving me about 1000 or 1200 total, and I saw a significant, significant slow down. So much so that actually adding a footnote to my document can take minutes, while I wait for it to complete the search for the entry.
    Melani
  • scot has a good point re. capacity. Maybe a full-blown wiki wouldn't be overkill!

    However, several people split across multiple tiddlywikis & the tiddlywiki ChangeLog shows that they have been adding features to help users who do this.
  • Melani99: It's true that the database gets slower as it gets bigger, though waiting minutes to insert a footnote does sound extreme. I have about 1100 items, and it can take 10-15 seconds to do certain database operations (especially involving tags). I don't use the Word plugin yet. I intended to start a new thread to ask if there were any thing that could be done to speed things along (delete attached links to database records, or whatever), but haven't had the chance.
    Are you searching via Quick Search? That can take a while if are full-text indexing. You'll find that searching goes faster if you open the advanced search window. If you want to solicit comments and advice, perhaps start a new thread, and see if you can gauge if your experience is 'normal' Don't forget to list OS, CPU speed and amount of computer memory, (and perhaps rough proportion of top-level items to attachments, and size of your database file zotero.sqlite).
  • Pretty old thread - I'll answer the initial question anyway and recommend a look at

    www.thebrain.com

    There's a free personal version of PersonalBrain, a powerful mindmapping software which helpes me in my research.
  • i teach writing at the university level
    I've been trying to find a way to use zotero for my students so that they could save/make notes, and reorganize them. I've spent a couple of hours trying to do this--really no luck with easily moving notes around (in the program I use (infoselect) i just drag my notes into the order in which I'm going to write about them.
  • because there was asked for a personal-wiki: i like zim a lot - it's a kind of desktop-wiki - a little bit like tomboy but much more powerful. It's the right tool to make some outline and to organize all your stuff which doesn't fit really to zotero.

    http://zim-wiki.org/ for linux it should be in the repository of the most distributions, and it's also installable under windows.
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