Data Management

As I continue to adjust to the new computer, I'm realizing that there's something I want to be doing my computer that I don't quite have the tools and/or cognitive capacity for.

I've sometimes joked that I have no business having such a powerful computer because the truth is that 80% or more of my digital work is a dealing with text files, plain text files that are technologically the same as text files from 30 years ago. For this we don't need a dual core processors, or 250 gigabyte hard drives.

But this is a digression. Probably the second biggest (in terms of import) collection of stuff I have on this computer is data and texts of one form or another. Lots of PDFs of academic articles and resources, lots of notes of my own creation, that sort of thing.

While I've tried almost all of the "personal database" managers over the past few years, I settled on using an interesting solution. That is programs like DEVONthink Pro, Mori, EagleFiler, that attempt to provide an additional layer of database management to all of the "things" in your digital life. They're good programs, but the truth is that they all provide a common set of very OS X-y tools, and they're all closed source, and they tend to obscure the organization of the data. [1]

I use BibDesk to index all of the published documents that I have on my computer, BibDesk is a great program for managing citations and frankly I use it for a lot less then its capable.

Anyway so there are a bunch of programs that do this kind of thing, and I used Devon Think at one point in the past, and I like it, but the database is proprietary and it's having a problem with a file extension I use [2].

In any case here are a list of features that I consider important for such a program and the task that I hope to accomplish with said features:

• Web Cliping when I run across something on the internet that is important to a project I'm working on, I want to be able to capture it to the database for later reference. The clip should capture key bibliographic data (URL, time, title, etc.) and keep this exposed to me so I can easily incorporate the information into what I'm working on without needing to either have a connection to the internet or trace down the source for a second time.
• Mange multiple formats, including PDF, HTML, and plain text.
• Needs to rely on external editing/viewing programs. I really like the programs I use to edit files, and don't really want to use some special wrapper on top of TextEdit.
• Needs to keep the data/files exposed to the directory structure, and keep synchronized with this. If I change a file name/title in the database it needs to propagate down the line. DTP will almost do this, if you index files, but it means keeping a finder open window.
• Something not Kludgey. As I've been writing this, I managed to hack together a shell script that does like eighty percent of what I need (in concert with ikiwiki, which I already use), but it's ugly, and doesn't do a very good job of capturing the citation information automatically. If someone knows how to get a url for the top most safari window into the shell as a variable, this will obviously be a lot easier, as it is, I think I can hack it.

Is there some solution that people are using for this sort of task? Do you have recommendations? I'd love to hear them.