For my dissertation, I am currently using the following tools:
- DTPO
- Sente 6
- Scrivener
- Nisus Writer Pro
I use Sente instead of Bookends. Overall, I find it an excellent tool for acquiring, organizing, reading, and annotating large numbers of journal pdf files, and for citation/bibliography production. It is definitely possible to keep your article-specific research notes in DTPO. In fact, in the DTPO action menu, you will find a template for linking notes directly to a citation in Sente or Bookends. I did try this, but in the end I decided to keep article-specific notes with the article itself - i.e. in Sente.
Scrivener is the greatest writing tool ever invented! Once I had my dissertation proposal approved, I set up the chapter/section structure in Scrivener. I then duplicated that structure into the “Research” binder. It is here that I assemble the ideas and quotes that will ultimately end up as the content in each section of the dissertation. As I am reading through an article, I will add specific quotes/ideas to whatever section of the dissertation that is most appropriate. Obviously, this does mean that those notes are pretty tied to both Scrivener, and to the one project - my dissertation. It also means that there is some duplication between the notes I keep in Sente and the notes that end up in the Scrivener “Research” binder. If you want an alternative that allows you more flexibility, you might check out these posts:
http://muninn.net/blog/2010/08/revisting-the-note-taking-problem-with-devonthink.html
http://blog.devontechnologies.com/2011/09/devonthink-and-history-research/
Although I can’t help you much further than that with specifics, DTPO is an amazingly flexible tool. It has so many different ways of connecting pieces of information in the database (links, tags, replicants, labels, smart groups, etc) that with a little effort, you’ll find a way to set up your notes as you want them. My main use of DTPO for my dissertation is as a repository for research sources that don’t fit easily into Sente. I also use it to keep all my “general” notes that aren’t related to a specific source. (My main use for DTPO in general is as a massive database of material related to my field - but that is a separate database from my dissertation database.)
Finally, I use Nisus Writer Pro for the final word processing. I have Word 2011, but I rarely use it. Nisus is fast, stable, and has most of the features you need for academic publishing minus the bloat of Word. It also plays nicely with Scrivener and Sente. It’s worth a look…
Here are a variety of related posts from forum threads and other sources. Some of it may be a bit dated now, but you never know what may spark an idea.
Other forum threads you may want to check out:
[url]DevonThink and (what?): Bookends, Endnote, Papers or Sente?]
[url]Sente and DevonThink Pro?]
[url]An Academic Writer's Suite- DT, BE, and Mellel]
Other sources:
http://parezcoydigo.wordpress.com/2008/12/18/posts-on-devonthink/
Enjoy DEVONthink!! And when you have a moment, check out DEVONagent Pro. It may well help you with some of your Internet research that involves specialized theological sites.