devonthink+bookends+scrivener for academic work

Hi all–

I’ve posted on my blog a series of three entries on my own workflow using devonthink, bookends, and scrivener. Granted, the posts are mostly about devonthink, but they all point towards scrivener. This is specifically for academic history and humanities research.


Great, that will definitly be useful to me ! I just bought Devonthink 2 and was wondering how to best integrate it to my actual workflow (I use Omnifocus for projects management, Scrivener to store all project-related info + project writing, and on the side Yojimbo for storing pieces of data that might be of use across many projects, the kind of general references).

At first glance, I felt that if I start using DT for each project (one database per project) I’d loose the benefit of the great Research portion of Scrivener (and really, having everything in the same place when I’m writing, with that split screen, is a godsend !).

So I’m still fiddling around…

I suggest placing all notes in DTP 2. You may always export project-specific files for importing into Scrivener as needed. DTP 2 gives you power searching and a single container for research files of all types. You may copy material to separate databases only as needed, but for the most part, they’re better off in one place.


Could you please post an update here once you discuss DTP 2.0 on your blog?



Will do-- but don’t expect anything soon! :laughing: I’m in the midst of writing my final two chapters, and I’m not going to migrate any of my existing database until that’s done. I just don’t have time to play that much right now. I’ll probably wait until DT2.0 comes out of beta before making the full switch, as I’m predisposed to be weary of beta software, even if it’s relatively stable as DT seems to be. By the way, I fixed the image links on the third post on the blog.

-chad black

I’m coming late to this thread, and am treading lightly. I realize that Scrivener was developed as a fiction tool, but I am working in history of science, not fiction. Thus, I may be a kindred spirit with the folks in this thread.

I have the latest release of DevonThink Pro and am very happy with it except for its complete lack of capability for internal documentation (other than just using the (author, year) designation after each note. This is almost a deal-killer for me. Not citing references in the sciences is tantamount to heresy. How does one bridge this enormous gap between DevonThink Pro and Scrivener? I am considering doing all of my work within Scrivener and Bookends, leaving DTP completely out of the mix despite having spent good money for it. Labels can be used for about 6 references, but after that I’m on my own.


In DevonThink, I put the citation in the comment field of imported documents. If it’s a note I took from a printed source, I put the note in the file itself.


I have been lying in bed awake for the past 2 hours trying to figure out how to deal with this. I guess I sort of came up with the same conclusion, i.e., that I would just put a reference in each note. To save time, I’ll just repeatedly paste the reference from the clipboard as long as I’m still taking notes from that same source.

After surfing for a few hours, I’ve found a way to link Bookends and DevonThink. Clicking on the note in DevonThink followed by going to Bookends and clicking on the reference, followed by Ctrl-Shift-Y will copy the reference back to Devonthink in the comments section. That beats just relying on the clipboard, but I wish that DevonThink would build some linkages for Bookends.

Hi Jeffrey–

I do two different things relative to citations. I’ve been using bookends, as I mentioned in the posts. If I import a whole source, I drag a link to the bookends citation into the source folder. This is done by double clicking on the source, then dragging the unique ID number of the source into DT.

When I take notes on sources, I put a citation at the end of each entry, so that when i do searches later and a note comes up that’s no longer anchored to the file structure, I have the exact citation/pg # on the note. as you figured out, you can do that with cmd-y, or cmd-k. The latter inserts a formated citation.

The same process works in linking scrivener and bookends during the writing process.

I you have more questions, the community over at the DT forums are very helpful

Thanks much for the reply. I’ll check out the DT forum. Hadn’t thought of checking to see if they had a forum.

I upgraded to DT2. I do not think its worth the effort . I am using Scrivener for my Phd and Bookends for reference and Skim for PDF. (I have also Notebook and Notetaker --useless except for clipping into ). I think that using Scrivener also for note taking is probably best and making extensive use of keywords , so you have your notes and main writing in one place . I am not sure what DT adds to all this, if some one can elaborate ! Problem with DT is that its meta tags are propriety and folders are not reflected in the Finder, which has put me off for using it as a mega collection tool and syncing means the whole database, which is time consuming and prone to errors. So actually I am not sure what to do with DT at this point . Eagle File is good, but its search index is propriety and you cannot move file directly from the finder nor search from spotligt! Its irritating . The best software so far for me is Scrivener !!

I hear you. I upgraded to DT2 and am completely put off by the cryptic file structure. It is impossible to sync files on iDisk with it (in fact, iDisk won’t sync correctly on my computers if DT2 is involved. I tried to get some information on the DT forum, but the only fellow who responded was a bit surly. So in the meantime I have dumped DT2 and DEVON Note 2 altogether for MacJournal. I’m not smitten with MacJournal, but it does sync properly with iDisk and gives me no unpleasant surprises. I still paid good money for Scrivener, and hope to use it in the future when it is time for writing a manuscript.

Synching DT to iDisk: follow the same procedure as with Scrivener.

  1. Zip the database
  2. Then copy it to iDisk.

DT becomes more valuable as you write more and more books. It serves as a central repository of data, which you may divide into sub-projects or keep intact as a single database.

For a dissertation, Scrivener may be sufficient.

I’m formerly (not that long ago) a purely PC guy, and the one place I’m having difficulty is in locating or recognizing data files. They don’t seem to be in “documents” even though I believe that I’m saving them in that folder and/or in the iDisk documents folder. That is what drove me to Eagle Filer. I know where that data is.

Your DevonThink database has a name, probably something like ReallyBigDatabase.dtbase.

The .dtbase “file” is actually a package: a folder containing as many files as necessary, plus DevonThink’s metadata. You can use the Finder’s “Show Package Contents” command to see what all is there. I’m still using DT version 1.x; I believe the database structure has become more transparent in DT 2.x.

Scrivener also uses the package structure. Use “Show Package Contents” on your BigProject.scriv file to see what’s inside.

I use DevonThink with all its quirks because I haven’t found another solution that scales as well. My main database has more than 2.5 million words in several thousand files. Everything else I’ve tried becomes unmanageable at a small fraction of that.


As Katherine says, the scalability of DT goes far beyond anything else I’ve used. My main DT database has some 2.5 million words and 5,000 entries. That is for a dissertation/book. With that much data, spotlight is useless for search anyway-- it throws every and anything at you. DT’s internal search capacity is much more robust. That size database is also too much, and too ponderous for Scrivener’s excellent research structure. I like pulling the pieces, in order, that I actually end up using when writing a chapter or section, or article into Scrivener. But, Scrivener is not a research database-- it’s a writing environment. Chose your tools for your task.

Spotlight can, and does index DT files if you want it to. For me, though, spotlight is essentially an application launcher. If I want to search my doc files, I do it from the Finder.

I’ve recently finished my book (well, pending readers reports), and am moving on to a next project. For the next book I’m upgrading to DT2.0 which has so many cool @ss improvements. But, apropos this forum, I’m also still using scrivener as my writing environment. Utilizing the two together has radically changed, and improved, my research and writing workflows. I’m hoping that with a 2010 copywrite, I can add my work to the list of books written with Scrivener (and DT).

Thank you for the reply Katherine. This is what has been confusing for me. I at first assumed that the dtbase2 file was the entire database, but moving that to the iDisk seemed to keep getting me in trouble. I asked about the issue on the DT forum and got some dismissive remarks along with the statement that the files are in the library part of the file structure, under application support. I left with the impression that they should remain in the library section of the files, not be placed in iDisk, and not run from a flash drive. That seemed to sort of paint me into a corner. I like the wiki-link feature of DT2 and also have the other DEVON applications. I would like to stick with them. Do you move or copy your DT2 files from computer to computer?


Thanks for the info parezcoydigo (yikes!). I would like to put all of my notes in DT2. I tried putting them into OmniOutliner Pro, but I don’t need that much structure during the information gathering/research phase. Instead, I need a giant repository of my research that can be accessed by keywords, etc. MacJournal has some of the capabilities, but it is no match for DT2.

If I can just figure out where all of my data is and how to copy it between 3 Macs, I’ll be a happy camper. Is it more complicated than just taking verybigfile.dtbase2 and putting it in my documents directory on the hard drive, copying it to a flash drive to transport it, and copying it to the documents directory on the other computer(s)?

Backing up the DT database:

Go to Library: Applications Support: DevonThink Pro
ZIP that file (Finder: File: Compress)
Then copy it to any external or network drive.

You might consider one copy the master file, and the others backup copies.
But if you add new material to any, modification dates will identify the latest version.