How I index my Zotero database from DEVONthink

The following is an explanation of how I set up indexing of Zotero's storage folder from DEVONthink.

First, do not to import the files into DEVONthink: leave them where they are in Zotero's database. In DEVONthink, use what they call indexing. In the PDF manual for DEVONthink 3.8 (which you can download for free from https://www.devontechnologies.com/support/download/extras), the description of indexing starts on p. 51.

In my case, I have a couple of additional folders ("groups" in DEVONthink-speak) related to Zotero, so what I did is first create one top-level group in DEVONthink called "Zotero". I opened this "Zotero" group in a separate window in DEVONthink, and then used the menu item File ▹ Index Files and Folders (which has keyboard shortcut ⌥ ⌘ x) and in the dialog that this produced, navigated to where I put my local Zotero database on disk outside of DEVONthink, and found the Zotero folder named "storage".

This will create a group in DEVONthink that is actually not a real group, but a pointer to the Zotero storage folder on disk. DEVONthink will proceed to create an index of all the files and folders it finds, and present them as if they were files and folders in your DEVONthink database. (They are not really "in" the database, and this is an important thing to keep in mind because it has implications for how you store things and whether you can synchronize the Zotero files between two computers running DEVONthink.)

An unfortunate thing about DEVONthink is that it doesn't provide a way to select which files are indexed: it indexes everything in your Zotero database, including HTML, CSS, JavaScript, and other files that end up there if you store (e.g.) web pages in Zotero. It also presents the exact Zotero folder hierarchy as it appears on disk, which is exactly what it should do, but is really inconvenient from the standpoint of human readability and navigation because of how Zotero's attachment storage is structured. To deal with that, what I did is create a DEVONthink smart group that searches the indexed "storage" folder in DEVONthink and finds only the most important file types (for me), like PDF and a few others. Here's what that rule looks like for me:

This produces in DEVONthink a nice flat listing of the articles, books, and other documents in my Zotero database:

Then, when I'm looking for something, I look in my "References" smart group instead of the "storage" group in DEVONthink.

Last note: I tried on two separate occasions to organize my materials in such a way that I kept the Zotero index in separate, dedicated DEVONthink database. I always ended up putting the index back into my main DEVONthink projects folder. The reasons are: (1) there's no way to share tags between databases in DEVONthink, and (2) the DEVONthink annotations facility only works within a single database and not across databases. Depending on how you use tags and annotations in DEVONthink, this may not matter to you, and maybe putting your Zotero index and other materials into a separate database may be more useful.

Hope this helps! Mike