Indexing Zotero PDFs but with multiple DT databases?

I’m a historian, I use Zotero and Devonthink, and have just learned about indexing my Zotero-stored PDFs to DT. I can’t wait to do it…

…except that not all of my references belong in the same database. While 80% of my Zotero references are for the book project I am currently working on (about the history of sugar; call it A), 10% of them are for an older project (about a river in London; call it B), and 10% are for my next project (about the history of doping in sports; call it C, and C will keep growing). I have a different DT database for each project. Within Zotero, I have a tag for each project so I can used saved searches effectively to identify the relevant references.

Does anyone have any ideas for how to differentiate the entries in Zotero, and the PDFs that Zotero stores, so that I can index the Zotero references for project A to DT database A, Zotero refs for B to DT database B, etc.?

In short I’d ideally like to
(a) keep PDFs organized alongside their references in Zotero
(b) index those PDFs to Devonthink so I can take advantage of them for research
(c) only index to a particular DT database those PDFs that are relevant to that project

At the moment I’m wondering if I should just give up on Zotero as a PDF storage. I could use the Zotero connector browser plugins to download the PDFs, insert a zotero select link using @mhucka 's Zowie program, and then import rather than index the PDF to Devonthink where I could annotate and manipulate it. The metadata in the imported PDF would still include a link to the relevant Zotero entry.

Thanks for your help!

You could organize your Zotero database using two (or more) collections and sort the references into the correct collection. Then just index the appropriate Zotero collection(s) folder(s) in the respective DEVONthink database.


Oh, brilliant—that seems like it could work! Do you know whether saved searches are legible as collections in Zotfile using the %c wildcard?

The Zotero documentation says that saved searches are “like collections” or “appear as collections” but that may not be quite the same thing.

Very grateful for the quick reply, too.

I don’t know for sure about saved searches–but my gut says no since it’s already a hack of Zotfile… I don’t really use collections or saved searches for my references though, so could be wrong!

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Thanks for all the help. I think, in the end, I am just going to switch to using Zotero as a reference and citation manager and use Devonthink to hold all my PDFs and notes. The fact that Zotero notes are not separate linked files, like DT annotations, makes me feel like it’s hard to swap from one to the other.

It’ll be useful to have Zotero capture the PDFs with its browser plugin, and possibly use Zotfile to sync/retrieve them from a tablet. But then I will just import the PDFs to Devonthink and work from there.

On the plus side, moving all my PDFs and notes from Zotero to Devonthink is going to be excellent procrastination.