How can I use Devonthink 3, PDF Expert and Zotero together?

I’m new to MacOS. I bought a Mac Air and I’d like to use Devonthink 3, PDF Expert and Zotero together, but I need some help.
I use PDF Expert for annotating and highlighting all my pdf files and Zotero for getting all the metadata from those files. I know Devonthink 3 is a powerful tool for managing and indexing files, but I don’t know how to build a workflow.
I’d like to keep using PDF Expert to annotate my files, but I don’t mind moving them to another folder/app.
Should I move all my pdf files to Devonthink 3? If I add a note or highlight using PDF Expert, will I be able to see it on Devonthink 3? Can I integrate Zotero and Devonthink?
I would appreciate some ideas for a workflow and some tips.

I do this. The missing link is Bookends. I may post a more complete outline of my workflow one day but here’s how it works in the abstract:

I use Zotero to import citations (particularly using its Safari extension). Nothing beats Zotero for this. However, as a reference manager, I much prefer Bookends. So, I use Zotero only as ‘front end’ for getting citations (metadata and PDFs) into Bookends (see here for how that’s done). Bookends has several import functions but none work as well for me as the Zotero method.

Once in Bookends, all imported PDFs are renamed according to the following pattern (which can be customised in Bookends preferences):

2020 Bloggs, Joe [[123456]] The Title of an Article.pdf

Here 123456 is Bookends’ own unique ID of that record. With that UID in the filename, you can easily refer back to the Bookends record wherever you are: looking at the file in Finder, reading it in PDF Expert, or wherever. You just need a macro or script (I use Keyboard Maestro or AppleScript) to read the front window name (so long as it contains the filename, which it usually does) and extract the UID via regex.

My Bookends library is indexed in DEVONthink. I have a script that automatically creates a custom metadata field in DEVONthink for the Bookends ID, and puts the DEVONthink UID for that same record in the Bookends user20 field. You can then query the Bookends and DEVONthink databases together via AppleScript.

From there, the only limit is your imagination (and your patience!…).

So, you’d need some familiarity with AppleScript and Keyboard Maestro, at a minimum. But it’s all possible. For example, if you’re reading an article in PDF Expert and you want to add a note about it in Bookends, instead of opening Bookends, typing the name of the article, clicking to add a note, etc. you could just have a script grab the UID, open a text input window, and add the note without ever having to leave PDF Expert. Same with adding a tag, copying a citation, and so on.


Thank you for your reply. It’s very good to know I can use PDF expert to open my pdf files, even if it’s storaged in Devonthink.

Thank you for posting your workflow and for the amazing link!
I bought David Sparks’s field guide and I’ll certainly download Bookends as well.
I don’t like Zotero as a database and I was considering to use Airtable for that, but I’ll see what I can do using Bookends.

A bit late to this party, but the Zotfile extension for Zotero can be used to manage PDFs for your collected references.

You can use this to make sure the PDFs are put in a DEVONthink-indexed folder, so you can then edit them with DEVONthink or PDF expert while keeping the metadata in Zotero.

I just use Zotero to import metadata, and then I export it to Bookends. I published how I do this here. nvm, hah, my post is linked by @prc above.