Hi @sfaj . I study ancient history and linguistics and use both DT and Zotero. I struggled to find a good workflow and finally settled on the following:
- Store all files in Zotero.
- Index files with DT.
Store all files in Zotero.
I chose to store all my files in Zotero for a couple of reasons. For my purposes, it did not make sense for me to keep the bibliographic info in Zotero and the PDFs in DT (which I did for quite some time to avoid paying the storage fees for Zotero). Zotero does a pretty good job of getting citation info when dropping in PDFs so that swayed me. But mainly I store my files in Zotero because the PDF isn’t modified when I mark it up in Zotero, but in DT it is. I was also an archivist by trade, so I like to preserve an original copy; this decision allowed me to keep a single copy rather than two. (And of course, I have backups.) Annotating PDFs in Zotero on my iPad is also a nice experience. Eventually, it also turned out to be even more beneficial because I now collaborate with other Zotero users, and I can simply drag and drop the Zotero entry to a shared Zotero library with the citation and the attached PDF to share.
Index files with DT.
Please use caution on the next step if you choose to go the same route: Indexing. What this means is that DT indexes the files or folders you choose (it does not make a copy in your DT database). But the integration is really tight with the Finder in that if you delete the file in DT, it will also do so in the Finder (if you are not careful, see below). So you can probably imagine the potential problems of deleting a file or folder in DT, only to find out your Zotero data is missing.
So with all that said, here is what I do: I index all my PDFs from the Zotero folder structure, but I index each file separately—NOT, I repeat, NOT—the folders. This allows one single advantage: It allows me to move the file anywhere in my DT database without moving it in the Finder. This makes possible the ability to store the indexed PDFs in the folder hierarchy I want in DT, rather than Zotero’s File structure and randomly generated folder names. If you index folders in the Finder with DT and then move a file within the indexed folder structure in DT, the changes will also be reflected in the Finder. But this does not apply to individually indexed files. (A major change on indexing from a couple of versions ago.) So moving individually indexed files in DT does not move them out of the folder structure for Zotero in the Finder. This does make my workflow a bit tedious, but it works for me.
One more thing to mention: If you delete an indexed file or folder in DT, the file or folder is moved to the trash in DT. I don’t empty my trash often (I am an archivist!), but when you do, you will get this popup:
Be sure to use “Only in database” if you don’t want any indexed items in the Finder to be deleted because if DT deletes the '“Files & Folders” of any indexed items, they will be deleted from the Finder as well. Take note of this, especially if you experiment with indexing with only a handful of files.
Well, that was long-winded, but I hope to spare you from the grief of inadvertently deleting any files and folders down the line. I hope this helps you to evaluate how best to integrate DT and Zotero for your own purposes.
Darryl
