Just wondering about this: keep pdfs and metadata separate – Why is that important? I just had a Zotero workshop in which I learned I get enough free space for about 300 pdfs, so why wouldn’t I use it for document storage? I also use DT3 and, indeed, it is a little confusing trying to toggle between DT and Zotero. I would probably be more efficient using one (DT3) for doc storage and one (Not) for biblio/referencing management – that’s what you’re suggesting, yes?
Hello! Yes that’s what I am suggesting. Zotero does store the PDFs in a local folder on your HD and allows for syncing across devices and online access, so that’s handy. However, I find Zotero’s native storage structure counter-intuitive. I prefer having my PDFs all in DT3 particulary because I can annotate there more easily, and move the files across to relevant project folders by creating replicants. I also like the idea that is I were ever to migrate to another bibliography manager, all I am transporting is a big XML file with all the citations, rather than an entire library. Also, my own storage needs rather outstripped free allocation (though I am still paying for Z, it’s wonderful and I want to support them). I also access my library on DTTG, which is much easier that way, there’s isnt’ a Zotero solution for iOS that really worked for me.
Zotero does have a plug-in (Zotfile) which allows for much more flexibility about storage and PDF renaming rules, which could play very nicely with an indexed folder in DT. I just went all in storing, not indexing, my research in DT (in part because I need to sync across two Macs) and personally like to have it all to hand there.
All that said, I think storing within Zotero is perfectly fine if it suits your needs. I like the flexibility of my set-up, but whatever works for you!
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Thanks very much for your response … I sure see a benefit to having my library in a single location (DT3) and using Zot as a meta-data respository, for convenience / efficiency and also matters of storage. Of course this leads to another Q, then: In ‘peeling out’ some files from Zotero, with an eye on transferring these into DT3, I want to leave the ‘parent’ info (metadata) in Zotero, obviously. So far this is a tedious, manual task … is there a way to do this more efficiently?
Mmmh alas no, I’ve not found a way to automate but sure it could be done (by some of the clever people on these forums!) At least, you can access the storage folder used by Zotero directly: locate it in Mac’s Finder, open it, then view ‘as list’, type ‘kind:PDF’ in the search bar, and then limit results to the Zotero storage folder (this shows in one view all the PDFs which are stored one level down, in their invididual, numbered folders, by Zotero). From here on you could simply copy the lot to wherever you want it. I’ve never tried deleting them from there, but I suspect you’ll confuse Zotero if you do so, leaving link to non-existent files. I simply spend a few hours over the summer recently, cleaning up my Zot library in this way.
I’d give some thought to using a native mac app with applescript support rather than zotero. I use BibDesk even though I don’t write in Latex because it’s so richly scriptable.
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Thanks again! I put my head down in the last couple of days and worked to harmonize the contents of DT3 - my library of working documents - with Zotero - now my archive of metadata. In Zot, I dragged in many docs from my DT3 library, ensured that metadata was accurately entered in the ‘Parent’ Info fields and then deleted the (mainly) pdfs. Original pdfs - some annotated, some not, as well as many other notes and artifacts are safely tucked away and indexed in DT3. Whew … I backed everything up and I’m ready to keep swerving down the road (on my PhD journey)! Ciao.
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A quick question about highlighting with PDFExpert on iOS - so you’re opening the PDFs on DTTG, but then opening them from DTTG to PDFExpert to highlight, and the changes are saved in DT?
I’m asking because I saw a lot of workflows that use Highlights app on iOS, but if you wanted your annotations synced (for example, having that folder indexed by DT), the folder needs to be in the cloud via iCloud or Dropbox or such.
So I’m hoping to find a simpler way to go about highlighting PDF’s without having to then export/copy them to a folder I index w DT (I used to highlight in Mendeley, and that works as a charm if it weren’t for the locked-in highlights, ugh.)
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On iPadOS, once a .PDF has been added to a DT database, I open PDFExpert and use the Files link in the sidebar to open the file. I select the DTTG Location and then navigate to the database and folder where I added the file to DT.
All highlights and annotations made in PDFExpert are there in DT when I access the database.
On the rare occasion I can’t access a file with this method, a reboot of the iPad fixes it.
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THANK YOU! Well, that just might make me buy their subscription.
Now when DTTG 3 is out, it’s time for sharing shortcuts! 
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