Agree - and equally important - rememeber that you can easily generate an item link for an indivdual entry in Zotero or for a specific Collection in Zotero. And that link can be to the citations on your local computer or synced to Zotero web. These items links can be added to Devonthink as bookmarks or can be pasted as active links into an Annotation note or any other RTF document in Devonthink.
Thus out of the box with no power user configuration needed, Zotero and DT3 integrate well together. Zotero works to maintain and search your whole collection of citations; and DT3 exists to organize specific citations or collections of citations in the context of a particular project or topic you are working on in Devonthink.
Bookends has similar capability so you can save some of your citations in Zotero and some in Zotero and still refer to either or both in Devonthink.
@rkaplan yes, sometimes I remember to put Zotero item links into the metadata of a devonthink file, and vice-versa…but mostly I forget! Fortunately, after spending a while looking for a script or tool that would do it for me, I’ve also found it’s just not that annoying to switch to Zotero and search for the reference I want to find.
Your pdfs are now in a place that Devonthink can easily index
When you open a pdf from Zotero and make highlights, those highlights are saved to the pdf and seen by Devonthink, or alternatively, if you make annotations in Devonthink, those annotations can be ingested into Zotero
You can sync all of your data to Zotero.org without hitting the file storage limit (re-installing on a new computer will work as long as you’ve backed up your pdfs and you don’t change the file structure on your next computer)
Copy the tags from an individual article and paste them onto the PDF in DEVONthink (it works, even with multi-word tags)
Create url links from articles, notes, snapshots, and other things that you can use in Zotero as bookmarks, etc. They look like this: zotero://select/library/items/MXJ9TA2T and open directly into Zotero
I’m having an issue that I believe stems from the PDF file type itself. Although Adobe attempts to define a standard for PDF annotations, many applications (including, I believe, Adobe’s own applications) do not fully conform to the standard. Especially when working on both Desktop and iOS, the OCR layer of PDF files becomes corrupt in some way. Sometimes the invisible OCR layer drifts out of alignment with the visible text (this even happens on digital-first, non-scanned PDF files), and other times the OCR letters become nonsense - maybe a unicode encoding issue introduced when geh annotated file saves?
Because of the ongoing corruption problems I experience when annotating and editing PDF files, I tend to prefer programs where the annotations are saved independently from the PDF file. This avoids editing the original file, and effectively bypasses the source of the problem, while still allowing me see highlighted text overlaid on the document. I know of two macOS applications that save annotations independently from the PDF file: Skim, and the new PDF viewer in Zotero 7.
DEVONthink is able to parse and display the annotation format used by Skim (thank god) but DT doesn’t “see” the new Zotero annotation format. (As an aside: this makes me wonder if someone has made a Zotero extension that turns Zotero annotations into Skim-style annotations.…)
On iOS, afaik there are no apps where I can annotate a PDF text without actually editing the file, aside from Zotero (which as I said above, is not compatible with DT’s annotation viewer). So I think I’m at a dead end for now. I can either a) stop using my mobile devices for annotating PDFs, b) switch out of DEVONthink for PDF reading and only use Zotero, or C) find other ways of dealing with the ongoing corruption problem, ie. always saving an unannotated backup that I can revert to if the file becomes damaged. Idk what else I can do… Maybe try to avoid PDFs and convert to EPUB whenever possible? Or use a more “analogue”-influenced annotation workflow similar to GoodNotes or Notability?
EPUBs would not be a good substitute for PDFs IMHO.
I tend to prefer programs where the annotations are saved independently from the PDF file.
But then you do run the risk of compatibility issues as shown with Zotero. Also, there’s another file to add to things you need to manage.
Although Adobe attempts to define a standard for PDF annotations, many applications (including, I believe, Adobe’s own applications) do not fully conform to the standard
PDF is an old and storied format that has many deviations from PDF producers for years. It amazes me more don’t break.
However, it’s still a great locked format that usually excels at retaining a visual appearance while still being searchable.
If you want to index the pdf files of Zotero to be indexed in DT, you can use Zotfile which moves the files from Zotero’s data folder to an external folder. But, the problem is, Zotfile will make your files inaccessible to the ios counterpart of Zotero.
Alternatively, you can index the parent folder where Zotero stores the pdf files.
I have files in Zotero database and index it in DT (before I used Zotfile and Dropbox for sync, now I moved to Zotero Storage because of the IPadOS and iOS app)
I only index storage folder, the only difference between previous setup and now is that I use smart rule for displaying all PDFs in a smart folder
And if someone has a problem with how new Annotations now work, is it still possible to use PDF reader (like DT) for annotation and not Zotero (there is an option in preferences to change it)
What are you using for file syncing? Before I switched to Zotero sync I was using Dropbox for my PDF with synced folder in the PDF Master on iOS and never had any problems with corrupted files
@bangersandmash With Hook app you could have a markdown link with article title and author (Zutilo also has a configurable quick copy shortcut)
You can use external pdf readers such as Pdf expert or adobe. They save the annotations into the pdf file itself. I think the standard annotation is visible inside Zotero’s reader; seems like you cannot edit it.
The reader in Zotero save the annotations into a database; not into the pdf itself. Personally, I don’t like to read inside Zotero because of the non-standard nature of the annotations. Bookends is better in that regard.
