Since you appear to be doing this on the Mac rather than iOS, DEVONthink Pro does allow you to (1) to extract quotes/annotate from a PDF in individual notes, (2) add comments to the note, (3) add tags (codes) and (4) link back to page/place in the PDF where the extract is.
You can then collect notes from the same or different papers by tag.
For a while I was able to do this in DTTG as well, but I haven’t been able to do this in DTTG for some time and certainly not with edit in place.
This app looks great. I’m using Highlights much the same way, but I like your approach to generating individual notes. Is there an option to have a single note per pdf? And is there a beta?
The app is built on the principle of atomic notes as one of its core concepts. All of the app’s filter, visualisation, PDF and data model features build (and depend) on this. So there likely will be no native support for having a single note per PDF.
That said, I plan to offer options to combine individual notes. Dragging multiple notes into a text editor will already combine them. In addition, I envision that one can export all selected notes to a single file, or preview all selected notes together (e.g. via integration with Marked 2). This could also include transcluded notes. And finally, I’d love to present multiple selected notes together in the app’s editor – similar to Scrivener’s “Scrivenings mode”.
Unfortunately, there’s no publicly available test version yet. Please see my reply here.
Exporting multiple notes to a single file — and especially a kind of Scrivenings mode and/or Marked 2 integration like you describe — would be fantastic. Looking forward to the app!
I think Highlights doesn’t perform too great with regards to it’s promises. Also, subscription models are a red flag for me. I own DT pro office but have nor figured out note export sorted by highlight color. This would be great for integration with tinderbox and further processing. Anyone have tips for that?
Does anybody use pdfpen pro? It seems to be able to select botes by color and then export them. Price is reasonably steep, though.