Integrate DT in scientific workflow with Papers3, LiquidText

Hi all.

I’m currently only using DT as a (dumb) file archive for important personal PDFs (bills, taxes, …).
However, reading other stories I always wanted to dig deeper and integrate it into my scientific/ academic workflow…

Maybe I need to read up more, but I struggle to see the light here.

So here is my setup:

  • All my literature is in Papers3 (approx. 3500 articles) with PDFs attached (I use this for inserting references in manuscripts and also to read)
  • I work on 2 Macs and just go a iPad Pro 10.5
  • On the iPad I’m test-driving LiquidText to better read new articles and it’s amazing. Notes and excerpts can be exported as PDFs or docx files (looking for a way to auto convert to txt or rtf). I plan on moving to LiquidText from reading on Papers3 iOS exclusively since it’s so much more efficient and better for note-taking in general
  • I use Magic Citations of Papers3 to cite while I write when composing an article in Word
  • However the knowledge mining in Papers3 sucks. Search is unreliable and I want to get better control to find relevant literature… Or related stuff

I do like the library aspect of Papers3 (also the interface to including literature in my manuscripts) and even though the future of Papers is unclear to me (been bought out) I’d prefer to keep it in my workflow. But I also want to take advantage of the advanced search capabilities (“see also” etc.) in DT… Also Papers can store notes of PDFs but I do not know how they can be accessed from other software or how best to exchange notes and excerpts between Papers3, Notetaking Apps & DT…
I really want to improve my efficiency in reading and searching articles but are a bit lost. :wink:

So the big questions for me are:

  • Do I need to have to dump my full library of PDFs into DT, too? The file names of the PDFs in Papers3 are unfortunately gibberish (some unique letter combinations I guess)? I don’t mind the space required I’m only concerned about keeping everything in sync (my Papers3 library lives on Dropbox, too, by the way).
  • Can I configure DT to parse the external Papers3 storage folder for deep searching my PDFs? Is there a drawback?
  • Can DT help to categorise PDFs based on work counts/ categories? Aka create tags/ labels (semi-)automatically and maybe even export them back to Papers3 to help categorize my library? Could I provide a list of topics or keywords and DT matches the literature against these?
  • If I want to associate notes/ excerpts to a PDF (somehow link a txt or rtf file to the PDF): what would be the best way?

Sorry for this incoherent mess… But maybe someone has solved this already?

You can use File > Index to link to the documents where they are - in Papers’ Library and Dropbox. This is a common thing to do.

DEVONthink is not going to automatically (or semi-automatically) Tag your files. Auto-tagging is fraught with more problems than benefits and would require highly structured and exact data for all documents coming in. This is a practical impossibility unless they were all documents made by one person / process. Not likely in the real world.

For notes relating to a PDF, you can try Data > New from Template > Annotation.