I’m an academic in the humanities and went all-in into DT some years ago. I’ve never looked back, it’s an outstanding research tool and my go-to brain for nearly everything now. I haven’t automated a great deal because I’ve never learned to Apple script and at this stage, it feels like the many (exciting, beautiful) integrations and scripts that people use to customise interaction between apps will take me more time to set-up than that I will win back in the end. I may be wrong. Anyway, some details of my set-up:
- DT3 contains all my research materials in a series of DBs (‘Research’, c. 40GB, one for ‘Images’ 30GB many taken from manuscripts, kept separately largely due to file size and syncing needs; and another I’ve ambitiously called ‘Zettelkasten’ following that broad philosophy of note-taking, but to be honest it never really took off).
- Reading notes are in many formats: handwritten (then scanned with iPhone and saved as PDFs) and typed. I’m forever streamlining this system in order to find stuff later – most importantly, each note is saved in a folder (‘Reading notes’) with the same file name as the original source PDF (Author - date - Title). At times I create link backs from note to PDF, but I don’t always bother.
- I am now a heavy user of replicants. This allows me to keep a central library of ‘Primary’ and ‘Secondary’ lit in a single place (and further such documents and notes, e.g. I run separate folders of notes that are essentially manuscript descriptions and indices), and replicate any relevant material to dedicated project folders (largely, these map onto writing projects, e.g. articles, books, chapters). It is this feature alone that sold DT to me.
- Because of my reliance on replicants I import everything. I dipped my toes in first, indexing a lot, but it just didn’t work as well. I trust DT to keep my data save, and of course, it’s a breeze to get it all out again.
- I sometimes create a top-level bibliography for new projects in such dedicated folders: an RTF or MD file that contains the bibl reference (copied from Zotero) and active links to the primary and secondary sources, and reading notes (stored in the central DB).
- I use Zotero for bibliographical management, but without any of the automation that the other author linked by cgrunenberg has suggested. I simply keep it running alongside and don’t use it to extract a bilbiography until the formatting stage (see below). I don’t use any ‘watched folders’ – rather, when I download articles into Zotero, they are renamed with Zotfile and then I use the ‘share’ sheet to push a copy into the DT database and file it there. I do this sporadically enough not to have invested in automating. See above!
- My writing workflow centres around Scrivener for any long-form writing: this lives on the left side of a 24" monitor, with the dedicated project folder in DT3 open on the right hand side. I might run another window on separate screen of the entire ‘Research’ db which contains the rest of my materials, for global searches.
- Bibl refs inserted into Scrivener drafts are my own short hand place holders (e.g. {Smith 2009, 123}. I compile the Scriv draft only at the very end of the writing process and then key in the references using the Zotero plug-in (with Word). I know that you can also scan your RTF drafts for automatic insertion, but I don’t use it. This is time-consuming and could be improved.
- I do shorter note-taking in Ulysses, or straight into DT by creating new notes in RTF. I am getting going with MD format now, having been persuaded on this forum that plain text is really the way forward for future-proofing and inter-device exchange, esp. to iOs.
- I’ve more recently got into mindmapping: Mindnote works well, and DT handles the file format okay. I also export the native format to MD since they the mindmaps are visually represented in DT but not searchable.
- I run DT2G on the iPad, which syncs selected chunks of the ‘Research’ database. It largely functions as my e-reader. I annotate using DT2G’s native annotation tools (highlighting, pens, etc) which are a little clunky but serve my needs perfectly.
- The ‘Readling list’ metadata offered by DT3 seems cool but doesnt’ sync to iOs at present (I think). So I run two smart groups which I use ALL THE TIME, ‘To Read Teaching’ and ‘To Read Research’. This looks for documents with tags of the same name in the DB, and if found, creates a replicant of those docs in a separate folder. It’s only these folders that I’ve set to ‘always download’ on my iPad. This really saves on having to sync an entire 40GB database (I don’t have the memory).
- Using DT2G as a note-taking tool on iOS is still awkward though the devs have hinted that this feature is in active development. MD is better than RTF (not supported, I think). This is the main reason that Ulysses is still in play for me. But I largely use the iPad as a tool to ‘consume’ (read, annotate) data, largely PDFs; for ‘production’ (any sort of writing and organisation), my MBP and Mac Mini do virtually all the work.
This is a broad overview of my workflow with DT3 proudly at the centre of it all. I’d be happy to elaborate if you have any questions!