I’m a medieval historian and I use a system that suits my historical research rather than any theoretical Zettelkasten system. It has similarities to rfreeborn56.
I have a list of sources, including manuscripts, that I want to consult for my research, perhaps with a note of the pages or sections to look up. The next stage is to find out where I can get hold of a copy, whether in my local university, a distant library somewhere, internet access, or perhaps buying it myself second hand. I download catalogue entries with Zotero or enter them by hand. When I’m ready to start reading a work, I create a note called e.g. Crouch English Aristocracy. I start with the full bibliography entry for the work, dragged over from Zotero. I then give details of where I found the work and the date(s) I read it. I leave space for comments on the author and the work as a whole, add a keyword or two, and finish with an automatic embedded list of any other notes I have that mention and .
I make separate notes, all linked to my first note, calling them e.g. CrouchE 51 Knights as a social group. This shows what the note is about, and it keeps all the notes from one source together and in order. I rarely note everything from a book, but instead choose to write notes on (a) details of relevant evidence, usually copied verbatim, to use for or against various interpretations, mine or other people’s; and (b) the comments that arise in my mind as I read the author’s interpretations; for this I need to paraphrase or copy verbatim enough of the passage to provide sufficient context to explain my comments. I like my notes to be self-contained, so that, with luck, I don’t have to go back to the original source again. I therefore distinguish carefully between quotes, paraphrases and my comments, and I include exact page numbers and all relevant footnotes. I add keywords, and links to other notes, and each note has an automatic footer listing its back links. All these notes are to be kept permanently for future reference.
When preparing for writing, I use what I think of as a Connection note, where I collect all my possibly relevant notes together. I start by using my keywords. I can collect all notes with keyword X and all notes with keyword Y, or I can limit them to notes that have both keyword X and keyword Y. These notes may have Out links or Back links that are relevant. I sort the notes into sections. Within each section I open the notes in separate floating windows which I can then arrange into a suitable order ready to use them for writing. The same Reading note may appear in more than one Connection note. I also keep all my Connection notes for future reference. I’m always worried that if I throw anything away I’m bound to need it later on. Fortunately, computer hard disks don’t need all the space that used to be taken up by my old index cards.
I therefore have the three types of notes, each type with its own icon. These are all kept in a single directory. I have a separate directory for pdf files of texts, and another one for images. I can put links to these in my Reading notes. For what it’s worth, I still use a very old personal wiki system, ConnectedText, for my notes. It may be that future changes to Windows will stop ConnectedText from working. I am therefore always on the lookout for a replacement. Obsidian looks as if it may well become a possibility.