When reading books, I take notes on the book--brief notes indicating points of interest as well as longer notes, especially if I disagree with some point. The typical direct product of these is a chapter-by-chapter summary, with a greater or lesser degree of detail depending on my interest.
For ebooks, my notes are often organized around highlights:
Each night, a cronjob runs that extracts my highlights and comments from calibre and imports them into my database:
The imported annotations are automatically tagged
inbox, and I have a weekly repeating item on my schedule to process items from this inbox. These are presented to me in a simple list, with highlights from the same source sorted together:
If those annotations are citations to some other book or article, I add the article to zotero, in an inbox collection, which I also work through weekly (removing the
inbox tag from the quotation, but retaining it as a record). Otherwise, I use them to construct my notes--either the summaries mentioned, or topical notes.
Highlights in my database can be transcluded into other notes or blog posts, like this:
Transclusion preserves the source of the quotation automatically. For annotations that aren't to be included directly, they remain linked in my database to the source document, included in searches, so I can refer to them in the future. My topic-oriented notes then come out like these notes on Newcomb's problem. I typically write them in emacs using
A post-save hook I've written automatically synchronizes my notes in org-roam with my database, translating org-roam links to ID links in the database, which can then be automatically exported in a form like this blog post. My database has support for making only some notes or some parts of notes public, so I can use this single system for all stages of the process.
For PDFs, I usually read either in polar or on my tablet (in Moon Reader+), manually adding the annotations to my database, since it's impractical to handle automatically. For paper books, I take notes on paper. The rest of the process is the same.