He converted a book into the most simple of formatting called Markdown which almost anything can read including a note taking application called Obsidian.

He's using Obsidian to link ideas, chapters, passages of the book to other ideas, chapters, passages of the book using the Obsidian tools.

In this way patterns emerge that are not always visible when reading a book.

Here are some screenshots from my Obsidian work.

This is a graph of how all the notes I have made on the books I have read start to "link up" with other ideas from other books. Each small dot is a note and the big dots are the books those notes come from. If I click a dot the note I wrote opens and also shows me what other notes I linked to that note.

It's like a second brain and as I go back through what I have done I start to see patterns.