You should look at logseq [1]. It is primarily an outliner but has a good integrated PDF reader with highlighting & annotation support. Content is saved as mark

You should look at logseq [1]. It is primarily an outliner but has a good integrated PDF reader with highlighting & annotation support. Content is saved as markdown. It has pretty much replaced other note taking tools for me, but I know of people who use it in conjunction with Obsidian/Zettlr/Zotero. [1] https://logseq.com/ https://logseq.com/