I have my own system of note taking Specifically for Academia. The main requirement here is that you have to keep meticulous track of your primary sources and are able to cite them.
I have a repository with the vault and in it is a link to the article explaining every aspect of the system.
The system is based on Zettelkasten, but is a bit more geared towards natural sciences I would say, as I found ZK not perfect for that. Here is a visual breakdown.
Recently I was playing around with replacing Zotero as a citation manager - and some of it is also already integrated into this vault.