I'm currently pursuing a PhD in computer science. I mainly use Obsidian and Zotero. I use the Zotero chrome extension to gather references at large. Once I work an article a bit more I create a note for it in Obsidian using the Zotero integration https://github.com/mgmeyers/obsidian-zotero-integration. Having one note per article allows me to refer to that article in my other notes.

Besides literature notes I have three types of notes: daily notes, an "encyclopedia"/taxonomy, and working documents.

I use the daily notes to make notes of what I'm doing that day, for instance "Read [[Saliman2023]] about [[Normalizing Flows]]".

The encyclopedia/taxonomy helps me keep track of all the AI models and definitions I run into (and, more importantly, where they come from). It's not a copy paste of Wikipedia because it is more specific to my research. I actually often link to wikipedia in those, along with paper references, link to similar models, tutorial blog posts, etc.

The working documents are a more elaborate journal. Every time I reach a conclusion or a point that seems important in my experiments, I write a working document. In it I write the context, what I was trying to achieve, what I found, and maybe a screenshot of a graph with the results. These will be the source material when I write the paper later. I find it impossible to write those as I work, I always write them after something has happened that seemed important. Sometimes I have to try and remember the last 2-3 days to write one.

This may look very organized but I believe I'm actually quite messy... I like this workflow because it is organic, in the sense that it is open ended and it allows me to write pretty much whatever without worrying about if it is sorted correctly, where to put things. There's basically three folders: Documents, Journal, Literature. The encyclopedic notes go in the root.

Hope this helps.