I highlight as a way to categorize my annotations. I highlight in Zotero as I go, and in the highlight's comment section briefly jot down why (e.g. something to follow up on, or whether this reminded me of something else it contrasts with). I dedicate a certain colour to "background references I should have", another to ~ "things I disagree with" etc., which I find useful when coming back over the paper to type up my notes.

In a sense the highlighting is just a way to localize my thoughts to a particular passage of the text, and the colours (or even highlighting at all) are secondary.

There's some considerable duplication of effort (notes in Zotero, then I type up notes in Obsidian, then also extract out some of those ideas into their own files). But, much like the recent posts about "outsourcing thinking" and GP noting that people sometimes do nothing with their highlights, I find that the work is useful for understanding and remembering.

Out of interest, why have you been considering Logseq?

> Out of interest, why have you been considering Logseq?

Primarily because it's FOSS; I love Obsidian (I even pay for it) but I have to consider the possibility that they'll be bullshit and start charging for stuff or start restricting things arbitrarily. If Logseq becomes bullshit then I (or someone else) can fork it and maintain/grow it. It's also written in ClojureScript, so legally I have to kind of like it :).

I've also kind of grown to like the way that the "unit" of Logseq is the "block" instead of the "page". Pages are more about aggregation than "units" of information, and as a result of this I find that the graph view is actually useful, instead of just something pretty in Obsidian.

There are some things I really don't like about Logseq (the lack of proper Vim keystrokes being a big one for me), but one of my biggest pet peeves is when people try software for five minutes, make zero effort to understand what the application is actually trying to do, give up, and declare the software as "bad". I felt like that's what happened with Gnome Shell, for example.

I will likely eventually go back to Obsidian, but I figured that I should give Logseq a fair shake, and it's different enough from Obsidian that I felt it's only fair to spend a few weeks properly learning it.