This is an excellent guide for web annotation but for those on Linux.
The author has forgotten about PowerNotes and WeavaTools.
Polar is an exciting project, but I found the implementation deplorable. If you are out of luck or can’t think beyond Evernote, then this guide isn’t for you.
For PDF annotation, I am using PDF Expert on Mac (for lack of better alternatives). Hypothesis is backed by a non-profit group, but they make the export nearly impossible. I don’t know why the people get creamed about the “non-profit-open-source” moniker. I am not impressed, and I don’t recommend it. I “might” use Liner but they don’t have compelling export options- yet.
Hypothesis.js
Already mentioned in the previous section, it’s also capable of annotating PDFs via pdf.js.
Check out their guide, especially if you’re using Chrome, apart from it it’s as easy as opening the PDF in your browser and activating Hypothesis. It fingerprints the PDFs so you don’t have to worry about losing your annotations and it’s easy to collaborate with other people.
It seems to work fast enough for big PDF books as well, however generally reading long things in browser is not very convenient as you lose reading position if you close the tab.
Polar
Polar is a new project which aims to be not just reader, but ‘personal knowledge repository’.supports highlights and comments
document repository, so you have overview of all the stuff you ever read/commented. It also keeps track of your reading position.
the PDFs are fingerprinted, so you don’t need to worry about moving them around your filesystem
~.polar directory holds all the data, which makes it easy to share among your computers (e.g. via git, or if you keep it on Dropbox and symlink)
metadata is in well structured json files, which makes it easy to access from scripts
highlight locators keep matched text alongside the absolute coordinates, which leaves potential for matching against different editions of the PDF file
it’s got builtin flashcards engine. Personally, I’m too used to org-drill now, but that’s a great a way of introducing spaced repetition to people.
the author is very passionate about this project, invests a lot of effort and quite ambitious
via How to annotate literally everything | Mildly entertainingᵝ
RadOncNotes 