A person who works with documents usually does three things: they underline items, highlight concepts using different colors, and make notes on the paper. Imagine being able to do all of these things on your computer. Well, yes, it is possible. The name of the program that allows you to do so is Skim, which is a complete PDF reader with a wide range of note-taking functions.
The shape and color of the notes that you can make will remind you of a typical post-it. You can stick them wherever you want and adjust their size.
There are two types: one that appears on top of the document and another one that is represented by a little icon that stores all of the note’s content. The second option is great when the text of the note is rather long. The other things that you can do with this program are: underline, cross things out, highlight text, circle things to point out concepts, etc.
The tree view on the left shows the relationship between the different pages in the document. On the right, it shows the relationship between notes, arrows, underlining, circles and all of the other objects that you have inserted in a page.