When one annotates, what is involved is usually whatever will help a student (or reader) do whatever it is he or she needs to be done by manner of in-text note taking in order to best understand the text being read. For instance, typically, in the margins of a text, notes can be taken that provide a summary of a paragraph. Areas of the text, too, can be highlighted/underlined that are confusing as a reminder to do additional research on otherwise confusing concepts presented in a text. Some students will circle key words and definitions and even write down questions or ideas he or she may have had when reading for later class discussion or future research. Thus, again, annotating is a type of in-text note taking one may do in order to help him or her better comprehend a text.
