Annotate simply means to make notes or comments. There are three ways of annotating ebooks
Note: You can only annotate books that you read online
You can bookmark pages in books. You might want to bookmark a page so that you know where you left off, or a page that contains information you find useful. To bookmark a page, click the 
button. This appears in the Read Online productivity menu bar and on each page of a book.
Like the bookmarking button, the highlighting button 
appears in the productivity menu bar. If you want to highlight text, either click the highlight button and then select the text to highlight it (click left mouse button and drag over the text, then release the mouse button) or select the text first to make a pop-up menu appear.
The first button is for copying
The different coloured pen buttons are for highlighting - in yellow (or orange, depending upon your display), blue or purple. So ,with your text selected, click a highlighting button to highlight the text. You might think about using different colours for different purposes - for example:
Like the bookmarking and highlighting buttons, the note button, 
appears twice - in the productivity menu bar above the text and in the pop-up menu that appears after you select text. Select your text as in the highlighting section and click the button.
Using the note button in the productivity menu bar lets you create a note on a page but does not highlight text.
In the online reader, you can see your annotations by clicking 
The annotations are listed by chapter or section. Click on a chapter title to see the annotations
In this example, in the book Practical Temperature Measurement, the preface has 5 annotations, 3 in Chapter 4 and three in Chapter 5, the first of which is a bookmark (see the bookmark icon, next to Page 139?). Clicking on Page 139 or the associated text will open that page in the online reader.
Annotations can also be accessed through the Bookshelf
Clicking on the Annotations link below the book details will open the book's annotations in the online reader as above
