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This explains in detail the architecture of SiphonTools, along with easy ways for you to extend the tools to suit your needs.

Siphon is composed of three different "main" component:

A Store for saving the annotations. There is a provided base store class that you should extend when implementing your own version of this.

A set of Annotations that are located in the store. These are basically "markup" on the current page. There is a large collection of subclasses that represent different functionality that you can extend.

Finally, Selectors -- interactions that connect user interactions to the generation of annotations. There might be multiple triggers / ways to trigger the creation of a single annotation type, or tiggers can differ based on the environment. Triggers will obviously return different types of data on their execution -- they can be HTML elements, a rectangle on a page, a point on a page, etc.