A navigation schema specifically focuses on the navigational structures and the relationships between these structures present within an interface. A very practical example of this as a deliverable would be: the global navigation (top nav), tool bar, and left rail (in various states) for a product facet search on product pages. These are important to tease out separately from other UI elements for many reasons, one of which is because they need to appear in a style/developer's guide.
You can also analyze the navigation schema in parts:
- Global Navigation
- Primary Navigation
- Secondary Navigation
- Breadcrumb Navigation
- Footer Navigation
As you can see here in the following image: