The EPUB framework relies heavliy on the Eclipse Modeling Framework (EMF) as the entire data structure is described using a set of Ecore models. The figures below shows the outline of an EPUB file and the purple boxes illustrates the components that are modeled. Note that only EPUB 2 is currently supported. The figure for EPUB 3 may change.
The Daisy NCX hold the table of contents and navigation hierarchy of the book. It has been deprecated and is replaced by the EPUB Navigation Document in version 3 of the specification. There are quite a few changes in the package document also which makes it unlikely that the EPUB 2 data model can be reused for EPUB 3 support.