If it is not meant to be hand coded then I would think that starting with Markdown is a bad idea. Markdown was meant to be human readable with minimal markup. T

If it is not meant to be hand coded then I would think that starting with Markdown is a bad idea. Markdown was meant to be human readable with minimal markup. This means that there are many limitations as to what you can represent in Markdown. To me, it would make sense to start with something more expressive. There are many different types of books (fiction, technical, poetry, interactive) and many types of semantic information that you will need to encode that publishers may require. Moreover, it is not just semantic information you need to capture. For some books the placement of the elements on the page, the font used, etc. may be important. If this format is also meant as an intermediate format for printed books then you only need to take a look at LaTeX and its numerous packages to get an idea of all the different things someone might require. Even if you decide to go with something like Markdown, it makes sense to look at mmd and pandoc extensions (e.g. for tables) before coming up with another syntax.