http://www.w3.org/ns/prov#value | - 64: PDF is fine for exactly the issues you sight, but for anything other than presenting a digital version of a piece of paper it is THE SUCK. The key concept here is that a PDF is a digital presentation of a physical object. ePub and other digital formats are designed to preserve the content (other than content that requires precise a4 formatting) and make that content easy to consume.
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