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Books aren't data The EPUB format is strictly XML-based. From the metadata to the table of contents to the book content, an EPUB file must be almost entirely composed of text marked up in well-defined XML schemas. Those schemas allow the EPUB book to be validated by a computer program that follows the schema and other well-defined business rules, ensuring consistent production. At the other end of the workflow, those same schemas would assure reading systems of the predictability of the books added to them.

PDF is a terrible format to convert from. For a list of the various issues you will encounter when converting PDF, see: Convert PDF documents.