Understanding large, structured documents like scholarly articles, requests for proposals or business reports is a complex and difficult task. It involves discovering a document's overall purpose and subject(s), understanding the function and meaning of its sections and subsections, and extracting low level entities and facts about them. In this research, we present a deep learning based document ontology to capture the general purpose semantic structure and domain specific semantic concepts from a large number of academic articles and business documents. The ontology is able to describe different functional parts of a document, which can be used to enhance semantic indexing for a better understanding by human beings and machines. We evaluate our models through extensive experiments on datasets of scholarly articles from arXiv and Request for Proposal documents.