While Isabelle is mostly known as part of Isabelle/HOL (an interactive theorem prover), it actually provides a framework for developing a wide spectrum of applications. A particular strength of the Isabelle framework is the combination of text editing, formal verification, and code generation.Up to now, Isabelle’s document preparation system lacks a mechanism for ensuring the structure of different document types (as, e.g., required in certification processes) in general and, in particular, mechanism for linking informal and formal parts of a document.In this paper, we present Isabelle/DOF, a novel Document Ontology Framework on top of Isabelle. Isabelle/DOF allows for conventional typesetting as well as formal development. We show how to model document ontologies inside Isabelle/DOF, how to use the resulting meta-information for enforcing a certain document structure, and discuss ontology-specific IDE support.