An ontology is a powerful way of representing knowledge for multiple purposes. There are several ontology languages for describing concepts, properties, objects, and relationships. However, ontologies in information systems are not primarily written for human reading and communication among humans. For many business, government, and scientific purposes, written documents are the primary description and communication media for human knowledge communication. Unfortunately, there is a significant gap between knowledge expressed as textual documents and knowledge represented as ontologies. Semantic documents aim at combining documents and ontologies, and allowing users to access the knowledge in multiple ways. By adding annotations to electronic-document formats and including ontologies in electronic documents, it is possible to reconcile documents and ontologies, and to provide new services, such as ontology-based searches of large document databases. To accomplish this goal, semantic documents require tools that support both complex ontologies and advanced document formats. The Protégé ontology editor, together with a custom-tailored documentation-handling extension, enables developers to create semantic documents by linking preexisting documents to ontologies. © 2007 Elsevier Ltd. All rights reserved.