Ontologies are complex knowledge representation artefacts used widely across biomedical, media and industrial domains. They are used for defining terminologies and providing metadata, especially for linked open data, and as such their use is rapidly increasing, but so far development tools have not benefited from empirical research into the ontology authoring process. This paper presents the results of a study that identifies common activity patterns through analysis of eyetracking data and the event logs of the popular authoring tool, Protégé. Informed by the activity patterns discovered, we propose design guidelines for bulk editing, efficient reasoning and increased situational awareness. Methodological implications go beyond the remit of knowledge artefacts: we establish a method for studying the usability of software designed for highly specialised complex domains.