The human karyotype has been used as a mechanism for describing and detecting gross abnormalities in the genome for many decades. It is used both for routine diagnostic purposes and for research to further our understanding of the causes of disease.Despite these important applications there has been no rigorous computational representation of the karyotype, rather an informal, string-based representation is used, making it hard to check, organise and search data of this form.In this paper, we describe our use of OWL, the Ontology Web Language, to generate a fully computational representation of the karyotype, the development of this ontology represents a significant advance from the traditional bioinformatics use for tagging and navigation and has necessitated the development of a new ontology development environment called Tawny-OWL.