Some problems in the formal representation of hierarchical knowledge

Much work has recently been devoted to the subject of ontological engineering. Although various methodologies have been developed to assist in this difficult task, these have necessarily focussed initial attempts on the overall process. Consequently, there is a need to provide advice to the ontological engineer on the details of developing ontologies. In this paper, we specifically address hierarchical relationships, which are a ubiquitous means of organising ontological knowledge. Little work has been done on developing principles for the representation of such knowledge. Towards the rectification of this, we identify five types of problem that can be met in moving from an informal description to a formal representation of hierarchical knowledge. Each of these problems is discussed in detail, giving examples from biological theories and addressing potential solutions to these examples.