The qualitative and time-dependent character of spatial relations in biomedical ontologies

The formal representation of mereological aspects of canonical anatomy (parthood relations) is relatively well understood. The formal representation of other aspects of canonical anatomy like connectedness relations between anatomical parts, shape and size of anatomical parts, the spatial arrangement of anatomical parts within larger anatomical structures are, however, much less well understood and only partial represented in computational anatomical ontologies. In this paper we propose a methodology of how to incorporate this kind of information into anatomical ontologies by applying techniques of qualitative spatial representation and reasoning from Artificial Intelligence. As a running example we use the human temporomandibular joint (TMJ).