There are a number of existing classifications and staging schemes for carcinomas, one of the most frequently used being the TNM classification. Such classifications represent classes of entities which exist at various anatomical levels of granularity. We argue that in order to apply such representations to the Electronic Health Records one needs sound ontologies which take into consideration the diversity of the domains which are involved in clinical bioinformatics. Here we outline a formal theory for addressing these issues in a (...) way that the ontologies can be used to support inferences relating to entities which exist at different anatomical levels of granularity. Our case study is the colon carcinoma, one of the most common carcinomas prevalent within the European population. (shrink)

We would first of all like to thank Thor Grünbaum and Andrea Raballo for their thoughtful and lively commentary on our work. We would also like to thank Daniel Rubin for taking this opportunity to describe in detail some of the research carried out in this domain since our paper was first written. Although their commentaries may seem to fall on opposite ends of the critical scale, so to speak, taken together they provide an opportunity to take stock of the (...) progress that has been made in this endeavor as well as some of the challenges that remain to be overcome. In this short response, we focus primarily on what we believe to be the most serious of Grünbaum and Raballo's criticisms to our work, arguing that our .. (shrink)

The word "ontology" presently encompasses two different meanings. In the philosophical sense, ontology has been defined since the days of Aristotle as the "science of being," also called "metaphysics." In this sense, ontology is concerned with categorizing discrete entities in reality and the relationships that hold between those entities (Aristotle 1952). Ontology, in the tradition of philosophical realism, aims to describe every day, mesoscopic entities and relations as they are in themselves, and not from the specific viewpoint of some particular (...) domain or conceptual schema. The type of entities realist ontology concerns are those that exist "out there" in the world (such as tables, chairs, mountains, streams .. (shrink)