|
Ontology for Anand Kumar, Yum Lina Yip, Barry Smith, Pierre Grenon, “Bridging the Gap between Medical and Bioinformatics: An Ontological Case Study in Colon Carcinoma”, Computers in Biology and Medicine, in press. Ontological
principles are needed in order to bridge the gap between medical and
biological information in a robust and computable fashion. This is essential
in order to draw inferences across the levels of granularity which span
medicine and biology, an example of which include the understanding of the
roles of tumor markers in the development and progress of carcinoma. Such
information integration is also important for the integration of genomics
information with the information contained in the electronic patient records
in such a way that real time conclusions can be drawn. In this paper we
describe a large multi-granular datasource built by using ontological
principles and focusing on the case of colon carcinoma. Anand
Kumar and Barry Smith, “Oncology Ontology in
the NCI Thesaurus”, AIME 2005 (Artificial Intelligence in Medicine The National Cancer Institute’s Thesaurus (NCIT) has been created with the goal of providing a controlled vocabulary which can be used by specialists in the various sub-domains of oncology. It is intended to be used for purposes of annotation in ways designed to ensure the integration of data and information deriving from these various sub-domains, and thus to support more powerful cross-domain inferences. In order to evaluate its suitability for this purpose, we examined the NCIT’s treatment of the kinds of entities which are fundamental to an ontology of colon carcinoma. We here describe the problems we uncovered concerning classification, synonymy, relations and definitions, and we draw conclusions for the work needed to establish the NCIT as a reference ontology for the cancer domain in the future. Anand
Kumar, Y. Lina Yip, Barry Smith, Dirk Marwede, Daniel Novotny, “An Ontology for
Carcinoma Classification for Clinical Bioinformatics”, Medical Informatics 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. |