Gary H. Merrill
(For a complete list, see my CV)

Abstract.This presentation was made to the technical experts session of the BioSynC Workshop and emphasizes several critical concepts, distinctions, and principles in constructing ontologies in the empirical sciences.

Abstract. In a series of papers over a period of several years Barry Smith andWerner Ceusters have offered a number of cogent criticisms of historical approaches to creating, maintaining, and applying biomedical terminologies and ontologies. And they have urged the adoption of what they refer to as a “realism-based” approach. Indeed, at times they insist that the realism-based approach not only offers clear advantages and a well-founded methodological basis for ontology development and evaluation, but that such a realist perspective is in fact necessary for understanding and using terminologies and ontologies in science.  This paper explores a number of questions surrounding such claims, provides a careful characterization of the type of realism recommended by Smith and Ceusters, and evaluates the role that realism plays in the critiques and recommendations that they offer. The conclusion reached is that while Smith’s and Ceusters’ criticisms of prior practice in the treatment of ontologies and terminologies in medical informatics are often both perceptive and well founded, and while at least some of their own proposals demonstrate obvious merit and promise, none of this either follows from or requires the brand of realism that they propose.

Abstract.This paper advances a detailed exploration of the complex relationships among terms, concepts, and synonymy in the UMLS (Unified Medical Language System) Metathesaurus, and proposes the study and understanding of the Metathesaurus from a model-theoretic perspective. Initial sections provide the background and motivation for such an approach, and a careful informal treatment of these notions is offered as a context and basis for the formal analysis. What emerges from this is a set of puzzles and confusions in the Metathesaurus and its literature pertaining to synonymy and its relation to terms and concepts. A model theory for a segment of the Metathesaurus is then constructed, and its adequacy relative to the informal treatment is demonstrated. Finally, it is shown how this approach clarifies and addresses the puzzles educed from the informal discussion, and how the model-theoretic perspective may be employed to evaluate some fundamental criticisms of the Metathesaurus. For users of the UMLS, two significant results of this analysis are a rigorous clarification of the different senses of synonymy that appear in treatments of the Metathesaurus and an illustration of the dangers in computing inferences involving ambiguous terms.

Abstract.MedDRA (the Medical Dictionary for Regulatory Activities Terminology) is a controlled vocabulary widely used as a medical coding scheme. However, MedDRA’s characterization of its structural hierarchy exhibits some confusing and paradoxical features. The goal of this paper is to examine these features, determine whether there is a coherent view of the MedDRA hierarchy that emerges, and explore what lessons are to be learned from this for using MedDRA and similar terminologies in a broad medical informatics context that includes relations among multiple disparate terminologies, thesauri, and ontologies.

Abstract.The primary goal of the SafetyWorks project has been the development of an integrated set of methodologies enabling the use of large observational data sources in monitoring and assessing drug safety concerns. To support its analytical and exploratory capabilities, SafetyWorks makes use of two large hierarchically structured ontologies – one for medical conditions, and one for drugs. In this paper we focus on the drug ontology employed in SafetyWorks and on its construction and annotation based on the SNOMED CT and RxNorm subsets of the Unified Medical Language System Metathesaurus. The result is a case study illustrating the value of SNOMED and its integration with UMLS and RxNorm in a critical and innovative drug safety application. We expose sufficient details of our methods to enable others to make use of these methods and to encourage the expanded use of both SNOMED and the UMLS in data exploration and analysis applications, particularly in the area of improving approaches to drug safety.

Abstract.The SafetyWorks project is oriented towards developing methodologies for the use of large observational data sources in drug safety signal screening and evaluation. The SafetyWorks application, as described here, is a prototype software application (or a set of prototypical components) implementing those methodologies. A feature of the overall SafetyWorks methodologies is the use of large formal biomedical ontologies for the purposes of data normalization and the exploration and inferencing of class eects pertaining to medical conditions and drugs. This paper describes the methods used in the creation and annotation of those ontologies within GSK's prototype application of the SafetyWorks methodologies.  Note (Added Sept. 15, 2009):  This paper describes the technology employed in the GlaxoSmithKline SafetyWorks project to create the drug and medical conditions ontologies employed in SafetyWorks. It was delivered to ProSanos Corporation as part of a licensing agreement and technology transfer covering their use of this and other intellectual property developed by GlaxoSmithKline, and it is hereby placed in the public domain.