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. (shrink)

Philosophers frequently struggle with the relation of metaphysics to the everyday world, with its practical value, and with its relation to empirical science. This paper distinguishes several different models of the relation between philosophical ontology and applied (scientific) ontology that have been advanced in the history of philosopy. Adoption of a strong participation model for the philosophical ontologist in science is urged, and requirements and consequences of the participation model are explored. This approach provides both a principled view and justification (...) of the role of the philosophical ontologist in contemporary empirical science as well as guidelines for integrating philosophers and philosophical contributions into the practice of science. (shrink)

In “Ontological realism: Methodology or misdirection?” I offered a detailed critique of the position referred to as “realism” taken by Barry Smith and Werner Ceusters. This position is claimed to serve as the basis for a “realist methodology” that they seek to impose on the development of scientific ontologies, particularly within the biomedical sciences. Here, in part responding to a reply to those criticisms by Smith and Ceusters, I return the focus to an examination of fundamental incoherencies in this realist (...) approach and propose an alternative that is amenable to much of what Smith and Ceusters hope to accomplish. And I sketch what I believe is needed to advance ontology theory and practice in the sciences. (shrink)

This paper advances a detailed exploration of the complex relationships among terms, concepts, and synonymy in the UMLS 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. (shrink)

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. (shrink)

Babylon Knowledge Explorer (BKE) is an integrated suite of tools and information sources developed in GlaxoSmithKline's Analysis, Applications, and Research Technologies Department to support the prototyping and implementation of ontology-driven information systems and ontology-enhanced knowledge applications. In this paper we describe the current state of BKE development and focus on some of its distinctive or novel approaches, highlighting -/- * How BKE makes use of multiple large pre-existing ontologies in support of text and data mining. * The methodology employed for (...) importing an ontology and making it immediately accessible to BKE's tools, interfaces, and API. * A formal description of BKE's ontology-based fact model and how this is employed in implementing information retrieval and data mining capabilities. * A sample application built on BKE that illustrates an ontologyenhanced machine learning tool. (shrink)

For centuries (indeed for millennia) philosophers have complained about pseudo-philosophy being practiced by others claiming to be philosophers — and about people being taken in and suffering in one way or another from the mimicry, exploitation, and fakery of the pseudo-philosophers. But no attempt at a careful, comprehensive, and useful characterization of pseudo-philosophy has emerged. This book is a comprehensive historical, theoretical, and practical treatment of pseudo-philosophy — a concept often encountered in both formal and popular philosophy, but rarely with (...) any degree of seriousness and precision. It presents a theory of pseudo-philosophy through the use of models of the genuine philosopher and pseudo-philosopher, and then applies that theory to specific real-world cases. -/- Available on Amazon in either KIndle or paperback format. More details — as well as the complete Preface, Postscript, and References sections — available on my False Wisdom blog (falsephilosophy on blogspot: see External Links below). (shrink)

In 'Notes on the Theory of Reference' Quine offers a brief argument, based on Tarski's Convention T and semantic definition of truth, that the theory of meaning is 'in a worse state' than is the theory of reference and that the concepts of the theory of meaning are inherently more 'foggy and mysterious' than those of thetheory of reference. A careful reconstruction of Quine's argument, however, is sufficient to show both that he covertly imposes a double standard of clarity on (...) the two theories in question and that in so far as Tarski's contributions clarify or explicate the notion of truth they do likewise for the notion of analyticity. Consequently, the appeal which Quine makes to Tarski's definition of truth cannot be used in the manner he wishes, to draw a clear boundary between the theories of meaning and reference. (shrink)

In 'Notes on the Theory of Reference' Quine offers a brief argument, based on Tarski's Convention T and semantic definition of truth, that the theory of meaning is 'in a worse state' than is the theory of reference and that the concepts of the theory of meaning are inherently more 'foggy and mysterious' than those of thetheory of reference. A careful reconstruction of Quine's argument, however, is sufficient to show both that he covertly imposes a double standard of clarity on (...) the two theories in question and that in so far as Tarski's contributions clarify or explicate the notion of truth they do likewise for the notion of analyticity. Consequently, the appeal which Quine makes to Tarski's definition of truth cannot be used in the manner he wishes, to draw a clear boundary between the theories of meaning and reference. (shrink)