Since 2002 we have been testing and refining a methodology for ontology development that is now being used by multiple groups of researchers in different life science domains. Gary Merrill, in a recent paper in this journal, describes some of the reasons why this methodology has been found attractive by researchers in the biological and biomedical sciences. At the same time he assails the methodology on philosophical grounds, focusing specifically on our recommendation that ontologies developed for scientific purposes should be (...) constructed in such a way that their terms are seen as referring to what we call universals or types in reality. As we show, Merrill’s critique is of little relevance to the success of our realist project, since it not only reveals no actual errors in our work but also criticizes views on universals that we do not in fact hold. However, it nonetheless provides us with a valuable opportunity to clarify the realist methodology, and to show how some of its principles are being applied, especially within the framework of the OBO (Open Biomedical Ontologies) Foundry initiative. (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)

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)

This paper addresses questions of universality related to ontological engineering, namely aims at substantiating (negative) answers to the following three basic questions: (i) Is there a ‘universal ontology’?, (ii) Is there a ‘universal formal ontology language’?, and (iii) Is there a universally applicable ‘mode of reasoning’ for formal ontologies? To support our answers in a principled way, we present a general framework for the design of formal ontologies resting on two main principles: firstly, we endorse Rudolf Carnap’s principle of logical (...) tolerance by giving central stage to the concept of logical heterogeneity, i.e. the use of a plurality of logical languages within one ontology design. Secondly, to structure and combine heterogeneous ontologies in a semantically well-founded way, we base our work on abstract model theory in the form of institutional semantics, as forcefully put forward by Joseph Goguen and Rod Burstall. In particular, we employ the structuring mechanisms of the heterogeneous algebraic specification language HetCasl for defining a general concept of heterogeneous, distributed, highly modular and structured ontologies, called hyperontologies. Moreover, we distinguish, on a structural and semantic level, several different kinds of combining and aligning heterogeneous ontologies, namely integration, connection, and refinement. We show how the notion of heterogeneous refinement can be used to provide both a general notion of sub-ontology as well as a notion of heterogeneous equivalence of ontologies, and finally sketch how different modes of reasoning over ontologies are related to these different structuring aspects. (shrink)

The philosophical study of what exists and what it means for something to exist is one of the core concerns of metaphysics. This introduction to ontology provides readers with a comprehensive account of the central ideas of the subject of being. This book is divided into two parts. The first part explores questions of pure philosophical ontology: what is meant by the concept of being, why there exists something rather than nothing, and why there is only one logically contingent actual (...) world. Dale Jacquette shows how logic provides the only possible answers to these fundamental problems. The second part of the book examines issues of applied scientific ontology. Jacquette offers a critical survey of some of the most influential traditional ontologies, such as the distinction between appearance and reality, and the categories of substance and transcendence. The ontology of physical entities - space, time, matter and causation - is examined as well as the ontology of abstract entities such as sets, numbers, properties, relations and propositions. The special problems posed by the subjectivity of mind and of postulating a god are also explored in detail. The final chapter examines the ontology of culture, language and art. (shrink)

The philosophical study of what exists and what it means for something to exist is one of the core concerns of metaphysics. This introduction to ontology provides readers with a comprehensive account of the central ideas of the subject of being. This book is divided into two parts. The first part explores questions of pure philosophical ontology: what is meant by the concept of being, why there exists something rather than nothing, and why there is only one logically contingent actual (...) world. Dale Jacquette shows how logic provides the only possible answers to these fundamental problems. The second part of the book examines issues of applied scientific ontology. Jacquette offers a critical survey of some of the most influential traditional ontologies, such as the distinction between appearance and reality, and the categories of substance and transcendence. The ontology of physical entities - space, time, matter and causation - is examined as well as the ontology of abstract entities such as sets, numbers, properties, relations and propositions. The special problems posed by the subjectivity of mind and of postulating a god are also explored in detail. The final chapter examines the ontology of culture, language and art. (shrink)

In a world that is overflowing with journals and other outlets for scientific publication, the appearance of any new periodical requires some justification. There are already more journals than we can read and more conferences than we can attend. In the case of applied Ontology, we believe that the creation of anew journal not only is completely justifiable, it is downright exciting. For too long, workers in computer science have assumed that content comes for free. “Theory” in computer science has (...) always meant the theory of processes and of computation. We measure the complexity of computer programs in terms of how long it takes machines to execute them, not in terms of how long it takes people to understand and to represent the data on which those programs might operate. We typically describe computer code in terms of algorithms that operate on formal parameters, often without pausing to discuss where the data that might satisfy those parameters come from. This journal was founded on the premise that workers in computer science, informatics, and information science are overdue in paying as much attention to contents as they do to algorithms. (shrink)

There is a long history of worrying about whether or not metaphysics is a legitimate philosophical discipline. Traditionally such worries center around issues of meaning and epistemological concerns. Do the metaphysical questions have any meaning? Can metaphysical methodology lead to knowledge? But these questions are, in my opinion, not as serious as they have sometimes (historically) been taken to be. What is much more concerning is another set of worries about metaphysics, which I take to the greatest threat to metaphysics (...) as a philosophical discipline. These worries, in effect, hold that the questions that metaphysics tries to answer have long been answered in other parts of inquiry, ones that have much greater authority. And if they haven’t been answered yet then one should not look to philosophy for an answer. What metaphysics tries to do has been or will be done by the sciences. There is nothing left to do for philosophy, or so the worry. Let me illustrate this with two examples, one of which is our main concern here. (shrink)

Metaphysics is concerned with the foundations of reality. It asks questions about the nature of the world, such as: Aside from concrete objects, are there also abstract objects like numbers and properties? Does every event have a cause? What is the nature of possibility and necessity? When do several things make up a single bigger thing? Do the past and future exist? And so on. -/- Metametaphysics is concerned with the foundations of metaphysics. It asks: Do the questions of metaphysics (...) really have answers? If so, are these answers substantive or just a matter of how we use words? And what is the best procedure for arriving at them—common sense and conceptual analysis? Or assessing competing hypotheses with quasi-scientific criteria? -/- This volume gathers together sixteen new essays that are concerned with the semantics, epistemology, and methodology of metaphysics. My aim is to introduce these essays within a more general (and mildly opinionated) survey of contemporary challenges to metaphysics . (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)

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)

Digital Rights Management (DRM) covers the description, identification, trading, protection, monitoring and tracking of all forms of rights over both tangible and intangible assets. The Digital Object Identifier (DOI) system provides a framework for the persistent identification of entities involved in this domain. Although the system has been very well designed to manage object identifiers, some important questions relating to the creation and assignment of identifiers are left open. The paradigm of a Referent Tracking System (RTS) recently advanced in the (...) healthcare and life sciences environment is able to fill these gaps. This is demonstrated by pointing out inconsistencies in the existing DOI models and by showing how they can be corrected using an RTS. (shrink)

The present essay is devoted to the application of ontology in support of research in the natural sciences. It defends the thesis that ontologies developed for such purposes should be understood as having as their subject matter, not concepts, but rather the universals and particulars which exist in reality and are captured in scientific laws. We outline the benefits of a view along these lines by showing how it yields rigorous formal definitions of the foundational relations used in many influential (...) ontologies, illustrating our results by reference to examples drawn from the domain of the life sciences. (shrink)