We propose an ontological theory that is powerful enough to describe both complex spatio-temporal processes and the enduring entities that participate therein. For this purpose we introduce the notion a directly depicting ontology. Directly depicting ontologies are based on relatively simple languages and fall into two major categories: ontologies of type SPAN and ontologies of type SNAP. These represent two complementary perspectives on reality and employ distinct though compatible systems of categories. A SNAP (snapshot) ontology comprehends enduring entities such as (...) organisms, geographic features, or qualities as they exist at some given moment of time. A SPAN ontology comprehends perduring entities such as processes and their parts and aggregates as they unfold themselves through some temporal interval. We give an axiomatic account of the theory of directly depicting ontologies and of the core parts of the metaontological fragment within which they are embedded. (shrink)

One of the tasks of ontology in information science is to support the classification of entities according to their kinds and qualities. We hold that to realize this task as far as entities such as material objects are concerned we need to distinguish four kinds of entities: substance particulars, quality particulars, substance universals, and quality universals. These form, so to speak, an ontological square. We present a formal theory of classification based on this idea, including both a semantics for the (...) theory and a provably sound axiomatization. (shrink)

The Foundational Model of Anatomy (FMA) symbolically represents the structural organization of the human body from the macromolecular to the macroscopic levels, with the goal of providing a robust and consistent scheme for classifying anatomical entities that is designed to serve as a reference ontology in biomedical informatics. Here we articulate the need for formally clarifying the is-a and part-of relations in the FMA and similar ontology and terminology systems. We diagnose certain characteristic errors in the treatment of these relations (...) and show how these errors can be avoided through adoption of the formalism we describe. We then illustrate how a consistently applied formal treatment of taxonomy and partonomy can support the alignment of ontologies. (shrink)

This paper provides an axiomatic formalization of a theory of foundational relations between three categories of entities: individuals, universals, and collections. We deal with a variety of relations between entities in these categories, including the is-a relation among universals and the part-of relation among individuals as well as cross-category relations such as instance-of, member-of, and partition-of. We show that an adequate understanding of the formal properties of such relations – in particular their behavior with respect to time – is critical (...) for formal ontology. We provide examples to support this thesis from the domain of biomedicine. (shrink)

Thinking about space is thinking about spatial things. The table is on the carpet; hence the carpet is under the table. The vase is in the box; hence the box is not in the vase. But what does it mean for an object to be somewhere? How are objects tied to the space they occupy? This book is concerned with these and other fundamental issues in the philosophy of spatial representation. Our starting point is an analysis of the interplay between (...) mereology (the study of part/whole relations), topology (the study of spatial continuity and compactness), and the theory of spatial location proper. This leads to a unified framework for spatial representation understood quite broadly as a theory of the representation of spatial entities. The framework is then tested against some classical metaphysical questions such as: Are parts essential to their wholes? Is spatial colocation a sufficient criterion of identity? What (if anything) distinguishes material objects from events and other spatial entities? The concluding chapters deal with applications to topics as diverse as the logical analysis of movement and the semantics of maps. (shrink)

'Mass terms', words like water, rice and traffic, have proved very difficult to accommodate in any theory of meaning since, unlike count nouns such as house or dog, they cannot be viewed as part of a logical set and differ in their grammatical properties. In this study, motivated by the need to design a computer program for understanding natural language utterances incorporating mass terms, Harry Bunt provides a thorough analysis of the problem and offers an original and detailed solution. An (...) extension of classical set theory, Ensemble Theory, is defined, and this provides the conceptual basis of a framework for the analysis of natural language meaning which Dr Bunt calls Two-level model-theoretic semantics. The validity of the framework is convincingly demonstrated by the formal analysis of a fragment of English including sentences with quantified and modified mass terms. Separate chapters of the book are devoted to an axiomatic definition of Ensemble Theory and a detailed discussion of its status as a mathematical formalism. (shrink)

We propose a modular ontology of the dynamic features of reality. This amounts, on the one hand, to a purely spatial ontology supporting snapshot views of the world at successive instants of time and, on the other hand, to a purely spatiotemporal ontology of change and process. We argue that dynamic spatial ontology must combine these two distinct types of inventory of the entities and relationships in reality, and we provide characterizations of spatiotemporal reasoning in the light of the interconnections (...) between them. (shrink)

An overview of contemporary part-whole theories, with reference to both their axiomatic developments and their philosophical underpinnings.

We can see mereology as a theory of parthood and topology as a theory of wholeness. How can these be combined to obtain a unified theory of parts and wholes? This paper examines various non-equivalent ways of pursuing this task, with specific reference to its relevance to spatio-temporal reasoning. In particular, three main strategies are compared: (i) mereology and topology as two independent (though mutually related) chapters; (ii) mereology as a general theory subsuming topology; (iii) topology as a general theory (...) subsuming mereology. Some more speculative strategies and directions for further research are also considered. (shrink)

The paper presents a new method for generating typologies of formal-ontological relations. The guiding idea is that formal relations are those sorts of relations which hold between entities which are constituents of distinct ontologies. We provide examples of ontologies (in the spirit of Zemach’s classic “Four Ontologies” of 1970), and show how these can be used to give a rich typology of formal relations in a way which also throws light on the opposition between threeand four-dimensionalism.

What are the relationships between an entity and the space at which it is located? And between a region of space and the events that take place there? What is the metaphysical structure of localization? What its modal status? This paper addresses some of these questions in an attempt to work out at least the main coordinates of the logical structure of localization. Our task is mostly taxonomic. But we also highlight some of the underlying structural features and we single (...) out the interactions between the notion of localization and nearby notions, such as the notions of part and whole, or of necessity and possibility. A theory of localization—we argue—is needed in order to account for the basic relations between objects and space, and runs afoul a pure part-whole theory. We also provide an axiomatization of the relation of localization and examine cases of localization involving entities different from material objects. (shrink)

There is a basic distinction, in the realm of spatial boundaries, between bona fide boundaries on the one hand, and fiat boundaries on the other. The former are just the physical boundaries of old. The latter are exemplified especially by boundaries induced through human demarcation, for example in the geographic domain. The classical problems connected with the notions of adjacency, contact, separation and division can be resolved in an intuitive way by recognizing this two-sorted ontology of boundaries. Bona fide boundaries (...) yield a notion of contact that is effectively modeled by classical topology; the analogue of contact involving fiat boundaries calls, however, for a different account, based on the intuition that fiat boundaries do not support the open/closed distinction on which classical topology is based. In the presence of this two-sorted ontology it then transpires that mereotopology—topology erected on a mereological basis—is more than a trivial formal variant of classical point-set topology. (shrink)

Persistence through time is like extension through space. A road has spatial parts in the subregions of the region of space it occupies; likewise, an object that exists in time has temporal parts in the various subregions of the total region of time it occupies. This view — known variously as four dimensionalism, the doctrine of temporal parts, and the theory that objects “perdure” — is opposed to “three dimensionalism”, the doctrine that things “endure”, or are “wholly present”.1 I will (...) attempt to resolve this dispute in favor of four dimensionalism by means of a novel argument based on considerations of vagueness. But before argument in this area can be productive, I believe we must become much clearer than is customary about exactly what the dispute is, for the usual ways of formulating the dispute are flawed, especially where three dimensionalism is concerned. (shrink)

Ontology as a branch of philosophy is the science of what is, of the kinds and structures of objects, properties, events, processes and relations in every area of reality. ‘Ontology’ in this sense is often used by philosophers as a synonym of ‘metaphysics’ (a label meaning literally: ‘what comes after the Physics’), a term used by early students of Aristotle to refer to what Aristotle himself called ‘first philosophy’. But in recent years, in a development hardly noticed by philosophers, the (...) term ‘ontology’ has gained currency in the field of computer and information science, and in information-driven research in bioinformatics and related areas. We examine these new developments in applied ontology, and show what lessons they might have for both philosophers and information scientists. (shrink)

Formal principles governing best practices in classification and definition have for too long been neglected in the construction of biomedical ontologies, in ways which have important negative consequences for data integration and ontology alignment. We argue that the use of such principles in ontology construction can serve as a valuable tool in error-detection and also in supporting reliable manual curation. We argue also that such principles are a prerequisite for the successful application of advanced data integration techniques such as ontology-based (...) multi-database querying, automated ontology alignment and ontology-based text-mining. These theses are illustrated by means of a case study of the Gene Ontology, a project of increasing importance within the field of biomedical data integration. (shrink)

To enhance the treatment of relations in biomedical ontologies we advance a methodology for providing consistent and unambiguous formal definitions of the relational expressions used in such ontologies in a way designed to assist developers and users in avoiding errors in coding and annotation. The resulting Relation Ontology can promote interoperability of ontologies and support new types of automated reasoning about the spatial and temporal dimensions of biological and medical phenomena.

That parthood is a transitive relation is among the most basic principles of classical mereology. Alas, it is also very controversial. In a recent paper, Ingvar Johansson has put forward a novel diagnosis of the problem, along with a corresponding solution. The diagnosis is on the right track, I argue, but the solution is misleading. And once the pieces are properly put together, we end up with a reinforcement of the standard defense of transitivity on behalf of classical mereology.

The relationship of part to whole is one of the most fundamental there is, yet until now there has been no full-length study of this concept. This book shows that mereology, the formal theory of part and whole, is essential to ontology. Peter Simons surveys and criticizes previous theories, especially the standard extensional view, and proposes a more adequate account which encompasses both temporal and modal considerations in detail. This has far-reaching consequences for our understanding of such classical philosophical concepts (...) as identity, individual, class, substance and accident, matter, form, essence, dependence, and integral whole. It also enables the author to offer new solutions to long-standing problems surrounding these concepts, such as the Ship of Theseus Problem and the issue of mereological essentialism. The author shows by his use of formal techniques that classical philosophical problems are amenable to rigorous treatment, and the book represents a synthesis of issues and methods from the analytical tradition and from the older continental realist tradition of Brentano and the early Husserl. (shrink)

The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or ‘ontologies’. Unfortunately, the very success of this approach has led to a proliferation of ontologies which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium has set in train a strategy to overcome this problem. Existing (...) OBO ontologies, including the Gene Ontology, are undergoing a process of coordinated reform and new ontologies being created on the basis of an evolving set of shared principles governing ontology development. The result is an expanding family of ontologies designed to be interoperable, logically well-formed, and to incorporate accurate representations of biological reality. We describe the OBO Foundry initiative, and provide guidelines for those who might wish to become involved. (shrink)

This volume is a self-contained introduction to interactive proof in high- order logic, using the proof assistant Isabelle 2002. Compared with existing Isabelle documentation, it provides a direct route into higher-order logic, which most people prefer these days. It bypasses?rst-order logic and minimizes discussion of meta-theory. It is written for potential users rather than for our colleagues in the research world. Another departure from previous documentation is that we describe Markus Wenzel’s proof script notation instead of ML tactic scripts. The (...) l- ter make it easier to introduce new tactics on the?y, but hardly anybody does that. Wenzel’s dedicated syntax is elegant, replacing for example eight simpli?cation tactics with a single method, namely simp, with associated - tions. The book has three parts. – The?rst part, Elementary Techniques, shows how to model functional programs in higher-order logic. Early examples involve lists and the natural numbers. Most proofs are two steps long, consisting of induction on a chosen variable followed by the auto tactic. But even this elementary part covers such advanced topics as nested and mutual recursion. – The second part, Logic and Sets, presents a collection of lower-level tactics that you can use to apply rules selectively. It also describes I- belle/HOL’s treatment of sets, functions, and relations and explains how to de?ne sets inductively. One of the examples concerns the theory of model checking, and another is drawn from a classic textbook on formal languages. (shrink)