This paper presents an axiomatic formalization of a theory of top-level relations between three categories of entities: individuals, universals, and collections. We deal with a variety of relations between entities in these categories, including the sub-universal relation among universals and the parthood relation among individuals, as well as cross-categorial relations such as instantiation and membership. We show that an adequate understanding of the formal properties of such relations – in particular their behavior with respect to time – is critical for (...) geographic information processing. The axiomatic theory is developed using Isabelle, a computational system for implementing logical formalisms. All proofs are computer verified and the computational representation of the theory is available online. (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)

The integration of biomedical terminologies is indispensable to the process of information integration. When terminologies are linked merely through the alignment of their leaf terms, however, differences in context and ontological structure are ignored. Making use of the SNAP and SPAN ontologies, we show how three reference domain ontologies can be integrated at a higher level, through what we shall call the OBR framework (for: Ontology of Biomedical Reality). OBR is designed to facilitate inference across the boundaries of domain ontologies (...) in anatomy, physiology and pathology. (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.

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)

The sorites paradox is the name given to a class of paradoxical arguments, also known as little by little arguments, which arise as a result of the indeterminacy surrounding limits of application of the predicates involved. For example, the concept of a heap appears to lack sharp boundaries and, as a consequence of the subsequent indeterminacy surrounding the extension of the predicate ‘is a heap’, no one grain of wheat can be identified as making the difference between being a heap (...) and not being a heap. Given then that one grain of wheat does not make a heap, it would seem to follow that two do not, thus three do not, and so on. In the end it would appear that no amount of wheat can make a heap. We are faced with paradox since from apparently true premises by seemingly uncontroversial reasoning we arrive at an apparently false conclusion. (shrink)

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

This paper deals with the truth-Conditions and the logic for vague languages. The use of supervaluations and of classical logic is defended; and other approaches are criticized. The truth-Conditions are extended to a language that contains a definitely-Operator and that is subject to higher order vagueness.

According to the prevalent 'sum view' of stuffs, each portion of stuff is a mereological sum of its subportions. The purpose of this paper is to re-examine the sum view in the light of a modal temporal mereology which distinguishes between different varieties of summation relations. While admitting David Barnett's recent counter-example to the sum view, we show that there is nonetheless an important sense in which all portions of stuff are sums of their subportions. We use our summation relations (...) to develop, as an alternative to the sum view, an analysis of stuffs that distinguisher between the ways in which different sorts of stuffs are sums of their subportions. (shrink)

The rapidly increasing wealth of genomic data has driven the development of tools to assist in the task of representing and processing information about genes, their products and their functions. One of the most important of these tools is the Gene Ontology (GO), which is being developed in tandem with work on a variety of bioinformatics databases. An examination of the structure of GO, however, reveals a number of problems, which we believe can be resolved by taking account of certain (...) organizing principles drawn from philosophical ontology. We shall explore the results of applying such principles to GO with a view to improving GO’s consistency and coherence and thus its future applicability in the automated processing of biological data. (shrink)

This volume succeeds the same authors' well-known An Introduction to Modal Logic and A Companion to Modal Logic. We designate the three books and their authors NIML, IML, CML and H&C respectively. Sadly, George Hughes died partway through the writing of NIML.

The relationship of part to whole is one of the most fundamental there is; this is the first and only 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. 'Parts could easily be the standard book on mereology for the next twenty (...) or thirty years.' Timothy Williamson, Grazer Philosophische Studien. (shrink)

This long-awaited book replaces Hughes and Cresswell's two classic studies of modal logic: _An Introduction to Modal Logic_ and _A Companion to Modal Logic_. _A New Introduction to Modal Logic_ is an entirely new work, completely re-written by the authors. They have incorporated all the new developments that have taken place since 1968 in both modal propositional logic and modal predicate logic, without sacrificing tha clarity of exposition and approachability that were essential features of their earlier works. The book takes (...) readers from the most basic systems of modal propositional logic right up to systems of modal predicate with identity. It covers both technical developments such as completeness and incompleteness, and finite and infinite models, and their philosophical applications, especially in the area of modal predicate logic. (shrink)

This book is a defense of modal realism; the thesis that our world is but one of a plurality of worlds, and that the individuals that inhabit our world are only a few out of all the inhabitants of all the worlds. Lewis argues that the philosophical utility of modal realism is a good reason for believing that it is true.

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 paradigm of referent tracking is based on a realist presupposition which rejects so-called negative entities (congenital absent nipple, and the like) as spurious. How, then, can a referent tracking-based Electronic Health Record deal with what are standardly called ‘negative findings’? To answer this question we carried out an analysis of some 748 sentences drawn from patient charts and containing some form of negation. Our analysis shows that to deal with these sentences we need to introduce a new ontological relationship (...) between a particular and a universal, which holds when no instance of the universal has a specific qualified ontological relation with the particular. This relation is found to be able to accommodate nearly all occurrences of negative findings in the examined sample, in ways which involve no reference to negative entities. (shrink)

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)

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)

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)

We are used to regarding actions and other events, such as Brutus’ stabbing of Caesar or the sinking of the Titanic, as occupying intervals of some underlying linearly ordered temporal dimension. This attitude is so natural and compelling that one is tempted to disregard the obvious difference between time periods and actual happenings in favor of the former: events become mere “intervals cum description”.1 On the other hand, in ordinary circumstances the point of talking about time is to talk about (...) what actually happens or might happen at some time or another. We talk about ‘now’ and ‘then’ in an effort to put some order in our description of what goes on. And since different events seem to overlap in so many different ways, a full account of their temporal relations seems to run afoul of a reductionist strategy. This raises two philosophical questions. The first is whether we can actually go beyond time, as it were, i.e., whether we can take events as bona fide entities and deal with them directly, just as we can deal with spatial entities such as physical bodies or masses without confining ourselves to their spatial representations. This is a controversial issue (though probably not as controversial as it used to be), and ties in with a number of unsettled problems concerning, e.g., the structure of causality or the definition of adequate identity and individuation criteria for events. 2 The second question is whether we can perhaps do without time, i.e., whether we can dispense with time points or intervals as an independent ontological category and focus only on actual or potential happenings, in opposition to the form of reductionism mentioned above—in short, whether we can account for the temporal dimension in terms of suitable relations among events. This is also a highly controversial issue, and relates to the classical dispute concerning relational vs. absolutist conceptions of (space and) time.3 It is this second question that we intend to focus on here.. (shrink)

We analyze and compare geometrical theories based on mereology (mereogeometries). Most theories in this area lack in formalization, and this prevents any systematic logical analysis. To overcome this problem, we concentrate on specific interpretations for the primitives and use them to isolate comparable models for each theory. Relying on the chosen interpretations, we introduce the notion of environment structure, that is, a minimal structure that contains a (sub)structure for each theory. In particular, in the case of mereogeometries, the domain of (...) an environment structure is composed of particular subsets of Rn. The comparison of mereogeometrical theories within these environment structures shows dependencies among primitives and provides (relative) definitional equivalences. With one exception, we show that all the theories considered are equivalent in these environment structures. (shrink)

In fields such as medicine, geography, and mechanics, spatial reasoning involves reasoning about entities that may coincide without overlapping. Some examples are: cavities and invading particles, passageways and valves, geographic regions and tropical storms. The purpose of this paper is to develop a formal theory of spatial relations for domains that include coincident entities. The core of the theory is a clear distinction between mereotopological relations, such as parthood and connection, and relative location relations, such as coincidence. To guide the (...) development of the formal theory, I construct mathematical models in which nontrivial relative location relations are defined. (shrink)