Barry Smith

While contemporary philosophers have devoted vast amounts of attention to the language we use in describing and finding our way about the world of everyday experience, they have, with few exceptions, refused to see this world itself as a fitting object of theoretical concern. In what follows I shall seek to show how the commonsensical world might be treated ontologically as an object of investigation in its own right. At the same time I shall seek to establish how such a treatment might help us better philosophically to understand the structures of both physical reality and cognition.

The influence of Kasimir Twardowski on modern Polish philosophy is all-pervasive. As is well known, almost all important 20th century Polish philosophers went through the hard training of his courses in Lvov. Twardowski instilled in his students an enduring concern for clarity and rigour. He taught them to regard philosophy as a collaborative effort, a matter of disciplined discussion and argument. And he encouraged them to work together with scientists from other disciplines — above all with psychologists, and also with mathematicians — so that the Lvov school of philosophy would gradually evolve into the Warsaw school of logic.

The pivotal role of the relation part-of in the description of living organisms is widely acknowledged. Organisms are open systems, which means that in contradistinction to mechanical artifacts they are characterized by a continuous flow and exchange of matter. A closer analysis of the spatial relations in biological organisms reveals that the decision as to whether a given particular is part-of a second particular or whether it is only contained-in the second particular is often controversial. We here propose a rule-based approach which allows us to decide on the basis of well-defined criteria which of the two relations holds between two anatomical objects, given that one spatially includes the other. We discuss the advantages and limitations of this approach, using concrete examples from human anatomy.

Two senses of ‘ontology’ can be distinguished in the current literature. First is the sense favored by information scientists, who view ontologies as software implementations designed to capture in some formal way the consensus conceptualization shared by those working on information systems or databases in a given domain. [Gruber 1993] Second is the sense favored by philosophers, who regard ontologies as theories of different types of entities (objects, processes, relations, functions) [Smith 2003]. Where information systems ontologists seek to maximize reasoning efficiency even at the price of simplifications on the side of representation, philosophical ontologists argue that representational adequacy can bring benefits for the stability and resistance to error of an ontological framework and also for its extendibility in the future. In bioinformatics, however, a third sense of ‘ontology’ has established itself, above all as a result of the successes of the Gene Ontology (hereafter: GO), which is a tool for the representation and processing of information about gene products and their biological functions [Gene Ontology Consortium 2000]. We show how Basic Formal Ontology (BFO) has established itself as an overarching ontology drawing on all three of the strands distinguished above, and describe applications of BFO especially in the treatment of biological granularity.

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.

Die Entwicklung der Philosophie in Österreich unterscheidet sich in markanter Weise von der Hauptlinie der philosophischen Entwicklung in Deutschland. Dabei fällt bei der österreichischen Philosophie vor allem die konsequente Orientierung an den Wissenschaften auf. In der philosophiegeschichtlichen Forschung sind für diese Besonderheit der österreichischen Philosophie z. B. von Otto Neurath, Rudolf Haller, Friedrich Stadier und J.C. Nyiri verschiedene Erklärungen vorgeschlagen worden. In diesen spielen in jeweils unterschiedlicher Weise Faktoren der spezifisch österreichischen Entwicklungen in historischer, institutioneller, politischer und religiöser Hinsicht eine Rolle. Der vorliegende Aufsatz kritisiert demgegenüber bereits die diese Erklärungsversuche tragende Fragestellung: Die philosophischen Entwicklungen in Österreich bedürfen - so lautet die neue These - gar nicht einer besonderen Erklärung; denn sie stellen den geistesgeschichtlichen Normalfall dar. Vielmehr ist eine Erklärung dafür notwendig, daß sich die wissenschaftliche Philosophie und die mit ihr verbundenen Charakterzüge stilistischer Klarheit, technischer Kompetenz, systematischer Orientierung, Spezialisierung und Professionalisierung im gleichen Zeitraum nicht auch in Deutschland entwickelt haben. Eine solche Erklärung läßt sich - so eine weitere These des Aufsatzes - ziemlich leicht aus der besonderen Rolle der (traditionellen idealistischen) Philosophie im deutschen Nationalbewußtsein herleiten.

What follows is an investigation of the ontology of Franz Brentano with special reference to Brentano's later and superficially somewhat peculiar doctrine to the effect that the substances of the material world are three dimensional places. Taken as a whole, Brentano's philosophy is marked by three, not obviously compatible, trait. In the first place, his work is rooted in the metaphysics of Aristotle, above all in Aristotle's substance/accident ontology and in the Aristotelian theory of categories. In the second place, Brentano embraced a Cartesian epistemology. He saw the source of all knowledge as residing in our direct awareness of our own mental phenomena and in our capacity to grasp evident incompatibilities in the realm of concepts.) Thirdly, he regarded the existence of an external world as at most probable, and denied outright the existence of a world similar to the world that is given in experience. Finally, and in some sense linking together these opposing strands, he propagated an idea of what he called "descriptive psychology", a discipline which would on the one hand yield exact knowledge of the structures and categories of mental life, and on the other hand provide an epistemologically sure foundation for other branches of philosophy. As we shall see, it is this psychological aspect of Brentano's philosophy which leads him to his conception of the substantiality of place. Surprisingly, however, the psychological considerations which underlie Brentano's thinking will be shown to raise a series of questions strictly ontological in nature, questions which are not without a systematic interest of their own.

In what respects is Western civilization superior or inferior to its rivals? In raising this question we are addressing a particularly strong form of the problem of relativism. For in order to compare civilizations one with another we would need to be in possession of a framework based on principles of evaluation which would be acceptable, in principle, to all human beings. Morality will surely provide one axis of such a framework (and we note in passing that believers in Islam might quite reasonably claim that their fellow-believers are characteristically more moral than are many in the West). Criteria such as material wellbeing, too, will need to play a role, as also will happiness or pleasure. Even happiness (pace some proponents of the utilitarian philosophy) comes in different types, and to count in the civilization stakes the happiness involved would presumably need to be of the right kind. We propose a specification for what this ‘right kind’ of happiness might be.

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.

Standard theories in mereotopology focus on relations of parthood and connection among spatial or spatio-temporal regions. Objects or processes which might be located in such regions are not normally directly treated in such theories. At best, they are simulated via appeal to distributions of attributes across the regions occupied or by functions from times to regions. The present paper offers a richer framework, in which it is possible to represent directly the relations between entities of various types at different levels, including both objects and the regions they occupy. What results is a layered mereotopology, a theory which can handle multiple layers (analogous to the layers of a lasagna) of spatially or spatiotemporally coincident but mereologically non-overlapping entities.

The theory of speech acts put forward by Adolf Reinach in his "The A Priori Foundations of the Civil Law" of 1913 rests on a systematic account of the ontological structures associated with various different sorts of language use. One of the most original features of Reinach's account lies in hIs demonstration of how the ontological structure of, say, an action of promising or of commanding, may be modified in different ways, yielding different sorts of non-standard instances of the corresponding speech act varieties. The present paper is an attempt to apply this idea of standard and modified instances of ontological structures to the realm of judgement and cognition, and thereby to develop a Reinachian theory of how intentionality is mediated through language in acts of thinking and speaking.

Ontology is one strategy for promoting interoperability of heterogeneous data through consistent tagging. An ontology is a controlled structured vocabulary consisting of general terms (such as “cell” or “image” or “tissue” or “microscope”) that form the basis for such tagging. These terms are designed to represent the types of entities in the domain of reality that the ontology has been devised to capture; the terms are provided with logical defi nitions thereby also supporting reasoning over the tagged data. Aim: This paper provides a survey of the biomedical imaging ontologies that have been developed thus far. It outlines the challenges, particularly faced by ontologies in the fields of histopathological imaging and image analysis, and suggests a strategy for addressing these challenges in the example domain of quantitative histopathology imaging. The ultimate goal is to support the multiscale understanding of disease that comes from using interoperable ontologies to integrate imaging data with clinical and genomics data.

Common sense is on the one hand a certain set of processes of natural cognition - of speaking, reasoning, seeing, and so on. On the other hand common sense is a system of beliefs (of folk physics, folk psychology and so on). Over against both of these is the world of common sense, the world of objects to which the processes of natural cognition and the corresponding belief-contents standardly relate. What are the structures of this world? How does the scientific treatment of this world relate to traditional and contemporary metaphysics and formal ontology? Can we embrace a thesis of common-sense realism to the effect that the world of common sense exists uniquely? Or must we adopt instead a position of cultural relativism which would assign distinct worlds of common sense to each group and epoch? The present paper draws on recent work in computer science (especially in the fields of naive and qualitative physics), in perceptual and developmental psychology, and in cognitive anthropology, in order to consider in a new light these and related questions and to draw conclusions for the methodology and philosophical foundations of the cognitive sciences.

In the era of “big data,” science is increasingly information driven, and the potential for computers to store, manage, and integrate massive amounts of data has given rise to such new disciplinary fields as biomedical informatics. Applied ontology offers a strategy for the organization of scientific information in computer-tractable form, drawing on concepts not only from computer and information science but also from linguistics, logic, and philosophy. This book provides an introduction to the field of applied ontology that is of particular relevance to biomedicine, covering theoretical components of ontologies, best practices for ontology design, and examples of biomedical ontologies in use. After defining an ontology as a representation of the types of entities in a given domain, the book distinguishes between different kinds of ontologies and taxonomies, and shows how applied ontology draws on more traditional ideas from metaphysics. It presents the core features of the Basic Formal Ontology (BFO), now used by over one hundred ontology projects around the world, and offers examples of domain ontologies that utilize BFO. The book also describes Web Ontology Language (OWL), a common framework for Semantic Web technologies. Throughout, the book provides concrete recommendations for the design and construction of domain ontologies.

Imagine a 5-stone weakling whose brain has been loaded with all the knowledge of a champion tennis player. He goes to serve in his first match – Wham! – His arm falls off. The 5-stone weakling just doesn’t have the bone structure or muscular development to serve that hard. There are, clearly, different types of knowledge/ability/skill, only some of which are a matter of what can be transferred simply by passing signals down a wire from one brain (or computer) to another. Sometimes it is the body (the hardware) which knows.

The ontology of language is concerned with the relations between uses of language, both overt and covert, and other entities, whether in the world or in the mind of the thinking subject. We attempt a first survey of the sorts of relations which might come into question for such an ontology, including: relations between referring uses of expressions and their objects, relations between the use of a (true) sentence and that in the world which makes it true, relations between mental acts on the one hand and underlying mental states (attitudes, beliefs), on the other, relations between my acts and states, associated uses of language and overt actions on my part and on the part of those other subjects with whom I communicate.

The Unified Medical Language System and the Gene Ontology are among the most widely used terminology resources in the biomedical domain. However, when we evaluate them in the light of simple principles for wellconstructed ontologies we find a number of characteristic inadequacies. Employing the theory of granular partitions, a new approach to the understanding of ontologies and of the relationships ontologies bear to instances in reality, we provide an application of this theory in relation to an example drawn from the context of the pathophysiology of hypertension. This exercise is designed to demonstrate how, by taking ontological principles into account we can create more realistic biomedical ontologies which will also bring advantages in terms of efficiency and robustness of associated software applications.

When the U.S. conducts warfare, elements of a force are drawn from different services and work together as a single team to accomplish an assigned mission. To achieve such unified action, it is necessary that the doctrines governing the actions of members of specific services be both consistent with and subservient to joint Doctrine. Because warfighting today increasingly involves not only live forces but also automated systems, unified action requires that information technology that is used in joint warfare must be aligned with joint doctrine. It requires also that the separate information systems used by the different elements of a joint force must be interoperable, in the sense that data and information that is generated by each element must be usable (understandable, processable) by all the other elements that need them. Currently, such interoperability is impeded by multiple inconsistencies among the different data and software standards used by warfighters. We describe here the on-going project of creating a Joint Doctrine Ontology (JDO), which uses joint doctrine to provide shared computer-accessible content valid for any field of military endeavor, organization, and information system. JDO addresses the two previously mentioned requirements of unified action by providing a widely applicable benchmark for use by developers of information systems that will both guarantee alignment with joint doctrine and support interoperability.

There are some who defend a view of vagueness according to which there are intrinsically vague objects or attributes in reality. Here, in contrast, we defend a view of vagueness as a semantic property of names and predicates. All entities are crisp, on this view, but there are, for each vague name, multiple portions of reality that are equally good candidates for being its referent, and, for each vague predicate, multiple classes of objects that are equally good candidates for being its extension. We provide a new formulation of these ideas in terms of a theory of granular partitions. We show that this theory provides a general framework within which we can understand the relation between vague terms and concepts on the one hand and correlated portions of reality on the other. We also sketch how it might be possible to formulate within this framework a theory of vagueness which dispenses with the notion of truth-value gaps and other artifacts of more familiar approaches.

We performed a qualitative analysis of the Thesaurus in order to assess its conformity with principles of good practice in terminology and ontology design. We used both the on-line browsable version of the Thesaurus and its OWL-representation (version 04.08b, released on August 2, 2004), measuring each in light of the requirements put forward in relevant ISO terminology standards and in light of ontological principles advanced in the recent literature. Version 04.08b of the NCI Thesaurus suffers from the same broad range of problems that have been observed in other biomedical terminologies. For its further development, we recommend the use of a more principled approach that allows the Thesaurus to be tested not just for internal consistency but also for its degree of correspondence to that part of reality which it is designed to represent.

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.