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. (shrink)

A novel rereading of the relationship between ethics and ontology in Aristotle.

Ontologies describe reality in specific domains in ways that can bridge various disciplines and languages. They allow easier access and integration of information that is collected by different groups. Ontologies are currently used in the biomedical sciences, geography, and law. A Biomedical Ethics Ontology would benefit members of ethics committees who deal with protocols and consent forms spanning numerous fields of inquiry. There already exists the Ontology for Biomedical Investigations (OBI); the proposed BMEO would interoperate with OBI, creating a powerful (...) information tool. We define a domain ontology and begin to construct a BMEO, focused on the process of evaluating human research protocols. Finally, we show how our BMEO can have practical applications for ethics committees. This paper describes ongoing research and a strategy for its broader continuation and cooperation. (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)

Medical practice is practiced morality, and clinical research belongs to normative ethics. The present book elucidates and advances this thesis by: 1. analyzing the structure of medical language, knowledge, and theories; 2. inquiring into the foundations of the clinical encounter; 3. introducing the logic and methodology of clinical decision-making, including artificial intelligence in medicine; 4. suggesting comprehensive theories of organism, life, and psyche; of health, illness, and disease; of etiology, diagnosis, prognosis, prevention, and therapy; and 5. investigating the moral and (...) metaphysical issues central to medical practice and research. Many systems of (classical, modal, non-classical, probability, and fuzzy) logic are introduced and applied. Fuzzy medical deontics, fuzzy medical ontology, fuzzy medical concept formation, fuzzy medical decision-making and biomedicine and many other techniques of fuzzification in medicine are introduced for the first time. -/- . (shrink)

The basic question of ontology is “What exists?”. The basic question of metaontology is: are there objective answers to the basic question of ontology? Here ontological realists say yes, and ontological anti-realists say no. (Compare: The basic question of ethics is “What is right?”. The basic question of metaethics is: are there objective answers to the basic question of ethics? Here moral realists say yes, and moral anti-realists say no.) For example, the ontologist may ask: Do numbers exist? The Platonist (...) says yes, and the nominalist says no. The metaontologist may ask: is there an objective fact of the matter about whether numbers exist? The ontological realist says yes, and the ontological anti-realist says no. Likewise, the ontologist may ask: Given two distinct entities, when does a mereological sum of those entities exist? The universalist says always, while the nihilist says never. The metaontologist may ask: is there an objective fact of the matter about whether the mereological sum of two distinct entities exists? The ontological realist says yes, and the ontological anti-realist says no. Ontological realism is often traced to Quine (1948), who held that we can determine what exists by seeing which entities are endorsed by our best scientific theory of the world. In recent years, the practice of ontology has often presupposed an ever-stronger ontological realism, and strong versions of ontological realism have received explicit statements by Fine (this volume), Sider (2001; this volume), van Inwagen (1998; this volume), and others. (shrink)

The hypothesis of the study was that the domains of color and form are structured into nonarbitrary, semantic categories which develop around perceptually salient “natural prototypes.” Categories which reflected such an organization (where the presumed natural prototypes were central tendencies of the categories) and categories which violated the organization (natural prototypes peripheral) were taught to a total of 162 members of a Stone Age culture which did not initially have hue or geometric-form concepts. In both domains, the presumed “natural” categories (...) were consistently easier to learn than the “distorted” categories. Even when not central, natural prototype stimuli tended to be more rapidly learned and more often chosen as the most typical example of the category than were other stimuli. Implications for general differences between natural categories and the artificial categories of concept formation research were discussed. (shrink)

In , Peter van Inwagen asked a good question. (Asking the right question is often the hardest part.) He asked: what do you have to do to some objects to get them to compose something---to bring into existence some further thing made up of those objects? Glue them together or what?1 Some said that you don’t have to do anything.2 No matter what you do to the objects, they’ll always compose something further, no matter how they are arranged. Thus we (...) learned of the fusion of the coins in our pockets and the Eiffel tower. (shrink)

This book contains selected papers from the First International Conference on the Ontology of Spacetime. Its fourteen chapters address two main questions: first, what is the current status of the substantivalism/relationalism debate, and second, what about the prospects of presentism and becoming within present-day physics and its philosophy? The overall tenor of the four chapters of the book’s first part is that the prospects of spacetime substantivalism are bleak, although different possible positions remain with respect to the ontological status of (...) spacetime. Part II and Part III of the book are devoted to presentism, eternalism, and becoming, from two different perspectives. In the six chapters of Part II it is argued, in different ways, that relativity theory does not have essential consequences for these issues. It certainly is true that the structure of time is different, according to relativity theory, from the one in classical theory. But that does not mean that a decision is forced between presentism and eternalism, or that becoming has proved to be an impossible concept. It may even be asked whether presentism and eternalism really offer different ontological perspectives at all. The writers of the last four chapters, in Part III, disagree. They argue that relativity theory is incompatible with becoming and presentism. Several of them come up with proposals to go beyond relativity, in order to restore the prospects of presentism. · Space and time in present-day physics and philosophy · Relatively low level of technicality, easily accessible · Introduction from scratch of the debates surrounding time · Top authors explaining their positions · Broad spectrum of approaches, coherently represented. (shrink)

According to four dimensionalism, the material world is divided into momentary stages. In a four-dimensional world, which objects are the ordinary things, the things we normally name and quantify over? Aggregates of stages, according to most four-dimensionalists, but according to stage theorists (or exdurantists), ordinary objects are instead to be identified with the stages themselves. (A temporal counterpart theoretic account of de re temporal predication is then given.) This paper argues that a stage theorist is best positioned to accept David (...) Lewis's argument from temporary intrinsics for four-dimensionalism, since stage theorists are the only four-dimensionalists who attribute monadic temporary intrinsic properties to ordinary things. (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)

In this brief book one of the most distinguished living American philosophers takes up the question of whether ethical judgments can properly be considered objective--a question that has vexed philosophers over the past century. Reviewing what he deems the disastrous consequences of ontology's influence on analytic philosophy--in particular, the contortions it imposes upon debates about the objective of ethical judgments--Putnam proposes abandoning the very idea of ontology.

Barry Smith recently discussed the diagraphs of book eight of Jacob Lorhard’s Ogdoas scholastica under the heading “birth of ontology” (Smith, 2022; this issue). Here, I highlight the commonalities between the original usage of diagraphs in the tradition of Ramus for didactic purposes and the the usage of their present-day successors–modern ontologies–for computational purposes. The modern ideas of ontology and of the universal computer were born just two generations apart in the breakthrough century of instrumental reason.

This review focuses on the Ogdoas scholastica by Jacob Lorhard, published in 1606. The importance of this document turns on the fact that it contains what is almost certainly the first published occurrence of the term “ontology.” The body of the work consists in a series of diagrams called “diagraphs.” Relevant features of this compendium of diagraphs are: 1. that it does not in fact contain the word “ontology,” and 2. that Lorhard himself was not responsible for its content.

Foundational ontologies, central constructs in ontological investigations and engineering alike, are based on ontological categories. Firstly proposed by Aristotle as the very ur- elements from which the whole of reality can be derived, they are not easy to identify, let alone partition and/or hierarchize; in particular, the question of their number poses serious challenges. The late medieval philosopher Dietrich of Freiberg wrote around 1286 a tutorial that can help us today with this exceedingly difficult task. In this paper, I discuss (...) ontological categories and their importance for foundational ontologies from both the contemporary perspective and the original Aristotelian viewpoint, I provide the translation from the Latin into English of Dietrich's De origine II with an introductory elaboration, and I extract a foundational ontology–that is in fact a single-category one–from this text rooted in Dietrich's specification of types of subjecthood and his conception of intentionality as causal operation. (shrink)

This essay is a response to Luis M. Augusto’s intriguing paper on the rift between mainstream and formal ontology. I will show that there are in fact two questions at issue here: 1. concerning the links between mainstream and formal approaches within philosophy, and 2. concerning the application of philosophy (and especially philosophical ontology) in support of information-driven research for example in the life sciences.

Ontologies are some of the most central constructs in today's large plethora of knowledge technologies, namely in the context of the semantic web. As their coinage indicates, they are direct heirs to the ontological investigations in the long Western philosophical tradition, but it is not easy to make bridges between them. Contemporary ontological commitments often take causality as a central aspect for the ur-segregation of entities, especially in scientific upper ontologies; theories of causality and philosophical ontological investigations often go hand-in-hand, (...) and were essentially inseparable in medieval thought. This constitutes the foundation for a bridge, and this article analyzes the causality-based ontology of the late medieval philosopher Dietrich of Freiberg from the viewpoint of today's upper-ontology engineering. In this bridging attempt, it offers a translation into English of the first part of Dietrich's De origine (abbreviated title) that is a compromise between traditional scholarly translations of medieval Latin philosophical texts and contemporary ontology. (shrink)

On how medieval philosophy is not (only) theology.

Abstract The purpose of this paper is twofold: (i) we will argue that formal semantics might have faltered due to its failure in distinguishing between two fundamentally very different types of concepts, namely ontological concepts, that should be types in a strongly-typed ontology, and logical concepts, that are predicates corresponding to properties of, and relations between, objects of various ontological types; and (ii) we show that accounting for these differences amounts to a new formal semantics; one that integrates lexical and (...) compositional semantics in one coherent framework and one where formal semantics is embedded with a strongly typed ontology; an ontology that reflects our commonsense knowledge of the world and the way we talk about it in ordinary language. We will show how in such a framework a number of challenges in the semantics of natural language are adequately and systematically treated. (shrink)

For millennia, knowledge has eluded a precise definition. The industrialization of knowledge (IoK) and the associated proliferation of the so-called knowledge communities in the last few decades caused this state of affairs to deteriorate, namely by creating a trio composed of data, knowledge, and information (DIK) that is not unlike the aporia of the trinity in philosophy. This calls for a general theory of knowledge (ToK) that can work as a foundation for a science of knowledge (SoK) and additionally distinguishes (...) knowledge from both data and information. In this paper, I attempt to sketch this generality via the establishing of both knowledge structures and knowledge systems that can then be adopted/adapted by the diverse communities for the respective knowledge technologies and practices. This is achieved by means of a formal–indeed, mathematical–approach to epistemological matters a.k.a. formal epistemology. The corresponding application focus is on knowledge systems implementable as computer programs. (shrink)

It is common in contemporary metaphysics to distinguish two levels of ontology: the ontology of ordinary objects and the ontology of fundamental reality. This papers argues that natural language reflects not only the ontology of ordinary objects, but also a language-driven ontology, which is involved in the mass-count distinction and part-structure-sensitive semantic selection, as well as perhaps the light ontology of pleonastic entities. The paper recasts my older theory of situated part structures without situations, making use of a primitive notion (...) of unity. (shrink)

2nd edition. Many-valued logics are those logics that have more than the two classical truth values, to wit, true and false; in fact, they can have from three to infinitely many truth values. This property, together with truth-functionality, provides a powerful formalism to reason in settings where classical logic—as well as other non-classical logics—is of no avail. Indeed, originally motivated by philosophical concerns, these logics soon proved relevant for a plethora of applications ranging from switching theory to cognitive modeling, and (...) they are today in more demand than ever, due to the realization that inconsistency and vagueness in knowledge bases and information processes are not only inevitable and acceptable, but also perhaps welcome. The main modern applications of (any) logic are to be found in the digital computer, and we thus require the practical knowledge how to computerize—which also means automate—decisions (i.e. reasoning) in many-valued logics. This, in turn, necessitates a mathematical foundation for these logics. This book provides both these mathematical foundation and practical knowledge in a rigorous, yet accessible, text, while at the same time situating these logics in the context of the satisfiability problem (SAT) and automated deduction. The main text is complemented with a large selection of exercises, a plus for the reader wishing to not only learn about, but also do something with, many-valued logics. (shrink)

Presents a good mapping of Williams’s argument in the larger context, relative to other thinkers, especially McDowell. With a short conclusion that there is something transcendent about ethical value that ecumenical projects reconciling the naturalist and the realist tend to miss.

Descriptive metaphysics investigates our naïve ontology as this is articulated in the content of our perception or of our pre-reflective thought about the world. But is access to such content reliable? Sceptics about the standard modes of access (introspection, or language-driven intuitions) may think that investigations in descriptive metaphysics can be aided by the controlled findings of cognitive science. Cognitive scientists have studied a promising range of representational advantages, that is, ways in which cognition favours one type of entity over (...) another. The notion of representational advantage is investigated and some scepticism is expressed as to its appropriateness for use in descriptive metaphysics. (shrink)

Intimate and medicalized, natural and technological, reproduction poses some of the most challenging ethical dilemmas of our time. This volume brings together scholars from multiple perspectives to address both traditional and novel questions about the rights and responsibilities of human reproducers, their caregivers, and the societies in which they live.

In der Vorlesung des Sommersemesters 1927 unter dem Titel Die Grundprobleme der Phanomenologie nimmt Martin Heidegger eine Neue Ausarbeitung des 3. Abschnitts des I. Teiles von 'Sein und Zeit' in Angriff. Der Gesamtbestand der Grundprobleme der Phanomenologie in ihrer Systematik und Begrundung besteht in der Diskussion der Grundfrage nach dem Sinn von Sein uberhaupt und der aus ihr entspringenden Probleme. Die so gekennzeichnete Thematik von Zeit und Sein wird auf dem Umweg einer phanomenologischen Erorterung von vier geschichtlichen Thesen uber das (...) Sein behandelt. Die phanomenologisch-kritische Diskussion dieser Thesen fuhrt zu der Einsicht, dass allem zuvor die Grundfrage nach dem Sinn von Sein uberhaupt beantwortet sein muss, um die aus den vier geschichtlichen Thesen herausgeschalten vier Grundprobleme in zureichender Weise systematisch ausarbeiten zu konnen. Wer Sein und Zeit als einen Weg zur Ausarbeitung der Seinsfrage uberhaupt als dem Ziel studiert, bleibt auf Die Grundprobleme der Phanomenologie verwiesen. (shrink)

Over two decades ago a "quite revolution" overwhelmingly replaced knowledgebased approaches in natural language processing (NLP) by quantitative (e.g., statistical, corpus-based, machine learning) methods. Although it is our firm belief that purely quantitative approaches cannot be the only paradigm for NLP, dissatisfaction with purely engineering approaches to the construction of large knowledge bases for NLP are somewhat justified. In this paper we hope to demonstrate that both trends are partly misguided and that the time has come to enrich logical semantics (...) with an ontological structure that reflects our commonsense view of the world and the way we talk about in ordinary language. In this paper it will be demonstrated that assuming such an ontological structure a number of challenges in the semantics of natural language (e.g., metonymy, intensionality, copredication, nominal compounds, etc.) can be properly and uniformly addressed. (shrink)

The question of whether biologists should continue to use the Linnaean hierarchy has been a hotly debated issue. Invented before the introduction of evolutionary theory, Linnaeus's system of classifying organisms is based on outdated theoretical assumptions, and is thought to be unable to provide accurate biological classifications. Marc Ereshefsky argues that biologists should abandon the Linnaean system and adopt an alternative that is more in line with evolutionary theory. He traces the evolution of the Linnaean hierarchy from its introduction to (...) the present. He illustrates how the continued use of this system hampers our ability to classify the organic world, and then goes on to make specific recommendations for a post-Linnaean method of classification. Accessible to a wide range of readers by providing introductory chapters to the philosophy of classification and the taxonomy of biology, the book will interest both scholars and students of biology and the philosophy of science. (shrink)

This volume is a collection of fourteen essays by leading philosophers on issues concerning the nature, existence, and our knowledge of animal minds. The nature of animal minds has been a topic of interest to philosophers since the origins of philosophy, and recent years have seen significant philosophical engagement with the subject. However, there is no volume that represents the current state of play in this important and growing field. The purpose of this volume is to highlight the state of (...) the debate. The issues which are covered include whether and to what degree animals think in a language or in iconic structures, possess concepts, are conscious, self-aware, metacognize, attribute states of mind to others, and have emotions, as well as issues pertaining to our knowledge of and the scientific standards for attributing mental states to animals. (shrink)

La célèbre querelle médiévale des universaux est une figure du débat qui, depuis l'antiquité tardive, oppose et rassemble à la fois le platonisme et l'aristotélisme. Ce débat dure encore. Il y a aujourd'hui des « nominalistes » et des « réalistes ». Mais ce livre est d'abord un livre d'histoire. Et quelle histoire! Comme le montre Alain de Libera, le problème des universaux est un condensateur d'innovations unique. Nul autre ne permet de voir se former, s'échanger et se codifier autant (...) de langages théoriques, de modèles ou d'instruments analytiques nouveaux : l'invention de l'intentionnalité, la théorie du signe, la refonte des concepts d'essence et d'existence, etc. Toutes ces « percées » typiquement médiévales trouvent, à partir de cet observatoire, l'horizon qui a fait d'elles autant de points de frayage de la modernité et de l'Âge classique le vrai Moyen Âge, celui qui espace, sépare et surtout interrompt.Un livre destiné à renouveler profondément les études médiévales et leur place dans l'histoire de la philosophie. (shrink)

In a series of publications, Eli Hirsch has presented a sustained defense of common-sense ontology. Hirsch's argument relies crucially on a meta-ontological position sometimes known as ‘superficialism’. Hirsch's argument from superficialism to common-sense ontology is typically resisted on the grounds that superficialism is implausible. In this paper, I present an alternative argument for common-sense ontology, one that relies on (what I argue is) a much more plausible meta-ontological position, which I call ‘constructivism’. Note well: I will not quite argue that (...) constructivism is true; merely that it is significantly more plausible than superficialism, and consequently affords a safer route to common-sense ontology. Thus my main goal in the paper is not quite to establish common-sense ontology, nor for that matter to refute Hirsch's argument for it. My goal is, in a way, more expressive than argumentative: I wish to articulate a novel meta-ontological position, one that I take to be in no way obviously less plausible than already familiar positions, and to point out that the position probably leads to common-sense ontology. I open, in section 1, with a discussion of Hirsch's argument and the main objection to it. I then develop, in section 2, a sketch of the alternative meta-ontology I have in mind. I close, in section 3, with the argument that this alternative meta-ontology, too, leads to common-sense ontology. (shrink)

This volume is dedicated to the centennial anniversary of Minkowski's discovery of spacetime.

The problem of universals is one of the main philosophical issues. In this book the author reconstructs the history of the problem from Boethius to John of Salisbury, considering a selection of medieval representative texts.

What happens to a person in a case of fission? Does it survive? Does it go out of existence? Or is the outcome indeterminate? Since each description of fission based on the persistence conditions associated with our ordinary concept of a person seems to clash with one or more platitudes of common sense about the spatiotemporal profile of macroscopic objects, fission threatens the common-sense conception of persons with inconsistency. Standard responses to this paradox agree that the common-sense conception of persons (...) is unstable, differing over which part of the conception requires revision. I will show that this entrenched view of fission is not compulsory. I will develop a solution to the paradox that maintains the consistency of the common-sense conception of persons on the basis of an ontology of persons and other ordinary objects as double-layered compounds. Each of various descriptions of the outcome of personal fission is compatible with principles about the spatiotemporal profile of persons, because the descriptions and the principles manifest different perspectives on persons and are made true or false by different ontological components of the latter. What holds for the fission of persons, holds for the fission of other kinds of objects. (shrink)

The representational nature of human cognition and thought in general has been a source of controversies. This is particularly so in the context of studies of unconscious cognition, in which representations tend to be ontologically and structurally segregated with regard to their conscious status. However, it appears evolutionarily and developmentally unwarranted to posit such segregations, as,otherwise, artifact structures and ontologies must be concocted to explain them from the viewpoint of the human cognitive architecture. Here, from a by-and-large Classical cognitivist viewpoint, (...) I show why this segregation is wrong, and elaborate on the need to postulate an ontological and structural continuity between unconscious and conscious representations. Specifically, I hypothesize that this continuity is to be found in the symbolic-based interplay between the syntax and the semantics of thought, and I propose a model of human information processing characterized by the integration of syntactic and semantic representations. (shrink)