[Stephen Yablo] The usual charge against Carnap's internal/external distinction is one of 'guilt by association with analytic/synthetic'. But it can be freed of this association, to become the distinction between statements made within make-believe games and those made outside them-or, rather, a special case of it with some claim to be called the metaphorical/literal distinction. Not even Quine considers figurative speech committal, so this turns the tables somewhat. To determine our ontological commitments, we have to ferret out all traces of (...) nonliterality in our assertions; if there is no sensible project of doing that, there is no sensible project of Quinean ontology. /// [Andre Gallois] I discuss Steve Yablo's defence of Carnap's distinction between internal and external questions. In the first section I set out what I take that distinction, as Carnap draws it, to be, and spell out a central motivation Carnap has for invoking it. In the second section I endorse, and augment, Yablo's response to Quine's arguments against Carnap. In the third section I say why Carnap's application of the distinction between internal and external questions runs into trouble. In the fourth section I spell out what I take to be Yablo's version of Carnap. In the last I say why that version is especially vulnerable to the objection raised in the second. (shrink)

Ontology is the philosophical discipline which aims to understand how things in the world are divided into categories and how these categories are related together. This is exactly what information scientists aim for in creating structured, automated representations, called 'ontologies,' for managing information in fields such as science, government, industry, and healthcare. Currently, these systems are designed in a variety of different ways, so they cannot share data with one another. They are often idiosyncratically structured, accessible only to those (...) who created them, and unable to serve as inputs for automated reasoning. This volume shows, in a nontechnical way and using examples from medicine and biology, how the rigorous application of theories and insights from philosophical ontology can improve the ontologies upon which information management depends. (shrink)

A ‘duality’ is a formal mapping between the spaces of solutions of two empirically equivalent theories. In recent times, dualities have been found to be pervasive in string theory and quantum field theory. Naïvely interpreted, duality-related theories appear to make very different ontological claims about the world—differing in e.g. space-time structure, fundamental ontology, and mereological structure. In light of this, duality-related theories raise questions familiar from discussions of underdetermination in the philosophy of science: in the presence of dual theories, (...) what is one to say about the ontology of the world? In this paper, we undertake a comprehensive and non-technical survey of the landscape of possible ontological interpretations of duality-related theories. We provide a significantly enriched and clarified taxonomy of options—several of which are novel to the literature. (shrink)

We describe a prototype ontology-driven information system (ODIS) that exploits what we call Portion of Reality (POR) representations. The system takes both sensor data and natural language text as inputs and composes on this basis logically structured POR assertions. The goal of our prototype is to represent both natural language and sensor data within a single framework that is able to support both axiomatic reasoning and computation. In addition, the framework should be capable of discovering and representing new kinds (...) of situations and thematic roles, (e.g., roles such as agent, patient and instrument), based on new compositions of existing representations. We applied our prototype in an intelligence analysis use case to test the hypothesis that a framework of this sort can produce usefully structured information from combined natural language and sensor data inputs. We further tested our hypothesis by adding an enhanced US Air Force ontology framework to our ODIS in order to (1) process a collection of sensor data, intel reports, and mission plans; (2) build composite POR representations from these data; and (3) machine analyze the fused results to infer mission threats. (shrink)

In this paper I will argue that critical theory needs to make its socio-ontological commitments explicit, whilst on the other hand I will posit that contemporary social ontology needs to amend its formalistic approach by embodying a critical theory perspective. In the first part of my paper I will discuss how the question was posed in Horkheimer’s essays of the 1930s, which leave open two options: (1) a constructive inclusion of social ontology within social philosophy, or else (2) (...) a program of social philosophy that excludes social ontology. Option (2) corresponds to Adorno’s position, which I argue is forced to recur to a hidden social ontology. Following option (1), I first develop a metacritical analysis of Searle, arguing that his social ontology presupposes a notion of 'recognition' which it cannot account for. Furthermore, by means of a critical reading of Honneth, I argue that critical theory could incorporate a socioontological approach, giving value to the constitutive socio-ontological role of recognition and to the socio-ontological role of objectification. I will finish with a proposal for a socio-ontological characterization of reification which involves that the basic occurrence of recognition is to be grasped at the level of background practices. (shrink)

The best arguments for possible worlds as states of affairs furnish us with equally good arguments for impossible worlds of the same sort. I argue for a theory of impossible worlds on which the impossible worlds correspond to maximal inconsistent classes of propositions. Three objections are rejected. In the final part of the paper, I present a menu of impossible worlds and explore some of their interesting formal properties.

'Ontology and Metaontology: A Contemporary Guide' is a clear and accessible survey of ontology, focussing on the most recent trends in the discipline. -/- Divided into parts, the first half characterizes metaontology: the discourse on the methodology of ontological inquiry, covering the main concepts, tools, and methods of the discipline, exploring the notions of being and existence, ontological commitment, paraphrase strategies, fictionalist strategies, and other metaontological questions. The second half considers a series of case studies, introducing and familiarizing (...) the reader with concrete examples of the latest research in the field. The basic sub-fields of ontology are covered here via an accessible and captivating exposition: events, properties, universals, abstract objects, possible worlds, material beings, mereology, fictional objects. -/- The guide's modular structure allows for a flexible approach to the subject, making it suitable for both undergraduates and postgraduates looking to better understand and apply the exciting developments and debates taking place in ontology today. (shrink)

The descriptions and theoretical laws scientists write down when they model a system are often false of any real system. And yet we commonly talk as if there were objects that satisfy the scientists’ assumptions and as if we may learn about their properties. Many attempt to make sense of this by taking the scientists’ descriptions and theoretical laws to define abstract or fictional entities. In this paper, I propose an alternative account of theoretical modelling that draws upon Kendall Walton’s (...) ‘make-believe’ theory of representation in art. I argue that this account allows us to understand theoretical modelling without positing any object of which scientists’ modelling assumptions are true. (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)

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic (...) expressivity to existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (shrink)

The discipline of applied ethics already has a certain familiarity in the Anglo-Saxon world, above all through the work of Peter Singer. Applied ethics uses the tools of moral philosophy to resolve practical problems of the sort which arise, for example, in the running of hospitals. In the University at Buffalo (New York) there was organized on April 24-25 1998 the world's first conference on a new, sister discipline, the discipline of applied ontology. Applied ontologists seek to apply ontological (...) tools to solving practical problems of the sort which arise in various extra-philosophical domains, including law and government administration. (shrink)

The aim of this paper is to summarize a particular approach of doing metaphysics through physics - the primitive ontology approach. The idea is that any fundamental physical theory has a well-defined architecture, to the foundation of which there is the primitive ontology, which represents matter. According to the framework provided by this approach when applied to quantum mechanics, the wave function is not suitable to represent matter. Rather, the wave function has a nomological character, given that its (...) role in the theory is to implement the law of evolution for the primitive ontology. (shrink)

The paper points out that the modern formulation of Bohm’s quantum theory known as Bohmian mechanics is committed only to particles’ positions and a law of motion. We explain how this view can avoid the open questions that the traditional view faces according to which Bohm’s theory is committed to a wave-function that is a physical entity over and above the particles, although it is defined on configuration space instead of three-dimensional space. We then enquire into the status of the (...) law of motion, elaborating on how the main philosophical options to ground a law of motion, namely Humeanism and dispositionalism, can be applied to Bohmian mechanics. In conclusion, we sketch out how these options apply to primitive ontology approaches to quantum mechanics in general. (shrink)

The paper offers an interpretation of a disputed portion of Plato’s Theaetetus that is often called the Secret Doctrine. It is presented as a process ontology that takes two types of processes, swift and slow motions, as fundamental building blocks for ordinary material objects. Slow motions are powers which, when realized, generate swift motions, which, in turn, are subjectively bundled to compose sensible objects and perceivers. Although the reading of the Secret Doctrine offered here—a new version of the “Causal (...) Theory interpretation”—is not without problems, these problems are acknowledged in Plato’s text, confirming that this interpretation is correct. (shrink)

Though the realm of biology has long been under the philosophical rule of the mechanistic magisterium, recent years have seen a surprisingly steady rise in the usurping prowess of process ontology. According to its proponents, theoretical advances in the contemporary science of evo-devo have afforded that ontology a particularly powerful claim to the throne: in that increasingly empirically confirmed discipline, emergently autonomous, higher-order entities are the reigning explanantia. If we are to accept the election of evo-devo as our (...) best conceptualisation of the biological realm with metaphysical rigour, must we depose our mechanistic ontology for failing to properly “carve at the joints” of organisms? In this paper, I challenge the legitimacy of that claim: not only can the theoretical benefits offered by a process ontology be had without it, they cannot be sufficiently grounded without the metaphysical underpinning of the very mechanisms which processes purport to replace. The biological realm, I argue, remains one best understood as under the governance of mechanistic principles. (shrink)

When we ask what natural kinds are, there are two different things we might have in mind. The first, which I’ll call the taxonomy question, is what distinguishes a category which is a natural kind from an arbitrary class. The second, which I’ll call the ontology question, is what manner of stuff there is that realizes the category. Many philosophers have systematically conflated the two questions. The confusion is exhibited both by essentialists and by philosophers who pose their accounts (...) in terms of similarity. It also leads to misreading philosophers who do make the distinction. Distinguishing the questions allows for a more subtle understanding of both natural kinds and their underlying metaphysics. (shrink)

How does the critical Kant view ontology? There is no shared scholarly answer to this question. Norbert Hinske sees in the Critique of Pure Reason a “farewell to ontology,” albeit one that took Kant long to bid (Hinske 2009). Karl Ameriks has found evidence in Kant’s metaphysics lectures from the critical period that he “was unwilling to break away fully from traditional ontology” (Ameriks 1992: 272). Gualtiero Lorini argues that a decisive break with the tradition of (...) class='Hi'>ontology is essential to Kant’s critical reform of metaphysics, as is reflected in his shift from “ontology” to “transcendental philosophy,” two notions that Lorini takes to be related by mere “analogy” (Lorini 2015). I agree with Lorini that a thorough reform of ontology is a pivotal part of Kant’s critical plan for metaphysics and that ontology somehow “survives within the critical philosophy” (Lorini 2015: 76). To make this case, however, I deem it important to identify “ontology” and “transcendental philosophy” in the sense of extensional equivalence. While we can detect this identification in Kant’s writings, only from his metaphysics lectures can we get a full sense of its historical and philosophical significance. In this chapter I focus on how it represents a definitive turn from as well as notable continuity with traditional treatments of ontology, particularly the Wolffian one. (shrink)

For a long time it was believed that it was impossible to be realist about quantum mechanics. It took quite a while for the researchers in the foundations of physics, beginning with John Stuart Bell [Bell 1987], to convince others that such an alleged impossibility had no foundation. Nowadays there are several quantum theories that can be interpreted realistically, among which Bohmian mechanics, the GRW theory, and the many-worlds theory. The debate, though, is far from being over: in what respect (...) should we be realist regarding these theories? Two diff erent proposals have been made: on the one hand, there are those who insist on a direct ontological interpretation of the wave function as representing physical bodies, and on the other hand there are those who claim that quantum mechanics is not really about the wave function. In this paper we will present and discuss one proposal of the latter kind that focuses on the notion of primitive ontology. (shrink)

The term ‘intelligence’ as used in this paper refers to items of knowledge collected for the sake of assessing and maintaining national security. The intelligence community (IC) of the United States (US) is a community of organizations that collaborate in collecting and processing intelligence for the US. The IC relies on human-machine-based analytic strategies that 1) access and integrate vast amounts of information from disparate sources, 2) continuously process this information, so that, 3) a maximally comprehensive understanding of world actors (...) and their behaviors can be developed and updated. Herein we describe an approach to utilizing outcomes-based learning (OBL) to support these efforts that is based on an ontology of the cognitive processes performed by intelligence analysts. Of particular importance to the Cognitive Process Ontology is the class Representation that is Warranted. Such a representation is descriptive in nature and deserving of trust in its veridicality. The latter is because a Representation that is Warranted is always produced by a process that was vetted (or successfully designed) to reliably produce veridical representations. As such, Representations that are Warranted are what in other contexts we might refer to as ‘items of knowledge’. (shrink)

This paper motivates taking seriously the possibility that brains are basically protean: that they make use of neural structures in inventive, on-the-fly improvisations to suit circumstance and context. Accordingly, we should not always expect cognition to divide into functionally stable neural parts and pieces. We begin by reviewing recent work in cognitive ontology that highlights the inadequacy of traditional neuroscientific approaches when it comes to divining the function and structure of cognition. Cathy J. Price and Karl J. Friston, and (...) Colin Klein identify the limitations of relying on forward and reverse inferences to cast light on the relation between cognitive functions and neural structures. There is reason to prefer Klein’s approach to that of Price and Friston’s. But Klein’s approach is neurocentric - it assumes that we ought to look solely at neural contexts to fix cognitive ontology. Using recent work on mindreading as a case study, we motivate adopting a radically different approach to cognitive ontology. Promoting the Protean Brain Hypothesis, we posit the possibility that we may need to look beyond the brain when deciding which functions are being performed in acts of cognition and in understanding how the brain contributes to such acts by adapting to circumstance. (shrink)

The study of viruses raises pressing conceptual and philosophical questions about their nature, their classification, and their place in the biological world. A major set of problems concerns the individuality and diachronic identity of a virus: what is the virus, the viral particle (virion) or the entire viral cycle? The correct identification of the virus has significant ontological consequences, also related to the place and time when biological entities begin and end. DOI: 10.13140/RG.2.2.35874.66241.

Words are indispensable linguistic tools for beings like us. However, there is not much philosophical work done about what words really are. In this paper, I develop a new ontology for words. I argue that words are abstract artifacts that are created to fulfill various kinds of purposes, and words are abstract in the sense that they are not located in space but they have a beginning and may have an end in time given that certain conditions are met. (...) What follows from this two-fold argument is that words, from an ontological point of view, are more like musical works, fictional characters or computer programs, than numbers or sets. (shrink)

Fictionalism in ontology is a mixed bag. Here I focus on three main variants—which I label after the names of Pascal, Berkeley, and Hume—and consider their relative strengths and weaknesses. The first variant is just a version of the epistemic Wager, applied across the board. The second variant builds instead on the fact that ordinary language is not ontologically transparent; we speak with the vulgar, but deep down we think with the learned. Finally, on the Humean variant it’s the (...) structure of the ontological inventory, not its content, that may turn out to involve fictional elements. That is, for the Humean the fiction lies, not in the reality of common-sense ontology, but in the laws—of unity, identity, causation, etc.—in terms of which we articulate our experience of that reality. In the end, this is the kind of fictionalism that I find most interesting, sensible, and tenable. And I argue that it is even compatible with the sort of “naive” realism we have all come to appreciate in the work of Paolo Bozzi, to whom the paper is dedicated. (shrink)

This is a contribution to a symposium on Amie Thomasson’s Ontology Made Easy (2015). Thomasson defends two deflationary theses: that philosophical questions about the existence of numbers, tables, properties, and other disputed entities can all easily be answered, and that there is something wrong with prolonged debates about whether such objects exist. I argue that the first thesis (properly understood) does not by itself entail the second. Rather, the case for deflationary metaontology rests largely on a controversial doctrine about (...) the possible meanings of ‘object’. I challenge Thomasson's argument for that doctrine, and I make a positive case for the availability of the contested, unrestricted use of ‘object’. (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)

Timothy Williamson has argued that in the debate on modal ontology, the familiar distinction between actualism and possibilism should be replaced by a distinction between positions he calls contingentism and necessitism. He has also argued in favor of necessitism, using results on quantified modal logic with plurally interpreted second-order quantifiers showing that necessitists can draw distinctions contingentists cannot draw. Some of these results are similar to well-known results on the relative expressivity of quantified modal logics with so-called inner and (...) outer quantifiers. The present paper deals with these issues in the context of quantified modal logics with generalized quantifiers. Its main aim is to establish two results for such a logic: Firstly, contingentists can draw the distinctions necessitists can draw if and only if the logic with inner quantifiers is at least as expressive as the logic with outer quantifiers, and necessitists can draw the distinctions contingentists can draw if and only if the logic with outer quantifiers is at least as expressive as the logic with inner quantifiers. Secondly, the former two items are the case if and only if all of the generalized quantifiers are first-order definable, and the latter two items are the case if and only if first-order logic with these generalized quantifiers relativizes. (shrink)

Current approaches to formal representation in biomedicine are characterized by their focus on either the static or the dynamic aspects of biological reality. We here outline a theory that combines both perspectives and at the same time tackles the by no means trivial issue of their coherent integration. Our position is that a good ontology must be capable of accounting for reality both synchronically (as it exists at a time) and diachronically (as it unfolds through time), but that these (...) are two quite different tasks, whose simultaneous realization is by no means trivial. The paper is structured as follows. We begin by laying out the methodological and philosophical background of our approach. We then summarize the structure and elements of the Basic Formal Ontology on which it rests, in particular the SNAP ontology of objects and the SPAN ontology of processes. Finally, we apply the general framework to the specific domain of biomedicine. (shrink)

What is the ontology of collective action? I have in mind three connected questions. 1. Do the truth conditions of action sentences about groups require there to be group agents over and above individual agents? 2. Is there a difference, in this connection, between action sentences about informal groups that use plural noun phrases, such as ‘We pushed the car’ and ‘The women left the party early’, and action sentences about formal or institutional groups that use singular noun phrases, (...) such as ‘The United States declared war on Japan on December 8th, 1941’ and ‘The Supreme Court ruled that segregation is unconstitutional in 1954 in Brown vs. Board of Education’? 3. Under what conditions does it make sense to speak of a group doing something together, and what, if anything, is a collective action? In this paper, I argue that a) understanding action sentences about groups does not commit us to the existence of group agents per se, but only to the existence of individual agents; b) there is no difference in this regard between sentences which attribute actions to informal groups on the one hand and institutional groups on the other; c) collective action can be both intentional and unintentional; d) any random group of agents each of whom does something is also a group which does something together; e) while there is a sense in which groups per se perform no primitive collective actions, and therefore no actions at all, f) there is a sensible extension of talk of actions to groups, though it should be treated strictly speaking, like talk of group agents, as a façon de parler, for g) the only agents per se are individuals and the only actions are theirs. -/-. (shrink)

Successful biomedical data mining and information extraction require a complete picture of biological phenomena such as genes, biological processes, and diseases; as these exist on different levels of granularity. To realize this goal, several freely available heterogeneous databases as well as proprietary structured datasets have to be integrated into a single global customizable scheme. We will present a tool to integrate different biological data sources by mapping them to a proprietary biomedical ontology that has been developed for the purposes (...) of making computers understand medical natural language. (shrink)

Although the relationship of part to whole is one of the most fundamental there is, this is the first full-length study of this key concept. Showing that mereology, or the formal theory of part and whole, is essential to ontology, Simons surveys and critiques previous theories--especially the standard extensional view--and proposes a new account that encompasses both temporal and modal considerations. Simons's revised theory not only allows him to offer fresh solutions to long-standing problems, but also has far-reaching consequences (...) for our understanding of a host of classical philosophical concepts. (shrink)

I argue that the most promising approach to understanding J.J. Gibson's "affordances" takes affordances themselves as ontological primitives, instead of treating them as dispositional properties of more primitive things, events, surfaces, or substances. These latter are best treated as coalescences of affordances present in the environment (or "coalescences of use-potential," as in Sanders (1994) and Hilditch (1995)). On this view, even the ecological approach's stress on the complementary organism/environment pair is seen as expressing a particular affordance relation between the world (...) and the analyst. That the world is parsed in any way among events and objects, perceivers and worlds, etc., reflects equally features of certain real or possible perspectives on the world and features of the world itself. In section 1, I begin by contending that, contrary to the apparent expectations of some in the field, the bare existence of affordances is surely quite uncontroversial. In section 2, I argue that the most reasonable approach to foundational ontology is a relativistic one. In section 3, I address the claim that affordances must be ontologically complemented by effectivities for the sake of completeness, and I shall argue against that claim on grounds that I take to reflect some of Gibson's most important insights. This work will help to clarify the way affordances are to be used in the fourth and final section, where I argue that ontological work, even within special sciences, should not be merely "regional," and that the most attractive general approach to ontological questions is one that is based on affordances, rather than upon things, events, surfaces, and the like. (shrink)

This paper advances a general argument, inspired by some remarks of Davidson, to show that appeal to meanings as entities in the theory of meaning is neither necessary nor sufficient for carrying out the tasks of the theory of meaning. The crucial point is that appeal to meaning as entities fails to provide us with an understanding of any expression of a language except insofar as we pick it out with an expression we understand which we tacitly recognize to be (...) a translation of the term whose meaning we want to illuminate by the appeal to assigning to it a meaning. The meaning drops out as irrelevant: the work is done, and can only be done, by matching terms already understood with terms they translate. (shrink)

Medical terminology collects and organizes the many different kinds of terms employed in the biomedical domain both by practitioners and also in the course of biomedical research. In addition to serving as labels for biomedical classes, these names reflect the organizational principles of biomedical vocabularies and ontologies. Some names represent invariant features (classes, universals) of biomedical reality (i.e., they are a matter for ontology). Other names, however, convey also how this reality is perceived, measured, and understood by health professionals (...) (i.e., they belong to the domain of epistemology). We analyze terms from several biomedical vocabularies in order to throw light on the interactions between ontological and epistemological components of these terminologies. We identify four cases: 1) terms containing classification criteria, 2) terms reflecting detectability, modality, uncertainty, and vagueness, 3) terms created in order to obtain a complete partition of a given domain, and 4) terms reflecting mere fiat boundaries. We show that epistemology-loaded terms are pervasive in biomedical vocabularies, that the “classes” they name often do not comply with sound classification principles, and that they are therefore likely to cause problems in the evolution and alignment of terminologies and associated ontologies. (shrink)

In this paper I present the common structure of quantum theories with a primitive ontology, and discuss in what sense the classical world emerges from quantum theories as understood in this framework. In addition, I argue that the primitive ontology approach is better at answering this question than the rival wave function ontology approach or any other approach in which the classical world is nonreductively ‘emergent:’ even if the classical limit within this framework needs to be fully (...) developed, the difficulties are technical rather than conceptual, while this is not true for the alternatives. (shrink)

The problem of merging several ontologies has important applications in the Semantic Web, medical ontology engineering and other domains where information from several distinct sources needs to be integrated in a coherent manner.We propose to view ontology merging as a problem of social choice, i.e. as a problem of aggregating the input of a set of individuals into an adequate collective decision. That is, we propose to view ontology merging as ontology aggregation. As a first step (...) in this direction, we formulate several desirable properties for ontology aggregators, we identify the incompatibility of some of these properties, and we define and analyse several simple aggregation procedures. Our approach is closely related to work in judgment aggregation, but with the crucial difference that we adopt an open world assumption, by distinguishing between facts not included in an agent’s ontology and facts explicitly negated in an agent’s ontology. (shrink)

In this paper recognition is taken to be a question of social ontology, regarding the very constitution of the social space of interaction. I concentrate on the question of whether certain aspects of the theory of recognition can be translated into the terms of a socio-ontological paradigm: to do so, I make reference to some conceptual tools derived from John Searle's social ontology and Robert Brandom's normative pragmatics. My strategy consists in showing that recognitive phenomena cannot be isolated (...) at the level of human interaction, and are, rather, in part proper to animal interaction as well. Furthermore, it is argued that recognitive powers are constitutive powers more basic than deontic ones and play a role much broader than the one they in fact assume in Searle and in Brandom. (shrink)

In a number of recent publications Thomasson has defended a deflationary approach to ontological disputes, according to which ontological disputes are relatively easy to settle, by either conceptual analysis, or conceptual analysis in conjunction with empirical investigation. Thomasson’s “easy” approach to ontology is intended to derail many prominent ontological disputes. In this paper I present an objection to Thomasson’s approach to ontology. Thomasson’s approach to existence assertions means that she is committed to the view that application conditions associated (...) with any term “K” with non-trivial application conditions must refer to the existence of things other than Ks. Given other components of her meta-ontological scheme, this leads to either an infinite regress or circularity of application conditions, both of which seem objectionable. Accordingly, some part of Thomasson’s meta-ontological scheme should be modified or abandoned. (shrink)

I shall attempt in what follows to show how mereology, taken together with certain topological notions, can yield the basis for future investigations in formal ontology. I shall attempt to show also how the mereological framework here advanced can allow the direct and natural formulation of a series of theses – for example pertaining to the concept of boundary – which can be formulated only indirectly (if at all) in set-theoretic terms.

Ontology is currently perceived as the solution of first resort for all problems related to biomedical terminology, and the use of description logics is seen as a minimal requirement on adequate ontology-based systems. Contrary to common conceptions, however, description logics alone are not able to prevent incorrect representations; this is because they do not come with a theory indicating what is computed by using them, just as classical arithmetic does not tell us anything about the entities that are (...) added or subtracted. In this paper we shall show that ontology is indeed an essential part of any solution to the problems of medical terminology – but only if it is understood in the right sort of way. Ontological engineering, we shall argue, should in every case go hand in hand with a sound ontological theory. (shrink)

Ontology, since Aristotle, has been conceived as a sort of highly general physics, a science of the types of entities in reality, of the objects, properties, categories and relations which make up the world. At the same time ontology has been for some two thousand years a speculative enterprise. It has rested methodologically on introspection and on the construction and analysis of elaborate world-models and of abstract formal-ontological theories. In the work of Quine and others this ontological theorizing (...) in abstract fashion about the world was supplemented by the study, based on the use of logical methods, of the ontological commitments or presuppositions embodied in scientific theories. In recent years both types of ontological study have found application in the world of information systems, for example in the construction of frameworks for knowledge representation and in database design and translation. As ontology is in this way drawn closer to the domain of real-world applications, the question arises as to whether it is possible to use empirical methods in studying ontological theories. More specifically: can we use empirical methods to test the ontological theories embodied in human cognition? We set forth the outlines of a framework for the formulation and testing of such theories as they relate to the specific domain of geographic objects and categories. (shrink)

Statistics play a critical role in biological and clinical research. To promote logically consistent representation and classification of statistical entities, we have developed the Ontology of Biological and Clinical Statistics (OBCS). OBCS extends the Ontology of Biomedical Investigations (OBI), an OBO Foundry ontology supported by some 20 communities. Currently, OBCS contains 686 terms, including 381 classes imported from OBI and 147 classes specific to OBCS. The goal of this paper is to present OBCS for community critique and (...) to describe a number of use cases designed to illustrate its potential applications. The OBCS project and source code are available at http://obcs.googlecode.com. (shrink)

In this paper I sketch some arguments that underlie Hegel's chapter on judgment, and I attempt to place them within a broad tradition in the history of logic. Focusing on his analysis of simple predicative assertions or ‘positive judgments’, I first argue that Hegel supplies an instructive alternative to the classical technique of existential quantification. The main advantage of his theory lies in his treatment of the ontological implications of judgments, implications that are inadequately captured by quantification. The second concern (...) of this paper is the manner in which Hegel makes logic not only dependent on ontology generally, but also variant in regard to domains of objects. In other words, he offers a domain-specific logical theory, according to which the form of judgment or inference is specific to the subject of judgment. My third concern lies with the metaphilosophical consequences of this theory, and this includes some more familiar Hegelian themes. It is well known that Hegel frequently questioned the adequacy of the sentential form for expressing higher order truths. My reading of his theory of predication explains and contextualizes this tendency by demystifying notions like the so-called speculative proposition. (shrink)

In this article I try to show that the most deep level ontology can have rich meaning for our understanding of such practical and everyday phenomena as education and interaction. With this deep level ontology I mean the problem of universals. Starting from famous traditional stances of realism and nominalism, which both are for the modern theories of growth and Bildung, I continue to the third and more recently developed ontological theory, trope theory according to which the properties (...) (qualities, relations etc.) are real (unlike in nominalism) but not universal (like in realisms). Then I will take a closer look at the trope theory of CB Martin. According to it every causal event is an interaction event between simple or complex beings in which their existing dispositions may produce manifesting properties. This point of view is radically anti dualistic because that basic level causal interaction has in the simplified forms all the elements of semiotic, meaningful of mental activity of such complex beings likes humans and animals. Ome of the main general conclusions of the article is that all causal affections contain a kind of “interpretation” from the side of affected object. (shrink)

In this paper I elicit a prediction from structural realism and compare it, not to a historical case, but to a contemporary scientific theory. If structural realism is correct, then we should expect physics to develop theories that fail to provide an ontology of the sort sought by traditional realists. If structure alone is responsible for instrumental success, we should expect surplus ontology to be eliminated. Quantum field theory (QFT) provides the framework for some of the best confirmed (...) theories in science, but debates over its ontology are vexed. Rather than taking a stand on these matters, the structural realist can embrace QFT as an example of just the kind of theory SR should lead us to expect. Yet, it is not clear that QFT meets the structuralist's positive expectation by providing a structure for the world. In particular, the problem of unitarily inequivalent representations threatens to undermine the possibility of QFT providing a unique structure for the world. In response to this problem, I suggest that the structuralist should endorse pluralism about structure. (shrink)

The aim of natural language ontology is to uncover the ontological categories and structures that are implicit in the use of natural language, that is, that a speaker accepts when using a language. This article aims to clarify what exactly the subject matter of natural language ontology is, what sorts of linguistic data it should take into account, how natural language ontology relates to other branches of metaphysics, in what ways natural language ontology is important, and (...) what may be distinctive of the ontological categories and structures reflected in natural language. (shrink)

This essay explores the possibility of constructing a structural realist interpretation of spacetime theories that can resolve the ontological debate between substantivalists and relationists. Drawing on various structuralist approaches in the philosophy of mathematics, as well as on the theoretical complexities of general relativity, our investigation will reveal that a structuralist approach can be beneficial to the spacetime theorist as a means of deflating some of the ontological disputes regarding similarly structured spacetimes.

The Salivaomics Knowledge Base (SKB) is designed to serve as a computational infrastructure that can permit global exploration and utilization of data and information relevant to salivaomics. SKB is created by aligning (1) the saliva biomarker discovery and validation resources at UCLA with (2) the ontology resources developed by the OBO (Open Biomedical Ontologies) Foundry, including a new Saliva Ontology (SALO). We define the Saliva Ontology (SALO; http://www.skb.ucla.edu/SALO/) as a consensus-based controlled vocabulary of terms and relations dedicated (...) to the salivaomics domain and to saliva-related diagnostics following the principles of the OBO (Open Biomedical Ontologies) Foundry. The Saliva Ontology is an ongoing exploratory initiative. The ontology will be used to facilitate salivaomics data retrieval and integration across multiple fields of research together with data analysis and data mining. The ontology will be tested through its ability to serve the annotation ('tagging') of a representative corpus of salivaomics research literature that is to be incorporated into the SKB. Background Saliva (oral fluid) is an emerging biofluid for non-invasive diagnostics used in the detection of human diseases. The need to advance saliva research is strongly emphasized by the National Institute of Dental and Craniofacial Research (NIDCR), and is included in the NIDCR's 2004- 2009 expert panel long-term research agenda [1]. The ability to monitor health status, disease onset, progression, recurrence and treatment outcome through noninvasive means is highly important to advancing health care management. Saliva is a perfect medium to be explored for personalized individual medicine including diagnostics, offering a non-invasive, easy to obtain means for detecting and monitoring diseases. Saliva testing potentially allows the patient to collect their own saliva samples at home, yielding convenience for the patient and savings in health costs, and facilitating multiple sampling. Specimen collection is less objectionable to patients and easier in children and elderly individuals. Due to these advantages. (shrink)

A standard art-ontological position is to construe repeatable artworks as abstract objects that admit multiple concrete instances. Since photographic artworks are putatively repeatable, the ontology of photographic art is by default modelled after standard repeatable-work ontology. I argue, however, that the construal of photographic artworks as abstracta mistakenly ignores photography’s printmaking genealogy, specifically its ontological inheritance. More precisely, I claim that the products of printmaking media (prints) minimally must be construed in a manner consistent with basic print (...) class='Hi'>ontology, the most plausible model of which looks decidedly nominalist (what I call the relevant similarity model) and that as such, photographic artworks must be likewise construed, not as abstracta but as individual and distinct concreta. That is, the correct ontological account of photographic art must be one according to which photographic artworks are individual and distinct concrete artworks. In the end, I show that the ontology of photographic art resists the standard repeatable-work model because the putative repeatability of photographic artworks is upon closer inspection nothing more than the relevant similarity relation between individual and distinct photographic prints. (shrink)

The central hypothesis of the collaboration between Language and Computing (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is that the methodology and conceptual rigor of a philosophically inspired formal ontology greatly benefits application ontologies. To this end r®, L&C’s ontology, which is designed to integrate and reason across various external databases simultaneously, has been submitted to the conceptual demands of IFOMIS’s Basic Formal Ontology (BFO). With this project we aim to move (...) beyond the level of controlled vocabularies to yield an ontology with the ability to support reasoning applications. Our general procedure has been the implementation of a meta-ontological definition space in which the definitions of all the concepts and relations in LinKBase® are standardized in a framework of first-order logic. In this paper we describe how this standardization has already led to an improvement in the LinKBase® structure that allows for a greater degree of internal coherence than ever before possible. We then show the use of this philosophical standardization for the purpose of mapping external databases to one another, using LinKBase® as translation hub, with a greater degree of success than possible hitherto. We demonstrate how this offers a genuine advance over other application ontologies that have not submitted themselves to the demands of philosophical scrutiny. LinKBase® is one of the world’s largest applications-oriented medical domain ontologies, and BFO is one of the world’s first philosophically driven reference ontologies. The collaboration of the two thus initiates a new phase in the quest to solve the so-called “Tower of Babel”. (shrink)