'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)

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)

I give shape to a neglected debate in metaphysics, the debate over the ontological priority between individuality and collectivity. I distinguish the debate from more familiar ones in the recent literature and articulate what I call ontological collectivism, the view that collectivity is prior to individuality. I defend the in-principle intelligibility of the view from forceful general objections and argue that not only is it coherent but also of significant interest to the literature: it allows for overlooked alternatives on a (...) variety of central discussions. (shrink)

This essay provides an opinionated survey of some recent developments in the literature on ontological dependence. Some of the most popular definitions of ontological dependence are formulated in modal terms; others in non-modal terms (e.g., in terms of the explanatory connective, ‘because’, or in terms of a non-modal conception of essence); some (viz., the existential construals of ontological dependence) emphasise requirements that must be met in order for an entity to exist; others (viz., the essentialist construals) focus on conditions that (...) must be satisfied in order for an entity to be the very entity it is at each time at which it exists; some are rigid, in the sense that they concern a relation between particular entities; others are generic, in the sense that they involve only a relation between an entity and some entities or other, which bear certain characteristics. I identify three potential measures of success with respect to which these different definitions of ontological dependence can be evaluated and consider the question of how well they in fact meet these desiderata. I end by noting that certain challenges face even the most promising essentialist construals of ontological dependence. (shrink)

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)

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)

Ontological pluralism is the view that there are different ways to exist. It is a position with deep roots in the history of philosophy, and in which there has been a recent resurgence of interest. In contemporary presentations, it is stated in terms of fundamental languages: as the view that such languages contain more than one quantifier. For example, one ranging over abstract objects, and another over concrete ones. A natural worry, however, is that the languages proposed by the pluralist (...) are mere notational variants of those proposed by the monist, in which case the debate between the two positions would not seem to be substantive. Jason Turner has given an ingenious response to this worry, in terms of a principle that he calls ‘logical realism’. This paper offers a counter-response on behalf of the ‘notationalist’. I argue that, properly applied, the principle of logical realism is no threat to the claim that the languages in question are notational variants. Indeed, there seems to be every reason to think that they are. (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)

In this chapter, I examine Lewis's ideas about ontological innocence, ontological commitment and double-counting, in his discussion of composition as identity in Parts of Classes. I attempt to understand these primarily as epistemic or methodological claims: how far can we get down this route without adopting radical metaphysical theses about composition as identity?

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)

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)

The gulf between philosophical and formal ontology can and should be bridged. In this Editorial, I elaborate briefly on this subject.

Bio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. They are a key component of the Semantic Web. This paper provides background on what bio-ontologies are, why they are relevant to botany, and the principles of ontology development. It includes an overview of ontologies and related resources that are relevant to plant (...) science, with a detailed description of the Plant Ontology (PO). We discuss the challenges of building an ontology that covers all green plants (Viridiplantae). Key results: Ontologies can advance plant science in four keys areas: 1. comparative genetics, genomics, phenomics, and development, 2. taxonomy and systematics, 3. semantic applications and 4. education. Conclusions: Bio-ontologies offer a flexible framework for comparative plant biology, based on common botanical understanding. As genomic and phenomic data become available for more species, we anticipate that the annotation of data with ontology terms will become less centralized, while at the same time, the need for cross-species queries will become more common, causing more researchers in plant science to turn to ontologies. (shrink)

Enterprise Risk Management and security have become a fundamental part of Enterprise Architecture, so several frameworks and modeling languages have been designed to support the activities associated with these areas. Archi- Mate’s Risk and Security Overlay is one of such proposals, endorsed by The Open Group. We investigate the capabilities of the proposed security-related con- structs in ArchiMate with regard to the necessities of enterprise security modeling. Our analysis relies on a well-founded reference ontology of security to uncover ambiguity, (...) missing modeling elements, and other deficiencies of the security mod- eling capabilities in ArchiMate. Based on this ontologically-founded analysis, we propose a redesign of security aspects of ArchiMate to overcome its original limitations. (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)

Ontological expressivism is the view that ontological existence claims express non-cognitive mental states. I develop a version of ontological expressivism that is modeled after Gibbard’s (2003) norm-expressivism. I argue that, when speakers assess whether, say, composite objects exist, they rely on assumptions with regard to what is required for composition to occur. These assumptions guide their assessment, similar to how norms may guide the assessment of normative propositions. Against this backdrop, I argue that “some objects have parts”, uttered in the (...) context of an ontological disagreement, expresses a noncognitive disposition to assess the truth of propositions by using only rules of assessment according to which the proposition that some objects have parts is to be evaluated as true. (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)

Ontological pluralism is the view that there are different fundamental ways of being. Trenton Merricks has recently raised three objections to combining pluralism with a generic way of being enjoyed by absolutely everything there is: first, that the resulting view contradicts the pluralist’s core intuition; second, that it is especially vulnerable to the charge—due to Peter van Inwagen—that it posits a difference in being where there is simply a difference in kind; and, third, that it is in tension with various (...) historically influential motivations for pluralism. I reply to each of these objections in turn. My replies will help to bring out the true nature of the pluralist’s basic commitments. (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)

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)

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)

According to standard trope nominalism, there are simple tropes that do not have parts or multiply distinct aspects. Douglas Ehring’s reductio ad absurdum against this standard view concludes that there are no simple tropes. In this paper, we provide a response to Ehring defending the standard view. Ehring’s argument may be refuted by (1) distinguishing the ontological form of tropes from their contribution to the ontological content of the world, and (2) construing tropes as having primitive identity. At the same (...) time, standard trope nominalism is elaborated on by distinguishing between ontological form and content, for which there are also independent reasons. (shrink)

Consider the most recent Yale-Harvard football game, an event which occurred on 11/20/21 in New Haven, lasting about three hours. This event, like many college football games before, was composed of four quarters, each of which was composed of possessions, each of which was composed of downs, each of which was composed of particular movements, tackles and decisions of the individual players. Each of these parts of the game was itself an event, occurring in a smaller region of space and (...) time than the game itself. Each of these events involved material objects like players, helmets, jerseys, etc. Each had causes and effects, and each instantiated qualitative properties, such as being a kickoff or being a tackle. These are paradigmatic examples of events. Events are many and varied; some other examples include the melting of an ice cube, the birth of a horse, the supernova of a star, the presidential election campaign and a winter snowstorm. Each of these took place in a certain region of spacetime, had other events as parts, involved certain objects, had causes and effects, and instantiated properties. Objects and their properties are not the only furniture in the world. Events are a crucial part of our manifest and scientific pictures of the world. We go to football games, think about and participate in elections, eagerly anticipate the birth of a child, and quantify over and explain such things in our scientific theories. Yet, events have received insufficient attention from metaphysicians. Some philosophers have been skeptical of events, holding that talk of events can be paraphrased away, or that events can be reduced to objects and properties.1 When philosophers have accepted events, their motivations have usually been extrinsic—events are introduced in order to play a role in a larger philosophical system. This tendency has led philosophers to miss a number of interesting features of events. In this paper, I wish to reverse that trend by developing an ontology of events which is not an afterthought with respect to another philosophical project. In so doing, I will provide answers to substantive metaphysical questions about the relations in which events stand and their identity conditions. In the next section, I identify four basic relations in which events stand: parthood, involvement, causation and instantiation, focusing in particular on involvement. Then, I argue that events are individuated by their involvements, and criticize the identity conditions which have been offered by other philosophers, notably Quine, Davidson and Kim. I then conclude. (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)

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)

Virtually everyone who has advanced an ontology of art has accepted a constraint to the effect that claims about ontology should cohere with the sort of appreciative claims made about artworks within a mature and reflective version of critical practice. I argue that such a constraint, which I agree is appropriate, rules out a one-size-fits-all ontology of contemporary visual art (and thus of visual art in general). Mature critical practice with respect to contemporary art accords artists a (...) significant degree of stipulative authority regarding the features and boundaries of their works. This results in ontological variation among visual artworks. Any claim to the effect that all works belong to the same ontological category will thus come out false or uninformative. Interesting, substantive claims about ontological status can be made only in relation to specific works; that is, we must consider the ontological status of each contemporary artwork individually. The only general ontological claim that can be made about visual artworks (and also about artworks in other forms) is that they belong to the sort of thing that artists create. But this is not a substantive ontological claim. (shrink)

I develop ontological pluralism about non-being, the view that there are multiple ways, kinds, or modes of non-being. I suggest that the view is both more plausible and defensible than it first seems, and that it has many useful applications across a wide variety of metaphysical and explanatory problems. After drawing out the relationship between pluralism about being and pluralism about non-being, I discuss quantificational strategies for the pluralist about non-being. I examine historical precedent for the view. Finally, I suggest (...) that pluralism about non-being has explanatory power across a variety of domains, and that the view can account for differences between nonexistent past and future times, between omissions and absences, and between different kinds of fictional objects. (shrink)

Because climate change can be seen as the blind spot of contemporary philosophy of technology, while the destructive side effects of technological progress are no longer deniable, this article reflects on the role of technologies in the constitution of the (post)Anthropocene world. Our first hypothesis is that humanity is not the primary agent involved in world-production, but concrete technologies. Our second hypothesis is that technological inventions at an ontic level have an ontological impact and constitutes world. As we object to (...) classical philosophers of technology like Ihde and Heidegger, we will sketch the progressive contribution of our conceptuality to understand the role of technology in the Anthropocene world. Our third hypothesis is that technology has emancipatory potential and in this respect, can inaugurate a post-Anthropocene World. We consider these three hypotheses to develop a philosophical account of the ontology of technology beyond an abstract and deterministic understanding. This concept enables us to philosophically reflect on the role of technology in the Anthropocene World in general, and its contribution to the transition to the post-Anthropocene World in particular. (shrink)

[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)

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)

This article is a brief overview of major ontological arguments. The most noteworthy feature of this article is the statement of a new parody of the Anselmian and Cartesian arguments that is obviously immune to objections adverting to intrinsic minima and maxima.

Software application ontologies have the potential to become the keystone in state-of-the-art information management techniques. It is expected that these ontologies will support the sort of reasoning power required to navigate large and complex terminologies correctly and efficiently. Yet, there is one problem in particular that continues to stand in our way. As these terminological structures increase in size and complexity, and the drive to integrate them inevitably swells, it is clear that the level of consistency required for such navigation (...) will become correspondingly difficult to maintain. While descriptive semantic representations are certainly a necessary component to any adequate ontology-based system, so long as ontology engineers rely solely on semantic information, without a sound ontological theory informing their modeling decisions, this goal will surely remain out of reach. In this paper we describe how Language and Computing nv (L&C), along with The Institute for Formal Ontology and Medical Information Sciences (IFOMIS), are working towards developing and implementing just such a theory, combining the open software architecture of L&C’s LinkSuiteTM with the philosophical rigor of IFOMIS’s Basic Formal Ontology. In this way we aim to move beyond the more or less simple controlled vocabularies that have dominated the industry to date. (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)

We present an ontological analysis of the notion of group agency developed by Christian List and Philip Pettit. We focus on this notion as it allows us to neatly distinguish groups, organizations, corporations – to which we may ascribe agency – from mere aggregates of individuals. We develop a module for group agency within a foundational ontology and we apply it to organizations.

In a world that is overflowing with journals and other outlets for scientific publication, the appearance of any new periodical requires some justification. There are already more journals than we can read and more conferences than we can attend. In the case of applied Ontology, we believe that the creation of anew journal not only is completely justifiable, it is downright exciting. For too long, workers in computer science have assumed that content comes for free. “Theory” in computer science (...) has always meant the theory of processes and of computation. We measure the complexity of computer programs in terms of how long it takes machines to execute them, not in terms of how long it takes people to understand and to represent the data on which those programs might operate. We typically describe computer code in terms of algorithms that operate on formal parameters, often without pausing to discuss where the data that might satisfy those parameters come from. This journal was founded on the premise that workers in computer science, informatics, and information science are overdue in paying as much attention to contents as they do to algorithms. (shrink)

This is a commentary on the article by Augusto (2022; this issue) on categories and foundation ontology (FO). We agree that the notion of categories of kinds of elements to devise a FO deserves more attention than it has received to date. From a practical point of view sensu developing domain ontologies, however, it probably does not matter much as long as a FO is used and that that one was understood.

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)

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)

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)

Increasingly, in data-intensive areas of the life sciences, experimental results are being described in algorithmically useful ways with the help of ontologies. Such ontologies are authored and maintained by scientists to support the retrieval, integration and analysis of their data. The proposition to be defended here is that ontologies of this type – the Gene Ontology (GO) being the most conspicuous example – are a part of science. Initial evidence for the truth of this proposition (which some will find (...) self-evident) is the increasing recognition of the importance of empirically-based methods of evaluation to the ontology development work being undertaken in support of scientific research. The ontologies created by scientists must, of course, be associated with implementations satisfying the requirements of software engineering. But these ontologies are not themselves engineering artifacts, and to conceive them as such brings grievous consequences. Rather, we shall argue, ontologies such as the GO are comparable to scientific theories, to scientific databases, or to scientific journal publications. Such a view implies a radically new conception of what is involved in the authoring, maintenance and application of ontologies in scientific contexts, and therewith also a radically new approach to the evaluation of ontologies and to the training of ontologists. (shrink)

The traditional approach to explanation in cognitive neuroscience is realist about psychological constructs, and treats them as explanatory. On the “standard framework,” cognitive neuroscientists explain behavior as the result of the instantiation of psychological functions in brain activity. This strategy is questioned by results suggesting the distribution of function in the brain, the multifunctionality of individual parts of the brain, and the overlap in neural realization of purportedly distinct psychological constructs. One response to this in the field has been to (...) employ the tools of databasing and machine learning to attempt to find and quantify specific correlations between psychological kinds such as ‘memory’ or ‘attention’ (or sub-kinds thereof) and patterns of activity in the brain. I assess the status and prospects of these projects. I argue that current proponents of the project are vague about their aims, vis-à-vis the standard framework, sometimes suggesting substantiation of the framework, sometimes suggesting retaining the framework but revising the ontology of mental constructs, and sometimes suggesting abandonment of the framework. I argue that extant results from within the projects fail to substantiate the standard framework, and propose an alternative. On my view, psychological constructs should not be viewed as explanantia, but instead as heuristic concepts that help us uncover ways that behaviors can vary and the ways that the brain implements those distinctions. I then discuss the normative upshot of these views for databasing and brain mapping projects. (shrink)

We begin at the beginning, with an outline of Aristotle’s views on ontology and with a discussion of the influence of these views on Linnaeus. We move from there to consider the data standardization initiatives launched in the 19th century, and then turn to investigate how the idea of computational ontologies developed in the AI and knowledge representation communities in the closing decades of the 20th century. We show how aspects of this idea, particularly those relating to the use (...) of the term 'concept' in ontology development, influenced SNOMED CT and other medical terminologies. Against this background we then show how the Foundational Model of Anatomy, the Gene Ontology, Basic Formal Ontology and other OBO Foundry ontologies came into existence and discuss their role in the development of contemporary biomedical informatics. (shrink)

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)

What are words? What makes two token words tokens of the same word-type? Are words abstract entities, or are they (merely) collections of tokens? The ontology of words tries to provide answers to these, and related questions. This article provides an overview of some of the most prominent views proposed in the literature, with a particular focus on the debate between type-realist, nominalist, and eliminativist ontologies of words.

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)

In recent years, there has been an increasing interest in thedevelopment of ontologically well-founded conceptual models for Information Systems in areas such as Service Management, Accounting Information Systems and Financial Reporting. Economic exchanges are central phenomena in these areas. For this reason, they occupy a prominent position in modelling frameworks such as the REA (Resource-EventAction) ISO Standard as well as the FIBO (Financial Industry BusinessOntology). In this paper, we begin a well-founded ontological analysisof economic exchanges inspired by a recent ontological (...) view on the nature of economic transactions. According to this view, what counts asan economic transaction is based on an agreement on the actions thatthe agents are committed to perform. The agreement is in turn based on convergent preferences about the course of action to bring about. This view enables a unified treatment of economic exchanges, regardless the object of the transaction, and complies with the view that all economictransactions are about services. In this paper, we start developing our analysis in the framework of the Unified Foundational Ontology (UFO). (shrink)

Statistics play a critical role in biological and clinical research. However, most reports of scientific results in the published literature make it difficult for the reader to reproduce the statistical analyses performed in achieving those results because they provide inadequate documentation of the statistical tests and algorithms applied. The Ontology of Biological and Clinical Statistics (OBCS) is put forward here as a step towards solving this problem. Terms in OBCS, including ‘data collection’, ‘data transformation in statistics’, ‘data visualization’, ‘statistical (...) data analysis’, and ‘drawing a conclusion based on data’, cover the major types of statistical processes used in basic biological research and clinical outcome studies. OBCS is aligned with the Basic Formal Ontology (BFO) and extends the Ontology of Biomedical Investigations (OBI), an OBO (Open Biological and Biomedical Ontologies) Foundry ontology supported by over 20 research communities. We discuss two examples illustrating how the ontology is being applied. In the first (biological) use case, we describe how OBCS was applied to represent the high throughput microarray data analysis of immunological transcriptional profiles in human subjects vaccinated with an influenza vaccine. In the second (clinical outcomes) use case, we applied OBCS to represent the processing of electronic health care data to determine the associations between hospital staffing levels and patient mortality. Our case studies were designed to show how OBCS can be used for the consistent representation of statistical analysis pipelines under two different research paradigms. By representing statistics-related terms and their relations in a rigorous fashion, OBCS facilitates standard data analysis and integration, and supports reproducible biological and clinical research. (shrink)

The Handbook of Metaphysics and Ontology reflects the conviction that the history of metaphysics and current work in metaphysics and ontology can each throw valuable light on the other. Thus it is designed to serve both äs a means of making more widely accessible the results of recent scholarship in the history of philosophy, and also äs a unique work of reference in reladon to the metaphysical themes at the centre of much current debate in analyüc philosophy. The (...) work contains more man 450 shorter articies on specific themes and methods in metaphysics and ontology, together with biographical essays summarizing the thinking of the most important philosophers within the traditions dealt with. In addition, it contains about 20 longer survey arücles mapping out both historically and systemadcally the main areas of metaphysics and ontology. AU contributions have been speciaüy commissioned for this project from leading authorities in their respective fields. A special feature of the work is the pardcular attention that is paid to topics and issues of relevance to contemporary philosophical debates. The work includes also a series of arücles on the logical and mathematical tools of metaphysics and on the applications of metaphysical ideas within linguisdcs, psychology, cognitive science, and mathemadcs. (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)

This essay focuses on realism in ontology and on the problem of defining reality. According to the definition given by many realists, reality is independent of our thoughts, conceptual schemes, linguistic practices, etc. Yet, this merely negative definition of reality has some disadvantages: it implies a dualistic view, and it is incompatible with scientific realism. As an alternative, I introduce and discuss the traditional definition of reality as effectiveness, or capability of acting. I then attempt to determine to what (...) extent this definition can be helpful in the debate concerning ontological realism. (shrink)