A repository of clinically associated Staphylococcus aureus (Sa) isolates is used to semi‐automatically generate a set of application ontologies for specific subfamilies of Sa‐related disease. Each such application ontology is compatible with the Infectious Disease Ontology (IDO) and uses resources from the Open Biomedical Ontology (OBO) Foundry. The set of application ontologies forms a lattice structure beneath the IDO‐Core and IDO‐extension reference ontologies. We show how this lattice can be used to define a strategy for the (...) class='Hi'>construction of a new taxonomy of infectious disease incorporating genetic, molecular, and clinical data. We also outline how faceted browsing and query of annotated data is supported using a lattice application ontology. (shrink)

In a first part, I defend that formal semantics can be used as a guide to ontological commitment. Thus, if one endorses an ontological view \(O\) and wants to interpret a formal language \(L\) , a thorough understanding of the relation between semantics and ontology will help us to construct a semantics for \(L\) in such a way that its ontological commitment will be in perfect accordance with \(O\) . Basically, that is what I call constructing formal semantics from (...) an ontological perspective. In the rest of the paper, I develop rigorously and put into practice such a method, especially concerning the interpretation of second-order quantification. I will define the notion of ontological framework: it is a set-theoretical structure from which one can construct semantics whose ontological commitments correspond exactly to a given ontological view. I will define five ontological frameworks corresponding respectively to: (i) predicate nominalism, (ii) resemblance nominalism, (iii) armstrongian realism, (iv) platonic realism, and (v) tropism. From those different frameworks, I will construct different semantics for first-order and second-order languages. Notably I will present different kinds of nominalist semantics for second-order languages, showing thus that we can perfectly quantify over properties and relations while being ontologically committed only to individuals. I will show in what extent those semantics differ from each other; it will make clear how the disagreements between the ontological views extend from ontology to logic, and thus why endorsing an ontological view should have an impact on the kind of logic one should use. (shrink)

I describe an account of ontological categories which does justice to the facts that not all categories are ontological categories and that ontological categories can stand in containment relations. The account sorts objects into different categories in the same way in which grammar sorts expressions . It then identifies the ontological categories with those which play a certain role in the systematization of collections of categories. The paper concludes by noting that on my account what ontological categories there are is (...) partially interest-relative, and that furthermore no object can belong essentially to its ontological category. (shrink)

(Report assembled for the Workshop of the AMIA Working Group on Formal Biomedical Knowledge Representation in connection with AMIA Symposium, Washington DC, 2005.) Best practices in ontology building for biomedicine have been frequently discussed in recent years. However there is a range of seemingly disparate views represented by experts in the field. These views not only reflect the different uses to which ontologies are put, but also the experiences and disciplinary background of these experts themselves. We asked six questions (...) related to biomedical ontologies to what we believe is a representative sample of ontologists in the biomedical field and came to a number conclusions which we believe can help provide an insight into the practical problems which ontology builders face today. (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)

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)

Ontology has been proposed as a solution to the 'Tower of Babel' problem that threatens the semantic interoperability of information systems constructed independently for the same domain. In information systems research and applications, ontologies are often implemented by formalizing the meanings of words from natural languages. However, words in different natural languages sometimes subdivide the same domain of reality in terms of different conceptual categories. If the words and their associated concepts in two natural languages, or even in two (...) terminological traditions within the same language, do not have common referents in the real world, an ontology based on word meanings will inherit the 'Tower of Babel' problem from the languages involved, rather than solve it. In this paper we present evidence from a preliminary comparison of landscape terms in English with those in the Yindjibarndi language of northwestern Australia demonstrating that this problem is not just hypothetical. Some possible solutions are suggested. (shrink)

Kant maintains that the only thing that is good in itself, and therefore good without limitation or qualification, is a good will. This is an objectionable claim in support of a controversial position. The problem is not just that the good will is not the only thing that is good in itself, which indeed it is not, but more importantly, that the good will is not so much a thing that is good in itself as it is the good kind (...) of a thing that is otherwise neither good nor bad in itself. The goodness of a good will is no more intrinsic than the goodness of a good act, good outcome, good attitude, good character, or good person. Nor is it even any more so than something as commonplace as a good laugh or a good cup of coffee. A good will, whatever else it may be, is a will that is good, much like how a good act is an act that is good, a good outcome is an outcome that is good, and so on with the other examples, not one of which is good for any reason other than the goodness predicated of the corresponding subject. This paper thus challenges Kant’s position on ontological grounds. It questions the validity of claiming intrinsic goodness for a complex construct whose goodness is, in fact, extrinsic to its substance. The objection is not that the good will might not turn out to be good after all, which is impossible by definition, designation, or stipulation, but that its goodness is axiomatic and derivative rather than intrinsic or fundamental. (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.

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)

The construction of complex ontologies can be facilitated by adapting existing vocabularies. There is little clarity and in fact little consensus as to what modifications of vocabularies are necessary in order to re-engineer them into ontologies. In this paper we present a method that provides clear steps to follow when re-engineering a thesaurus. The method makes use of top-level ontologies and was derived from the structural differences between thesauri and ontologies as well as from best practices in modeling, some (...) of which have been advocated in the biomedical domain. We illustrate each step of our method with examples from a re-engineering case study about agricultural fertilizers based on the AGROVOC thesaurus. Our method makes clear that re-engineering thesauri requires far more than just a syntactic conversion into a formal language or other easily automatable steps. The method can not only be used for re-engineering thesauri, but does also summarize steps for building ontologies in general, and can hence be adapted for the re-engineering of other types of vocabularies or terminologies. (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)

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

World food production is facing exorbitant challenges like climate change, use of resources, population growth, and dietary changes. These, in turn, raise major ethical and political questions, such as how to uphold the right to adequate nutrition, or the right to enact a gastronomic culture and to preserve the conditions to do so. Proposals for utopic solutions vary from vertical farming and lab meat to diets filled with the most fanciful insects and seaweeds. Common to all proposals is a polarized (...) understanding of food and diets, famously captured by Warren Belasco in the contraposition between technological fixes and anthropological fixes. According to the first, technology will deliver clean, just, pleasurable, affordable food; future generations will not need to adjust much of their dietary cultures. According to the second, future generations should dramatically change their dietary habits (what they eat and how they eat it) to achieve a sustainable diet. The two fixes found remarkably distinct perspectives over dietary politics and the ethics of food production and consumption. In this paper we argue that such polarized thinking rests on a misrepresentation of the ontological status of food, which in turn affects the underlying ethical and political issues. Food is a socially constructed object that draws in specific ways on habits, norms, traditions, geographical, and climatic conditions. Although this thesis seems somewhat obvious, its consequences on the ethical and political perspectives on the future of food have not been derived properly. After introducing the issue at stake (¤1), we point out the polarities that characterize food utopias (¤2) and their ontological faults (¤3). We hence suggest that a socio-ontological analysis of food can better deliver the principles for a foundation of food utopias (¤4). (shrink)

This paper gives significance to the concept of continuity in addressing the contemporary mind-body problem. Building upon philosophical definitions and insights from empirical brain science, the paper argues for "ontology of continuity" as a way to bridge between the mental and physical. To overcome the challenge of Kim’s causal overdetermination, the paper introduces a dual-neural process model, where subjective experiences and neural activities co-depend and influence each other in a quasi-parallel manner. This model seeks to reconcile idealism and physicalism, (...) proposing that continuity serves as a fundamental ontological construct connecting the mental and physical realms. (shrink)

How should scientists carve up cognition to generate good predictions, explanations, and models of cognition? This chapter argues that cognitive categories should be constructed the same way that biological categories are: in terms of homology. The chapter adapts a developmental account of trait identity from evolutionary-developmental biology to make sense of the notion of “cognitive homology.” The consequence is that both brain structures and the organism’s ongoing interactions with the environment are crucial for individuating cognitive homologies, and thus for cognitive (...) ontology. (shrink)

Formal principles governing best practices in classification and definition have for too long been neglected in the construction of biomedical ontologies, in ways which have important negative consequences for data integration and ontology alignment. We argue that the use of such principles in ontology construction can serve as a valuable tool in error-detection and also in supporting reliable manual curation. We argue also that such principles are a prerequisite for the successful application of advanced data integration (...) techniques such as ontology-based multi-database querying, automated ontology alignment and ontology-based text-mining. These theses are illustrated by means of a case study of the Gene Ontology, a project of increasing importance within the field of biomedical data integration. (shrink)

We examine how insights made in socio-anthropological and evolutionary schools of thought necessitate us to reevaluate the classic philosophical distinction between epistemology and ontology. We adopt an applied evolutionary epistemological stance and demonstrate that both epistemology and ontology evolve. Epistemology is broadened to include all knowledge and information that all life forms evolve, and ontology encompasses all biologically informed realities that life builds. Through processes such as symbiosis and niche construction, organisms acquire and extend information and (...) knowledge into their offspring, onto unrelated organisms, and onto their niches. Life builds biorealities that change over time. Consequently, knowledge and reality are mutable and truth is spatiotemporally bounded. We conclude that the classic distinction between epistemology and ontology has become superfluous and instead, we argue that the evolving knowledge that comes in the form of organisms and their extended niches equals ontological realities. (shrink)

Enterprise Risk Management involves the process of identification, evaluation, treatment, and communication regarding risks throughout the enterprise. To support the tasks associated with this process, several frameworks and modeling languages have been proposed, such as the Risk and Security Overlay (RSO) of ArchiMate. An ontological investigation of this artifact would reveal its adequacy, capabilities, and limitations w.r.t. the domain of risk and security. Based on that, a language redesign can be proposed as a refinement. Such analysis and redesign have been (...) executed for the risk elements of the RSO grounded in the Common Ontology of Value and Risk. The next step along this line of research is to address the following research problems: What would be the outcome of an ontological analysis of security-related elements of the RSO? That is, can we identify other semantic deficiencies in the RSO through an ontological analysis? Once such an analysis is provided, can we redesign the security elements of the RSO accordingly, in order to produce an improved artifact? Here, with the aid of the Reference Ontology for Security Engineering (ROSE) and the ontological theory of prevention behind it, we address the remaining gap by proceeding with an ontological analysis of the security-related constructs of the RSO. The outcome of this assessment is an ontology-based redesign of the ArchiMate language regarding security modeling. In a nutshell, we report the following contributions: (1) an ontological analysis of the RSO that identifies six limitations concerning security modeling; (2) because of the key role of the notion of prevention in security modeling, the introduction of the ontological theory of prevention in ArchiMate; (3) a well-founded redesign of security elements of ArchiMate; and (4) ontology-based security modeling patterns that are logical consequences of our proposal of redesign due to its underlying ontology of security. As a form of evaluation, we show that our proposal can describe risk treatment options, according to ISO 31000. Finally, besides presenting multiple examples, we proceed with a real-world illustrative application taken from the cybersecurity domain. (shrink)

Systems theory offers a language in which one might formulate a metaphysics (or more specifically an ontology) of problems. This proposal is based upon a conception of systems theory shared by vonBertalanffy, Wiener, Boulding, Rapoport, Ashby, Klir, and others,and expressed succinctly by Bunge, who considered game theory, information theory, feedback control theory, and the like to be attempts to construct an "exact and scientific metaphysics." Our prevailing conceptions of "problems" are concretized yet also fragmented, and in fact dissolved, by (...) the standard reductionist model of science, which cannot provide a general framework for analysis. The idea of a "systems theory," however, suggests the possibility of an abstract and coherent account of the origin and essence of problems. Such an account would constitute a secular theodicy. (shrink)

Response to the paper “The Biomedical Ethics Ontology Proposal: Excellent Aims, Questionable Methods" by James DuBois, published in the Journal of Empirical Research on Human Research Ethics.

Since 2002 we have been testing and refining a methodology for ontology development that is now being used by multiple groups of researchers in different life science domains. Gary Merrill, in a recent paper in this journal, describes some of the reasons why this methodology has been found attractive by researchers in the biological and biomedical sciences. At the same time he assails the methodology on philosophical grounds, focusing specifically on our recommendation that ontologies developed for scientific purposes should (...) be constructed in such a way that their terms are seen as referring to what we call universals or types in reality. As we show, Merrill’s critique is of little relevance to the success of our realist project, since it not only reveals no actual errors in our work but also criticizes views on universals that we do not in fact hold. However, it nonetheless provides us with a valuable opportunity to clarify the realist methodology, and to show how some of its principles are being applied, especially within the framework of the OBO (Open Biomedical Ontologies) Foundry initiative. (shrink)

The paper proposes a simple method for constructing ontological theories—an ‘ontology generator’. It shows that such a generator manages to produce major existing ontological theories, e.g., Realism, Nominalism, Trope theory, Bundle theory, Perdurantism, Endurantism, Possibilism, Actualism and more. It thus turns out, surprisingly, that all these seemingly unrelated different ontological theories that were designed by thinkers hundreds of years apart, can all be generated using the same simple mechanism. Moreover, this same generator manages to produce entirely novel ontological theories, (...) that fare no worse than existing ones in meeting the same common metaphysical challenges. (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)

When an entity ontologically depends on another entity, the former ‘presupposes’ or ‘requires’ the latter in some metaphysical sense. This paper defends a novel view, Dependence Deflationism, according to which ontological dependence is what I call an aggregative cluster concept: a concept which can be understood, but not fully analysed, as a ‘weighted total’ of constructive and modal relations. The view has several benefits: it accounts for clear cases of ontological dependence as well as the source of disagreement in controversial (...) ones; it gives a nice story about the evidential relevance of modal, mereological and set-theoretic facts to ontological dependence; and it makes sense of debates over the relation's formal properties. One important upshot of the deflationary account is that questions of ontological dependence are generally less deep and less interesting than usually thought. (shrink)

This paper addresses the use of dispositions in the Infectious Disease Ontology (IDO). IDO is an ontology constructed according to the principles of the Open Biomedical Ontology (OBO) Foundry and uses the Basic Formal Ontology (BFO) as an upper ontology. After providing a brief introduction to disposition types in BFO and IDO, we discuss three general techniques for representing combinations of dispositions under the headings blocking dispositions, complementary dispositions, and collective dispositions. Motivating examples for each (...) combination of dispositions is given along with a specific use case in IDO. Description logic restrictions are used to formalize statements relating to these combinations. (shrink)

Where humans can manipulate and integrate the information they receive in subtle and ever changing ways from context to context, computers need structured and context-free background information of a sort which ontologies can help to provide. A domain ontology captures the stable, highly general and commonly accepted core knowledge for an application domain. The domain at issue here is that of the life sciences, in particular molecular biology and bioinformatics. Contemporary life science research includes components drawn from physics, chemistry, (...) mathematics, medicine and many other areas, and all of these dimensions, as well as fundamental philosophical issues, must be taken into account in the construction of a domain ontology. Here we describe the basic features of domain ontologies in the life sciences and show how they can be used. (shrink)

In Ontological Catastrophe, Joseph Carew takes up the central question guiding Slavoj Žižek’s philosophy: How could something like phenomenal reality emerge out of the meaninglessness of the Real? Carefully reconstructing and expanding upon his controversial reactualization of German Idealism, Carew argues that Žižek offers us an original, but perhaps terrifying, response: experience is possible only if we presuppose a prior moment of breakdown as the ontogenetic basis of subjectivity. Drawing upon resources found in Žižek, Lacanian psychoanalysis, and post-Kantian philosophy, Carew (...) thus develops a new critical metaphysics—a metaphysics which is a variation upon the late German Idealist theme of balancing system and freedom, realism and idealism, in a single, self-reflexive theoretical construct—that challenges our understanding of nature, culture, and the ultimate structure of reality. (shrink)

As conceived by analytic philosophers ontology consists in the application of the methods of mathematical logic to the analysis of ontological discourse. As conceived by realist philosophers such as Meinong and the early Husserl, Reinach and Ingarden, it consists in the investigation of the forms of entities of various types. The suggestion is that formal methods be employed by phenomenological ontologists, and that phenomenological insights may contribute to the construction of adequate formal-ontological languages. The paper sketches an account (...) of what might be involved in this new discipline, an account which is illustrated in application to the formal-ontological problems raised by negative states of affairs. (shrink)

The goal of the Department of Defense Net-Centric Data Strategy is to improve data sharing throughout the DoD. Data sharing is a critical element of interoperability in the emerging system-of-systems. Achieving interoperability requires the elimination of two types of data heterogeneity: differences of syntax and differences of semantics. This paper builds a path toward semantic uniformity through application of a disciplined approach to ontology. An ontology is a consensus framework representing the types of entities within a given domain (...) and the relations between them. The construction of an ontology begins when a Community of Interest (COI) identifies its authoritative data sources (ADS), which are usually manifest in relevant doctrinal publications, glossaries, data dictionaries, and logical data models. The identified terms are then defined in relation to a common logical framework that has been designed to ensure interoperability with other ontologies created on the basis of the same strategy. As will be described, the Command and Control (C2) Ontology will include representations of a substantial number of entities within the Command and Control (C2) domain. If domain ontologies (e.g. Strike and Counterinsurgency) semantically align with the C2 Ontology, then a substantial barrier to systems interoperability is thereby crossed. (shrink)

Kant's reasoning in his special metaphysics of nature is often opaque, and the character of his a priori foundation for Newtonian science is the subject of some controversy. Recent literature on the Metaphysical Foundations of Natural Science has fallen well short of consensus on the aims and reasoning in the work. Various of the doctrines and even the character of the reasoning in the Metaphysical Foundations have been taken to present insuperable obstacles to accepting Kant's claim to ground Newtonian science. (...) Gordon Brittan and Gerd Buchdahl, amongst others, have argued that Kant's stated aims in this case are not to be taken at face value, and that prior ontological commitments play a hidden but central role in Kant's special metaphysics. ;Michael Friedman has shown how Kant's stated aims can be taken seriously with his ingenious reconstruction of the Metaphysical Foundations as a demonstration of the a priori basis for our thinking bodies to be in true motion and in absolute space. However, Friedman does not address the issue of matter theory--despite the importance of the issue to Kant. I argue that a strict reading of both the stated aims and doctrines of the Metaphysical Foundations is possible, since much of Kant's reasoning about the empirical concept of matter can be explained by his views on how the construction of empirical concepts is possible. ;Kant's quasi-mathematical constructions are pivotal in Friedman's interpretation. Constructibility is Kant's criterion of acceptability for the concepts of natural science. Yet Kant notoriously fails to construct the dynamical concept of matter, and accepts this failure with an equally notorious complacency. I argue that Kant's criteria of empirical concept construction, apart from any prior ontological commitments, are enough to generate his views on matter. Kant's failure to construct the requisite concept of matter can be ascribed to a missing law of nature, a law of the relation of forces the discovery of which Kant thought imminent. I conclude that matter theory is central to the Metaphysical Foundations, but that this does not undermine Kant's stated aim of giving the a priori ground of Newtonian science. (shrink)

The game of life is an excellent framework for metaphysical modeling. It can be used to study ontological categories like space, time, causality, persistence, substance, emergence, and supervenience. It is often said that there are many levels of existence in the game of life. Objects like the glider are said to exist on higher levels. Our goal here is to work out a precise formalization of the thesis that there are various levels of existence in the game of life. To (...) formalize this thesis, we develop a set-theoretic construction of the glider. The method of this construction generalizes to other patterns in the game of life. And it can be extended to more realistic physical systems. The result is a highly general method for the set-theoretical construction of substances. (shrink)

Total ontological unification of matter at all levels of reality as a whole, its “grasp” of its dialectical structure, space dimensionality and structure of the language of nature – “house of Being” [1], gives the opportunity to see the “place” and to understand the nature of information as a phenomenon of Ontological (structural) Memory (OntoMemory), the measure of being of the whole, “the soul of matter”, qualitative quantity of the absolute forms of existence of matter (absolute states). “Information” and “time” (...) are multivalent phenomena of Ontological Memory substantiating the essential unity of the world on the “horizontal” and “vertical”. Ontological constructing of dialectics of Logos self-motion, total unification of matter, “grasp” of the nature of information leads to the necessity of introducing a new unit of information showing the ideas of dialectical formation and generation of new structures and meanings, namely Delta-Logit (Δ-Logit), qualitative quantum-prototecton, fundamental organizing, absolute existential-extreme. The simplest mathematical symbol represents the dialectical microprocessor of the Nature. Ontological formula of John A. Wheeler «It from Bit» [2] is “grasped” as the first dialectic link in the chain of ontological formulas → “It from Δ-Logit” → “It from OntoMemory” → “It from Logos, Logos into It”. Ontological Memory - core, semantic attractor of the new conceptual structure of the world of the Information Age, which is based on Absolute generating structure («general framework structure»), the representant of onto-genetic code and algorithm of the Universe. (shrink)

Could a person ever transcend what it is like to be in the world as a human being? Could we ever know what it is like to be other creatures? Questions about the overcoming of a human perspective are not uncommon in the history of philosophy. In the last century, those very interrogatives were notably raised by American philosopher Thomas Nagel in the context of philosophy of mind. In his 1974 essay What is it Like to Be a Bat?, Nagel (...) offered reflections on human subjectivity and its constraints. Nagel’s insights were elaborated before the social diffusion of computers and could not anticipate the cultural impact of technological artefacts capable of materializing interactive simulated worlds as well as disclosing virtual alternatives to the “self.” In this sense, this article proposes an understanding of computers as epistemological and ontological instruments. The embracing of a phenomenological standpoint entails that philosophical issues are engaged and understood from a fundamentally practical perspective. In terms of philosophical praxis, or “applied philosophy,” I explored the relationship between human phenomenologies and digital mediation through the design and the development of experimental video games. For instance, I have conceptualized the first-person action-adventure video game Haerfest (Technically Finished 2009) as a digital re-formulation of the questions posed in Nagel’s famous essay. Experiencing a bat’s perceptual equipment in Haerfest practically corroborates Nagel’s conclusions: there is no way for humans to map, reproduce, or even experience the consciousness of an actual bat. Although unverifiable in its correspondence to that of bats, Haerfest still grants access to experiences and perceptions that, albeit still inescapably within the boundaries of human kinds of phenomenologies, were inaccessible to humans prior to the advent of computers. Phenomenological alterations and virtual experiences disclosed by interactive digital media cannot take place without a shift in human kinds of ontologies, a shift which this study recognizes as the fundamental ground for the development of a new humanism (I deem it necessary to specify that I am not utilizing the term “humanism” in its common connotation, that is to say the one that emerged from the encounter between the Roman civilization and the late Hellenistic culture. According to this conventional acceptation, humanism indicates the realization of the human essence through “scholarship and training in good conduct” (Heidegger 1998, p. 244). However, Heidegger observed that this understanding of humanism does not truly cater to the original essence of human beings, but rather “is determined with regard to an already established interpretation of nature, history, world, and […] beings as a whole.” (Heidegger 1998, p. 245) The German thinker found this way of embracing humanism reductive: a by-product of Western metaphysics. As Heidegger himself specified in his 1949 essay Letter on Humanism, his opposition to the traditional acceptation of the term humanism does not advocate for the “inhuman” or a return to the “barbaric” but stems instead from the belief that the humanism can only be properly understood and restored in culture as more original way of meditating and caring for humanity and understanding its relationship with Being.). Additionally, this study explicitly proposes and exemplifies the use of interactive digital technology as a medium for testing, developing and disseminating philosophical notions, problems and hypotheses in ways which are alternative to the traditional textual one. Presented as virtual experiences, philosophical concepts can be accessed without the filter of subjective imagination. In a persistent, interactive, simulated environment, I claim that the crafting and the mediation of thought takes a novel, projective (In Martin Heidegger’s 1927 Being and Time, the term “projectivity” indicates the way a Being opens to the world in terms of its possibilities of being (Heidegger 1962, pp. 184–185, BT 145). Inspired by Heidegger’s and Vilem Flusser’s work in the field of philosophy of technology as well as Helmuth Plessner’s anthropological position presented in his 1928 book Die Stufen des Organischen und der Mensch. Einleitung in die philosophische Anthropologie, this study understands the concept of projectivity as the innate openness of human beings to construct themselves and their world by means of technical artefacts. In this sense, this study proposes a fundamental understanding of technology as the materialization of mankind’s tendency to overcome its physical, perceptual and communicative limitations.) dimension which I propose to call “augmented ontology.”. (shrink)

Ontologies represent principled, formalised descriptions of agents’ conceptualisations of a domain. For a community of agents, these descriptions may differ among agents. We propose an aggregative view of the integration of ontologies based on Judgement Aggregation (JA). Agents may vote on statements of the ontologies, and we aim at constructing a collective, integrated ontology, that reflects the individual conceptualisations as much as possible. As several results in JA show, many attractive and widely used aggregation procedures are prone to return (...) inconsistent collective ontologies. We propose to solve the possible inconsistencies in the collective ontology by applying suitable weakenings of axioms that cause inconsistencies. (shrink)

Building Information Modelling (BIM) is a process for managing construction project information in such a way as to provide a basis for enhanced decision-making and for collaboration in a construction supply chain. One impediment to the uptake of BIM is the limited interoperability of different BIM systems. To overcome this problem, a set of Industry Foundation Classes (IFC) has been proposed as a standard for the construction industry. Building on IFC, the ifcOWL ontology was developed in (...) order to facilitate representation of building data in a consistent fashion across the Web by using the Web Ontology Language (OWL). This study presents a critical analysis of the ifcOWL ontology and of the associated interoperability issues. It shows how these issues can be resolved by using Basic Formal Ontology (ISO/IEC 21838-2) as top-level architecture. A set of competency questions is used as the basis for comparison of the original ifcOWL with the enhanced ontology, and the latter is used to align with a second ontology – the ontology for building intelligent environments (DOGONT) – in order to demonstrate the added value derived from BFO by showing how querying the enhanced ifcOWL yields useful additional information. (shrink)

The Plant Ontology (PO) is a community resource consisting of standardized terms, definitions, and logical relations describing plant structures and development stages, augmented by a large database of annotations from genomic and phenomic studies. This paper describes the structure of the ontology and the design principles we used in constructing PO terms for plant development stages. It also provides details of the methodology and rationale behind our revision and expansion of the PO to cover development stages for all (...) plants, particularly the land plants (bryophytes through angiosperms). As a case study to illustrate the general approach, we examine variation in gene expression across embryo development stages in Arabidopsis and maize, demonstrating how the PO can be used to compare patterns of expression across stages and in developmentally different species. Although many genes appear to be active throughout embryo development, we identified a small set of uniquely expressed genes for each stage of embryo development and also between the two species. Evaluating the different sets of genes expressed during embryo development in Arabidopsis or maize may inform future studies of the divergent developmental pathways observed in monocotyledonous versus dicotyledonous species. The PO and its annotation databasemake plant data for any species more discoverable and accessible through common formats, thus providing support for applications in plant pathology, image analysis, and comparative development and evolution. (shrink)

The article will expose the problem of the nature of reality stablished in the first sections of Wittgenstein"s “Tractatus Logico-Philosophicus”, especially the aphorisms 1 to 2.063 seeking to show points of contact between the Aristotelian-Thomistic and Suarezian thought. Initially, (I) a distinction is made between metaphysics and ontology in order to understand why Wittgenstein, notorious for his anti-metaphysical thought, actually ends up producing a theory of reality. Subsequently, (II) the relationship between reality and language will be drawn from the (...) characteristic isomorphism of the Tractatus in which a structural similarity will appear with the Aristotelian-Thomistic thought. This relationship will be the basis for (III) the construction of an ontological image of reality as the condition of possibility for a meaningful language. With this outlook, the (IV) hypothesis of the influence of Francisco Suárez"s thought as the content behind this Wittgensteinian description of reality will be advanced. (shrink)

The essay presents the main ideas of the philosophical system «OntoTopoLogia», developed and promoted since 1990 at the I-IV, VIII Russian Philosophical Congresses, the XX World Philosophical Congress (Boston, 1998), Conference «Problems of Consciousness in Philosophy and Science» (Institute of Philosophy RAS, 1996), Conference «Philosophy of Physics: Current Problems» (MSU, 2010), seven International contests The Foundational Questions Institute (USA, FQXi Essay 2012-2020), International scientific conference «Modern Ontology» (St. Petersburg , 2013, 2017, 2019, 2023), Third All-Russian Scientific Conference «Philosophy of (...) Mathematics: Current Problems» (MSU, 2013), International Congress «Fundamental Problems of Natural Science» (St. Petersburg, 2013, 2016, 2022), Conference «Foundations of Fundamental Physics and Mathematics» (RUDN University, 2023). The ideas of the «OntoTopoLogia» system are aimed at overcoming the conceptual-paradigmatic crisis in the metaphysical/ontological basis of fundamental science (mathematics, physics, cosmology) on the basis of a holistic paradigm («paradigm of understanding»), a comprehensive conceptual-figurative synthesis, a method of dialectical-ontological construction, MetaCategory, MetaAxiom, SuperPrinciple and Metasymbol, a new holistic understanding of matter, its ontological unification across all levels of existence of the Universe as eternal holistic process of generating more and more new meanings, forms and structures. A model of the Primordial (absolute) generating structure is being built - a single ontological basis of knowledge: ontological frameworc, carcass, foundation as an all-encompassing Ideality, a single basis for the «sciences of nature» and «sciences of the spirit». (shrink)

For over a decade now, a community of researchers has contributed to the development of the Unified Foundational Ontology (UFO) - aimed at providing foundations for all major conceptual modeling constructs. This ontology has led to the development of an Ontology-Driven Conceptual Modeling language dubbed OntoUML, reflecting the ontological micro-theories comprising UFO. Over the years, UFO and OntoUML have been successfully employed in a number of academic, industrial and governmental settings to create conceptual models in a variety (...) of different domains. These experiences have pointed out to opportunities of improvement not only to the language itself but also to its underlying theory. In this paper, we take the first step in that direction by revising the theory of types in UFO in response to empirical evidence. The new version of this theory shows that many of the meta-types present in OntoUML (differentiating Kinds, Roles, Phases, Mixins, etc.) should be considered not as restricted to Substantial types but instead should be applied to model Endurant Types in general, including Relator types, Quality types and Mode types. We also contribute a formal characterization of this fragment of the theory, which is then used to advance a metamodel for OntoUML 2.0. Finally, we propose a computational support tool implementing this updated metamodel. (shrink)

I defend a one category ontology: an ontology that denies that we need more than one fundamental category to support the ontological structure of the world. Categorical fundamentality is understood in terms of the metaphysically prior, as that in which everything else in the world consists. One category ontologies are deeply appealing, because their ontological simplicity gives them an unmatched elegance and spareness. I’m a fan of a one category ontology that collapses the distinction between particular and (...) property, replacing it with a single fundamental category of intrinsic characters or qualities. We may describe the qualities as qualitative charactersor as modes, perhaps on the model of Aristotelian qualitative (nonsubstantial) kinds, and I will use the term “properties” interchangeably with “qualities”. The qualities are repeatable and reasonably sparse, although, as I discuss in section 2.6, there are empirical reasons that may suggest, depending on one’s preferred fundamental physical theory, that they include irreducibly intensive qualities. There are no uninstantiated qualities. I also assume that the fundamental qualitative natures are intrinsic, although physics may ultimately suggest that some of them are extrinsic. On my view, matter, concrete objects, abstract objects, and perhaps even spacetime are constructed from mereological fusions of qualities, so the world is simply a vast mixture of qualities, including polyadic properties (i.e., relations). This means that everything there is, including concrete objects like persons or stars, is a quality, a qualitative fusion, or a portion of the extended qualitative fusion that is the worldwhole. I call my view mereological bundle theory. (shrink)

Fundamental Science is undergoing an acute conceptual-paradigmatic crisis of philosophical foundations, manifested as a crisis of understanding, crisis of interpretation and representation, “loss of certainty”, “trouble with physics”, and a methodological crisis. Fundamental Science rested in the "first-beginning", "first-structure", in "cogito ergo sum". The modern crisis is not only a crisis of the philosophical foundations of Fundamental Science, but there is a comprehensive crisis of knowledge, transforming by the beginning of the 21st century into a planetary existential crisis, which has (...) exacerbated the question of the existence of Humanity and life on Earth. Due to the unsolved problem of justification of Mathematics, paradigm problems in Computational mathematics have arisen. It's time to return ↔ Into Dialectics. The solution to the problem of the foundations of Mathematics, and therefore knowledge in general, is the solution to the problem of modeling (constructing) the ontological basis of knowledge - the ontological model of the primordial generating process. The idea and model of the primordial generating process, its ontological structure directs thinking to the need for the introduction of superconcept → ontological (cosmic, structural) memory, concept-attractor, supercategory, substantial semantic core of the scientific picture of the world of the nuclear-ecological-information age. Model of basic Ideality→ “Space-MatterMemory-Time” [S-MM-T]. (shrink)

Simple partial logic (=SPL) is, broadly speaking, an extensional logic which allows for the truth-value gap. First I give a system of propositional SPL by partializing classical logic, as well as extending it with several non-classical truth-functional operators. Second I show a way based on SPL to construct a system of tensed ontology, by representing tensed statements as two kinds of necessary statements in a linear model that consists of the present and future worlds. Finally I compare that way (...) with other two ways based on Łukasiewicz’s three-valued logic and branching temporal logic. (shrink)

The hard problem of consciousness has held center stage in the philosophy of mind for the past two decades. It claims that the phenomenal character of conscious experiences—what it’s like to be in them—cannot be explained by appeal to the operation of physiological subsystems. The hard problem arises, however, only given the assumption that hylomorphism is false. Hylomorphism claims that structure is a basic ontological and explanatory principle. A human is not a random collection of physical materials, but an individual (...) composed of physical materials with a structure that accounts for what it is and what it can do—the powers it has. What is true of humans is true of their activities as well. The latter are not random physiological changes, but structured ones: we engage in them by coordinating the ways our parts manifest their powers. Structured activities include perceptual experiences. Consequently, everything about a perceptual experience, including its phenomenal character, can be explained by describing the perceiver’s perceptual subsystems, the powers of those subsystems, and the coordination that unifies their activities into the activity of the perceiver as a whole. Conscious experiences thus fit unproblematically into the natural world—just as unproblematically as the phenomenon of life. Even exponents of the hard problem of consciousness agree that there is no hard problem of life. Consequently, if hylomorphism is true, there can be no hard problem of consciousness. To insist that there is such a problem, then, is implicitly to reject hylomorphism. The concept of consciousness that motivates the hard problem is as much a theoretical construct, therefore, as the concept of life that motivates an obstinate vitalist. (shrink)

Noam Chomsky’s well-known claim that linguistics is a “branch of cognitive psychology” has generated a great deal of dissent—not from linguists or psychologists, but from philosophers. Jerrold Katz, Scott Soames, Michael Devitt, and Kim Sterelny have presented a number of arguments, intended to show that this Chomskian hypothesis is incorrect. On both sides of this debate, two distinct issues are often conflated: (1) the ontological status of language and (2) the relation between psychology and linguistics. The ontological issue is, I (...) will argue, not the relevant issue in the debate. Even if this Chomskian position on the ontology of language is false, linguistics may still be a subfield of psychology if the relevant methods in linguistic theory construction are psychological. Two options are open to the philosopher who denies Chomskian conceptualism: linguistic nominalism or linguistic platonism. The former position holds that syntactic, semantic, and phonological properties are primarily properties, not of mental representations, but rather of public languagesentence tokens; The latter position holds that the linguistic properties are properties of public language sentence types. I will argue that both of these positions are compatible with Chomsky’s claim that linguistics is a branch of psychology, and the arguments that have been given for nominalism and platonism do not establish that linguistics and psychology are distinct disciplines. (shrink)

Applied ontologies have been used more and more frequently to enhance systems engineering. In this paper, we argue that adopting principles of ontological realism can increase the benefits that ontologies have already been shown to provide to the systems engineering process. Moreover, adopting Basic Formal Ontology (BFO), an ISO standard for top-level ontologies from which more domain specific ontologies are constructed, can lead to benefits in four distinct areas of systems engineering: (1) interoperability, (2) standardization, (3) testing, and (4) (...) data exploitation. Reaping these benefits in a model-based systems engineering (MBSE) context requires utilizing an ontology’s vocabulary when modeling systems and entities within those systems. If the chosen ontology abides by the principles of ontological realism, a semantic standard capable of uniting distinct domains, using BFO as a hub, can be leveraged to promote greater interoperability among systems. As interoperability and standardization increase, so does the ability to collect data during the testing and implementation of systems. These data can then be reasoned over by computational reasoners using the logical axioms within the ontology. This, in turn, generates new data that would have been impossible or too inefficient to generate without the aid of computational reasoners. (shrink)

Because the techno-economic paradigm of contemporary conceptualizations of innovation is often taken for granted in the literature, this chapter opens up this self-evident notion. First, the chapter consults the work of Joseph Schumpeter, who can be seen as the founding father of the current conceptualization of innovation as technological and commercial. Second, we open up the concept by reflecting on two aspects of Schumpeter’s conceptualization of innovation, namely its destructive and its constructive aspect, based on findings in the history of (...) innovation. Finally, we synthesize our findings and propose an ontic-ontological conceptualization of innovation as ontogenetic process and outcome with six dimensions—newness, political dimension, economic dimension, temporal dimension, human dimension and risk—that moves beyond its technological and commercial orientation. (shrink)

Abstract: We propose a dichotomy between object-entities and meaning-entities. The former are entities such as molecules, cells, organisms, organizations, numbers, shapes, and so forth. The latter are entities such as concepts, propositions, and theories belonging to the realm of logic. Frege distinguished analogously between a ‘realm of reference’ and a ‘realm of sense’, which he presented in some passages as mutually exclusive. This however contradicts his assumption elsewhere that every entity is a referent (even Fregean senses can be referred to (...) by means of suitably constructed expressions). We apply the meaning/object dichotomy to mathematical and fictional entities, and develop a view of mathematical and other abstract objects as the results of certain types of demarcation – as for example the North Sea is the result of demarcations built into naval charts. Such demarcations reflect demarcatory acts, which presuppose complex cognitive and social structures enabling the creation of maps, of theories (of mathematics, of natural science), and of novels. (shrink)

Research on the human microbiome has gen- erated a staggering amount of sequence data, revealing variation in microbial diversity at the community, species (or phylotype), and genomic levels. In order to make this complexity more manageable and easier to interpret, new units—the metagenome, core microbiome, and entero- type—have been introduced in the scientific literature. Here, I argue that analytical tools and exploratory statisti- cal methods, coupled with a translational imperative, are the primary drivers of this new ontology. By reducing (...) the dimensionality of variation in the human microbiome, these new units render it more tractable and easier to interpret, and hence serve an important heuristic role. Nonetheless, there are several reasons to be cautious about these new categories prematurely ‘‘hardening’’ into natural units: a lack of constraints on what can be sequenced metagenomically, freedom of choice in taxonomic level in defining a ‘‘core microbiome,’’ typological framing of some of the concepts, and possible reification of statistical constructs. Finally, lessons from the Human Genome Project have led to a translational imperative: a drive to derive results from the exploration of microbiome variation that can help to articulate the emerging paradigm of per- sonalized genomic medicine (PGM). There is a tension between the typologizing inherent in much of this research and the personal in PGM. (shrink)