Preference relations are intensively studied in Economics, but they are also approached in AI, Knowledge Representation, and Conceptual Modelling, as they provide a key concept in a variety of domains of application. In this paper, we propose an ontological foundation of preference relations to formalise their essential aspects across domains. Firstly, we shall discuss what is the ontological status of the relata of a preference relation. Secondly, we investigate the place of preference relations within a rich taxonomy (...) of relations (e.g. we ask whether they are internal or external, essential or contingent, descriptive or nondescriptive relations). Finally, we provide an ontological modelling of preference relation as a module of a foundational (or upper) ontology (viz. OntoUML). The aim of this paper is to provide a sharable foundational theory of preference relation that foster interoperability across the heterogeneous domains of application of preference relations. (shrink)

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

It is now increasingly accepted that many existing biological and medical ontologies can be improved by adopting tools and methods that bring a greater degree of logical and ontological rigor. In this chapter we will focus on the merits of a logically sound approach to ontologies from a methodological point of view. As we shall see, one crucial feature of a logically sound approach is that we have clear and functional definitions of the relational expressions such as ‘is a’ (...) and ‘part of ’. (shrink)

Patient-centered care (PCC) is an approach to healthcare that values patients’ preference, need, and autonomy. The estimation of healthcare partly depends on how well PCC is implemented. In addition, the result of clinical research can inform the assessment of the implementation of PCC. In clinical research, health-related quality of life (HRQL) theoretical models offer a conceptual toolbox that informs clinical research and guides the hypotheses generation. Wilson and Cleary (1995) developed the most widely used HRQL theoretical model (Bakas et al., (...) 2012). Ontological assumptions about causation in Wilson and Cleary’s model will influence which kind of hypotheses will be generated. I will argue that Wilson and Cleary’s model instilled a kind of causal bias into hypothesis generation in clinical research on HRQL. Causation from biomedical factors to non-biomedical factors is frequently hypothesized while causation from non-biomedical factors to biomedical factors is rarely hypothesized. It leads to that the interdependence and interaction between constituent parts of patients are ignored, which is an obstacle to the implementation of PCC. In addition, I will propose a revised HRQL theoretical model which avoids the causal bias brought by Wilson and Cleary’s model. By doing so, I leave room for the improvement of the practice of healthcare by analyzing the ontological assumptions about causation. (shrink)

I argue that a two-dimensional model of social objects is uniquely positioned to deliver explanations for some of the puzzling metaphysical features of words. I consider how a type-token model offers explanations for the metaphysical features of words, but I give reasons to find the model wanting. In its place, I employ an alternative model from social ontology to explain the puzzling data and questions that are generated from the metaphysical features of words. In the end I chart a new (...) path that foregrounds the agent-dependence and social conditions for word kinds. (shrink)

Levins and Lewontin have contributed significantly to our philosophical understanding of the structures, processes, and purposes of biological mathematical theorizing and modeling. Here I explore their separate and joint pleas to avoid making abstract and ideal scientific models ontologically independent by confusing or conflating our scientific models and the world. I differentiate two views of theorizing and modeling, orthodox and dialectical, in order to examine Levins and Lewontin’s, among others, advocacy of the latter view. I compare the positions of these (...) two views with respect to four points regarding ontological assumptions: (1) the origin of ontological assumptions, (2) the relation of such assumptions to the formal models of the same theory, (3) their use in integrating and negotiating different formal models of distinct theories, and (4) their employment in explanatory activity. Dialectical is here used in both its Hegelian–Marxist sense of opposition and tension between alternative positions and in its Platonic sense of dialogue between advocates of distinct theories. I investigate three case studies, from Levins and Lewontin as well as from a recent paper of mine, that show the relevance and power of the dialectical understanding of theorizing and modeling. (shrink)

This paper addresses the question of what constitutes an apt interpreted model for the purpose of analyzing causation. I first collect universally adopted aptness principles into a basic account, flagging open questions and choice points along the way. I then explore various additional aptness principles that have been proposed in the literature but have not been widely adopted, the motivations behind their proposals, and the concerns with each that stand in the way of universal adoption. I conclude that the remaining (...) work of articulating aptness for a SEM analysis of causation is tied up with issue to do with modality, ontology, and mereology. Continuing this work is therefore likely to shed light on the relationship between these areas and causation more generally. (shrink)

Elimination controversies are ubiquitous in philosophy and the human sciences. For example, it has been suggested that human races, hysteria, intelligence, mental disorder, propositional attitudes such as beliefs and desires, the self, and the super-ego should be eliminated from the list of respectable entities in the human sciences. I argue that eliminativist proposals are often presented in the framework of an oversimplified “phlogiston model” and suggest an alternative account that describes ontological elimination on a gradual scale between criticism of (...) empirical assumptions and conceptual choices. (shrink)

The theory of granular partitions (TGP) is a new approach to the understanding of ontologies and other classificatory systems. The paper explores the use of this new theory in the treatment of task-based clinical guidelines as a means for better understanding the relations between different clinical tasks, both within the framework of a single guideline and between related guidelines. We used as our starting point a DAML+OIL-based ontology for the WHO guideline for hypertension management, comparing this with related guidelines and (...) attempting to show that TGP provides a flexible and highly expressive basis for the manipulation of ontologies of a sort which might be useful in providing more adequate Computer Interpretable Guideline Models (CIGMs) in the future. (shrink)

Current controversies about knowledge integration reflect conflicting ideas of what it means to “take Indigenous knowledge seriously”. While there is increased interest in integrating Indigenous and Western scientific knowledge in various disciplines such as anthropology and ethnobiology, integration projects are often accused of recognizing Indigenous knowledge only insofar as it is useful for Western scientists. The aim of this article is to use tools from philosophy of science to develop a model of both successful integration and integration failures. On the (...) one hand, I argue that cross-cultural recognition of property clusters leads to an ontological overlap that makes knowledge integration often epistemically productive and socially useful. On the other hand, I argue that knowledge integration is limited by ontological divergence. Adequate models of Indigenous knowledge will therefore have to take integration failures seriously and I argue that integration efforts need to be complemented by a political notion of ontological self-determination. (shrink)

In conceptual modeling (CM) as a subdiscipline of software engineering, current proposed ontologies (categorical analysis of entities) are typically established through whole adoption of philosophical theories (e.g. Bunge’s). In this paper, we pursue an interdisciplinary research approach to develop a diagrammatic-based ontological foundation for CM using philosophical ontology as a secondary source. It is an endeavor to escape an offshore procurement of ontology from philosophy and implant it in CM. In such an effort, the CM diagrammatic language plays an (...) important role in contrast to dogmatic philosophical languages’ obsession with abstract entities. Specifically, this paper is about developing a descriptive (in contrast to formal) ontology that a modeler accepts as a supplementary account of reality when using thinging machines (TMs; i.e. a reality that uncovers the ontology of things that TM modeling discusses or “talks about,” akin to the ontology of natural language). Although existence is a well-established notion, we defend subsistence (Stoic term) as a supplementary mode of reality (e.g. reflection of event). The aim here is aligned toward developing CM notions and processes that are firm enough. Classical analysis of being per se (e.g. identity, substance, classes, objects) is de-emphasized in this work; nevertheless, philosophical concepts form an acknowledged authority to compare to. As a case study, such a methodology is applied to the notion of information that provides a common-sense understanding of the world. This application would enhance understanding of the TM methodology and clarify some of the issues that shed light on the question of the nature of information as an important concept in software engineering. Information is defined as about events; that is, it is about existing things. It is viewed as having a subsisting nature that exists only through being “carried on” by other things. The results seem to indicate a promising approach to define information and understand its nature. (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)

All eyes are turned towards genomic data and models as the source of knowledge about whether human races exist or not. Will genomic science make the final decision about whether racial realism (e.g., racial population naturalism) or anti-realism (e.g., racial skepticism) is correct? We think not. We believe that the results of even our best and most impressive genomic technologies underdetermine whether bio-genomic races exist, or not. First, different sub-disciplines of biology interested in population structure employ distinct concepts, aims, measures, (...) and models, producing cross-cutting categorizations of population subdivisions rather than a single, universal bio-genomic concept of "race." Second, within each sub-discipline (e.g., conservation biology, phylogenetics), genomic results are consistent with, and map multiply to, racial realism and anti-realism. Indeed, racial ontologies are constructed conventionally, rather than discovered. We thus defend a /constructivist conventionalism/ about bio-genomic racial ontology. Choices and conventions must always be made in identifying particular kinds of groups. Political agendas, social programs, and moral questions premised on the existence of naturalistic race must accept that no scientifically grounded racial ontology is forthcoming, and adjust presumptions, practices, and projects accordingly. (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)

Despite the recent advances in information and communication technology that have increased our ability to store and circulate information, the task remains of ensuring that the right sorts of information reach the right sorts of people. In what follows we defend the thesis that efforts to develop efficient means for sharing information across healthcare systems and organizations would benefit from a careful analysis of human action in healthcare organizations, and that the communication of healthcare information and knowledge needs to rest (...) on a sound ontology of social interaction. We illustrate this thesis in relation to the HL7 RIM, which is one centrally important tool for communication in the healthcare domain. (shrink)

Abstract: The following is an outline of an emerging foundation for science that begins to explain living forms and their patterns of movement beyond the sphere of mechanistic interactions. Employing an event ontology based on a convergence of quantum physics and Alfred North Whitehead’s process philosophy, coupled with the controversial yet promising theory of formative causation, this development will explore possible influences on the outcomes of events beyond any combination of external forces, laws of Nature, and chance. If it turns (...) out there are no such additional influences--beyond mechanistic causes--it is difficult to see how agency or free will could exist. Assuming agency exists, as Whitehead apparently does, while committing to an event ontology in which process is fundamental leads to interesting questions about the natures of any entities that might participate in events. Furthermore, what might the purposes and agendas of such entities be based upon, beyond memory traces or DNA code? This ontological model, recognizing processes as fundamental, leads to a revised cosmology where the trajectory of a series of events may be due to more than rearrangement of material bits according to external forces and where goal-directed, recurring processes and the emergence of mind are not so surprising. Just as special relativity reduces to classical treatment when speeds slow down, this scientific model for a living world reduces to mechanistic materialism whenever conditions are more limited. Though this development is based on a philosophy of process, there are some dissimilarities with respect to Whitehead’s particular version. (shrink)

We show that logic has more to offer to ontologists than standard first order and modal operators. We first describe some operators of linear logic which we believe are particularly suitable for ontological modeling, and suggest how to interpret them within an ontological framework. After showing how they can coexist with those of classical logic, we analyze three notions of artifact from the literature to conclude that these linear operators allow for reducing the ontological commitment needed for (...) their formalization, and even simplify their logical formulation. (shrink)

The view of nature we adopt in the natural attitude is determined by common sense, without which we could not survive. Classical physics is modelled on this common-sense view of nature, and uses mathematics to formalise our natural understanding of the causes and effects we observe in time and space when we select subsystems of nature for modelling. But in modern physics, we do not go beyond the realm of common sense by augmenting our knowledge of what is going (...) on in nature. Rather, we have measurements that we do not understand, so we know nothing about the ontology of what we measure. We help ourselves by using entities from mathematics, which we fully understand ontologically. But we have no ontology of the reality of modern physics; we have only what we can assert mathematically. In this paper, we describe the ontology of classical and modern physics against this background and show how it relates to the ontology of common sense and of mathematics. (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)

A formal model of the processes of digestion in a hypothetical cell is developed and discussed as a case study of how the threefold logic of Peircean semiotics works within Rosen’s paradigm of relational ontology. The formal model is used to demonstrate several fundamental differences between a relational description of biological processes and a mechanistic description. The formal model produces a logic of embodied generalization that is mediated and determined by the cell through its interactions with the environment. Specifically, the (...) synchronization of the functions of pattern recognition and semantic attribution results in an open and adaptive learning system that is stabilized by a hermeneutical circle. The relational principles of biosemiotics demonstrated through this case study are applicable to other biological systems, as well as to the relational ontology of systems theory, artificial intelligence systems, and relativistic quantum theory. (shrink)

It is widely recognized that accurately identifying and classifying competitors is a challenge for many companies and entrepreneurs. Nonetheless, it is a paramount activity which provide valuable insights that affect a wide range of strategic decisions. One of the main challenges in competitor identification lies in the complex nature of the competitive relationships that arise in business envi- ronments. These have been extensively investigate over the years, which lead to a plethora of competition theories and frameworks. Still, the concept of (...) competition remains conceptually complex, as none of these approaches properly formalized their assumptions. In this paper, we address this issue by means of an ontological analysis on the notion of competition in general, and of business competition, in particular, leveraging theories from various fields, including Marketing, Strategic Management, Ecology, Psychology and Cognitive Sciences. Our analysis, the first of its kind in the literature, is grounded on the Unified Foundational Ontology (UFO) and allows us to formally characterize why competition arises, as well as to distinguish between three types of business competitive relationships, namely market-level, firm-level and potential competition. (shrink)

In this article, we analyse the ontological import of adding classes to set theories. We assume that this increment is well represented by going from ZF system to NBG. We thus consider the standard techniques of reducing one system to the other. Novak proved that from a model of ZF we can build a model of NBG (and vice versa), while Shoenfield have shown that from a proof in NBG of a set-sentence we can generate a proof in ZF (...) of the same formula. We argue that the first makes use of a too strong metatheory. Although meaningful, this symmetrical reduction does not equate the ontological content of the theories. The strong metatheory levels the two theories. Moreover, we will modernize Shoenfields proof, emphasizing its relation to Herbrands theorem and that it can only be seen as a partial type of reduction. In contrast with symmetrical reductions, we believe that asymmetrical relations are powerful tools for comparing ontological content. In virtue of this, we prove that there is no interpretation of NBG in ZF, while NBG trivially interprets ZF. This challenges the standard view that the two systems have the same ontological content. (shrink)

The desideratum of semantic interoperability has been intensively discussed in medical informatics circles in recent years. Originally, experts assumed that this issue could be sufficiently addressed by insisting simply on the application of shared clinical terminologies or clinical information models. However, the use of the term ‘ontology’ has been steadily increasing more recently. We discuss criteria for distinguishing clinical ontologies from clinical terminologies and information models. Then, we briefly present the role clinical ontologies play in two multicentric research projects. Finally, (...) we discuss the interactions between these different kinds of knowledge representation artifacts and the stakeholders involved in developing interoperational real-world clinical applications. We provide ontology engineering examples from two EU-funded projects. (shrink)

dolce, the first top-level ontology to be axiomatized, has remained stable for twenty years and today is broadly used in a variety of domains. dolce is inspired by cognitive and linguistic considerations and aims to model a commonsense view of reality, like the one human beings exploit in everyday life in areas as diverse as socio-technical systems, manufacturing, financial transactions and cultural heritage. dolce clearly lists the ontological choices it is based upon, relies on philosophical principles, is richly formalized, (...) and is built according to well-established ontological methodologies, e.g. OntoClean. Because of these features, it has inspired most of the existing top-level ontologies and has been used to develop or improve standards and public domain resources. Being a foundational ontology, dolce is not directly concerned with domain knowledge. Its purpose is to provide the general categories and relations needed to give a coherent view of reality, to integrate domain knowledge, and to mediate across domains. In these 20 years dolce has shown that applied ontologies can be stable and that interoperability across reference and domain ontologies is a reality. This paper briefly introduces the ontology and shows how to use it on a few modeling cases. (shrink)

A conspicuous feature of contemporary modelling practices is the use of the same mathematical forms and modelling methods across different scientific domains. This model transfer raises many philosophical questions concerning, for example, the exact object of transfer, the relationship between the model and the target domain, the specific challenges such transfer confronts, and the ways in which model transfer relates to scientific progress. While the interest in studying model transfer has increased among philosophers of science in recent years, (...) the phenomenon has not yet received its due attention. The literature is scattered and much of it has addressed questions around the factors that might explain model transfer, such as whether the different target phenomena to which a model is applied eventually prove to be structurally and dynamically similar, or whether they have to share more fundamental ontological features that explain the interdisciplinary success of distinct models. This chapter surveys the existing literature on model transfer with the main goal of highlighting the main findings of existing discussions and pointing out open issues whose discussion would improve our understanding of this highly relevant phenomenon in science. (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)

The book is a collection of papers and aims to unify the questions of syntax and semantics of language, which are included in logic, philosophy and ontology of language. The leading motif of the presented selection of works is the differentiation between linguistic tokens (material, concrete objects) and linguistic types (ideal, abstract objects) following two philosophical trends: nominalism (concretism) and Platonizing version of realism. The opening article under the title “The Dual Ontological Nature of Language Signs and the Problem (...) of Their Mutual Relations” provides a broad introduction into the problem area connected with this differentiation, while the logic-formal characteristics of the distinction are framed in the work entitled “On the Type-Token Relationships” (Chapter 1). The basic part of the book deals with issues relating to syntax (Chapters 2-4) and semantics of language (Chapters 5-6), as well as pertaining to syntactic-semantic pragmatic questions (Chapters 7-13). Throughout the book, language, categorial language, is characterized syntactically as generated by classical categorial grammar (Chapter 2) and formalized on two opposing levels: as language of expression-tokens (level of tokens) and language of expression-types (level of types). The author’s considerations contained in Chapters 2 and 4 lead to the important philosophical conclusion that in formal-logical syntactic studies on language the assumption that expression-types constitute the primary language layer while expression-tokens make the secondary one, can be neglected; thus, this speaks in favour of the opposing standpoint—the concretistic one—in the ontology of language syntax. In the works “Meaning and Interpretations”, Parts I and II (Chapters 5 and 6), it is underlined, however, that such semantic concepts as: meaning, denotation and interpretation are defined on the types level, yet their formal definitions require making use of notions of the tokens level. The semantic notions introduced in the above-mentioned articles are also used in the following works of the present selection, under the titles: “Three Principles of Compositionality” and “On Metaknowledge and Truth” (Chapters 7 and 8). They formalize two principles of compositionality that are well known in the literature on the subject, deriving from Frege, i.e. those of meaning and of denotation; they are related to the syntactic principle of compositionality which was introduced by the author. All the three principles are, at the same time, three conditions of homomorphism of categorial language algebra into three kinds of non-standard models of language (one syntactic and two semantic ones: intensional and extensional), which allows introducing three definitions of truthfulness into these models. The next two works in the collection, entitled: “On Language Adequacy” and “What is the Sense in Logic and Philosophy of Language” (Chapters 9 and 10) concern adequacy of categorial language syntax along with its dual semantics: intensional and extensional, and categorial compatibility of any of its syntactic categories with two corresponding semantic categories: intensional and extensional, based on the compatibility the syntactic category of each language expression with the ontological category assigned to its denotatum. The well-known problem of categorial compatibility for first-order quantifiers finds its solution in the paper “Categories of First-Order Quantifiers” (Chapter 11). In the work “Logic and Ontology of Language” (Chapter 12), being in a sense a summary of the considerations presented in the preceding chapters of the book, language is treated as an ontological being, characterized in compliance with the logical conception of language proposed by Ajdukiewicz. Application—like throughout the book—of tools of classical logic and set theory has resulted in emergence of a general formal logical theory of syntax, semantics and pragmatics of language, which takes into account duality in the understanding of linguistic expressions as tokens (concretes) and types (abstract objects). In terms that take into account a functional approach to language itself, there comes out an ontological neutrality of logic with respect to existential assumptions relating to the ontological nature of linguistic expressions and their extra-linguistic ontological counterparts. The issues connected with applying logic while explaining the manner of using linguistic tokens and linguistic types to determine notions of language communication are raised and illustrated in the last chapter of the work, bearing the title “A Logical Conceptualization of Knowledge on the Notion of Language Communication”. (shrink)

While representation learning techniques have shown great promise in application to a number of different NLP tasks, they have had little impact on the problem of ontology matching. Unlike past work that has focused on feature engineering, we present a novel representation learning approach that is tailored to the ontology matching task. Our approach is based on embedding ontological terms in a high-dimensional Euclidean space. This embedding is derived on the basis of a novel phrase retrofitting strategy through which (...) semantic similarity information becomes inscribed onto fields of pre-trained word vectors. The resulting framework also incorporates a novel outlier detection mechanism based on a denoising autoencoder that is shown to improve performance. An ontology matching system derived using the proposed framework achieved an F-score of 94% on an alignment scenario involving the Adult Mouse Anatomical Dictionary and the Foundational Model of Anatomy ontology (FMA) as targets. This compares favorably with the best performing systems on the Ontology Alignment Evaluation Initiative anatomy challenge. We performed additional experiments on aligning FMA to NCI Thesaurus and to SNOMED CT based on a reference alignment extracted from the UMLS Metathesaurus. Our system obtained overall F-scores of 93.2% and 89.2% for these experiments, thus achieving state-of-the-art results. (shrink)

I discuss the ontological assumptions and implications of General Relativity. I maintain that General Relativity is a theory about gravitational fields, not about space-time. The latter is a more basic ontological category, that emerges from physical relations among all existents. I also argue that there are no physical singularities in space-time. Singular space-time models do not belong to the ontology of the world: they are not things but concepts, i.e. defective solutions of Einstein’s field equations. I briefly discuss (...) the actual implication of the so-called singularity theorems in General Relativity and some problems related to ontological assumptions of Quantum Gravity. (shrink)

The notion of Mathematics as Ontology (as defined by Badiou in his work) is brought into question from a working mathematician's perspective. Notions of independence in set theory and model theory are contrasted with the original equation Mathematics=Ontology. The author builds an extension of mathematical ontology from set theory to a foliated, étale, setting.

Discourse carries thin commitment to objects of a certain sort iff it says or implies that there are such objects. It carries a thick commitment to such objects iff an account of what determines truth-values for its sentences say or implies that there are such objects. This paper presents two model-theoretic semantics for mathematical discourse, one reflecting thick commitment to mathematical objects, the other reflecting only a thin commitment to them. According to the latter view, for example, the semantic role (...) of number-words is not designation but rather the encoding of cardinality-quantifiers. I also present some reasons for preferring this view. (shrink)

The ontological turn (OT) is a loose cluster of theoretical approaches within cultural anthropology that advocates a synthetic, overarching way forward for ethnographically oriented cultural anthropology. We argue that in order to contribute substantively to ethnobiology the OT needs to distance itself from a long-standing tradition of thinking within ethnography that assumes some kind of fundamental divide between the natural and the social sciences. This distancing seems especially unlikely in light of the meta-anthropological nature of the OT as primarily (...) a perspective on ethnographic methodology. Instead, we advocate for naturalistic theoretical alternatives for thinking about human sociality, where philosophical innovation develops in concert with ongoing empirical work across the biological, cognitive, and social sciences. We illustrate this perspective by drawing on two naturalistic accounts likely to prove more fruitful for ethnobiological practice, namely, trans-genera models of sociality and progenerative views of kinship. (shrink)

Scientists and philosophers frequently speak about levels of description, levels of explanation, and ontological levels. In this paper, I propose a unified framework for modelling levels. I give a general definition of a system of levels and show that it can accommodate descriptive, explanatory, and ontological notions of levels. I further illustrate the usefulness of this framework by applying it to some salient philosophical questions: (1) Is there a linear hierarchy of levels, with a fundamental level at (...) the bottom? And what does the answer to this question imply for physicalism, the thesis that everything supervenes on the physical? (2) Are there emergent properties? (3) Are higher-level descriptions reducible to lower-level ones? (4) Can the relationship between normative and non-normative domains be viewed as one involving levels? Although I use the terminology of “levels”, the proposed framework can also represent “scales”, “domains”, or “subject matters”, where these are not linearly but only partially ordered by relations of supervenience or inclusion. (shrink)

In his work on the open future, Patrick Todd outlines three models of how to deal with future contingents. These models must answer two questions: one metaphysical, about what facts there are in the world; one semantic, about how to deal with sentences involving ‘will.’ Model 1 has a privileged timeline. Model 2 has an actual future timeline but leaves it indeterminate which timeline that is. Model 3 has no future timeline. All three give will-sentences a modal treatement, as a (...) box over available futures. I will argue that Todd’s second model has problems and should be improved. The first is that it denies what Todd labels as the basic metaphysical intuition behind open-futurism. The second is that indeterminacy about the facts that characterize the actual timeline breaks through into indeterminate identity. I propose a fix to model 2 eliminating its actual future and resolving an issue that arises in applying the neutral semantics Todd endorses to indeterminate sentences. This improved model, I suggest, may even compare favorably to Todd’s preferred model 3. (shrink)

The research presented in this article is motivated by the increasing importance of complex human relations in linked data, either extracted from social networks, or found in existing databases. The FOAF vocabulary, targeted in our research, plays a central role in those data, and is a model for lightweight ontologies largely used in linked data, such as the DBpedia ontology and schema-org. We provide an overview of FOAF and other approaches for describing human relations, followed by a detailed analysis and (...) critique of the FOAF Relationship Vocabulary, the most important FOAF extension. We propose an explicit formal axiomatization of this vocabulary, and an ontological analysis concerning the properties used to describe human relationships. We analyze the distribution of human relations based on their epistemological status, and define an ontoepistemic meta-property as characteristic of some of these predicates. Our analysis is generalizable to semantic modeling of social networks. Additionally, the modeling patterns used in other relevant linked data vocabularies are analyzed for comparison. (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)

In Risk Management, security issues arise from complex relations among objects and agents, their capabilities and vulnerabilities, the events they are involved in, and the value and risk they ensue to the stakeholders at hand. Further, there are patterns involving these relations that crosscut many domains, ranging from information security to public safety. Understanding and forming a shared conceptualization and vocabulary about these notions and their relations is fundamental for modeling the corresponding scenarios, so that proper security countermeasures can be (...) devised. Ontologies are instruments developed to address these conceptual clarification and terminological systematization issues. Over the years, several ontologies have been proposed in Risk Management and Security Engineering. However, as shown in recent literature, they fall short in many respects, including generality and expressivity - the latter impacting on their interoperability with related models. We propose a Reference Ontology for Security Engineering (ROSE) from a Risk Treatment perspective. Our proposal leverages on two existing Reference Ontologies: the Common Ontology of Value and Risk and a Reference Ontology of Prevention, both of which are grounded on the Unified Foundational Ontology (UFO). ROSE is employed for modeling and analysing some cases, in particular providing clarification to the semantically overloaded notion of Security Mechanism. (shrink)

This article presents a simple derivation of optimization models for reaction networks leading to a generalized form of the mass-action law, and compares the formal structure of Minimum Information Divergence, Quadratic Programming and Kirchhoff type network models. These optimization models are used in related articles to develop and illustrate the operation of ontology alignment algorithms and to discuss closely connected issues concerning the epistemological and statistical significance of sharp or precise hypotheses in empirical science.

In this paper, we review and connect the three essential conditions needed by the collapse model to achieve a complete and exact formulation, namely the theoretical, the experimental, and the ontological ones. These features correspond to the three parts of the paper. In any empirical science, the first two features are obviously connected but, as is well known, among the different formulations and interpretations of non-relativistic quantum mechanics, only collapse models, as the paper well illustrates with a richness of (...) details, have experimental consequences. Finally, we show that a clarification of the ontological intimations of collapse models is needed for at least three reasons: (1) to respond to the indispensable task of answering the question ’what are collapse models (and in general any physical theory) about?’; (2) to achieve a deeper understanding of their different formulations; (3) to enlarge the panorama of possible readings of a theory, which historically has often played a fundamental heuristic role. (shrink)

In what follows, I will give examples of the sorts of step that can be taken towards spelling out the intuition that, after all, good models might be true. Along the way, I provide an outline of my account of models as ontologically and pragmatically constrained representations. And I emphasize the importance of examining models as functionally composed systems in which different components play different roles and only some components serve as relevant truth bearers. This disputes the standard approach that (...) proceeds by simply counting true and false elements in models in their entirety and concludes that models are false since they contain so many false elements. I call my alternative the functional decomposition approach. (shrink)

We present a preliminary high-level formal theory, grounded on knowledge representation techniques and foundational ontologies, for the uniform and integrated representation of the different kinds of (quali- tative and quantitative) knowledge involved in the designing process. We discuss the conceptual nature of engineering design by individuating and analyzing the involved notions. These notions are then formally charac- terized by extending the DOLCE foundational ontology. Our ultimate purpose is twofold: (i) to contribute to foundational issues of design; and (ii) to support (...) the development of advanced modelling systems for (qualitative and quantitative) representation of design knowledge. (shrink)

While classifications of mental disorders have existed for over one hundred years, it still remains unspecified what terms such as 'mental disorder', 'disease' and 'illness' might actually denote. While ontologies have been called in aid to address this shortfall since the GALEN project of the early 1990s, most attempts thus far have sought to provide a formal description of the structure of some pre-existing terminology or classification, rather than of the corresponding structures and processes on the side of the patient. (...) We here present a view of mental disease that is based on ontological realism and which follows the principles embodied in Basic Formal Ontology and in the application of BFO in the Ontology of General Medical Science. We analyzed statements about what counts as a mental disease provided in the research agenda for the DSM-V, and in Pies' model. The results were used to assess whether the representational units of BFO and OGMS were adequate as foundations for a formal representation of the entities in reality that these statements attempt to describe. We then analyzed the representational units specific to mental disease and provided corresponding definitions. Our key contributions lie in the identification of confusions and conflations in the existing terminology of mental disease and in providing what we believe is a framework for the sort of clear and unambiguous reference to entities on the side of the patient that is needed in order to avoid these confusions in the future. (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)

This article shows how the MISS account of models—as isolations and surrogate systems—accommodates and elaborates Sugden’s account of models as credible worlds and Hausman’s account of models as explorations. Theoretical models typically isolate by means of idealization, and they are representatives of some target system, which prompts issues of resemblance between the two to arise. Models as representations are constrained both ontologically (by their targets) and pragmatically (by the purposes and audiences of the modeller), and these relations are coordinated by (...) a model commentary. Surrogate models are often about single mechanisms. They are distinguishable from substitute models, which are examined without any concern about their connections with the target. Models as credible worlds are surrogate models that are believed to provide access to their targets on account of their credibility (of which a few senses are distinguished). (shrink)

According to the PubMed resource from the U.S. National Library of Medicine, over 750,000 scientific articles have been published in the ~5000 biomedical journals worldwide in the year 2007 alone. The vast majority of these publications include results from hypothesis-driven experimentation in overlapping biomedical research domains. Unfortunately, the sheer volume of information being generated by the biomedical research enterprise has made it virtually impossible for investigators to stay aware of the latest findings in their domain of interest, let alone to (...) be able to assimilate and mine data from related investigations for purposes of meta-analysis. While computers have the potential for assisting investigators in the extraction, management and analysis of these data, information contained in the traditional journal publication is still largely unstructured, free-text descriptions of study design, experimental application and results interpretation, making it difficult for computers to gain access to the content of what is being conveyed without significant manual intervention. In order to circumvent these roadblocks and make the most of the output from the biomedical research enterprise, a variety of related standards in knowledge representation are being developed, proposed and adopted in the biomedical community. In this chapter, we will explore the current status of efforts to develop minimum information standards for the representation of a biomedical experiment, ontologies composed of shared vocabularies assembled into subsumption hierarchical structures, and extensible relational data models that link the information components together in a machine-readable and human-useable framework for data mining purposes. (shrink)

I argue that there are no physical singularities in space–time. Singular space–time models do not belong to the ontology of the world, because of a simple reason: they are concepts, defective solutions of Einstein’s field equations. I discuss the actual implication of the so-called singularity theorems. In remarking the confusion and fog that emerge from the reification of singularities I hope to contribute to a better understanding of the possibilities and limits of the theory of general relativity.

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

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)