The relevance of analytic metaphysics has come under criticism: Ladyman & Ross, for instance, have suggested do discontinue the field. French & McKenzie have argued in defense of analytic metaphysics that it develops tools that could turn out to be useful for philosophy of physics. In this article, we show first that this heuristic defense of metaphysics can be extended to the scientific field of applied ontology, which uses constructs from analytic metaphysics. Second, we elaborate on a parallel (...) by French & McKenzie between mathematics and metaphysics to show that the whole field of analytic metaphysics, being useful not only for philosophy but also for science, should continue to exist as a largely autonomous field. (shrink)

We begin by describing recent developments in the burgeoning discipline of applied ontology, focusing especially on the ways ontologies are providing a means for the consistent representation of scientific data. We then introduce Basic Formal Ontology (BFO), a top-level ontology that is serving as domain-neutral framework for the development of lower level ontologies in many specialist disciplines, above all in biology and medicine. BFO is a bicategorial ontology, embracing both three-dimensionalist (continuant) and four-dimensionalist (occurrent) perspectives (...) within a single framework. We examine how BFO-conformant domain ontologies can deal with the consistent representation of scientific data deriving from the measurement of processes of different types, and we outline on this basis the first steps of an approach to the classification of such processes within the BFO framework. (shrink)

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

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

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

On March 14-15, 2006, at the US National Institute of Standards and Technology (NIST) in Gaithersburg, MD there took place the first Upper Ontology Summit (UOS). This was a convening of custodians of several prominent upper ontologies, key technology participants, and interested other parties, with the purpose of finding a means to relate the different ontologies to each other. The result is reflected in a joint communiqué, directed to the larger ontology community and the general public, and expressing (...) a joint intent to build bridges among the existing upper ontologies in ways designed to increase and rationalize their utilization and to enhance their semantic interoperability. (shrink)

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

The ability to access and share data is key to optimizing and streamlining any industrial production process. Unfortunately, the manufacturing industry is stymied by a lack of interoperability among the systems by which data are produced and managed, and this is true both within and across organizations. In this paper, we describe our work to address this problem through the creation of a suite of modular ontologies representing the product life cycle and its successive phases, from design to end of (...) life. We call this suite the Product Life Cycle (PLC) Ontologies. The suite extends proximately from The Common Core Ontologies (CCO) used widely in defense and intelligence circles, and ultimately from the Basic Formal Ontology (BFO), which serves as top level ontology for the CCO and for some 300 further ontologies. The PLC Ontologies were developed together, but they have been factored to cover particular domains such as design, manufacturing processes, and tools. We argue that these ontologies, when used together with standard public domain alignment and browsing tools created within the context of the Semantic Web, may offer a low-cost approach to solving increasingly costly problems of data management in the manufacturing industry. (shrink)

The notion of function is indispensable to our understanding of distinctions such as that between being broken and being in working order (for artifacts) and between being diseased and being healthy (for organisms). A clear account of the ontology of functions and functioning is thus an important desideratum for any top-level ontology intended for application to domains such as engineering or medicine. The benefit of using top-level ontologies in applied ontology can only be realized when each (...) of the categories identified and defined by a top-level ontology is integrated with the others in a coherent fashion. Basic Formal Ontology (BFO) has from the beginning included function as one of its categories, exploiting a version of the etiological account of function that is framed at a level of generality sufficient to accommodate both biological and artifactual functions. This account has been subjected to a series of criticisms and refinements. We here articulate BFO’s account of function, provide some reasons for favoring it over competing views, and defend it against objections. (shrink)

This introduction to the second international conference on Formal Ontology and Information Systems presents a brief history of ontology as a discipline spanning the boundaries of philosophy and information science. We sketch some of the reasons for the growth of ontology in the information science field, and offer a preliminary stocktaking of how the term ‘ontology’ is currently used. We conclude by suggesting some grounds for optimism as concerns the future collaboration between philosophical ontologists and information (...) scientists. (shrink)

Basic Formal Ontology was created in 2002 as an upper-level ontology to support the creation of consistent lower-level ontologies, initially in the subdomains of biomedical research, now also in other areas, including defense and security. BFO is currently undergoing revisions in preparation for the release of BFO version 2.0. We summarize some of the proposed revisions in what follows, focusing on BFO’s treatment of material entities, and specifically of the category object.

This paper proposes a reformulation of the treatment of boundaries, at parts and aggregates of entities in Basic Formal Ontology. These are currently treated as mutually exclusive, which is inadequate for biological representation since some entities may simultaneously be at parts, boundaries and/or aggregates. We introduce functions which map entities to their boundaries, at parts or aggregations. We make use of time, space and spacetime projection functions which, along the way, allow us to develop a simple temporal theory.

This paper develops the ontology of space objects for theoretical and computational ontology applied to the space (astronautical/astronomical) domain. It follows “An ontological architecture for Orbital Debris Data” (Rovetto, 2015) and “Preliminaries of a Space Situational Awareness Ontology” (Rovetto, Kelso, 2016). Important considerations for developing a space object ontology, or more broadly, a space domain ontology are presented. The main category term ‘Space Object’ is analyzed from a philosophical perspective. The ontological commitments of legal (...) definitions for artificial space objects are also discussed. Space object taxonomies are offered and space object terms are defined. (shrink)

The National Center for Biomedical Ontology is now in its seventh year. The goals of this National Center for Biomedical Computing are to: create and maintain a repository of biomedical ontologies and terminologies; build tools and web services to enable the use of ontologies and terminologies in clinical and translational research; educate their trainees and the scientific community broadly about biomedical ontology and ontology-based technology and best practices; and collaborate with a variety of groups who develop and (...) use ontologies and terminologies in biomedicine. The centerpiece of the National Center for Biomedical Ontology is a web-based resource known as BioPortal. BioPortal makes available for research in computationally useful forms more than 270 of the world's biomedical ontologies and terminologies, and supports a wide range of web services that enable investigators to use the ontologies to annotate and retrieve data, to generate value sets and special-purpose lexicons, and to perform advanced analytics on a wide range of biomedical data. (shrink)

Two senses of ‘ontology’ can be distinguished in the current literature. First is the sense favored by information scientists, who view ontologies as software implementations designed to capture in some formal way the consensus conceptualization shared by those working on information systems or databases in a given domain. [Gruber 1993] Second is the sense favored by philosophers, who regard ontologies as theories of different types of entities (objects, processes, relations, functions) [Smith 2003]. Where information systems ontologists seek to maximize (...) reasoning efficiency even at the price of simplifications on the side of representation, philosophical ontologists argue that representational adequacy can bring benefits for the stability and resistance to error of an ontological framework and also for its extendibility in the future. In bioinformatics, however, a third sense of ‘ontology’ has established itself, above all as a result of the successes of the Gene Ontology (hereafter: GO), which is a tool for the representation and processing of information about gene products and their biological functions [Gene Ontology Consortium 2000]. We show how Basic Formal Ontology (BFO) has established itself as an overarching ontology drawing on all three of the strands distinguished above, and describe applications of BFO especially in the treatment of biological granularity. (shrink)

[ES] En recientes décadas se ha observado un renovado interés por algunos de los temas clásicos de la ontología, desde áreas de conocimiento externas a la filosofía, sin embargo, este renacimiento ontológico ha «estimulado» una multiplicidad y diversidad de teorías y concepciones «ontológicas» que ha dado como consecuencia una proliferación de «ontologías» y de interminables batallas para determinar qué tipo de «entidades» estudian sus respectivos «dominios», que a su vez se consideran autónomos e independientes entre sí, inclusive de la propia (...) ontología. En este sentido, el propósito de este trabajo es caracterizar y representar de manera adecuada estas «ontologías», dentro del marco general del debate acerca de la naturaleza de la ontología. Es así que, en la primera sección haré un diagnostico de la ontología contemporánea; en la segunda proporcionaré algunas definiciones y caracterizaciones de las principales concepciones, en especial de las denominadas «ontologías aplicadas»; y en la tercera analizaré sí estas concepciones pueden ser consideradas diversos tipos de ontología o simplemente son diversos niveles de ontología. El marco de la discusión no se centrará en confrontar todas estas nociones, sino en describirlas y analizarlas para ofrecer un enfoque sobre el estado actual de la ontología y sus problemas. [EN] In recent decades there has been a renewed interest in some of the classic themes of ontology, from areas of knowledge external to philosophy; however, this ontological revival has «stimulated» a multiplicity and diversity of «ontological» theories and concepts that has resulted in a proliferation of «ontologies» and endless battles to determine what kind of «entities» study their respective «domains», which in turn are considered autonomous and independent, even of ontology itself. In this sense, the purpose of this work is to adequately characterize and represent these «ontologies», within the general framework of the debate about the nature of ontology. Thus, in the first section I will make a diagnosis of contemporary ontology; in the second I will provide some definitions and characterizations of the main concepts, especially the so-called «applied ontologies»; and in the third I will analyze whether these concepts can be considered different types of ontology or simply are different levels of ontology. The framework of the discussion will not center on confronting all these notions, but to describe and analyze them to provide a focus on the current state of ontology and its problems. (shrink)

Ontology as a branch of philosophy is the science of what is, of the kinds and structures of objects, properties, events, processes and relations in every area of reality. ‘Ontology’ in this sense is often used by philosophers as a synonym of ‘metaphysics’ (a label meaning literally: ‘what comes after the Physics’), a term used by early students of Aristotle to refer to what Aristotle himself called ‘first philosophy’. But in recent years, in a development hardly noticed by (...) philosophers, the term ‘ontology’ has gained currency in the field of computer and information science, and in information-driven research in bioinformatics and related areas. We examine these new developments in applied ontology, and show what lessons they might have for both philosophers and information scientists. (shrink)

Space situational awareness (SSA) is vital for international safety and security, and for the future of space travel. The sharing of SSA data and information should improve the state of global SSA for planetary defense and spaceflight safety. I take steps toward a Space Situational Awareness (SSA) Ontology, and outline some central objectives, requirements and desiderata in the ontology development process for this domain. The purpose of this ontological system is to explore the potential for the ontology (...) research topic to (i) represent SSA general knowledge, data, and entities/objects, (ii) clearly express the meaning of SSA data, and (iii) foster SSA data-sharing. The overall goal and motivation is to (iv) improve our capacity for planetary defense, e.g., from near- or deep-space objects and phenomena, and (v) facilitate safer and peaceful space access, navigation and travel, by improving global SSA. This research is thereby intended only for peaceful space-domain applications and uses, with particular interests in orbital debris. There is little application of ontology to the space domain as compared with other disciplines and little if any ontological development of SSA and related domains. In this respect, this paper offers novel concepts. (shrink)

This paper presents an ontology architecture concept for the European Space Agency‘s (ESA) Space Situational Awareness (SSA) Program. It incorporates the author‘s domain ontology, The Space Situational Awareness Ontology and related ontology work. I summarize computational ontology, discuss the segments of ESA SSA, and introduce an option for a modular ontology framework reflecting the divisionsof the SSA program. Among other things, ontologies are used for data sharing and integration. By applying ontology to ESA (...) data, the ESA may better achieve its integration and innovation goals, while simultaneously improving the state of peaceful SSA. (shrink)

This article presents a formal ontology which accounts for the general nature of artefacts. The objective is to help structure application ontologies in areas where specific artefacts are present - in other words, virtually any area of activity. The conceptualization relies on recent philosophical and psychological research on artefacts, having resulted in a largely consensual theoretical basis. Furthermore, this ontology of artefacts extends the foundational DOLCE ontology and supplements its axiomatization. The conceptual primitives are as follows: artificial (...) entity, intentional production of entities, (state of) capacity, capacity to play a role in actions of a given type, function and functional object. These primitives enable artefacts in general to be characterized as intentionally and successfully produced entities, and isolate an important subclass of “technical” artefacts to which a function is ascribed. Lastly, we emphasize the novelty of this ontology by comparing it with other works with similar objectives. (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)

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

In this article, the results of conceptualization of the definition of mind as an object of interdisciplinary applied research are described. The purpose of the theoretical analysis is to generate a methodological discourse suitable for a functional understanding of the mind in the context of the problem of natural language processing as one of the components of developments in the field of artificial intelligence. The conceptual discourse was realized with the help of the author's method of structural-ontological analysis, and (...) developed in the mainstream of the system-methodological tradition of the school of G.P. Shchedrovitsky and intended for descriptive research of subject areas of interdisciplinary objects of scientific study. As a result of the structural and ontological analysis of the super-system, the relevant place and role of the directly studied system (mind) are determined, and its primary process and material are localized and structural and functional connections are described. At the basic level, the mind is conceptualized as an energy process unfolding in a spatio-temporal environment and accompanied by archetypal structuring of neural impulses into images. The genesis of the system is separately analyzed by constructing a structural-ontological matrix that reflects the initial stage of the development of the mind. The primary process is concretized with the help of hetero- and homeostatic dichotomy, and also the most significant features of the consistent transformation of the material of the system and its ascent to verbal morphology are described. The structural-ontological comparison of the functioning of the verbal intelligence with the preverbal level has been carried out. The transformation of neural impulses of needs into words, as verbal units fixing semiotic values is analyzed. Structural-ontological connections that determine the reactive and prospective characteristics of the functioning of the system are disclosed. The position of the chronological primacy of "semiotic readiness" for language with respect to the debut of the latter as an information-sign model of the environment is argued. The hypothesis of domination at the initial stage of the development of the mind of exopsychic functions over endopsychic ones is formulated. The theoretical substantiation of the hypothesis of the inevitability of the ontology of language in the functional understanding of the mind is given, corresponding structural and ontological arguments are given, including those based on the ideas about the information relationship between affects and needs, according to the views of P.V. Simonov. The arguments are presented in favor of the non-alternative methodology of A. Turing in studies of artificial intelligence. (shrink)

The paper shows how the Bohmian approach to quantum physics can be applied to develop a clear and coherent ontology of non-perturbative quantum gravity. We suggest retaining discrete objects as the primitive ontology also when it comes to a quantum theory of space-time and therefore focus on loop quantum gravity. We conceive atoms of space, represented in terms of nodes linked by edges in a graph, as the primitive ontology of the theory and show how a (...) non-local law in which a universal and stationary wave-function figures can provide an order of configurations of such atoms of space such that the classical space-time of general relativity is approximated. Although there is as yet no fully worked out physical theory of quantum gravity, we regard the Bohmian approach as setting up a standard that proposals for a serious ontology in this field should meet and as opening up a route for fruitful physical and mathematical investigations. (shrink)

Formal ontology as it is presented in Husserl`s Third Logical Investigation can be interpreted as a fundamental tool to describe objects in a formal sense. It is presented one of the main sources: chapter five of Carl Stumpf`s Ûber den psycholoogischen Ursprung der Raumovorstellung (1873), and then it is described how Husserlian Formal Ontology is applied in Fifth Logical Investigation. Finally, it is applied to dramatic structures, in the spirit of Roman Ingarden.

In the domain of ontology design as well as in Knowledge Representation, modeling universals is a challenging problem.Most approaches that have addressed this problem rely on Description Logics (DLs) but many difficulties remain, due to under-constrained representation which reduces the inferences that can be drawn and further causes problems in expressiveness. In mathematical logic and program checking, type theories have proved to be appealing but, so far they have not been applied in the formalization of ontologies. To bridge (...) this gap, we present in this paper a theory for representing ontologies in a dependently typed framework which relies on strong formal foundations including both a constructive logic and a functional type system. The language of this theory defines in a precise way what ontological primitives such as classes, relations, properties, etc., and thereof roles, are. The first part of the paper details how these primitives are defined and used within the theory. In a second part, we focus on the formalization of the role primitive. A review of significant role properties leads to the specification of a role profile and most of the remaining work details through numerous examples, how the proposed theory is able to fully satisfy this profile. It is demonstrated that dependent types can model several non-trivial aspects of roles including a formal solution for generalization hierarchies, identity criteria for roles and other contributions. A discussion is given on how the theory is able to cope with many of the constraints inherent in a good role representation. (shrink)

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

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

Representing the kinetic state of a patient (posture, motion, and activity) during vital sign measurement is an important part of continuous monitoring applications, especially remote monitoring applications. In contextualized vital sign representation, the measurement result is presented in conjunction with salient measurement context metadata. We present an automated annotation system for vital sign measurements that uses ontologies from the Open Biomedical Ontology Foundry (OBO Foundry) to represent the patient’s kinetic state at the time of measurement. The annotation system is (...) applied to data generated by a wearable personal status monitoring (PSM) device. We demonstrate how annotated PSM data can be queried for contextualized vital signs as well as sensor algorithm configuration parameters. (shrink)

Festschrift in Honor of Barry Smith on the occasion of his 65th Birthday. Published as issue 4:4 of the journal Cosmos + Taxis: Studies in Emergent Order and Organization. Includes contributions by Wolfgang Grassl, Nicola Guarino, John T. Kearns, Rudolf Lüthe, Luc Schneider, Peter Simons, Wojciech Żełaniec, and Jan Woleński.

Dieses Buch betritt Neuland. Es ist eine Einführung in das neue Gebiet der angewandten Ontologie, jenem multidisziplinären Arbeitsgebiet, in dem Philosophen gemeinsam mit Informatikern und Vertretern der jeweils thematischen Wissenschaftsbereiche, in unserem Fall mit Biologen und Medizinern, daran arbeiten, wissenschaftliches Wissen informationstechnisch zu repräsentieren. Es zeigt, wie Philosophie eine praktische Anwendung findet, die von zunehmender Wichtigkeit nicht nur in den heutigen Lebenswissenschaften ist. Und so richtet sich dieses Buch an Philosophen, aber auch an interessierte Biologen, Mediziner und Informatiker.

The orbital debris problem presents an opportunity for inter-agency and international cooperation toward the mutually beneficial goals of debris prevention, mitigation, remediation, and improved space situational awareness (SSA). Achieving these goals requires sharing orbital debris and other SSA data. Toward this, I present an ontological architecture for the orbital debris and broader SSA domain, taking steps in the creation of an orbital debris ontology (ODO). The purpose of this ontological system is to (I) represent general orbital debris and SSA (...) domain knowledge, (II) structure, and standardize where needed, orbital data and terminology, and (III) foster semantic interoperability and data-sharing. In doing so I hope to (IV) contribute to solving the orbital debris problem, improving peaceful global SSA, and ensuring safe space travel for future generations. (shrink)

This text aims to introduce Knowledge Ontology (OK) as an ontological model. According to OK these are not the world and its forms that make themselves intelligible to the subject but a principle of knowledge: the Logos, which gives meaning, which gives forms to a Reality that is otherwise formless, unspeakable. The Spirit, as a logical system, thus plays the central role; it creates forms, gives existence to the objects it represents, animates the representation it has of itself and (...) the world. The OK, however, is not idealism because knowledge is conceived as a principle of order: the Logos, applied to a reality of pure logic, free of any materialist, anthropologic or psychological a-priori. In that sense, Reality and Spirit have the same nature. That’s where the OK fills the gaps left open by Kant and Schopenhauer. The OK does not propose another reality than that described by common sense or science but another mode of representation. The OK is compatible with the current state of science and common sense, even though it opens the door to breakthrough interpretations. This text shows that the laws of the world, as we know them, are what appear to the knowledge at the same time as the Logos gives meaning to all Facts and Beings of our representation. (shrink)

ABSTRACT In previous work I explored how Integral Theory can be applied as a metatheoretical and transdisciplinary framework, in an attempt to arrive at an integrally informed metatheory of addiction. There was an overemphasis on Integral Methodological Pluralism in that thread of research, without clarifying the ontological pluralism of addiction as a multiple object enacted by various methodologies. To arrive at a comprehensive integral metatheory and integral ontology of addiction, I believe it is necessary to include the conception (...) of Integral Pluralism and Integral Enactment Theory as posited by Sean Esbjörn-Hargens. Integral Enactment Theory highlights the phenomenon of addiction as a multiple and dynamic object arising along a continuum of ontological complexity; it adeptly points out how etiological models “co-arise” in relation to methodology (methodological pluralism) to enact a particular reality of addiction (ontological pluralism) while being mediated by the worldview of the subject (epistemological pluralism) applying the method. This article briefly explores the significance of including Integral Pluralism and Integral Enactment Theory in the quest of an integral metatheory and integral ontology of addiction. (shrink)

The development of manufacturing technologies for new materials involves the generation of a large and continually evolving volume of information. The analysis, integration and management of such large volumes of data, typically stored in multiple independently developed databases, creates significant challenges for practitioners. There is a critical need especially for open-sharing of data pertaining to engineering design which together with effective decision support tools can enable innovation. We believe that ontology applied to engineering (OE) represents a viable strategy (...) for the alignment, reconciliation and integration of diverse and disparate data. The scope of OE includes: consistent capture of knowledge pertaining to the types of entities involved; facilitation of cooperation among diverse group of experts; more effective ongoing curation, and update of manufacturing data; collaborative design and knowledge reuse. As an illustrative case study we propose an ontology focused on the representation of composite materials focusing in particular on the class of Functionally Graded Materials (FGM) in particular. The scope of the ontology is to provide information about the components of such materials, the manufacturing processes involved in creation, and diversity of application ranging from additive manufacturing to restorative dentistry. The ontology is developed using Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations (OBI). (shrink)

What are we? Despite much discussion in historical and contemporary philosophy, we have not yet settled on an answer. A satisfactory personal ontology, an account of our metaphysical nature, will be informed by issues in the metaphysics of material objects. In the dissertation, I target two prominent materialist ontologies: animalism, the view that we are numerically identical to human organisms, and constitutionalism, the view that we are constituted by, but not identical to, human organisms. Because of the problems that (...) arise from endorsing these ontologies, I instead advance immaterialism, the view that we are essentially immaterial. In Chapter 2, I discuss how animalists must respond to a widely-discussed metaphysical puzzle, the problem of the many. This puzzle prompts some to endorse revisionary ontologies of material objects, and I argue that the animalist cannot appeal to these revisionary ontologies to solve the puzzle as it arises for personal ontology. In addition, solutions that don’t involve a commitment to revisionary ontology will be unavailable to the animalist: I argue that if animalists make use of non-revisionary solutions to the problem, they must abandon the most successful argument for their view. Absent their most successful argument, animalists will need to motivate the view in some other way. Some new arguments for animalism have been proposed, and I argue that they fail to give us reason to endorse animalism over competing ontologies. Without a strong argument, we should not prefer animalism over the other, more attractive, views. In Chapter 3, I show how constitutionalists face a different problem: explaining how the person is not the very same thing as the human organism, despite sharing the very same parts and occupying the very same physical space. We think that the person and the organism are different things because they have different modal profiles – the human organism can survive permanent loss of psychological life, but the person, presumably, cannot. Constitutionalists must then explain what grounds the difference in modal profiles, but such an explanation is hard to come by. This is an instance of the grounding problem, which is notoriously intractable. While the grounding problem is a well-known challenge to constitutional accounts of objects, I demonstrate that this puzzle is even more threatening when applied to persons. Some “solutions” to the problem fail to solve it at all, and solutions that might get the right result for ordinary objects require accepting that there are a multitude of persons where we ordinarily take there to be only one. We should not accept a personal ontology that requires a commitment to that multitude. I argue that the threat of the grounding problem is so great that we must reject the constitutionalist personal ontology. We will see from these puzzles in personal ontology that materialist solutions are either unsuccessful or yield unacceptable consequences. This should prompt us toward considering, instead, immaterialism. According to immaterialism, persons are not material objects, and the immaterialist can then provide solutions to the puzzles that threatened materialist ontologies. In Chapter 4, I outline these immaterialist solutions and show that the puzzles cannot be reinstantiated successfully against the immaterialist. I then discuss different available varieties of immaterialism and argue in defense of my preferred version. Ultimately, I argue that we are simple, immaterial entities that come into existence at the proper functioning of the brain. Endorsing this view of personal ontology permits us to adequately respond to metaphysical puzzles and retain judgments about persons that should be most important to us. In particular, the immaterialist has the resources to avoid the problem of too many thinkers and retain the judgment that there is exactly one person in circumstances where we take there to be just one. The immaterialist also has the resources to plausibly analyze thought experiments, such as cerebrum-swap cases, that threaten materialist ontologies. All things considered, it remains to be seen which personal ontology has the most evidence in its favor. In the context of debates that arise from material object metaphysics, however, evidence weighs in favor of immaterialism. Materialist personal ontologies are saddled with unacceptable responses to metaphysical puzzles, and endorsing materialism about persons requires taking on a very high cost: Either there are far more of us than we ordinarily take there to be, or there are no persons – far fewer of us than we ordinarily take there to be. Some might argue that these are the only acceptable options, so cost be damned. But we cannot afford to be so cavalier about our personal ontology. Instead, I advance immaterialist solutions to puzzles in personal ontology and propose that, in the interest of saving ourselves and everyone we love, we should seriously consider accounts according to which we are immaterial entities. (shrink)

The collaboration of Language and Computing nv (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is guided by the hypothesis that quality constraints on ontologies for software ap-plication purposes closely parallel the constraints salient to the design of sound philosophical theories. The extent of this parallel has been poorly appreciated in the informatics community, and it turns out that importing the benefits of phi-losophical insight and methodology into application domains yields a variety of improvements. L&C’s (...) LinKBase® is one of the world’s largest medical domain ontologies. Its current primary use pertains to natural language processing ap-plications, but it also supports intelligent navigation through a range of struc-tured medical and bioinformatics information resources, such as SNOMED-CT, Swiss-Prot, and the Gene Ontology (GO). In this report we discuss how and why philosophical methods improve both the internal coherence of LinKBase®, and its capacity to serve as a translation hub, improving the interoperability of the ontologies through which it navigates. (shrink)

In this paper, I develop a criticism to a method for metaontology, namely, the idea that a discourse’s or theory’s ontological commitments can be read off its sentences’ truth- conditions. Firstly, I will put forward this idea’s basis and, secondly, I will present the way Quine subscribed to it. However, I distinguish between two readings of Quine’s famous ontological criterion, and I center the focus on the one currently dubbed “ontological minimalism”, a kind of modern Ockhamism applied to the (...) mentioned metaontological view. I show that this view has a certain application via Quinean thesis of reference inscrutability but that it is not possible to press that application any further and, in particular, not for the ambitious metaontological task some authors try to employ. The conclusion may sound promising: having shown the impossibility of a semantic ontological criterion, intentionalist or subjectivist ones should be explored. (shrink)

We propose a formal framework to examine the relationship between models and observations. To make our analysis precise,models are reduced to first-order theories that represent both terminological knowledge – e.g., the laws that are supposed to regulate the domain under analysis and that allow for explanations, predictions, and simulations – and assertional knowledge – e.g., information about specific entities in the domain of interest. Observations are introduced into the domain of quantification of a distinct first-order theory that describes their nature (...) and their organization and takes track of the way they are experimentally acquired or intentionally elaborated. A model mainly represents the theoretical knowledge or hypotheses on a domain, while the theory of observations mainly represents the empirical knowledge and the given experimental practices. We propose a precise identity criterion for observations and we explore different links between models and observations by assuming a degree of independence between them. By exploiting some techniques developed in the field of social choice theory and judgment aggregation, we sketch some strategies to solve inconsistencies between a given set of observations and the assumed theoretical hypotheses. The solutions of these inconsistencies can impact both the observations – e.g., the theoretical knowledge and the analysis of the way observations are collected or produced may highlight some unreliable sources – and the models – e.g. empirical evidences may invalidate some theoretical laws. (shrink)

Equipped with the ultimate query answering system, computers would finally be in a position to address all our information needs in a natural way. In this paper, we describe how Language and Computing nv (L&C), a developer of ontology-based natural language understanding systems for the healthcare domain, is working towards the ultimate Question Answering (QA) System for healthcare workers. L&C’s company strategy in this area is to design in a step-by-step fashion the essential components of such a system, each (...) component being designed to solve some one part of the total problem and at the same time reflect well-defined needs on the prat of our customers. We compare our strategy with the research roadmap proposed by the Question Answering Committee of the National Institute of Standards and Technology (NIST), paying special attention to the role of ontology. (shrink)

The pathbreaking scientific advances of recent years call for a new philosophical consideration of the fundamental categories of biology and its neighboring disciplines. Above all, the new information technologies used in biomedical research, and the necessity to master the continuously growing flood of data that is associated therewith, demand a profound and systematic reflection on the systematization and classification of biological data. This, however, demands robust theories of basic concepts such as kind, species, part, whole, function, process, fragment, sequence, expression, (...) boundary, locus, environment, system, and so on. Concepts which belong to the implicit stock of knowledge of every biologist. They amount to a dimension of biological reality which remains constant in the course of biological evolution and whose theoretical treatment requires contemporary analogues of the tools developed in traditional Aristotelian metaphysics. To provide the necessary theories and definitions is a task for philosophy, which is thus called upon to play an important role as intermediary between biology and informatics. (shrink)

This study asserts that W.V.O. Quine’s eliminative philosophical gaze into mereological composition affects inevitably his interpretations of composition theories of ontology. To investigate Quine’s property monism from the account of modal eliminativism, I applied to his solution for the paradoxes of de re modalities’ . Because of its vital role to figure out how dispositions are encountered by Quine, it was significantly noted that the realm of de re modalities doesn’t include contingent and impossible inferences about things. Therefore, (...) for him, all the intrinsic forces and elements of entities such as powers and causal or teleological dispositions for ontology demand to be seen necessarily as bound variables from a monist perspective. Although his denial of analyticity and the elimination of dispositional field of ontology, S. Mumford criticizes the monist perspective of Quine’s paradoxical approach to superveniences. Because superveniences create problems while determining type-type identities from a monist mereological perspective. It is observed that Quine faces with a reduction again in terms of his dispositional monism despite his critiques to repulse vagueness from the ontology in his well-known article Two Dogmas of Empiricism. -/- . (shrink)

A new book by Timothy Morton, Humankind: Solidarity with Nonhuman People, is reviewed. Humankind: Solidarity with Nonhuman People is a project into the applied political ethics that emerge between speculative realism and Marxism. This book is intended to build on the object-oriented ontology that Morton has espoused in previous volumes, however with a greater emphasis on normative politics. The book’s core methodology is to outline the various neologisms that Morton employs and incorporate those speculative realist terms into a (...) retooling of Marxist. The book dialogue prose is a poetic tour de force that is both academically and philosophically rigorous. Morton provides a novel reworking of Marxist theory that can exist on the cutting edge of continental philosophy. -/- . (shrink)

The Foundational Model of Anatomy (FMA) symbolically represents the structural organization of the human body from the macromolecular to the macroscopic levels, with the goal of providing a robust and consistent scheme for classifying anatomical entities that is designed to serve as a reference ontology in biomedical informatics. Here we articulate the need for formally clarifying the is-a and part-of relations in the FMA and similar ontology and terminology systems. We diagnose certain characteristic errors in the treatment of (...) these relations and show how these errors can be avoided through adoption of the formalism we describe. We then illustrate how a consistently applied formal treatment of taxonomy and partonomy can support the alignment of ontologies. (shrink)

Quality assurance in large terminologies is a difficult issue. We present two algorithms that can help terminology developers and users to identify potential mistakes. We demon­strate the methodology by outlining the different types of mistakes that are found when the algorithms are applied to SNOMED-CT. On the basis of the results, we argue that both formal logical and linguistic tools should be used in the development and quality-assurance process of large terminologies.

‘What is characteristic of every mental activity’, according to Brentano, is ‘the reference to something as an object. In this respect every mental activity seems to be something relational.’ But what sort of a relation, if any, is our cognitive access to the world? This question – which we shall call Brentano’s question – throws a new light on many of the traditional problems of epistemology. The paper defends a view of perceptual acts as real relations of a subject to (...) an object. To make this view coherent, a theory of different types of relations is developed, resting on ideas on formal ontology put forward by Husserl in his Logical Investigations and on the theory of relations sketched in my "Acta cum fundamentis in re". The theory is applied to the notion of a Cambridge change, which proves to have an unforeseen relevance to our understanding of perception. (shrink)

The paper is an exercise in descriptive ontology, with specific applications to problems in the geographical sphere. It presents a general typology of spatial boundaries, based in particular on an opposition between bona fide or physical boundaries on the one hand, and fiat or human-demarcation-induced boundaries on the other. Cross-cutting this opposition are further oppositions in the realm of boundaries, for example between: crisp and indeterminate, complete and incomplete, enduring and transient, symmetrical and asymmetrical. The resulting typology generates a (...) corresponding categorization of the different sorts of objects which (complete) boundaries determine or demarcate. The theory is applied first of all in the areas of geography and of administrative and property law. Indications are then given as to how the typology may be applied also in other fields where physical and fiat boundaries are at work, including the field of cognitive linguistics and the related field of the ontology of truth. (shrink)

Statements about the behavior of biochemical entities (e.g., about the interaction between two proteins) abound in the literature on molecular biology and are increasingly becoming the targets of information extraction and text mining techniques. We show that an accurate analysis of the semantics of such statements reveals a number of ambiguities that have to be taken into account in the practice of biomedical ontology engineering: Such statements can not only be understood as event reporting statements, but also as ascriptions (...) of dispositions or tendencies that may or may not refer to collectives of interacting molecules or even to collectives of interaction events. (shrink)

In their paper “Sixteen Days” Barry Smith and Berit Brogaard try to answer the question: when does a human being begin to exist? In this paper we will address some methodological issues connected with this exercise in ontology. We shall begin by sketching the argument of “Sixteen Days”. We shall then attempt to characterize what is special about the ontological realism of “Sixteen Days” as contrasted to the linguistic constructivism which represents the more dominant current in contemporary analytic philosophy. (...) This will allow us to infer guidelines for assessing the quality of ontological theories of various types. We shall argue that ontological parsimony, groundedness, faithfulness to ordinary language, consistency with science, coherence, and fruitfulness are at least part of the adequacy criteria for such theories. These criteria will then be applied to the theory presented in “Sixteen Days”, and they will lead us to some revisions of this theory as well as to some reflections on its ethical implications. (shrink)