The promotion of patient welfare is a central goal of medical professionals and serves as a fundamental principle of medical professionalism. Despite its importance, however, it is unclear what is meant by patient welfare. In my dissertation, I explore patient welfare by analyzing the ordinary notion of welfare and applying this analysis to the patient population. I argue that welfare is best understood and expressed in terms of capabilities, which I define using the structure and vocabulary of Basic Formal (...) class='Hi'>Ontology. I conclude that patient welfare is a multi-dimensional quality of the human organism corresponding to the degree to which that patient has realized the array of capabilities typical of the human kind. I then identify certain important implications for this view on the practice of medicine. (shrink)

As engineering applications require management of ever larger volumes of data, ontologies offer the potential to capture, manage, and augment data with the capability for automated reasoning and semantic querying. Unfortunately, considerable barriers hinder wider deployment of ontologies in engineering. Key among these is lack of a shared top-level ontology to unify and organise disparate aspects of the field and coordinate co-development of orthogonal ontologies. As a result, many engineering ontologies are limited to their scope, and functionally difficult to (...) extend or interoperate with other engineering ontologies. This paper demonstrates how the use of a top-level ontology, specifically the Basic Formal Ontology (BFO), greatly facilitates interoperability of multiple engineering-related ontologies. We constructed a system of formal linked ontologies by re-engineering legacy ontologies to be conformant with BFO and developing new BFO-conformant ontologies to capture knowledge in the engineering design, enterprise, human factors, manufacturing, and application domain of additive manufacturing. The resulting Integrated Framework for Additively Manufactured Products (IFAMP), including the body knowledge instantiated on its basis, serve as the basis for a proposed Design with Additive Manufacturing Method (DWAM), which we believe can support the design of innovative products with semantically enhanced ideation tools and enhanced access to application domain knowledge. The method and its facilitation through the ontological framework are demonstrated using a case study in medicine. (shrink)

When approaching the nature and etiology of psychophysical problems in a given population, it is important to understand the causal relations, the mechanisms, and the processes which underlie given problems, issues, and disorders. This examination attempts to investigate the connection between neural pathophysiology and proprioceptive ontology of olfactory and visual cortical circuitry on the basis of the current scientific evidence indicated by the results of studies in which subjects underwent a series of therapeutic modalities focused on the improvement of (...) overall wellbeing with the utilization of devices and technologies to stimulate multiple motor vs. somatosensory processes. More specifically, the studies at the centers of this analysis incorporated physical movement and virtual reality interactions, with the supplement of olfactory stimulation. In this examination, such research is also investigated from a theoretical standpoint, with the ultimate goal to better determine which interventions are justified under the premise of a mutual support between empirical values (through laboratory examination) and logical deduction (via philosophical investigation). (shrink)

One way to detect, monitor and prevent adverse events with the help of Information Technology is by using ontologies capable of representing three levels of reality: what is the case, what is believed about reality, and what is represented. We report on how Basic Formal Ontology and Referent Tracking exhibit this capability and how they are used to develop an adverse event ontology and related data annotation scheme for the European ReMINE project.

In this article, I present a new interpretation of the pro-life view on the status of early human embryos. In my understanding, this position is based not on presumptions about the ontological status of embryos and their developmental capabilities but on the specific criteria of rational decisions under uncertainty and on a cautious response to the ambiguous status of embryos. This view, which uses the decision theory model of moral reasoning, promises to reconcile the uncertainty about the ontological status of (...) embryos with the certainty about normative obligations. I will demonstrate that my interpretation of the pro-life view, although seeming to be stronger than the standard one, has limited scope and cannot be used to limit destructive research on human embryos. (shrink)

We propose a definition of capability as a class intermediate between function and disposition as the latter are defined in Basic Formal Ontology (BFO). A disposition inheres in a material entity and is realized in a certain kind of process. An example is the disposition of a glass to break when struck, which is realized when it shatters. A function is a disposition which is (simply put) the rationale for the existence of its bearer. To say for example that (...) a water pump has the function to pump water is to say that the pump exists because something was needed that would pump water. Capabilities are a special sort of disposition in that that, like functions, they can be evaluated on the basis of how well they are realized. They differ from functions in that their realizations are not the rationale – not the primary reason – for the existence of their bearers. Thus, a water pump may have many capabilities, including to be weatherproof, to run without lubricant, and so forth, but only one function. All functions are capabilities on the view we defend, but not all capabilities are functions. We develop a series of axioms to distinguish capabilities formally from both dispositions and functions and provide examples of the use of ‘capability’ in a variety of domains. (shrink)

This paper compares the capability approach (CA) and libertarian paternalism (LP) to see whether they are compatible. The comparison focuses on rationality, wellbeing, and freedom. The main theoretical framework is Sen’s ‘reason to value’ (RtV). The relevance of this to CA, and LP is analysed, and whether the primacy that CA and LP both accord to reason leads to paternalism is examined. Although the principal focus is on Sen’s, Sunstein’s and Thaler’s original ideas, their key concepts are analysed in the (...) context of the contemporary critical literature on the topic. This critical analysis not only makes it possible to assess whether CA and LP are compatible, but also to see how they perceive rationality, wellbeing, and freedom. The critical analysis further differentiates the various interpretations of RtV in the literature and explains how CA and LP function. (shrink)

A principal rationale for public policy is to address market failures. Pareto efficiency is therefore a highly common and relatively non-controversial evaluative criterion for many policy analyses and is discussed at length in policy analysis texts. This makes sense, for Pareto improvements involve making at least one person better off without making anyone worse off. Who could object to that? But does efficiency deserve the prominence it enjoys in public policy? Is one policy option better than another, at least in (...) one respect, simply because it is more Pareto efficient? Or, is efficiency valuable for some other reason? In this chapter, I discuss Pareto efficiency as an evaluative criterion and argue that it is a stand-in for a more foundational criterion: wellbeing. I begin with an overview of Pareto efficiency, discuss the various ways in which it is operationalized to evaluate policy options, and argue that it is valuable insofar as more efficient states of affairs promise more wellbeing than less efficient states of affairs. I then raise questions regarding whether the conception of wellbeing presupposed by Pareto efficiency – preference satisfaction – is a defensible conception of wellbeing. I go on to introduce three alternative conceptions of wellbeing which have been proposed and defended by both philosophers and policy scholars, namely, hedonism, objective goods views, and the capability approach, and suggest ways in which each can be operationalized as an evaluative criterion. I close by discussing four ‘theory-free’ approaches to thinking about the impact of policies on the quality of people’s lives. Such approaches reject the idea that there is one single theory of wellbeing that should be used to evaluate policy options, and instead develop ways to evaluate the impact of policies on people’s lives that are not grounded in a specific theory. (shrink)

Biomedical ontologies exist to serve integration of clinical and experimental data, and it is critical to their success that they be put to widespread use in the annotation of data. How, then, can ontologies achieve the sort of user-friendliness, reliability, cost-effectiveness, and breadth of coverage that is necessary to ensure extensive usage? Methods: Our focus here is on two different sets of answers to these questions that have been proposed, on the one hand in medicine, by the SNOMED CT community, (...) and on the other hand in biology, by the OBO Foundry. We address more specifically the issue as to how adherence to certain development principles can advance the usability and effectiveness of an ontology or terminology resource, for example by allowing more accurate maintenance, more reliable application, and more efficient interoperation with other ontologies and information resources. Results: SNOMED CT and the OBO Foundry differ considerably in their general approach.Nevertheless, a general trend towards more formal rigor and cross-domain interoperability can be seen in both and we argue that this trend should be accepted by all similar initiatives in the future. Conclusions: Future efforts in ontology development have to address the need for harmonization and integration of ontologies across disciplinary borders, and for this, coherent formalization of ontologies is a prerequisite. (shrink)

Breeders of purebred dogs usually have several goals they want to accomplish, of which canine wellbeing is one. The purpose of this article is to investigate what we ought to do given this goal. Breeders typically think that they fulfil their wellbeing-related duties by doing the best they can within their breed of choice. However, it is true of most breeders that they could produce physically and mentally healthier dogs if they switched to a healthier breed. There are a few (...) breeds that are healthier than other breeds as well as mutts; we could maximize wellbeing for the next generations by focusing all our breeding resources on those. However, in the long run such a strategy would severely deplete the canine gene pool. If we are to breed for wellbeing in the long run, we must thus weigh the benefits of selection against physical and mental problems against the benefits of genetic diversity. The optimal breeding strategy for canine wellbeing is to preserve many breeds, though not all of them. Furthermore, we ought to combine strict health programs with looser barriers between breeds. Such a policy conflicts with the goal of breed preservation, at least if we think of breeds as populations registered within kennel clubs rather than types of dogs, but not with the goal of producing good working dogs capable of performing various tasks. (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)

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)

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

Programming artificial intelligence to make fairness assessments of texts through top-down rules, bottom-up training, or hybrid approaches, has presented the challenge of defining cross-cultural fairness. In this paper a simple method is presented which uses vectors to discover if a verb is unfair or fair. It uses already existing relational social ontologies inherent in Word Embeddings and thus requires no training. The plausibility of the approach rests on two premises. That individuals consider fair acts those that they would be willing (...) to accept if done to themselves. Secondly, that such a construal is ontologically reflected in Word Embeddings, by virtue of their ability to reflect the dimensions of such a perception. These dimensions being: responsibility vs. irresponsibility, gain vs. loss, reward vs. sanction, joy vs. pain, all as a single vector. The paper finds it possible to quantify and qualify a verb as fair or unfair by calculating the cosine similarity of the said verb’s embedding vector against FairVec—which represents the above dimensions. We apply this to Glove and Word2Vec embeddings. Testing on a list of verbs produces an F1 score of 95.7, which is improved to 97.0. Lastly, a demonstration of the method’s applicability to sentence measurement is carried out. (shrink)

We propose capability as a universal or type intermediate between function and disposition. A capability is, broadly speaking, a disposition that is of a type whose instances can be evaluated on the basis of how well they are realized. A function, on the view we are proposing, is a capability the possession of which is the rationale for the existence of its bearer. To say for example that a water pump has the function to pump water is to say that (...) the pump exists because something was needed that would pump water. A water pump may have many capabilities, including: to be weatherproof, to run without lubricant, to be transportable, and so forth. But its function is to pump water. We focus here on capabilities possessed by humans – such as piano playing or language using – and we explore the relation between capabilities of these sorts and structures in the brain. (shrink)

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

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

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

Over the last two decades, the capabilities approach has become an increasingly influential theory of development. It conceptualises human wellbeing in terms of an individual's ability to achieve functionings we have reason to value. In contrast, the African ethic of ubuntu views human flourishing as the propensity to pursue relations of fellowship with others, such that relationships have fundamental value. These two theoretical perspectives seem to be in tension with each other; while the capabilities approach focuses on individuals as the (...) locus of ethical value, an ubuntu ethic concentrates on the relations between individuals. In this article, we ask: to what extent is the capabilities approach compatible with this African ethical theory? We argue that, on reflection, relations play a much stronger role in the capabilities approach than often assumed. There is good reason to believe that relationality is part of the concept of a capability itself, where such relationality has intrinsic ethical value. This understanding of the ethical centrality of relations grounds new normative perspectives on the capabilities approach, and offers a more comprehensive grasp of the relevance of relationships to empirical enquiry. (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)

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

We present a novel methodology for calculating the improvements obtained in successive versions of biomedical ontologies. The theory takes into account changes both in reality itself and in our understanding of this reality. The successful application of the theory rests on the willingness of ontology authors to document changes they make by following a number of simple rules. The theory provides a pathway by which ontology authoring can become a science rather than an art, following principles analogous to (...) those that have fostered the growth of modern evidence-based medicine. Although in this paper we focus on ontologies, the methodology can be generalized to other sorts of terminology-based artifacts, including Electronic Patient Records. (shrink)

Basic Formal Ontology (BFO) is a top-level ontology consisting of thirty-six classes, designed to support information integration, retrieval, and analysis across all domains of scientific investigation, presently employed in over 350 ontology projects around the world. BFO is a genuine top-level ontology, containing no terms particular to material domains, such as physics, medicine, or psychology. In this paper, we demonstrate how a series of cases illustrating common types of change may be represented by universals, defined classes, (...) and relations employing the BFO framework. We provide discussion of these cases to provide a template for other ontologists using BFO, as well as to facilitate comparison with the strategies proposed by ontologists using different top-level ontologies. (shrink)

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

Evidence based medicine (EBM) is under critical debate, and person centered healthcare (PCH) has been proposed as an improvement. But is PCH offered as a supplement or as a replacement of EBM? Prima facie PCH only concerns the practice of medicine, while the contended features of EBM also include methods and medical model. I here argue that there are good philosophical reasons to see PCH as a radical alternative to the existing medical paradigm of EBM, since the two seem committed (...) to conflicting ontologies. This paper aims to make explicit some of the most fundamental assumptions that motivate EBM and PCH, respectively, in order to show that the choice between them ultimately comes down to ontological preference. While EBM has a solid foundation in positivism, or what I here call Humeanism, PCH is more consistent with causal dispositionalism. I conclude that if there is a paradigmatic revolution on the way in medicine, it is first of all one of ontology. (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)

In intelligence, the ontological problem is related to the nature and characteristics of entities that threaten and are threatened. Developing a threat ontology requires a taxonomy. An ontology for threat analysis and action must be able to shape ontological distinctions between potential and viable threats. This provides a better understanding of how threats (ie intentions, capabilities, and opportunities) can exist and can be changed over time. Escalating threats from a state of potency to a state of viability could (...) be avoided by using appropriate threat mitigation techniques. DOI: 10.13140/RG.2.2.25163.54569 . (shrink)

Achieving space situational awareness requires, at a minimum, the identification, characterization, and tracking of space objects. Leveraging the resultant space object data for purposes such as hostile threat assessment, object identification, and conjunction assessment presents major challenges. This is in part because in characterizing space objects we reference a variety of identifiers, components, subsystems, capabilities, vulnerabilities, origins, missions, orbital elements, patterns of life, operational processes, operational statuses, and so forth, which tend to be defined in highly heterogeneous and sometimes inconsistent (...) ways. The Space Domain Ontologies are designed to provide a consensus-based realist framework for formulating such characterizations in a way that is both consistent and computable. Space object data are aligned with classes and relations in a suite of ontologies built around the existing Space Object Ontology. They are stored in a dynamically updated Resource Description Framework triple store, which can be queried to support space situational awareness and the needs of spacecraft operators and analysts. This paper provides an overview of the Space Domain Ontologies and their development and use. It presents the motivation for and advantages of the Space Domain Ontologies, including the benefits they provide for enhancing and maintaining long-term space situational awareness. (shrink)

Based on the Ontology for General Medical Science, we propose definitions for biomarkers of various types of. These definitions provide not only a complete formal representation of what biomarkers are according to the Institute of Medicine (IOM), but also remove the ambiguities and inconsistencies encountered in the documentation provided by the IOM.

The work of Gregory Bateson offers a metaphysical basis for a “process psychology,” that is, a view of psychological practice and research guided by an ontology of becoming—identifying change, difference, and relationship as the basic elements of a foundational metaphysics. This article explores the relevance of Bateson's recursive epistemology, his re-conception of the Great Chain of Being, a first-principles approach to defining the nature of mind, and understandings of interaction and difference, pattern and symmetry, interpretation and context. Bateson's philosophical (...) contributions will be drawn into relationship with Wittgenstein's philosophy of language as use, Melnyk's theory of causal levels of explanation, Korzybski's account of map and territory, the rejection of the heuristic rigidity of substantialist ontologies, and a cybernetics communication science-informed approach to contextual bi-directionality of causality. We thereby arrive at an understanding of Bateson's process psychology that, given its ecological-systemic nature, is explanatorily applicable across the mind sciences. This process psychology equips us to answer the question: What is mind? Not by explanatory appeal to substantial entities contained within mind, but instead by recourse to the contextually relevant patterns for understanding mind to a particular purpose. We have thereby attended to the gulf between heuristics and fundamentals, between psychological models and an onto-epistemic account of reality. Insufficient attention has been given to characterising the vital nature of Bateson's philosophical oeuvre to psychological practice. This article draws out Bateson's relevance to establishing foundational principles for a process psychology capable of reinvigorating psychological thought. (shrink)

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

Background: Systematized Nomenclature of Medicine—Clinical Terms (SNOMED CT, hereafter abbreviated SCT) is acomprehensive medical terminology used for standardizing the storage, retrieval, and exchange of electronic healthdata. Some efforts have been made to capture the contents of SCT as Web Ontology Language (OWL), but theseefforts have been hampered by the size and complexity of SCT. Method: Our proposal here is to develop an upper-level ontology and to use it as the basis for defining the termsin SCT in a way (...) that will support quality assurance of SCT, for example, by allowing consistency checks ofdefinitions and the identification and elimination of redundancies in the SCT vocabulary. Our proposed upper-levelSCT ontology (SCTO) is based on the Ontology for General Medical Science (OGMS). Results: The SCTO is implemented in OWL 2, to support automatic inference and consistency checking. Theapproach will allow integration of SCT data with data annotated using Open Biomedical Ontologies (OBO) Foundryontologies, since the use of OGMS will ensure consistency with the Basic Formal Ontology, which is the top-levelontology of the OBO Foundry. Currently, the SCTO contains 304 classes, 28 properties, 2400 axioms, and 1555annotations. It is publicly available through the bioportal athttp://bioportal.bioontology.org/ontologies/SCTO/. Conclusion: The resulting ontology can enhance the semantics of clinical decision support systems and semanticinteroperability among distributed electronic health records. In addition, the populated ontology can be used forthe automation of mobile health applications. (shrink)

Ontology is a burgeoning field, involving researchers from the computer science, philosophy, data and software engineering, logic, linguistics, and terminology domains. Many ontology-related terms with precise meanings in one of these domains have different meanings in others. Our purpose here is to initiate a path towards disambiguation of such terms. We draw primarily on the literature of biomedical informatics, not least because the problems caused by unclear or ambiguous use of terms have been there most thoroughly addressed. We (...) advance a proposal resting on a distinction of three levels too often run together in biomedical ontology research: 1. the level of reality; 2. the level of cognitive representations of this reality; 3. the level of textual and graphical artifacts. We propose a reference terminology for ontology research and development that is designed to serve as common hub into which the several competing disciplinary terminologies can be mapped. We then justify our terminological choices through a critical treatment of the ‘concept orientation’ in biomedical terminology research. (shrink)

When and why does awareness of a belief's genealogy render it irrational to continue holding that belief? According to explanationism, awareness of a belief’s genealogy gives rise to an epistemic defeater when and because it reveals that the belief is not explanatorily connected to the relevant worldly facts. I argue that an influential recent version of explanationism, due to Korman and Locke, incorrectly implies that it is not rationally permissible to adopt a “sparse” ontology of worldly facts or states (...) of affairs. I then propose a new explanationist account of genealogical defeat capable of accommodating rational belief in ontological sparsity. According to my account, awareness of a belief’s genealogy gives rise to a defeater when and because it reveals that the belief is not explanatorily connected to its truthmaker. (shrink)

We present a novel methodology for calculating the improvements obtained in successive versions of biomedical ontologies. The theory takes into account changes both in reality itself and in our understanding of this reality. The successful application of the theory rests on the willingness of ontology authors to document changes they make by following a number of simple rules. The theory provides a pathway by which ontology authoring can become a science rather than an art, following principles analogous to (...) those that have fostered the growth of modern evidence-based medicine. Although in this paper we focus on ontologies, the methodology can be generalized to other sorts of terminology-based artifacts, including Electronic Patient Records. (shrink)

Evidence-based medicine relies on the execution of clinical practice guidelines and protocols. A great deal of of effort has been invested in the development of various tools which automate the representation and execution of the recommendations contained within such guidelines and protocols by creating Computer Interpretable Guideline Models (CIGMs). Context-based task ontologies (CTOs), based on standard terminology systems like UMLS, form one of the core components of such a model. We have created DAML+OIL-based CTOs for the tasks mentioned in the (...) WHO guideline for hypertension management, drawing comparisons also with other related guidelines. The advantages of CTOs include: contextualization of ontologies, providing ontologies tailored to specific aspects of the phenomena of interest, dividing the complexity involved in creating ontologies into different levels, providing a methodology by means of which the task recommendations contained within guidelines can be integrated into the clinical practices of a health care set-up. (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)

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

Through this contribution I aim to explore the horizons and limits of digital medicine in light of an embodied approach to the issue of care. I will sketch the historical background of digital medicine and show the contemporary status of this interdisciplinary field, as well as its applications and outcomes. Then, I will address a critique of the computational theory of mind (CTM) upon which many contemporary mental health apps are designed. This approach to the mind is inscribed into the (...) modern trend of neuromania, which conceives the embodied, living human being as a mere series of data analyses and algorithms, with the brain as the seat of the person. Drawing on continental philosophy and classical phenomenology I will develop a notion of health conceived as a moral enterprise, showing how wellbeing and vitality are not reducible to a product made by technologies or doctors, but rather they are the results of an embodied encounter. As such, empathy and person-centered care cannot be achieved by digital medicine. They are the result of a journey into the regions of recognition, embodied presence and the aliveness constituting the person. Finally, I will show how the issue of care cannot be separated from an embodied encounter between people, especially in case of dementia. (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)

In this article, we deal with the evaluation of the losses suffered by persons living in urban areas as a result of energy services. In the first part, we analyse how by adopting different informational foci we obtain contrasting interpersonal evaluations regarding the same loss. In the second part, we distinguish between a diachronic and a hypothetical/moralised threshold for harm in order to assess whether individuals are benefiting from or being harmed by a given energy service. Our argument is that (...) the most accurate evaluation of an individual damage caused by an energy service can be obtained by using capabilities as informational focus, instead of realised wellbeing or means to wellbeing, and by interpreting the loss in relation to a hypothetical/moralised threshold that corresponds to a list of central capabilities. In the last part, we address monetary and non-monetary compensations for a loss that is evaluated in terms of capabilities. Accordingly, we expound how compensation policies can either restore the capabilities lost due to energy services or monetarily compensate the individual for the fact that a given capability (or set of capabilities) has been irremediably lost. (shrink)

Achieving space domain awareness requires the identification, characterization, and tracking of space objects. Storing and leveraging associated space object data for purposes such as hostile threat assessment, object identification, and collision prediction and avoidance present further challenges. Space objects are characterized according to a variety of parameters including their identifiers, design specifications, components, subsystems, capabilities, vulnerabilities, origins, missions, orbital elements, patterns of life, processes, operational statuses, and associated persons, organizations, or nations. The Space Object Ontology provides a consensus-based realist (...) framework for formulating such characterizations in a computable fashion. Space object data are aligned with classes and relations in the Space Object Ontology and stored in a dynamically updated Resource Description Framework triple store, which can be queried to support space domain awareness and the needs of spacecraft operators. This paper presents the core of the Space Object Ontology, discusses its advantages over other approaches to space object classification, and demonstrates its ability to combine diverse sets of data from multiple sources within an expandable framework. Finally, we show how the ontology provides benefits for enhancing and maintaining longterm space domain awareness. (shrink)

Justice for children and during childhood and the particular political, social and moral status of children has long been a neglected issue in ethics, and in social and political philosophy. The application of general, adult-oriented theories of justice to children can be regarded as particularly problematic. Philosophers have only recently begun to explore what it means to consider children as equals, what goods are especially valuable to them, and what are the obligations of justice different agents have toward children. In (...) addition, while philosophers have extensively written about global poverty and inequality, the issue of disadvantages during childhood, especially child poverty, has only been superficially addressed. This also applies to the Capability Approach (CA) as a normative theory. Although the socio-scientific and economic literature on how to conceptualize capabilities and functionings of children and how to measure them in the context of poverty and wellbeing is steadily growing, the normative aspects of these issues are still under-theorized. The CA offers a unique framework to engage with both the topic of justice for children and questions concerning what justice implies and demands with regard to children living and growing up in disadvantaged circumstances. Furthermore, justice and disadvantage during childhood is a compellingly interdisciplinary topic that invites the combination of ethical and philosophical reasoning together with socio-scientific theories and empirical knowledge. In this special issue of Ethical Perspectives we bring together theoretical and empirically informed discussions that explore the CA in relation to children and the many disadvantages they can face in their lives. (shrink)

The meeting focused on uses of ontologies, with a special focus on spatial ontologies, in addressing the ever increasing needs faced by biology and medicine to cope with ever expanding quantities of data. To provide effective solutions computers need to integrate data deriving from myriad heterogeneous sources by bringing the data together within a single framework. The meeting brought together leaders in the field of what are called "top-level ontologies" to address this issue, and to establish strategies among leaders in (...) the field of biomedical ontology for the creation of interoperable biomedical ontologies which will serve the goal of useful data integration. (shrink)

The automatic integration of rapidly expanding information resources in the life sciences is one of the most challenging goals facing biomedical research today. Controlled vocabularies, terminologies, and coding systems play an important role in realizing this goal, by making it possible to draw together information from heterogeneous sources – for example pertaining to genes and proteins, drugs and diseases – secure in the knowledge that the same terms will also represent the same entities on all occasions of use. In the (...) naming of genes, proteins, and other molecular structures, considerable efforts are under way to reduce the effects of the different naming conventions which have been spawned by different groups of researchers. Electronic patient records, too, increasingly involve the use of standardized terminologies, and tremendous efforts are currently being devoted to the creation of terminology resources that can meet the needs of a future era of personalized medicine, in which genomic and clinical data can be aligned in such a way that the corresponding information systems become interoperable. (shrink)

The National Cancer Institute’s Thesaurus (NCIT) has been created with the goal of providing a controlled vocabulary which can be used by specialists in the various sub-domains of oncology. It is intended to be used for purposes of annotation in ways designed to ensure the integration of data and information deriving from these various sub-domains, and thus to support more powerful cross-domain inferences. In order to evaluate its suitability for this purpose, we examined the NCIT’s treatment of the kinds of (...) entities which are fundamental to an ontology of colon carcinoma. We here describe the problems we uncovered concerning classification, synonymy, relations and definitions, and we draw conclusions for the work needed to establish the NCIT as a reference ontology for the cancer domain in the future. (shrink)

Digital me ontology and ethics. 21 December 2020. -/- Ljupco Kocarev and Jasna Koteska. -/- This paper addresses ontology and ethics of an AI agent called digital me. We define digital me as autonomous, decision-making, and learning agent, representing an individual and having practically immortal own life. It is assumed that digital me is equipped with the big-five personality model, ensuring that it provides a model of some aspects of a strong AI: consciousness, free will, and intentionality. As (...) computer-based personality judgments are more accurate than those made by humans, digital me can judge the personality of the individual represented by the digital me, other individuals’ personalities, and other digital me-s. We describe seven ontological qualities of digital me: a) double-layer status of Digital Being versus digital me, b) digital me versus real me, c) mind-digital me and body-digital me, d) digital me versus doppelganger (shadow digital me), e) non-human time concept, f) social quality, g) practical immortality. We argue that with the advancement of AI’s sciences and technologies, there exist two digital me thresholds. The first threshold defines digital me having some (rudimentarily) form of consciousness, free will, and intentionality. The second threshold assumes that digital me is equipped with moral learning capabilities, implying that, in principle, digital me could develop their own ethics which significantly differs from human’s understanding of ethics. Finally we discuss the implications of digital me metaethics, normative and applied ethics, the implementation of the Golden Rule in digital me-s, and we suggest two sets of normative principles for digital me: consequentialist and duty based digital me principles. -/- Authors are ordered alphabetically and equally contributed to the paper. (shrink)

Extensionalism is, roughly, the view that perception occurs in episodes that are temporally extended (and thus capable of accomodating in their entirety phenomena taking a nonzero lapse of time to occur). This view is widely acknowledged to be incompatible with thin presentism, the second most popular position in temporal ontology. In this paper, I argue that extensionalism is also incompatible with several other positions in temporal ontology, namely those positing the existence of non-present times that host sentience—positions I (...) collectively refer to as the sentient non-present view. Most notably, extensionalism proves to be incompatible with B-theoretical eternalism, which is the most popular position in temporal ontology. (shrink)

Intelligent neurotechnology is an emerging field that combines neurotechnologies like brain-computer interface (BCI) with artificial intelligence. This paper introduces a capability framework to assess the responsible use of intelligent BCI systems and provide practical ethical guidance. It proposes two tests, the threshold and flourishing tests, that BCI applications must meet, and illustrates them in a series of cases. After a brief introduction (Section 1), Section 2 sets forth the capability view and the two tests. It illustrates the threshold test using (...) examples from clinical medicine of BCI applications that enable patients with profound disabilities to function at a threshold level through computer mediation. Section 3 illustrates the flourishing test by exploring possible future applications of BCI involving neuroenhancements for healthy people, using examples adapted from research currently underway in the US military. Section 3 applies a capability lens to a complex case involving dual effects, both therapeutic and non-therapeutic, showing how the threshold and flourishing tests resolve the case. Section 4 replies to three objections: neurorights are the best tool for assessing BCI; the two tests are moving targets; and the analysis utilizes a capability view to do work it is not designed for. The paper concludes that a capability view offers unique advantages and gives practical guidance for evaluating the responsible use of present and future BCI applications. Extrapolating from our analysis may help guide other emerging technologies, such as germline gene editing, expected to impact central human capabilities. (shrink)