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  1. Towards a dispositionalist (and unifying) account of addiction.Robert M. Kelly - 2023 - Theoretical Medicine and Bioethics 44 (1):21-40.
    Addiction theorists have often utilized the metaphor of the blind men and the elephant to illustrate the complex nature of addiction and the varied methodological approaches to studying it. A common purported upshot is skeptical in nature: due to these complexities, it is not possible to offer a unifying account of addiction. I think that this is a mistake. The elephant is real–there is a _there_ there. Here, I defend a dispositionalist account of addiction as _the systematic disposition to fail (...)
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  • BFO and DOLCE: So Far, So Close….Nicola Guarino - 2017 - Cosmos + Taxis 4 (4):10-18.
    A survey of the similarities and differences between BFO and DOLCE, and of the mutual interactions between Nicola Guarino and Barry Smith.
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  • The Industrial Ontologies Foundry (IOF) perspectives.Mohamed Karray, Neil Otte, Rahul Rai, Farhad Ameri, Boonserm Kulvatunyou, Barry Smith, Dimitris Kiritsis, Chris Will, Rebecca Arista & Others - 2021 - Proceedings: Industrial Ontology Foundry (IOF) Achieving Data Interoperability Workshop, International Conference on Interoperability for Enterprise Systems and Applications, Tarbes, France, March 17-24, 2020.
    In recent years there has been a number of promising technical and institutional developments regarding use of ontologies in industry. At the same time, however, most industrial ontology development work remains within the realm of academic research and is without significant uptake in commercial applications. In biomedicine, by contrast, ontologies have made significant inroads as valuable tools for achieving interoperability between data systems whose contents derive from widely heterogeneous sources. In this position paper, we present a set of principles learned (...)
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  • Ontology-based fusion of sensor data and natural language.Erik Thomsen & Barry Smith - 2018 - Applied ontology 13 (4):295-333.
    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 (...)
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  • Explaining ambiguity in scientific language.Beckett Sterner - 2022 - Synthese 200 (5):1-27.
    The idea that ambiguity can be productive in data science remains controversial. Efforts to make scientific publications and data intelligible to computers generally assume that accommodating multiple meanings for words, known as polysemy, undermines reasoning and communication. This assumption has nonetheless been contested by historians, philosophers, and social scientists, who have applied qualitative research methods to demonstrate the generative and strategic value of polysemy. Recent quantitative results from linguistics have also shown how polysemy can actually improve the efficiency of human (...)
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  • Coordinating dissent as an alternative to consensus classification: insights from systematics for bio-ontologies.Beckett Sterner, Joeri Witteveen & Nico Franz - 2020 - History and Philosophy of the Life Sciences 42 (1):1-25.
    The collection and classification of data into meaningful categories is a key step in the process of knowledge making. In the life sciences, the design of data discovery and integration tools has relied on the premise that a formal classificatory system for expressing a body of data should be grounded in consensus definitions for classifications. On this approach, exemplified by the realist program of the Open Biomedical Ontologies Foundry, progress is maximized by grounding the representation and aggregation of data on (...)
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  • Functions in Basic Formal Ontology.Andrew D. Spear, Werner Ceusters & Barry Smith - 2016 - Applied ontology 11 (2):103-128.
    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 (...)
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  • Formal ontologies in manufacturing.Emilio M. Sanfilippo, Yoshinobu Kitamura & Robert I. M. Young - 2019 - Applied ontology 14 (2):119-125.
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  • BFO: Basic Formal Ontology.J. Neil Otte, John Beverley & Alan Ruttenberg - 2022 - Applied ontology 17 (1):17-43.
    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 (...)
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  • An Ontological Approach to Representing the Product Life Cycle.J. Neil Otte, Dimitris Kiritsi, Munira Mohd Ali, Ruoyu Yang, Binbin Zhang, Ron Rudnicki, Rahul Rai & Barry Smith - 2019 - Applied ontology 14 (2):1-19.
    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 (...)
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  • Analytic Metaphysics versus Naturalized Metaphysics: The Relevance of Applied Ontology.Baptiste Le Bihan & Adrien Barton - 2021 - Erkenntnis 86 (1):21-37.
    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 (...)
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  • Mapping the Patient’s Experience: An Applied Ontological Framework for Phenomenological Psychopathology.Rasmus Rosenberg Larsen & Janna Hastings - 2020 - Phenomenology and Mind 18:200-219.
    Mental health research faces a suite of unresolved challenges that have contributed to a stagnation of research efforts and treatment innovation. One such challenge is how to reliably and validly account for the subjective side of patient symptomatology, that is, the patient’s inner experiences or patient phenomenology. Providing a structured, standardised semantics for patient phenomenology would enable future research in novel directions. In this contribution, we aim at initiating a standardized approach to patient phenomenology by sketching a tentative formalisation within (...)
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  • Making AI Meaningful Again.Jobst Landgrebe & Barry Smith - 2021 - Synthese 198 (March):2061-2081.
    Artificial intelligence (AI) research enjoyed an initial period of enthusiasm in the 1970s and 80s. But this enthusiasm was tempered by a long interlude of frustration when genuinely useful AI applications failed to be forthcoming. Today, we are experiencing once again a period of enthusiasm, fired above all by the successes of the technology of deep neural networks or deep machine learning. In this paper we draw attention to what we take to be serious problems underlying current views of artificial (...)
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  • A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology.Yongqun He, Hong Yu, Anthony Huffman, Asiyah Yu Lin, Darren A. Natale, John Beverley, Ling Zheng, Yehoshua Perl, Zhigang Wang, Yingtong Liu, Edison Ong, Yang Wang, Philip Huang, Long Tran, Jinyang Du, Zalan Shah, Easheta Shah, Roshan Desai, Hsin-hui Huang, Yujia Tian, Eric Merrell, William D. Duncan, Sivaram Arabandi, Lynn M. Schriml, Jie Zheng, Anna Maria Masci, Liwei Wang, Hongfang Liu, Fatima Zohra Smaili, Robert Hoehndorf, Zoë May Pendlington, Paola Roncaglia, Xianwei Ye, Jiangan Xie, Yi-Wei Tang, Xiaolin Yang, Suyuan Peng, Luxia Zhang, Luonan Chen, Junguk Hur, Gilbert S. Omenn, Brian Athey & Barry Smith - 2022 - Journal of Biomedical Semantics 13 (1):25.
    The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of developing effective and safe vaccines and drugs and to better understand coronaviruses and associated disease mechenisms it is necessary to integrate the large and exponentially growing body of heterogeneous coronavirus data. Ontologies play an important role in standard-based knowledge and data representation, integration, sharing, and analysis. Accordingly, we initiated the (...)
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  • Une ontologie dispositionnelle du risque.Olivier Grenier & Adrien Barton - 2021 - Lato Sensu: Revue de la Société de Philosophie des Sciences 8 (2):58-69.
    Risk is an ubiquitous entity in the biomedical domain. Thus, a coherent ontological characterization of risk, which can be used by informatical tools named "applied ontologies", is necessary to help with the exchange and the collection of data for clinical and research uses. We analyze some definitions of risk and draw two general characteristics that risks and dispositions share. We thus suggest that a risk is a disposition which has an undesirable realization for an agent. This definition conciliates the objective (...)
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  • Ontology: A Bridge between Bioethics and Data-Driven Inquiry.David Gordon Limbaugh, Peter Maloy Koch & Eric C. Merrell - 2021 - American Journal of Bioethics 21 (6):51-53.
    Pavarini et al. argue for the potential benefits of using games and other technologies to collect empirical data to enhance bioethics research. They propose a methodology called “design bioe...
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  • Advancing Methods in Empirical Bioethics: Bioxphi Meets Digital Technologies.Brian D. Earp, Ivar R. Hannikainen & Emilian Mihailov - 2021 - American Journal of Bioethics 21 (6):53-56.
    Historically, empirical research in bioethics has drawn on methods developed within the social sciences, including qualitative interviews, focus groups, ethnographic studies, and opinion surveys, t...
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  • Ontology of language, with applications to demographic data.S. Clint Dowland, Barry Smith, Matthew A. Diller, Jobst Landgrebe & William R. Hogan - 2023 - Applied ontology 18 (3):239-262.
    Here we present what we believe is a novel account of what languages are, along with an axiomatically rich representation of languages and language-related data that is based on this account. We propose an account of languages as aggregates of dispositions distributed across aggregates of persons, and in doing so we address linguistic competences and the processes that realize them. This paves the way for representing additional types of language-related entities. Like demographic data of other sorts, data about languages may (...)
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  • Cognitive metaphysics.Lieven Decock - 2018 - Frontiers in Psychology 11:1700.
    In recent years philosophers have been interested in the methodology of metaphysics. Most of these developments are related to formal work in logic or physics, often against the backdrop of the Carnap-Quine debate on ontology. Drawing on Quine’s later work, I argue that a psychological or cognitive perspective on metaphysical topics may be a valuable addition to contemporary metametaphysics. The method is illustrated by means of cognitive studies of the notions “identity,” “vagueness,” and “object” and is compared to other extant (...)
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  • Ontology Development Strategies and the Infectious Disease Ontology Ecosystem.Giacomo De Colle, Ali Hasanzadeh & John Beverley - 2023 - Proceedings of the International Conference on Biomedical Ontologies.
    After motivating a framework for evaluating top-down, middle-out, middle-in, and bottom-up ontology development strategies, we apply our framework to investigate whether infectious disease ontologies - specifically, the Virus Infectious Disease Ontology (VIDO) and the Coronavirus Infectious Disease Ontology (CIDO) - effectively promote semantic interoperability.
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  • Coordinating virus research: The Virus Infectious Disease Ontology.John Beverley, Shane Babcock, Gustavo Carvalho, Lindsay G. Cowell, Sebastian Duesing, Yongqun He, Regina Hurley, Eric Merrell, Richard H. Scheuermann & Barry Smith - 2024 - PLoS ONE 1.
    The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Rapid, accurate, and consistent interpretation of generated data is thereby of fundamental concern. Ontologies––structured, controlled, vocabularies––are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the COVID-19 research domain, by following principles of the Open Biological and Biomedical Ontology (OBO) Foundry and by reusing existing ontologies such as the Infectious Disease Ontology (...)
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  • ARGO: Arguments Ontology.John Beverley, Neil Otte, Francesco Franda, Brian Donohue, Alan Ruttenberg, Jean-Baptiste Guillion & Yonatan Schreiber - manuscript
    Although the last decade has seen a proliferation of ontological approaches to arguments, many of them employ ad hoc solutions to representing arguments, lack interoperability with other ontologies, or cover arguments only as part of a broader approach to evidence. To provide a better ontological representation of arguments, we present the Arguments Ontology (ArgO), a small ontology for arguments that is designed to be imported and easily extended by researchers who work in different upper-level ontology frameworks, different logics, and different (...)
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  • Ontology of finance: an introduction.Gloria Sansò & Barry Smith - 2023 - Rivista di Estetica 84 (3):3-6.
    One famous scene in The Wolf of Wall Street (2013) is the dialogue between the young Jordan Belfort (Leonardo DiCaprio) and the expert trader Mark Hanna (Matthew McConaughey). Hanna is complaining that the stock market is unpredictable; it’s “fugazi … it’s fairy dust. It doesn’t exist. It’s never landed. It is not matter. It’s not on the element chart. It’s not real”. But the fact that something is unpredictable and non-physical does not imply that it does not exist. On the (...)
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  • Formal Ontology.Jani Hakkarainen & Markku Keinänen - 2023 - Cambridge: Cambridge University Press.
    Formal ontology as a main branch of metaphysics investigates categories of being. In the formal ontological approach to metaphysics, these ontological categories are analysed by ontological forms. This analysis, which we illustrate by some category systems, provides a tool to assess the clarity, exactness and intelligibility of different category systems or formal ontologies. We discuss critically different accounts of ontological form in the literature. Of ontological form, we propose a character- neutral relational account. In this metatheory, ontological forms of entities (...)
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  • Barry Smith an sich.Gerald J. Erion & Gloria Zúñiga Y. Postigo (eds.) - 2017 - Cosmos + Taxis.
    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.
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  • Ontology of plays for autonomous teaming and collaboration.David Kasmier, Eric Merrell, Robert Kelly, Barry Smith, Curtis Heisey, Donald Evan Maki, Marc Brittain, Ronald Ankner & Kevin Bush - 2021 - Proceedings of the 14Th Seminar on Ontology Research in Brazil (Ontobras 2021), Ceur 3050, 9-22.
    We propose a domain-level ontology of plays for the facilitation of play-based collaborative autonomy among unmanned and manned-unmanned aircraft teams in the Army’s Unmanned Aircraft System (UAS) mission domain. We define a play as a type of plan that prescribes some pattern of intentional acts that are intended to reliably result in some goal in some competitive context, and which specifies one or more roles that are realized by those prescribed intentional acts. The ontology is well suited to be extended (...)
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  • Coordinating Coronavirus Research: The COVID-19 Infectious Disease Ontology.John Beverley, Shane Babcock, Barry Smith, Yongqun He, Eric Merrell, Lindsay Cowell, Regina Hurley & Sebastian Duesing - 2022 - Proceedings of the International Conference on Biomedical Ontologies.
    The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Ontologies – structured, controlled, vocabularies – are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the virus research domain, following the principles of the Open Biological and Biomedical Ontology (OBO) Foundry and drawing on the resources of the Infectious Disease Ontology (IDO) Core. We report the development of the Virus Infectious (...)
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  • Biomedical Ontologies.Barry Smith - 2023 - In Peter Elkin (ed.), Terminology, Ontology and their Implementations. Cham, Switzerland: Springer Nature Switzerland AG. pp. 125-169.
    We begin at the beginning, with an outline of Aristotle’s views on ontology and with a discussion of the influence of these views on Linnaeus. We move from there to consider the data standardization initiatives launched in the 19th century, and then turn to investigate how the idea of computational ontologies developed in the AI and knowledge representation communities in the closing decades of the 20th century. We show how aspects of this idea, particularly those relating to the use of (...)
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  • The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis.Jie Zheng, Marcelline R. Harris, Anna Maria Masci, Lin Yu, Alfred Hero, Barry Smith & Yongqun He - 2016 - Journal of Biomedical Semantics 7 (53).
    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 (...)
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  • OntONeo: The Obstetric and Neonatal Ontology.Fernanda Farinelli, Mauricio Almeida, Peter Elkin & Barry Smith - 2016 - In Dealing with elements of medical encounters: An approach based on ontological realism. Aachen: CEUR, vol. 1747.
    This paper presents the Obstetric and Neonatal Ontology (OntONeo). This ontology has been created to provide a consensus representation of salient electronic health record (EHR) data and to serve interoperability of the associated data and information systems. More generally, it will serve interoperability of clinical and translational data, for example deriving from genomics disciplines and from clinical trials. Interoperability of EHR data is important to ensuring continuity of care during the prenatal and postnatal periods for both mother and child. As (...)
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  • Dealing with elements of medical encounters: An approach based on ontological realism.Farinelli Fernanda, Almeida Mauricio, Elkin Peter & Barry Smith - 2016 - Proceedings of the Joint International Conference on Biological Ontology and Biocreative 1747.
    Electronic health records (EHRs) serve as repositories of documented data collected in a health care encounter. An EHR records information about who receives, who provides the health care and about the place where the encounter happens. We also observe additional elements relating to social relations in which the healthcare consumer is involved. To provide a consensus representation of common data and to enhance interoperability between different EHR repositories we have created a solution grounded in formal ontology. Here, we present how (...)
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  • Biomedical ontology alignment: An approach based on representation learning.Prodromos Kolyvakis, Alexandros Kalousis, Barry Smith & Dimitris Kiritsis - 2018 - Journal of Biomedical Semantics 9 (21).
    While representation learning techniques have shown great promise in application to a number of different NLP tasks, they have had little impact on the problem of ontology matching. Unlike past work that has focused on feature engineering, we present a novel representation learning approach that is tailored to the ontology matching task. Our approach is based on embedding ontological terms in a high-dimensional Euclidean space. This embedding is derived on the basis of a novel phrase retrofitting strategy through which semantic (...)
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  • Conceptual Spaces for Space Event Characterization via Hard and Soft Data Fusion.Jeremy R. Chapman, David Kasmier, David Limbaugh, Stephen R. Gagnon, John Crassidis, James Llinas, Barry Smith & Alexander P. Cox - 2021 - AIAA (American Institute of Aeronautics and Astronautics) Scitech 2021 Forum.
    The overall goal of the approach developed in this paper is to estimate the likelihood of a given kinetic kill scenario between hostile spacebased adversaries using the mathematical framework of Complex Conceptual Spaces Single Observation. Conceptual spaces are a cognitive model that provide a method for systematically and automatically mimicking human decision making. For accurate decisions to be made, the fusion of both hard and soft data into a single decision framework is required. This presents several challenges to this data (...)
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  • Understanding and Modeling Prevention.Riccardo Baratella, Mattia Fumagalli, Ítalo Oliveira & Giancarlo Guizzardi - 2022 - In Renata Guizzardi, Jolita Ralyté & Xavier Franch (eds.), Research Challenges in Information Science - 16th International Conference, RCIS 2022. Cham, Svizzera: Springer. pp. 389-405.
    Prevention is a pervasive phenomenon. It is about blocking an effect before it happens or stopping it as it unfolds: vaccines prevent (the unfolding of) diseases; seat belts prevent events causing serious injuries; circuit breaks prevent the manifestation of overcurrents. Many disciplines in the information sciences deal with modeling and reasoning about prevention. Examples include risk and security management as well as medical and legal informatics. Having a proper conceptualization of this phenomenon is crucial for devising proper modeling mechanisms and (...)
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  • The Birth of Ontology and the Directed Acyclic Graph.Jobst Landgrebe - 2022 - Journal of Knowledge Structures and Systems 3 (1):72-75.
    Barry Smith recently discussed the diagraphs of book eight of Jacob Lorhard’s Ogdoas scholastica under the heading “birth of ontology” (Smith, 2022; this issue). Here, I highlight the commonalities between the original usage of diagraphs in the tradition of Ramus for didactic purposes and the the usage of their present-day successors–modern ontologies–for computational purposes. The modern ideas of ontology and of the universal computer were born just two generations apart in the breakthrough century of instrumental reason.
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  • SNOMED CT standard ontology based on the ontology for general medical science.Shaker El-Sappagh, Francesco Franda, Ali Farman & Kyung-Sup Kwak - 2018 - BMC Medical Informatics and Decision Making 76 (18):1-19.
    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 (...)
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  • Biomedical imaging ontologies: A survey and proposal for future work.Barry Smith, Sivaram Arabandi, Mathias Brochhausen, Michael Calhoun, Paolo Ciccarese, Scott Doyle, Bernard Gibaud, Ilya Goldberg, Charles E. Kahn Jr, James Overton, John Tomaszewski & Metin Gurcan - 2015 - Journal of Pathology Informatics 6 (37):37.
    Ontology is one strategy for promoting interoperability of heterogeneous data through consistent tagging. An ontology is a controlled structured vocabulary consisting of general terms (such as “cell” or “image” or “tissue” or “microscope”) that form the basis for such tagging. These terms are designed to represent the types of entities in the domain of reality that the ontology has been devised to capture; the terms are provided with logical defi nitions thereby also supporting reasoning over the tagged data. Aim: This (...)
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  • Reification and Truthmaking Patterns.Nicola Guarino, Giancarlo Guizzardi & Tiago Prince Sales - 2018 - In J. Trujillo (ed.), Proceedings of 37th International Conference on Conceptual Modeling, ER 2018, Xi'an, China, October 22-25, 2018. Cham: Springer. pp. 151-165.
    Reification is a standard technique in conceptual modeling, which consists of including in the domain of discourse entities that may otherwise be hidden or implicit. However, deciding what should be rei- fied is not always easy. Recent work on formal ontology offers us a simple answer: put in the domain of discourse those entities that are responsible for the (alleged) truth of our propositions. These are called truthmakers. Re-visiting previous work, we propose in this paper a systematic analysis of truthmaking (...)
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  • Peer Review Report: Ontologies relevant to behaviour change interventions, version 3.Robert M. Kelly, David Limbaugh & Barry Smith - 2021 - Human Behaviour Change Project.
    In the present review we focus on what we take to be some remaining issues with the Behaviour Change Intervention Ontology (BCIO). We are in full agreement with the authors’ endorsement of the principles of best practice for ontology development In particular, we agree that an ontology should be “logically consistent and having a clear structures [sic], preferably a well-organised hierarchical structure,” and that “Maximising the new ontology’s interoperability with existing ontologies by reusing entities from existing ontologies where appropriate” is (...)
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  • Benefits of Realist Ontologies to Systems Engineering.Eric Merrell, Robert M. Kelly, David Kasmier, Barry Smith, Marc Brittain, Ronald Ankner, Evan Maki, Curtis W. Heisey & Kevin Bush - 2021 - 8th International Workshop on Ontologies and Conceptual Modelling (OntoCom).
    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 (...)
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  • Peer Review Report: Ontologies Relevant to Behaviour Change Interventions, version 1.Robert M. Kelly, David Limbaugh & Barry Smith - 2020 - Human Behaviour Change Project.
    In “Ontologies Relevant to behaviour change interventions: A Method for their Development” Wright, et al. outline a step by step process for building ontologies of behaviour modification – what the authors call the Refined Ontology Developmental Method (RODM) – and demonstrate its use in the development of the Behaviour Change Intervention Ontology (BCIO). RODM is based on the principles of good ontology building used by the Open Biomedical Ontology (OBO) Foundry in addition to those outlined in (Arp, Smith, and Spear (...)
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  • Understanding Addiction.Robert M. Kelly - 2021 - Dissertation, University at Buffalo
    The addiction literature is fraught with conceptual confusions, stalled debates, and an unfortunate lack of clear and careful attempts to delineate the phenomenon of addiction in a way that might lead to consensus. My dissertation has two overarching aims, one metaphysical and one practical. -/- The first aim is to defend an account of addiction as the systematic disposition to fail to control one’s desires to engage in certain types of behaviors. I defend the inclusion of desires and impaired control (...)
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  • Capabilities.Eric Merrell, David Limbaugh, Peter Koch & Barry Smith - manuscript
    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 (...)
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  • The Formal Cause in the Posterior Analytics.Petter Sandstad - 2016 - Filozofski Vestnik 37 (3):7-26.
    I argue that Aristotle’s account of scientific demonstrations in the Posterior Analytics is centred upon formal causation, understood as a demonstration in terms of essence (and as innocent of the distinction between form and matter). While Aristotle says that all four causes can be signified by the middle term in a demonstrative syllogism, and he discusses at some length efficient causation, much of Aristotle’s discussion is foremost concerned with the formal cause. Further, I show that Aristotle had very detailed procedures (...)
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  • Entities and their genera: Slicing up the world the medieval way--and does it matter to formal ontology?Luis M. Augusto - 2022 - Journal of Knowledge Structures and Systems 3 (2):4-47.
    Genera, typically hand-in-hand with their branching species, are essential elements of vocabulary-based information constructs, in particular scientific taxonomies. Should they also feature in formal ontologies, the highest of such constructs? I argue in this article that the answer is “Yes” and that the question posed in its title also has a Yes-answer: The way medieval ontologists sliced up the world into genera does matter to formal ontology. More specifically, the way Dietrich of Freiberg, a Latin scholastic, conceived and applied strictly (...)
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  • Foundational Ontologies: From Theory to Practice and Back.C. Maria Keet & Zubeida Khan - 2022 - Journal of Knowledge Structures and Systems 3 (1):67-71.
    This is a commentary on the article by Augusto (2022; this issue) on categories and foundation ontology (FO). We agree that the notion of categories of kinds of elements to devise a FO deserves more attention than it has received to date. From a practical point of view sensu developing domain ontologies, however, it probably does not matter much as long as a FO is used and that that one was understood.
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  • PROMES: An ontology‐based messaging service for semantically interoperable information exchange during disaster response.Linda Elmhadhbi, Mohamed‐Hedi Karray, Bernard Archimède, J. Neil Otte & Barry Smith - 2020 - Journal of Contingencies and Crisis Management 28 (3):324-338.
    Disaster response requires the cooperation of multiple emergency responder organizations (EROs). However, after‐action reports relating to large‐scale disasters identity communication difficulties among EROs as a major hindrance to collaboration. On the one hand, the use of two‐radio communication, based on multiple orthogonal frequencies and uneven coverage, has been shown to degrade inter‐organization communication. On the other hand, because they reflect different areas of expertise, EROs use differing terminologies, which are difficult to reconcile. These issues lead to ambiguities, misunderstandings, and inefficient (...)
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  • Bridging mainstream and formal ontology: A causality-based upper ontology in Dietrich of Freiberg.Luis M. Augusto - 2021 - Journal of Knowledge Structures and Systems 2 (2):35.
    Ontologies are some of the most central constructs in today's large plethora of knowledge technologies, namely in the context of the semantic web. As their coinage indicates, they are direct heirs to the ontological investigations in the long Western philosophical tradition, but it is not easy to make bridges between them. Contemporary ontological commitments often take causality as a central aspect for the ur-segregation of entities, especially in scientific upper ontologies; theories of causality and philosophical ontological investigations often go hand-in-hand, (...)
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  • Social Ontology and Social Normativity.Brian Donohue - 2020 - Dissertation, University at Buffalo
    Many recent accounts of the ontology of groups, institutions, and practices have touched upon the normative or deontic dimensions of social reality (e.g., social obligations, claims, permissions, prohibitions, authority, and immunity), as distinct from any specifically moral values or obligations. For the most part, however, the ontology of such socio-deontic phenomena has not received the attention it deserves. In what sense might a social obligation or a claim exist? What is the ontological status of such an obligation (e.g., is it (...)
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  • Conceptual Space Modeling for Space Event Characterization.Jeremy R. Chapman, David Kasmier, David Limbaugh, Stephen R. Gagnon, John L. Crassidis, James Llinas, Barry Smith & Alexander P. Cox - 2020 - IEEE 23rd International Conference on Information Fusion (FUSION).
    This paper provides a method for characterizing space events using the framework of conceptual spaces. We focus specifically on estimating and ranking the likelihood of collisions between space objects. The objective is to design an approach for anticipatory decision support for space operators who can take preventive actions on the basis of assessments of relative risk. To make this possible our approach draws on the fusion of both hard and soft data within a single decision support framework. Contextual data is (...)
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