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  1. Events, Their Names, and Their Synchronic Structure.Nicola Guarino, Riccardo Baratella & Giancarlo Guizzardi - forthcoming - Applied ontology.
    We present in this paper a novel ontological theory of events whose central tenet is the Aristotelian distinction between the object that changes and the actual subject of change, which is what we call an individual quality. While in the Kimian tradition events are individuated by a triple ⟨o, P, t⟩, where o is an object, P a property, and t an interval of time, for us the simplest events are qualitative changes, individuated by a triple ⟨o, q, t⟩, where (...)
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  2. Implementing Dempster-Shafer Theory for Property Similarity in Conceptual Spaces Modeling.Jeremy R. Chapman, John L. Crassidis, James Llinas, Barry Smith & David Kasmier - 2022 - Sensor Systems and Information Systems IV, American Institute of Aeronautics and Astronautics (AIAA) SCITECH Forum 2022.
    Previous work has shown that the Complex Conceptual Spaces − Single Observation Mathematical framework is a useful tool for event characterization. This mathematical framework is developed on the basis of Conceptual Spaces and uses integer linear programming to find the needed similarity values. The work of this paper is focused primarily on space event characterization. In particular, the focus is on the ranking of threats for malicious space events such as a kinetic kill. To make the Conceptual Spaces framework work, (...)
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  3. 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 - forthcoming - 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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  4. What is a Situation?Mercedes Valmisa - 2021 - In Livia Kohn (ed.), Coming to Terms with Timelessness. Daoist Time in Comparative Perspective. St. Petersburg, FL, USA: pp. 26-49.
    This paper leads us in reflections regarding the ontological status of a situation inspired by two main sources: the Zhuangzi--a multifarious compilation from Warring States China (ca. 4th c. BCE)--and José Ortega y Gasset's (1883-1955) Unas Lecciones de Metafísica (Some Lessons in Metaphysics)--the transcripts of a course on metaphysics by a Spanish philosopher of the early 20th century. Much as other ontologically subjective entities and events, situations do not preexist the intentional subject: instead, they are created alongside our act of (...)
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  5. Capabilities.Eric Merrell, David Limbaugh, Peter Koch & Barry Smith - manuscript
    A disposition, in Basic Formal Ontology (BFO), is defined as an intrinsic property of an entity that is realized by processes of a specific type in which that entity participates. We define capability as a disposition in whose realization one or more organisms have an interest. A function in BFO is (simplifying somewhat) a disposition whose realization is the rationale for the existence of its bearer. To say, for example, that a water pump has the function to pump water is (...)
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  6. A Conceptual Framework for Legal Personality and its Application to AI.Claudio Novelli, Giorgio Bongiovanni & Giovanni Sartor - forthcoming - Jurisprudence:1-26.
    In this paper we provide an analysis of the concept of legal personality and discuss whether personality may be conferred on artificial intelligence systems. Legal personality will be present...
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  7. 房地产的形而上学.Barry Smith & Leo Zaibert - 2021 - In Francesco Di Iorio & Jun Hu (eds.), 能动性与社会动力学——经济学哲学与社会科学哲学论文集 (Agency and Social Dynamics: Essays in the Philosophy of Economics and the Social Sciences). Beijing: Nankai University Press. pp. 111-125.
    The parceling of land into real estate is more than a simple geometrical affair. Real estate is a historical product of interaction between human beings, political, legal and economic institutions, and the physical environment. And while many authors, from Jeremy Bentham to Hernando de Soto, have drawn attention to the ontological (metaphysical) aspect of property in general, no comprehensive analysis of landed property has been attempted. The paper presents such an analysis and shows how landed property differs from other types (...)
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  8. Ontologia em Ciência da Informação. Teoria e Método.Mauricio B. Almeida - 2020 - Curitiba - Brasil: Editora CRV.
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  9. BFO-Based Ontology Enhancement to Promote Interoperability in BIM.Justine Flore Tchouanguem, Mohamed Hedi Karray, Bernard Kamsu Foguem, Camille Magniont, F. Henry Abanda & Barry Smith - 2021 - Applied ontology 16 (4):1–27.
    Building Information Modelling (BIM) is a process for managing construction project information in such a way as to provide a basis for enhanced decision-making and for collaboration in a construction supply chain. One impediment to the uptake of BIM is the limited interoperability of different BIM systems. To overcome this problem, a set of Industry Foundation Classes (IFC) has been proposed as a standard for the construction industry. Building on IFC, the ifcOWL ontology was developed in order to facilitate representation (...)
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  10. An Ontological Approach to Enhancing Information Sharing in Disaster Response.Linda Elmhadhbi, Mohamed-Hedi Karray, Bernard Archimède, J. Neil Otte & Barry Smith - 2021 - Information 12 (10).
    Managing complex disaster situations is a challenging task because of the large number of actors involved and the critical nature of the events themselves. In particular, the different terminologies and technical vocabularies that are being exchanged among Emergency Responders may lead to misunderstandings. Maintaining a shared semantics for exchanged data is a major challenge. To help to overcome these issues, we elaborate a modular suite of ontologies called POLARISCO that formalizes the complex knowledge of the ERs. Such a shared vocabulary (...)
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  11. 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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  12. Common Core Conformant Definitions for an Ontology of Commercial Exchange.Eric C. Merrell, Olivier Massin & Barry Smith - 2021 - 2nd International Workshop on Ontology of Social, Legal and Economic Entities (SoLEE).
    In “Toward an Ontology of Commercial Exchange” [11], we proposed human readable definitions for terms that are central to an ontology of commercial exchange. This paper furthers that project in two ways. First, the definitions have been modified to be compatible with the Common Core Ontologies (CCO). CCO is used in a wide variety of domains including the industrial and military domains. Having a commerce ontology compatible with CCO allows data about the exchange of goods relevant to those domains to (...)
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  13. 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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  14. Ontology-Driven Multicriteria Decision Support for Victim Evacuation.Linda Elmhadhbi, Mohamed-Hedi Karray, Bernard Archimède, J. Neil Otte & Barry Smith - forthcoming - International Journal of Information Technology and Decision Making:1–30.
    Abstract In light of the complexity of unfolding disasters, the diversity of rapidly evolving events, the enormous amount of generated information, and the huge pool of casualties, emergency responders (ERs) may be overwhelmed and in consequence poor decisions may be made. In fact, the possibility of transporting the wounded victims to one of several hospitals and the dynamic changes in healthcare resource availability make the decision process more complex. To tackle this problem, we propose a multicriteria decision support service, based (...)
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  15. 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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  16. The Toolbox Dialogue Initiative: The Power of Cross-Disciplinary Practice.Graham Hubbs, Michael O'Rourke & Steven Hecht Orzack (eds.) - 2020 - New York, NY, USA: CRC Press.
    Cross-disciplinary scientific collaboration is emerging as standard operating procedure for many scholarly research enterprises. And yet, the skill set needed for effective collaboration is neither taught nor mentored. The goal of the Toolbox Dialogue Initiative is to facilitate cross-disciplinary collaboration. This book, inspired by this initiative, presents dialogue-based methods designed to increase mutual understanding among collaborators so as to enhance the quality and productivity of cross-disciplinary collaboration. It provides a theoretical context, principal activities, and evidence for effectiveness that will assist (...)
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  17. Making Space: The Natural, Cultural, Cognitive and Social Niches of Human Activity.Barry Smith - 2021 - Cognitive Processing 22 (supplementary issue 1):77-87.
    This paper is in two parts. Part 1 examines the phenomenon of making space as a process involving one or other kind of legal decision-making, for example when a state authority authorizes the creation of a new highway along a certain route or the creation of a new park in a certain location. In cases such as this a new abstract spatial entity comes into existence – the route, the area set aside for the park – followed only later by (...)
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  18. 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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  19. Ontology (Science).Barry Smith - 2008 - In Carola Eschenbach & Mike Grüninger (eds.), Formal Ontology in Information Systems. Proceedings of the Fifth International Conference (FOIS 2008). Amsterdam: IOS Press. pp. 21-35.
    Increasingly, in data-intensive areas of the life sciences, experimental results are being described in algorithmically useful ways with the help of ontologies. Such ontologies are authored and maintained by scientists to support the retrieval, integration and analysis of their data. The proposition to be defended here is that ontologies of this type – the Gene Ontology (GO) being the most conspicuous example – are a part of science. Initial evidence for the truth of this proposition (which some will find self-evident) (...)
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  20. Wind Turbine Analysis Project.Neil Otte, Rahul Rai, Clare Paul & Barry Smith - 2018 - Final Project Report.
    The report describes an application of ontologies to the analysis of wind turbine manufacturing data. We show how applying ontologies to composite materials data may facilitate the discovery of optimum composite material designs that will deliver maximum wind turbine blade performance within environmental constraints.
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  21. SNAPVis and SPANVis: Ontologies for Recognizing Variable Vista Spatial Environments.Tiansi Dong - 2004 - In International Conference on Spatial Cognition. Springer. pp. 344-365.
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  22. 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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  23. 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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  24. 本体:广谱的知识集成工具.Barry Smith - 2020 - In 基于基本形式化本体的本体构建. Beijing: pp. 4-8.
    Ontology: Tool for Broad Spectrum Knowledge Integration (Foreword to Chinese translation of Building Ontologies with Basic Formal Ontology).
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  25. 基于基本形式化本体的本体构建.Robert Arp, Barry Smith & Andrew D. Spear - 2020 - Beijing: People's Medical Publishing House.
    In the era of “big data,” science is increasingly information driven, and the potential for computers to store, manage, and integrate massive amounts of data has given rise to such new disciplinary fields as biomedical informatics. Applied ontology offers a strategy for the organization of scientific information in computer-tractable form, drawing on concepts not only from computer and information science but also from linguistics, logic, and philosophy. This book provides an introduction to the field of applied ontology that is of (...)
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  26. Modeling Artificial Agents’ Actions in Context – a Deontic Cognitive Event Ontology.Miroslav Vacura - 2020 - Applied Ontology 15 (4):493-527.
    Although there have been efforts to integrate Semantic Web technologies and artificial agents related AI research approaches, they remain relatively isolated from each other. Herein, we introduce a new ontology framework designed to support the knowledge representation of artificial agents’ actions within the context of the actions of other autonomous agents and inspired by standard cognitive architectures. The framework consists of four parts: 1) an event ontology for information pertaining to actions and events; 2) an epistemic ontology containing facts about (...)
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  27. 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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  28. Enriching the Functionally Graded Materials (FGM) Ontology for Digital Manufacturing.Munira Mohd Ali, Ruoyu Yang, Binbin Zhang, Francesco Furini, Rahul Rai, J. Neil Otte & Barry Smith - 2021 - International Journal of Production Research 59 (18):5540-5557.
    Functionally graded materials (FGMs) have been used in many different kinds of applications in recent years and have attracted significant research attention. However, we do not yet have a commonly accepted way of representing the various aspects of FGMs. Lack of standardised vocabulary creates obstacles to the extraction of useful information relating to pertinent aspects of different applications. A standard resource is needed for describing various elements of FGMs, including existing applications, manufacturing techniques, and material characteristics. This motivated the creation (...)
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  29. An Ontological Account of the Action Theory of Economic Exchanges.Daniele Porello, Giancarlo Guizzardi, Tiago Prince Sales, Glenda C. M. Amaral & Nicola Guarino - 2020 - In Proceedings of 14th International Workshop on Value Modelling and Business Ontologies, Brussels, Belgium, January 16-17, 2020. pp. 157-169.
    In recent years, there has been an increasing interest in thedevelopment of ontologically well-founded conceptual models for Information Systems in areas such as Service Management, Accounting Information Systems and Financial Reporting. Economic exchanges are central phenomena in these areas. For this reason, they occupy a prominent position in modelling frameworks such as the REA (Resource-EventAction) ISO Standard as well as the FIBO (Financial Industry BusinessOntology). In this paper, we begin a well-founded ontological analysisof economic exchanges inspired by a recent ontological (...)
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  30. CIDO, a Community-Based Ontology for Coronavirus Disease Knowledge and Data Integration, Sharing, and Analysis.Oliver He, John Beverley, Gilbert S. Omenn, Barry Smith, Brian Athey, Luonan Chen, Xiaolin Yang, Junguk Hur, Hsin-hui Huang, Anthony Huffman, Yingtong Liu, Yang Wang, Edison Ong & Hong Yu - 2020 - Scientific Data 181 (7):5.
    Ontologies, as the term is used in informatics, are structured vocabularies comprised of human- and computer-interpretable terms and relations that represent entities and relationships. Within informatics fields, ontologies play an important role in knowledge and data standardization, representation, integra- tion, sharing and analysis. They have also become a foundation of artificial intelligence (AI) research. In what follows, we outline the Coronavirus Infectious Disease Ontology (CIDO), which covers multiple areas in the domain of coronavirus diseases, including etiology, transmission, epidemiology, pathogenesis, diagnosis, (...)
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  31. On Credentials.Barry Smith, Olimpia Giuliana Loddo & Giuseppe Lorini - 2020 - Journal of Social Ontology 6 (1):47-67.
    Credentials play an important role in all modern societies, but the analysis of their nature and function has thus far been neglected by social philosophers. We present a view according to which the function of credentials is certify the identity and the institutional status (including the rights) of individuals. More importantly, credentials enable rights-holders to exercise their rights, so that for a particular right to be exercisable the right-holder should possess, carry and sometimes show to an authority (or QR code (...)
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  32. Ontology and Cognitive Outcomes.David Limbaugh, Jobst Landgrebe, David Kasmier, Ronald Rudnicki, James Llinas & Barry Smith - 2020 - Journal of Knowledge Structures and Systems 1 (1): 3-22.
    The term ‘intelligence’ as used in this paper refers to items of knowledge collected for the sake of assessing and maintaining national security. The intelligence community (IC) of the United States (US) is a community of organizations that collaborate in collecting and processing intelligence for the US. The IC relies on human-machine-based analytic strategies that 1) access and integrate vast amounts of information from disparate sources, 2) continuously process this information, so that, 3) a maximally comprehensive understanding of world actors (...)
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  33. Realitätsrepräsentation: Das Ziel der Ontologie.Barry Smith - 2008 - In Ludger Jansen & Barry Smith (eds.), Biomedizinische Ontologie. Philosophie – Lebenswissenschaften - Informationstechnik. Zurich: vdf (UTB Forum). pp. 31-46.
    The development of ontologies for the purposes of data curation is an important element in modern-day data and information sciences. Unfortunately, much of the work on these applied ontologies is associated with a relativist or conceptualist point of view, according to which ontologies represent (for example) the concepts in the minds of human beings. The paper describes a series of problems with such views, and defends an alternative realist interpretation.
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  34. Interdyscyplinarne perspektywy rozwoju, integracji i zastosowań ontologii poznawczych.Janna Hastings, Gwen Frishkoff, Barry Smith, Mark Jensen, Russell Poldrack, Jane Lomax, Anita Bandrowski, Fahim Imam, Jessica Turner, Maryann Martone & Przemysław Nowakowski - 2016 - Avant: Trends in Interdisciplinary Studies 7 (3):101-117.
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  35. An Ontological Analysis of Drug Prescriptions.Jean-François Ethier, Adrien Barton & Ryeyan Taseen - 2018 - Applied ontology 13 (4):273-294.
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  36. Foundation for a Realist Ontology of Cognitive Processes.David Kasmier, David Limbaugh & Barry Smith - 2019 - In Proceedings of the International Conference on Biomedical Ontology (ICBO), University at Buffalo, NY.
    What follows is a first step towards an ontology of conscious mental processes. We provide a theoretical foundation and characterization of conscious mental processes based on a realist theory of intentionality and using BFO as our top-level ontology. We distinguish three components of intentional mental process: character, directedness, and objective referent, and describe several features of the process character and directedness significant to defining and classifying mental processes. We arrive at the definition of representational mental process as a process that (...)
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  37. Proceedings of the ECAI-02 Workshop on Ontologies and Semantic Interoperability Lyon, July 22, 2002.Jerome Euzenat, Asuncion Gomez-Perez, Nicola Guarino & Heiner Stuckenschmidt (eds.) - 2002 - CEUR Workshop Proceedings.
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  38. 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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  39. The Industrial Ontologies Foundry Proof-of-Concept Project.Evan Wallace, Dimitris Kiritsis, Barry Smith & Chris Will - 2018 - In Ilkyeong Moon, Gyu M. Lee, Jinwoo Park, Dimitris Kiritsis & Gregor von Cieminski (eds.), Advances in Production Management Systems. Smart Manufacturing for Industry 4.0. IFIP. pp. 402-409.
    The current industrial revolution is said to be driven by the digitization that exploits connected information across all aspects of manufacturing. Standards have been recognized as an important enabler. Ontology-based information standard may provide benefits not offered by current information standards. Although there have been ontologies developed in the industrial manufacturing domain, they have been fragmented and inconsistent, and little has received a standard status. With successes in developing coherent ontologies in the biological, biomedical, and financial domains, an effort called (...)
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  40. Ontology.Barry Smith - 2003 - In Luciano Floridi (ed.), Blackwell Guide to the Philosophy of Computing and Information. Oxford: Blackwell. pp. 155-166.
    Ontology as a branch of philosophy is the science of what is, of the kinds and structures of objects, properties, events, processes and relations in every area of reality. ‘Ontology’ in this sense is often used by philosophers as a synonym of ‘metaphysics’ (a label meaning literally: ‘what comes after the Physics’), a term used by early students of Aristotle to refer to what Aristotle himself called ‘first philosophy’. But in recent years, in a development hardly noticed by philosophers, the (...)
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  41. ImmPort, Toward Repurposing of Open Access Immunological Assay Data for Translational and Clinical Research.Sanchita Bhattacharya, Patrick Dunn, Cristel Thomas, Barry Smith, Henry Schaefer, Jieming Chen, Zicheng Hu, Kelly Zalocusky, Ravi Shankar & Shai Shen-Orr - 2018 - Scientific Data 5:180015.
    Immunology researchers are beginning to explore the possibilities of reproducibility, reuse and secondary analyses of immunology data. Open-access datasets are being applied in the validation of the methods used in the original studies, leveraging studies for meta-analysis, or generating new hypotheses. To promote these goals, the ImmPort data repository was created for the broader research community to explore the wide spectrum of clinical and basic research data and associated findings. The ImmPort ecosystem consists of four components–Private Data, Shared Data, Data (...)
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  42. A Visual Representation of Part-Whole Relationships in BFO-Conformant Ontologies.Jose M. Parente de Oliveira & Barry Smith - 2017 - In Á Rocha, A. M. Correia, H. Adeli, L. P. Reis & S. Costanzo (eds.), Recent Advances in Information Systems and Technologies (Advances in Intelligent Systems and Computing, 569). New York: Springer. pp. 184-194.
    In the visual representation of ontologies, in particular of part-whole relationships, it is customary to use graph theory as the representational background. We claim here that the standard graph-based approach has a number of limitations, and we propose instead a new representation of part-whole structures for ontologies, and describe the results of experiments designed to show the effectiveness of this new proposal especially as concerns reduction of visual complexity. The proposal is developed to serve visualization of ontologies conformant to the (...)
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  43. OmniSearch: A Semantic Search System Based on the Ontology for MIcroRNA Target Gene Interaction Data.Huang Jingshan, Gutierrez Fernando, J. Strachan Harrison, Dou Dejing, Huang Weili, A. Blake Judith, Barry Smith, Eilbeck Karen, A. Natale Darren & Lin Yu - 2016 - Journal of Biomedical Semantics 7 (1):1.
    In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the (...)
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  44. OBCS: The Ontology of Biological and Clinical Statistics.Jie Zheng, Marcelline R. Harris, Anna Maria Masci, Yu Lin, Alfred Hero, Barry Smith & Yongqun He - 2014 - Proceedings of the Fifth International Conference on Biomedical Ontology 1327:65.
    Statistics play a critical role in biological and clinical research. To promote logically consistent representation and classification of statistical entities, we have developed the Ontology of Biological and Clinical Statistics (OBCS). OBCS extends the Ontology of Biomedical Investigations (OBI), an OBO Foundry ontology supported by some 20 communities. Currently, OBCS contains 686 terms, including 381 classes imported from OBI and 147 classes specific to OBCS. The goal of this paper is to present OBCS for community critique and to describe a (...)
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  45. Engineering Ontologies: Foundations and Theories From Philosophy and Logical Theory.Nicola Guarino & Barry Smith - 2006 - In SemanticMining: Semantic Interoperability and Data Mining in Biomedicine (NoE 507505). 1 Deliverable D.21.2. pp. 1-13.
    Ontology as a branch of philosophy is the science of what is, of the kinds and structures of objects, properties, events, processes and relations in every area of reality. ‘Ontology’ is often used by philosophers as a synonym for ‘metaphysics’ (literally: ‘what comes after the Physics’), a term which was used by early students of Aristotle to refer to what Aristotle himself called ‘first philosophy’. The term ‘ontology’ (or ontologia) was itself coined in 1613, independently, by two philosophers, Rudolf Göckel (...)
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  46. The Functions of Definitions in Ontologies.Selja Seppälä, Alan Ruttenberg, & Barry Smith - 2016 - In R. Ferrario & W. Kuhn (eds.), Formal Ontology in Information Systems. Proceedings of the Ninth International Conference (FOIS 2016). IOS Pres. pp. 37-50.
    To understand what ontologies do through their definitions, we propose a theoretical explanation of the functions of definitions in ontologies backed by empirical neuropsychological studies. Our goal is to show how these functions should motivate (i) the systematic inclusion of definitions in ontologies and (ii) the adaptation of definition content and form to the specific context of use of ontologies.
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  47. 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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  48. Bootstrapping the Applied Ontology Practice: Ontology Communities, Then and Now.Peter P. Yim - 2015 - Applied ontology 10 (3-4):229-241.
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  49. Applied Ontology: The Next Decade Begins.Nicola Guarino & Mark Musen - 2015 - Applied ontology 10 (1):1-4.
    In 2005, IOS Press published the first issue of applied Ontology. At the time, we argued that, at the core of the journal, there was “a desire to understand the nature of reality and how people construe their world”. We declared that ontology was both “fundamental to human thought” and “to translating our thoughts into computational artifacts” (Guarino & Musen,2005). With an editorial board of distinguished scholars representing the fields of computer science, informatics, information science, philosophy, linguistics, psychology, and social (...)
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  50. Joint Doctrine Ontology: A Benchmark for Military Information Systems Interoperability.Peter Morosoff, Ron Rudnicki, Jason Bryant, Robert Farrell & Barry Smith - 2015 - In Semantic Technology for Intelligence, Defense and Security (STIDS). CEUR vol. 1325. pp. 2-9.
    When the U.S. conducts warfare, elements of a force are drawn from different services and work together as a single team to accomplish an assigned mission. To achieve such unified action, it is necessary that the doctrines governing the actions of members of specific services be both consistent with and subservient to joint Doctrine. Because warfighting today increasingly involves not only live forces but also automated systems, unified action requires that information technology that is used in joint warfare must be (...)
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