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194Coordinating virus research: The Virus Infectious Disease OntologyPLoS ONE 1. 2024.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 Biomed…Read more
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651Coordinating Coronavirus Research: The COVID-19 Infectious Disease OntologyProceedings of the International Conference on Biomedical Ontologies. 2022.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) Co…Read more
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281A new framework for host-pathogen interaction researchFrontiers in Immunology 13. 2022.COVID-19 often manifests with different outcomes in different patients, highlighting the complexity of the host-pathogen interactions involved in manifestations of the disease at the molecular and cellular levels. In this paper, we propose a set of postulates and a framework for systematically understanding complex molecular host-pathogen interaction networks. Specifically, we first propose four host-pathogen interaction (HPI) postulates as the basis for understanding molecular and cellular host…Read more
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399A comprehensive update on CIDO: the community-based coronavirus infectious disease ontologyJournal of Biomedical Semantics 13 (1): 25. 2022.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, integ…Read more
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310Ontology of plays for autonomous teaming and collaborationProceedings of the 14Th Seminar on Ontology Research in Brazil (Ontobras 2021), Ceur 3050, 9-22. 2021.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…Read more
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837We 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 …Read more
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558Benefits of Realist Ontologies to Systems Engineering8th International Workshop on Ontologies and Conceptual Modelling (OntoCom). 2021.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) int…Read more
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551Common Core Conformant Definitions for an Ontology of Commercial Exchange2nd International Workshop on Ontology of Social, Legal and Economic Entities (SoLEE). 2021.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 domai…Read more
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34Ontology: A Bridge between Bioethics and Data-Driven InquiryAmerican Journal of Bioethics 21 (6): 51-53. 2021.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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33Why We Should Not Let the Cheerfully Demented DieAmerican Journal of Bioethics 20 (8): 96-98. 2020.Volume 20, Issue 8, August 2020, Page 96-98.
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912Mental CapabilitiesIn David Kasmier, David Limbaugh & Barry Smith (eds.), Proceedings of the International Conference on Biomedical Ontology (ICBO), University at Buffalo, NY, . 2019.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…Read more
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1060Toward an Ontology of Commercial ExchangeIn Jonathan Vajda, Eric Merrell & Barry Smith (eds.), Proceedings of the Joint Ontology Workshops (JOWO), Graz, . 2019.In this paper we propose an Ontology of Commercial Exchange (OCE) based on Basic Formal Ontology. OCE is designed for re-use in the Industrial Ontologies Foundry (IOF) and in other ontologies addressing different aspects of human social behavior involving purchasing, selling, marketing, and so forth. We first evaluate some of the design patterns used in the Financial Industry Business Ontology (FIBO) and Product Types Ontology (PTO). We then propose terms and definitions that we believe will imp…Read more
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State University of New York (SUNY)Doctoral student
Newburgh, New York, United States of America
Areas of Specialization
Epistemology |
Ontology, Misc |
Areas of Interest
1 more
Ontology, Misc |
Epistemology |
Epistemic Normativity |
Ontological Categories |
Formal Epistemology |
Knowledge |