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418Ontology-based error detection in SNOMED-CTProceedings of Medinfo 2004 482-6. 2004.Quality assurance in large terminologies is a difficult issue. We present two algorithms that can help terminology developers and users to identify potential mistakes. We demonstrate the methodology by outlining the different types of mistakes that are found when the algorithms are applied to SNOMED-CT. On the basis of the results, we argue that both formal logical and linguistic tools should be used in the development and quality-assurance process of large terminologies.
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417PROMES: An ontology‐based messaging service for semantically interoperable information exchange during disaster responseJournal of Contingencies and Crisis Management 28 (3): 324-338. 2020.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…Read more
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416L'ontologia del senso communeIn Evandro Agazzi (ed.), Valore E Limiti Del Senso Comune, Milan: Francoangeli. pp. 261-284. 2004.Common sense is on the one hand a certain set of processes of natural cognition – of speaking, reasoning, seeing, and so on. On the other hand common sense is a system of beliefs (of folk physics, folk psychology and so on). Over against both of these is the world of common sense, the world of objects to which the processes of natural cognition and the corresponding belief-contents standardly relate. What are the structures of this world? How does the scientific treatment of this world relate to…Read more
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415Biomarkers in the Ontology for General Medical ScienceIn Ronald Cornet (ed.), Digital Healthcare Empowering Europeans, Ios Press. pp. 155-159. 2015.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.
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415Pleasure and its modifications: Stephan Witasek and the aesthetics of the Grazer SchuleAxiomathes 7 (1-2): 203-232. 1996.The most obvious varieties of mental phenomena directed to non- existent objects occur in our experiences of works of art. The task of applying the Meinongian ontology of the non-existent to the working out of a theory of aesthetic phenomena was however carried out not by Meinong by his disciple Stephan Witasek in his Grundzüge der allgemeinen Ästhetik of 1904. Witasek shows in detail how our feelings undergo certain sorts of structural modifications when they are directed towards what does not …Read more
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415An improved ontological representation of dendritic cells as a paradigm for all cell typesBMC Bioinformatics 10 (1): 70. 2009.
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413In a development that has still been hardly noticed by philosophers, a conception of ontology has been advanced in recent years in a series of extra-philosophical disciplines as researchers in linguistics, psychology, geography and anthropology have sought to elicit the ontological commitments (‘ontologies’, in the plural) of different cultures or disciplines. Exploiting the terminology of Quine, researchers in psychology and anthropology have sought to establish what individual human subjects, …Read more
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411Biodynamic Ontology: Applying BFO in the Biomedical DomainStudies in Health and Technology Informatics 102. 2004.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 tw…Read more
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409Vantagens e limitações das ontologias formais na área biomédicaRECIIS: Revista Electronica de Comunicacao Informacao, Inovacao Em Saude 3 (1). 2009.Propomos uma tipologia dos artefatos de representação para as áreas de saúde e ciências biológicas, e a associação dessa tipologia com diferentes tipos de ontologia formal e lógica, chegando a conclusões quanto aos pontos fortes e limitações da ontologia de diferentes tipos de recursos lógicos, enquanto mantemos o foco na lógica descritiva. Consideramos quatro tipos de representação de área: (i) representação léxico-semântica, (ii) representação de tipos de entidades, (iii) representação de conh…Read more
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409A plant disease extension of the Infectious Disease OntologyIn Walls Ramona, Smith Barry, Justin Elser, Albert Goldfain & Stevenson Dennis W. (eds.), Proceeedings of the Third International Conference on Biomedical Ontology (CEUR 897), . pp. 1-5. 2012.Plants from a handful of species provide the primary source of food for all people, yet this source is vulnerable to multiple stressors, such as disease, drought, and nutrient deficiency. With rapid population growth and climate uncertainty, the need to produce crops that can tolerate or resist plant stressors is more crucial than ever. Traditional plant breeding methods may not be sufficient to overcome this challenge, and methods such as highOthroughput sequencing and automated scoring of phen…Read more
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406We have begun work on two separate but related ontologies for the study of neurological diseases. The first, the Neurological Disease Ontology (ND), is intended to provide a set of controlled, logically connected classes to describe the range of neurological diseases and their associated signs and symptoms, assessments, diagnoses, and interventions that are encountered in the course of clinical practice. ND is built as an extension of the Ontology for General Medical Sciences — a high-level can…Read more
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404From concepts to clinical reality: An essay on the benchmarking of biomedical terminologiesJournal of Biomedical Informatics 39 (3): 288-298. 2006.It is only by fixing on agreed meanings of terms in biomedical terminologies that we will be in a position to achieve that accumulation and integration of knowledge that is indispensable to progress at the frontiers of biomedicine. Standardly, the goal of fixing meanings is seen as being realized through the alignment of terms on what are called ‘concepts’. Part I addresses three versions of the concept-based approach – by Cimino, by Wüster, and by Campbell and associates – and surveys som…Read more
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404Textual DeferenceAmerican Philosophical Quarterly 28 (1). 1991.It is a truism that the attitude of deference to the text plays a lesser role in Anglo-Saxon philosophy than in other philosophical traditions. Works of philosophy written in English have, it is true, spawned a massive secondary literature dealing with the ideas, problems or arguments they contain. But they have almost never given rise to works of commentary in the strict sense, a genre which is however a dominant literary form not only in the Confucian, Vedantic, Islamic, Jewish and Scholastic …Read more
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396Novel sequence feature variant type analysis of the HLA genetic association in systemic sclerosisHuman Molecular Genetics 19 (4): 707-719. 2009.Significant associations have been found between specific human leukocyte antigen (HLA) alleles and organ transplant rejection, autoimmune disease development, and the response to infection. Traditional searches for disease associations have conventionally measured risk associated with the presence of individual HLA alleles. However, given the high level of HLA polymorphism, the pattern of amino acid variability, and the fact that most of the HLA variation occurs at functionally important sites,…Read more
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396Logic and formal ontologyManuscrito 23 (2): 275-323. 2000.Revised version of chapter in J. N. Mohanty and W. McKenna (eds.), Husserl’s Phenomenology: A Textbook, Lanham: University Press of America, 1989, 29–67. Logic for Husserl is a science of science, a science of what all sciences have in common in their modes of validation. Thus logic deals with universal laws relating to truth, to deduction, to verification and falsification, and with laws relating to theory as such, and to what makes for theoretical unity, both on the side of the propositions of…Read more
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395How Many Kafka's Are There?Polish Journal of Aesthetics 53 (2): 9-13. 2019.The aim of this volume is to present Kafka not as a writer, or not only as a writer, but as a philosopher. However, even after narrowing the scope of our interest down, there will still be several Kafka’s left on the table. Themes treated in the volume include: the so-called Brentano School in Prague, Kafka’s affiliation to the Louvre Circle, Kafka and existentialist philosophy, Kafka’s Jewish heritage, his love of Nietzsche and Meister Eckhart and—last but not least, since he was such an except…Read more
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393Theories of JudgmentIn Thomas Baldwin (ed.), The Cambridge History of Philosophy 1870-1945, Cambridge University Press. pp. 157--173. 2003.The dominant theory of judgment in 1870 was one or other variety of combination theory: the act of judgment is an act of combining concepts or ideas in the mind of the judging subject. In the decades to follow a succession of alternative theories arose to address defects in the combination theory, starting with Bolzano’s theory of propositions in themselves, Brentano’s theory of judgment as affirmation or denial of existence, theories distinguishing judgment act from judgment content advanced by…Read more
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393Development of FuGO: An ontology for functional genomics investigationsOmics: A Journal of Integrative Biology 10 (2): 199-204. 2006.The development of the Functional Genomics Investigation Ontology (FuGO) is a collaborative, international effort that will provide a resource for annotating functional genomics investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. FuGO will contain both terms that are universal to all functional genomics investigations and those that are domain specific. In this way, the ontology will serve as the “sem…Read more
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389Layers: A New Approach to Locating Objects in SpaceIn W. Kuhn M. F. Worboys & S. Timpf (eds.), Spatial Information Theory: Foundations of Geographic Information Science, Springer. pp. 50-65. 2003.Standard theories in mereotopology focus on relations of parthood and connection among spatial or spatio-temporal regions. Objects or processes which might be located in such regions are not normally directly treated in such theories. At best, they are simulated via appeal to distributions of attributes across the regions occupied or by functions from times to regions. The present paper offers a richer framework, in which it is possible to represent directly the relations between entities of var…Read more
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388Rationality and Irrationality: Proceeedings of the 23rd International Wittgenstein Symposium, 13-19 August 2000, Kirchberg Am Wechsel (edited book, review)Öbv&Hpt. 2001.This volume consists of the invited papers presented at the 23rd International Wittgenstein Conference held in Kirchberg, Austria in August 2000. Among the topics treated are: truth, psychologism, science, the nature of rational discourse, practical reason, contextualism, vagueness, types of rationality, the rationality of religious belief, and Wittgenstein. Questions addressed include: Is rationality tied to special sorts of contexts? ls rationality tied to language? Is scientific rationality t…Read more
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387Establishing and Harmonizing Ontologies in an Interdisciplinary Health Care and Clinical Research EnvironmentStudies in Health, Technology and Informatics 134 219-234. 2008.Ontologies are being ever more commonly used in biomedical informatics and we provide a survey of some of these uses, and of the relations between ontologies and other terminology resources. In order for ontologies to become truly useful, two objectives must be met. First, ways must be found for the transparent evaluation of ontologies. Second, existing ontologies need to be harmonised. We argue that one key foundation for both ontology evaluation and harmonisation is the adoption of a realist p…Read more
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385Boundaries: An essay in mereotopologyIn Lewis H. Hahn (ed.), Philosophy of Roderick Chisholm (Library of Living Philosophers), Open Court. pp. 534--561. 1997.Of Chisholm’s many signal contributions to analytic metaphysics, perhaps the most important is his treatment of boundaries, a category of entity that has been neglected, to say the least, in the history of ontology. We can gain some preliminary idea of the sorts of problems which the Chisholmian ontology of boundaries is designed to solve, if we consider the following Zeno-inspired thought-experiment.
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385that can serve as a foundation for more refined ontologies in the field of proteomics. Standard data sources classify proteins in terms of just one or two specific aspects. Thus SCOP (Structural Classification of Proteins) is described as classifying proteins on the basis of structural features; SWISSPROT annotates proteins on the basis of their structure and of parameters like post-translational modifications. Such data sources are connected to each other by pairwise term-to-term mappings. Howe…Read more
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384The Ontogenesis of Mathematical ObjectsJournal of the British Society for Phenomenology 6 (2): 91-101. 1975.Mathematical objects are divided into (1) those which are autonomous, i.e., not dependent for their existence upon mathematicians’ conscious acts, and (2) intentional objects, which are so dependent. Platonist philosophy of mathematics argues that all objects belong to group (1), Brouwer’s intuitionism argues that all belong to group (2). Here we attempt to develop a dualist ontology of mathematics (implicit in the work of, e.g., Hilbert), exploiting the theories of Meinong, Husserl and Ingarden…Read more
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383The Role of Foundational Relations in the Alignment of Biomedical OntologiesIn M. Fieschi, E. Coiera & Y.-C. J. Li (eds.), Medinfo, Ios Press. pp. 444-448. 2004.The Foundational Model of Anatomy (FMA) symbolically represents the structural organization of the human body from the macromolecular to the macroscopic levels, with the goal of providing a robust and consistent scheme for classifying anatomical entities that is designed to serve as a reference ontology in biomedical informatics. Here we articulate the need for formally clarifying the is-a and part-of relations in the FMA and similar ontology and terminology systems. We diagnose certain characte…Read more
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383Ontology for task-based clinical guidelines and the theory of granular partitionsIn Michel Dojat, Elpida T. Keravnou & Pedro Barahona (eds.), Proceedings of 9th Conference on Artificial Intelligence in Medicine Europe (AIME 2003), Springer. pp. 71-75. 2003.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, compa…Read more
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382The role of ontologies for sustainable, semantically interoperable and trustworthy EHR solutionsStudies in Health Technology and Informatics 150 953-957. 2009.As health systems around the world turn towards highly distributed, specialized and cooperative structures to increase quality and safety of care as well as efficiency and efficacy of delivery processes, there is a growing need for supporting communication and collaboration of all parties involved with advanced ICT solutions. The Electronic Health Record (EHR) provides the information platform which is maturing towards the eHealth core application. To meet the requirements for sustainable, seman…Read more
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377Interdisciplinary perspectives on the development, integration and application of cognitive ontologiesFrontiers in Neuroinformatics 8 (62): 1-7. 2014.We discuss recent progress in the development of cognitive ontologies and summarize three challenges in the coordinated development and application of these resources. Challenge 1 is to adopt a standardized definition for cognitive processes. We describe three possibilities and recommend one that is consistent with the standard view in cognitive and biomedical sciences. Challenge 2 is harmonization. Gaps and conflicts in representation must be resolved so that these resources can be combined for…Read more
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376NiszaFilozofia Nauki 3. 2000.Pojęcie niszy (otoczenia, kontekstu, siedliska, środowiska) nie cieszy się specjalnym zainteresowaniem ontologów, mimo że ma szerokie zastosowanie w rozmaitych dyscyplinach, od biologii ewolucyjnej po ekonomię. Niniejszy artykuł zawiera pierwszą teorię formalną tego pojęcia — teorię relacji pomiędzy przedmiotami a ich niszami. Teoria ta opiera się na istniejącym dorobku mereologii, topologii i teorii lokalizacji przestrzennej, które są narzędziami ontologii formalnej. Jest ona tutaj ilustrowana …Read more
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376Foundations for a Realist Ontology of Mental DiseaseJournal of Biomedical Semantics 1 (10): 1-23. 2010.While classifications of mental disorders have existed for over one hundred years, it still remains unspecified what terms such as 'mental disorder', 'disease' and 'illness' might actually denote. While ontologies have been called in aid to address this shortfall since the GALEN project of the early 1990s, most attempts thus far have sought to provide a formal description of the structure of some pre-existing terminology or classification, rather than of the corresponding structures and processe…Read more
Barry Smith
University at Buffalo
National Center for Ontological Research
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University at BuffaloDepartment of Philosophy
Biomedical Informatics
Neurology
Computer Science and EngineeringDistinguished Professor, Julian Park Chair -
National Center for Ontological ResearchAdministrator
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APA Eastern Division
Buffalo, New York, United States of America
Areas of Specialization
Metaphysics |
Ontology |
Philosophy of Artificial Intelligence |
Philosophy of Biology |