-
665Controlled vocabularies in bioinformatics: A case study in the Gene OntologyDrug Discovery Today: Biosilico 2 (6): 246-252. 2004.The automatic integration of information resources in the life sciences is one of the most challenging goals facing biomedical informatics today. Controlled vocabularies have played an important role in realizing this goal, by making it possible to draw together information from heterogeneous sources secure in the knowledge that the same terms will also represent the same entities on all occasions of use. One of the most impressive achievements in this regard is the Gene Ontology (GO), which is …Read more
-
430Ontology-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.
-
243An ontology for carcinoma classification for clinical bioinformaticsStudies in Health Technology and Informatics 116 (1): 635-640. 2005.There are a number of existing classifications and staging schemes for carcinomas, one of the most frequently used being the TNM classification. Such classifications represent classes of entities which exist at various anatomical levels of granularity. We argue that in order to apply such representations to the Electronic Health Records one needs sound ontologies which take into consideration the diversity of the domains which are involved in clinical bioinformatics. Here we outline a formal the…Read more
-
521WüsteriaStudies in Health Technology and Informatics 116 647-652. 2005.The last two decades have seen considerable efforts directed towards making Electronic Health Records interoperable through improvements in medical ontologies, terminologies and coding systems. Unfortunately, these efforts have been hampered by a number of influential ideas inherited from the work of Eugen Wüster, the father of terminology standardization and the founder of ISO TC 37. We here survey Wüster’s ideas – which see terminology work as being focused on the classification of concepts in…Read more
-
249Clinical guidelines as plans: An ontological theoryMethods of Information in Medicine 45 (2): 204-210. 2006.Clinical guidelines are special types of plans realized by collective agents. We provide an ontological theory of such plans that is designed to support the construction of a framework in which guideline-based information systems can be employed in the management of workflow in health care organizations. The framework we propose allows us to represent in formal terms how clinical guidelines are realized through the actions of are realized through the actions of individuals organized into teams.…Read more
-
377Referent tracking for corporate memoriesIn Peter Rittgen (ed.), Handbook of Ontologies for Business Interaction, Idea Group Publishing. pp. 34-46. 2007.For corporate memory and enterprise ontology systems to be maximally useful, they must be freed from certain barriers placed around them by traditional knowledge management paradigms. This means, above all, that they must mirror more faithfully those portions of reality which are salient to the workings of the enterprise, including the changes that occur with the passage of time. The purpose of this chapter is to demonstrate how theories based on philosophical realism can contribute to this obje…Read more
-
287Ontology as the core discipline of biomedical informatics: Legacies of the past and recommendations for the future direction of researchIn Gordana Dodig Crnkovic & Susan Stuart (eds.), Computation, Information, Cognition: The Nexus and the Liminal.f, Cambridge Scholars Press. pp. 104-122. 2007.The automatic integration of rapidly expanding information resources in the life sciences is one of the most challenging goals facing biomedical research today. Controlled vocabularies, terminologies, and coding systems play an important role in realizing this goal, by making it possible to draw together information from heterogeneous sources – for example pertaining to genes and proteins, drugs and diseases – secure in the knowledge that the same terms will also represent the same entities on a…Read more
-
446Negative findings in electronic health records and biomedical ontologies: a realist approachInternational Journal of Medical Informatics 76 (3). 2007.PURPOSE—A substantial fraction of the observations made by clinicians and entered into patient records are expressed by means of negation or by using terms which contain negative qualifiers (as in “absence of pulse” or “surgical procedure not performed”). This seems at first sight to present problems for ontologies, terminologies and data repositories that adhere to a realist view and thus reject any reference to putative non-existing entities. Basic Formal Ontology (BFO) and Referent Tracking (…Read more
-
2609The Mystery of Capital and the Construction of Social Reality (edited book)Open Court. 2008.John Searle’s The Construction of Social Reality and Hernando de Soto’s The Mystery of Capital shifted the focus of current thought on capital and economic development to the cultural and conceptual ideas that underpin market economies and that are taken for granted in developed nations. This collection of essays assembles 21 philosophers, economists, and political scientists to help readers understand these exciting new theories.
-
249New desiderata for biomedical terminologiesIn Katherine Munn & Barry Smith (eds.), Applied Ontology: An Introduction, Ontos. pp. 83-109. 2008.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 some of t…Read more
-
349Referent Tracking for Command and Control Messaging SystemsCEUR, Volume 555. 2009.The Joint Battle Management Language (JBML) is an XML-based language designed to allow Command and Control (C2) systems to interface easily with Modeling and Simulation (M&S) systems. While some of the XML-tags defined in this language correspond to types of entities that exist in reality, others are mere syntactic artifacts used to structure the messages themselves. Because these two kinds of tags are not formally distinguishable, JBML messages in effect confuse data with what the data represen…Read more
-
394The 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
-
201Letter to the Editor: Dealing with socially constructed concepts in an ontologyJournal of Empirical Research on Human Research Ethics 4 (2): 75-76. 2009.Response to the paper “The Biomedical Ethics Ontology Proposal: Excellent Aims, Questionable Methods" by James DuBois, published in the Journal of Empirical Research on Human Research Ethics
-
482Saliva Ontology: An ontology-based framework for a Salivaomics Knowledge BaseBMC Bioinformatics 11 (1): 302. 2010.The Salivaomics Knowledge Base (SKB) is designed to serve as a computational infrastructure that can permit global exploration and utilization of data and information relevant to salivaomics. SKB is created by aligning (1) the saliva biomarker discovery and validation resources at UCLA with (2) the ontology resources developed by the OBO (Open Biomedical Ontologies) Foundry, including a new Saliva Ontology (SALO). We define the Saliva Ontology (SALO; http://www.skb.ucla.edu/SALO/) as a consensus…Read more
-
231More about ontology: ResponseJournal of the American Dental Association 142 (3): 252-254. 2011.Letter commenting on the paper Barry Smith, Louis J. Goldberg, Alan Ruttenberg & Michael Glick, "Ontology and the Future of Dental Research Informatics", Journal of the American Dental Association 141 2010;(10):1173-75 with responses by the authors of the paper.
-
189Guest Editorial: Ontologies for clinical and translational researchJournal of Biomedical Informatics 44 (1): 3--7. 2011.
-
286The representation of protein complexes in the Protein OntologyBMC Bioinformatics 12 (371): 1-11. 2011.Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consor…Read more
-
240ARGOS policy brief on semantic interoperabilityStudies in Health Technology and Informatics 170 (1): 1-15. 2011.Semantic interoperability requires the use of standards, not only for Electronic Health Record (EHR) data to be transferred and structurally mapped into a receiving repository, but also for the clinical content of the EHR to be interpreted in conformity with the original meanings intended by its authors. Accurate and complete clinical documentation, faithful to the patient’s situation, and interoperability between systems, require widespread and dependable access to published and maintained coll…Read more
-
428Wanting what we don't want to want: Representing Addiction in Interoperable Bio-OntologiesIn Janna Hastings, Werner Ceusters, Mark Jensen, Kevin Mulligan & Barry Smith (eds.), Towards an Ontology of Mental Functioning (ICBO Workshop), Ceur. pp. 56-60. 2012.Ontologies are being developed throughout the biomedical sciences to address standardization, integration, classification and reasoning needs against the background of an increasingly data-driven research paradigm. In particular, ontologies facilitate the translation of basic research into benefits for the patient by making research results more discoverable and by facilitating knowledge transfer across disciplinary boundaries. Addressing and adequately treating mental illness is one of our most p…Read more
-
380Bioinformatics advances in saliva diagnosticsInternational Journal of Oral Science 4 (2): 85--87. 2012.There is a need recognized by the National Institute of Dental & Craniofacial Research and the National Cancer Institute to advance basic, translational and clinical saliva research. The goal of the Salivaomics Knowledge Base (SKB) is to create a data management system and web resource constructed to support human salivaomics research. To maximize the utility of the SKB for retrieval, integration and analysis of data, we have developed the Saliva Ontology and SDxMart. This article reviews the in…Read more
-
397Interdisciplinary 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
-
466The Protein Ontology provides terms for and supports annotation of species-specific protein complexes in an ontology framework that relates them both to their components and to species-independent families of complexes. Comprehensive curation of experimentally known forms and annotations thereof is expected to expose discrepancies, differences, and gaps in our knowledge. We have annotated the early events of innate immune signaling mediated by Toll-Like Receptor 3 and 4 complexes in human, mouse…Read more
-
531The development of non-coding RNA ontologyInternational Journal of Data Mining and Bioinformatics 15 (3): 214--232. 2016.Identification of non-coding RNAs (ncRNAs) has been significantly improved over the past decade. On the other hand, semantic annotation of ncRNA data is facing critical challenges due to the lack of a comprehensive ontology to serve as common data elements and data exchange standards in the field. We developed the Non-Coding RNA Ontology (NCRO) to handle this situation. By providing a formally defined ncRNA controlled vocabulary, the NCRO aims to fill a specific and highly needed niche in semant…Read more
-
472Une théorie unifiée de la vérité et de la référenceIn Jean-Maurice Monnoyer (ed.), La Structure Du Monde, Vrin, Paris. pp. 141-184. 2004.The truthmaker theory rests on the thesis that the link between a true judgment and that in the world to which it corresponds is not a one-to-one but rather a one-to-many relation. An analogous thesis in relation to the link between a singular term and that in the world to which it refers is already widely accepted. This is the thesis to the effect that singular reference is marked by vagueness of a sort that is best understood in supervaluationist terms. In what follows we show that the superva…Read more
-
632Aristotelianism, apriorism, essentialismIn Boettke Peter (ed.), The Elgar Companion to Austrian Economics, Edward Elgard. pp. 33-37. 1994.
-
504A Taxonomy of Granular PartitionsIn Thomas Bittner (ed.), Spatial Information Theory. Foundations of Geographic Information Science, Lecture Notes in Computer Science 2205. pp. 28-43. 2001.In this paper we propose a formal theory of partitions (ways of dividing up or sorting or mapping reality) and we show how the theory can be applied in the geospatial domain. We characterize partitions at two levels: as systems of cells (theory A), and in terms of their projective relation to reality (theory B). We lay down conditions of well-formedness for partitions and we define what it means for partitions to project truly onto reality. We continue by classifying well-formed partitions along…Read more
-
372Les objects sociauxPhilosophique 26 (2). 2002.One reason for the renewed interest in Austrian philosophy, and especially in the work of Brentano and his followers, turns on the fact that analytic philosophers have become once again interested in the traditional problems of metaphysics. It was Brentano, Husserl, and the philosophers and psychologists whom they influenced, who drew attention to the thorny problem of intentionality, the problem of giving an account of the relation between acts and objects or, more generally, between the psycho…Read more
-
725How to Do Things with DocumentsRivista di Estetica 50 179-198. 2012.This essay is a contribution to social ontology, drawing on the work of John Searle and of Hernando de Soto. At the center of the argument is the proposition advanced by de Soto in his Mystery of Capital to the effect that many of the entities which structure our contemporary social reality are entities which exist in virtue of the fact that there are (paper or digital) documents which support their existence. I here develop de Soto’s argument further, focusing specifically on the ontological pr…Read more
Barry Smith
University at Buffalo
National Center for Ontological Research
-
University at BuffaloDepartment of Philosophy
Biomedical Informatics
Neurology
Computer Science and EngineeringDistinguished Professor, Julian Park Chair -
National Center for Ontological ResearchAdministrator
-
APA Eastern Division
Buffalo, New York, United States of America
Areas of Specialization
Metaphysics |
Ontology |
Philosophy of Artificial Intelligence |
Philosophy of Biology |