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647On the application of formal principles to life science data: A case study in the Gene OntologyIn Köhler Jacob, Kumar Anand & Smith Barry (eds.), Proceedings of DILS 2004 (Data Integration in the Life Sciences), (Lecture Notes in Bioinformatics 2994), Springer. pp. 79-94. 2004.Formal principles governing best practices in classification and definition have for too long been neglected in the construction of biomedical ontologies, in ways which have important negative consequences for data integration and ontology alignment. We argue that the use of such principles in ontology construction can serve as a valuable tool in error-detection and also in supporting reliable manual curation. We argue also that such principles are a prerequisite for the successful application o…Read more
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248Ontobull and BFOConvert: Web-based programs to support automatic ontology conversionProceedings of the Joint International Conference on Biological Ontology and Biocreative 1747. 2016.When a widely reused ontology appears in a new version which is not compatible with older versions, the ontologies reusing it need to be updated accordingly. Ontobull has been developed to automatically update ontologies with new term IRI(s) and associated metadata to take account of such version changes. To use the Ontobull web interface a user is required to (i) upload one or more ontology OWL source files; (ii) input an ontology term IRI mapping; and (where needed) (iii) provide update settin…Read more
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269New foundations for qualitative physicsIn J. E. Tiles, G. T. McKee & G. C. Dean (eds.), Evolving knowledge in natural science and artificial intelligence, Pitman. pp. 231-49. 1990.Physical reality is all the reality we have, and so physical theory in the standard sense is all the ontology we need. This, at least, was an assumption taken almost universally for granted by the advocates of exact philosophy for much of the present century. Every event, it was held, is a physical event, and all structure in reality is physical structure. The grip of this assumption has perhaps been gradually weakened in recent years as far as the sciences of mind are concerned. When it comes t…Read more
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423Novel 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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641National Center for Biomedical Ontology: Advancing biomedicine through structured organization of scientific knowledgeOmics: A Journal of Integrative Biology 10 (2): 185-198. 2006.The National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality op…Read more
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241Methodology for semantic enhancement of intelligence dataCUBRC Report. 2013.What follows is a contribution to the horizontal integration of warfighter intelligence data as defined in Chairman of the Joint Chiefs of Staff Instruction J2 CJCSI 3340.02AL: Horizontally integrating warfighter intelligence data improves the consumers’ production, analysis and dissemination capabilities. HI requires access (including discovery, search, retrieval, and display) to intelligence data among the warfighters and other producers and consumers via standardized services and architecture…Read more
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284Medical WordNet: A new methodology for the construction and validation of information resources for consumer healthIn Barry Smith & Christiane Fellbaum (eds.), Proceedings of Coling: The 20th International Conference on Computational Linguistics, . pp. 371-382. 2004.A consumer health information system must be able to comprehend both expert and non-expert medical vocabulary and to map between the two. We describe an ongoing project to create a new lexical database called Medical WordNet (MWN), consisting of medically relevant terms used by and intelligible to non-expert subjects and supplemented by a corpus of natural-language sentences that is designed to provide medically validated contexts for MWN terms. The corpus derives primarily from online health in…Read more
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320OBCS: The Ontology of Biological and Clinical StatisticsProceedings of the Fifth International Conference on Biomedical Ontology 1327 65. 2014.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 pres…Read more
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272Investigating subsumption in DL-based terminologies: A case study in SNOMED CTIn Olivier Bodenreider, Barry Smith, Anand Kumar & Anita Burgun (eds.), Proceedings of the First International Workshop on Formal Biomedical Knowledge Representation (KR-MED 2004), . pp. 12-20. 2004.Formalisms such as description logics (DL) are sometimes expected to help terminologies ensure compliance with sound ontological principles. The objective of this paper is to study the degree to which one DL-based biomedical terminology (SNOMED CT) complies with such principles. We defined seven ontological principles (for example: each class must have at least one parent, each class must differ from its parent) and examined the properties of SNOMED CT classes with respect to these principles. O…Read more
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735Finding Our Way through PhenotypesPLoS Biol 13 (1). 2015.Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systemat…Read more
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358Informatics: the fuel for pharmacometric analysisAAPS Journal 9 (1). 2007.The current informal practice of pharmacometrics as a combination art and science makes it hard to appreciate the role that informatics can and should play in the future of the discipline and to comprehend the gaps that exist because of its absence. The development of pharmacometric informatics has important implications for expediting decision making and for improving the reliability of decisions made in model-based development. We argue that well-defined informatics for pharmacometrics can lea…Read more
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306The emphasis on evidence based medicine (EBM) has placed increased focus on finding timely answers to clinical questions in presence of patients. Using a combination of natural language processing for the generation of clinical excerpts and information theoretic distance based clustering, we evaluated multiple approaches for the efficient presentation of context-sensitive EBM excerpts.
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3676In Defense of Truth: Skepticism, Morality, and The MatrixIn W. Irwin (ed.), Philosophy and The Matrix, Open Court. pp. 16-27. 2002.The Matrix exposes us to the uncomfortable worries of philosophical skepticism in an especially compelling way. However, with a bit more reflection, we can see why we need not share the skeptic’s doubts about the existence of the world. Such doubts are appropriate only in the very special context of the philosophical seminar. When we return to normal life we see immediately that they are groundless. Furthermore, we see also the drastic mistake that Cypher commits in turning his back upon reality…Read more
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225Foundation for the Electronic Health Record: An ontological analysis of the HL7 Reference Information ModelIn Vizenor Lowell, Smith Barry & Ceusters Werner (eds.), Ifomis Reports, Ifomis. pp. 1-14. 2004.Despite the recent advances in information and communication technology that have increased our ability to store and circulate information, the task remains of ensuring that the right sorts of information reach the right sorts of people. In what follows we defend the thesis that efforts to develop efficient means for sharing information across healthcare systems and organizations would benefit from a careful analysis of human action in healthcare organizations, and that the communication of heal…Read more
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228Formalizing UMLS Relations Using Semantic Partitions in the Context of a Task-Based Clinical Guidelines ModelIn Anand Kumar, Matteo Piazza, Barry Smith, Silvana Quaglini & Mario Stefanelli (eds.), Formalizing UMLS Relations Using Semantic Partitions in the Context of a Task-Based Clinical Guidelines Model, Ifomis. 2004.An important part of the Unified Medical Language System (UMLS) is its Semantic Network, consisting of 134 Semantic Types connected to each other by edges formed by one or more of 54 distinct Relation Types. This Network is however for many purposes overcomplex, and various groups have thus made attempts at simplification. Here we take this work further by simplifying the relations which involve the three Semantic Types – Diagnostic Procedure, Laboratory Procedure and Therapeutic or Preventive P…Read more
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406Development 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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250Dealing with elements of medical encounters: An approach based on ontological realismProceedings of the Joint International Conference on Biological Ontology and Biocreative 1747. 2016.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 groun…Read more
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688Adolf Reinach: An annotated bibliographyIn Kevin Mulligan (ed.), Speech Act and Sachverhalt: Reinach and the Foundations of Realist Phenomenology, Reidel. pp. 299-332. 1987.Ever since its appearance in 1913, Reinach's work on a The A Priori Foundations of the Civil Law has served as the principal representative of phenomenological, aprioristic and ontological/realist approaches to the philosophy of law. This annotated bibliography provides an overview of the reception of Reinach's thinking, which has been of influence also in the realm of speech act theory.
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492An improved ontological representation of dendritic cells as a paradigm for all cell typesBMC Bioinformatics 10 (1): 70. 2009.
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292The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and compu…Read more
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265Representing disease courses: An application of the Neurological Disease Ontology to Multiple Sclerosis TypologyIn Jensen Mark, Cox Alexander P., Diehl Alexander & Smith Barry (eds.), Proceedings of the Fourth International Conference on Biomedical Ontology (ICBO), CEUR 1060, . 2013.The Neurological Disease Ontology (ND) is being developed to provide a comprehensive framework for the representation of neurological diseases (Diehl et al., 2013). ND utilizes the model established by the Ontology for General Medical Science (OGMS) for the representation of entities in medicine and disease (Scheuermann et al., 2009). The goal of ND is to include information for each disease concerning its molecular, genetic, and environmental origins, the processes involved in its etiology and …Read more
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322A diagrammatic representation for entities and mereotopological relations in ontologiesIn José M. Parente de Oliveira & Barry Smith (eds.), CEUR, vol. 1908, . 2017.In the graphical representation of ontologies, 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. We focus here on a problem in the graph-based representation of ontologies in complex domains such as biomedical, engineering and manufacturing: lack of mereotopological representation. Based on such limitation, we proposed a diagrammatic way to represent an entity’s structure and various forms of …Read more
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552Functional Anatomy: A Taxonomic ProposalActa Biotheoretica 53 (3): 153-166. 2005.It is argued that medical science requires a classificatory system that (a) puts functions in the taxonomic center and (b) does justice ontologically to the difference between the processes which are the realizations of functions and the objects which are their bearers. We propose formulae for constructing such a system and describe some of its benefits. The arguments are general enough to be of interest to all the life sciences.
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389OntONeo: The Obstetric and Neonatal OntologyIn Farinelli Fernanda, Almeida Mauricio, Elkin Peter & Barry Smith (eds.), Dealing with elements of medical encounters: An approach based on ontological realism, Ceur, Vol. 1747. 2016.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…Read more
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361The ImmPort Antibody OntologyProceedings of the International Conference on Biological Ontology 1747. 2016.Monoclonal antibodies are essential biomedical research and clinical reagents that are produced by companies and research laboratories. The NIAID ImmPort (Immunology Database and Analysis Portal) resource provides a long-term, sustainable data warehouse for immunological data generated by NIAID, DAIT and DMID funded investigators for data archiving and re-use. A variety of immunological data is generated using techniques that rely upon monoclonal antibody reagents, including flow cytometry, immu…Read more
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248The Ontology of DocumentsIn Okada Mitsuhiro (ed.), Proceedings of the Conference on Ontology and Analytical Metaphysics, February 24-25, 2011, Keio University Press. pp. 1-6. 2011.As is well known, speech acts such as acts of promising can have ontological consequences. For example an act of promising can give rise to a mutually correlated claim and obligation. Increasingly, speech acts in the narrow sense are being augmented by the use of documents of multiple different sorts. In this paper we analyze the results of this augmenta-tion from the ontological point of view, considering especially the domains of law and com-merce. We show how document acts are not isolated ph…Read more
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285Kognitionsforskningens topologiske grundlagSemikolon 3 (7): 91-105. 2003.The paper introduces the concepts at the heart of point-set-topology and of mereotopology (topology founded in the non-atomistic theory of parts and wholes) in an informal and intuitive fashion. It will then seek to demonstrate how mereotopological ideas can be of particular utility in cognitive science applications. The prehistory of such applications (in the work of Husserl, the Gestaltists, of Kurt Lewin and of J. J. Gibson) will be sketched, together with an indication of the field of possib…Read more
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5261OntologíaIn Hurtado G. & Nudler O. (eds.), El mobiliario del mundo. Ensayos de ontología, Universidad Autónoma De México. 2007.Presentiamo qui la traduzione di un lungo saggio sull’ontologia e i sistemi informativi. Abbiamo tradotto la parte più generale con le distinzioni base tra ontologia, metafisica e scienza. L’autore, fornendo un suo punto di vista peculiare sull’ontologia, descrive le diverse questioni e distinzioni connesse all’impresa ontologica, considerando sia il punto di vista dei filosofi che degli informatici.
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341Rationality 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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256Bela Zalai und die Metaphysik des reinen SeinsBrentano Studien. Internationales Jahrbuch der Franz Brentano Forschung 5. 1994.Between 1910 und 1915 the Hungarian philosopher Béla Zalai (1882-1915) developed his “comparative metaphysics of systems”, which had a significant influence on both the young Georg Lukács and also on Karl Mannheim. Through an analysis of Zalai’s approach to metaphysics, we show how he served to mediate between the realist Austrian philosophy of Meinong and of the early Husserl on the one side, and the German (idealistic, Kantian) philosophy then dominant in Hungary.
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 |