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458Physics and the phenomenal worldIn Roberto Poli & Peter Simons (eds.), Formal Ontology: Papers Presented at the International Summer School in Philosophy and Artificial Intelligence on "Formal Ontology", Bolzano, Italy, July 1-5, 1991, Central European Institute of Culture, Kluwer. pp. 233-254. 1996.The paper challenges the assumption, common amongst philosophers, that the reality described in the fundamental theories of microphysics is all the reality we have. It will be argued that this assumption is in fact incompatible with the nature of such theories. It will be shown further that the macro-world of three-dimensional bodies and of such qualitative structures as colour and sound can be treated scientifically on its own terms, which is to say not only from the perspective of psychology b…Read more
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599Ontology-based knowledge representation of experiment metadata in biological data miningIn Jake Chen & Stefano Lonardi (eds.), Biological Data Mining, Chapman Hall / Taylor and Francis. pp. 529-559. 2009.According to the PubMed resource from the U.S. National Library of Medicine, over 750,000 scientific articles have been published in the ~5000 biomedical journals worldwide in the year 2007 alone. The vast majority of these publications include results from hypothesis-driven experimentation in overlapping biomedical research domains. Unfortunately, the sheer volume of information being generated by the biomedical research enterprise has made it virtually impossible for investigators to stay awar…Read more
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380Ontology 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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360Ontology-assisted database integration to support natural language processing and biomedical data-miningJournal of Integrative Bioinformatics. Repr. In: Yearbook of Bioinformatics , 39–48 1 1-10. 2004.Successful biomedical data mining and information extraction require a complete picture of biological phenomena such as genes, biological processes, and diseases; as these exist on different levels of granularity. To realize this goal, several freely available heterogeneous databases as well as proprietary structured datasets have to be integrated into a single global customizable scheme. We will present a tool to integrate different biological data sources by mapping them to a proprietary biome…Read more
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211Information may be defined as the conceptual or communicable part of the content of mental acts. The content of mental acts includes sensory data as well as concepts, particular as well as general information. An information system is an external (non-mental) system designed to store such content. Information systems afford indirect transmission of content between people, some of whom may put information into the system and others who are among those who use the system. In order for communicatio…Read more
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224Representing the kinetic state of a patient (posture, motion, and activity) during vital sign measurement is an important part of continuous monitoring applications, especially remote monitoring applications. In contextualized vital sign representation, the measurement result is presented in conjunction with salient measurement context metadata. We present an automated annotation system for vital sign measurements that uses ontologies from the Open Biomedical Ontology Foundry (OBO Foundry) to re…Read more
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524Ontology and medical terminology: Why description logics are not enoughIn Proceedings of the Conference: Towards an Electronic Patient Record (TEPR 2003), Medical Records Institute. 2003.Ontology is currently perceived as the solution of first resort for all problems related to biomedical terminology, and the use of description logics is seen as a minimal requirement on adequate ontology-based systems. Contrary to common conceptions, however, description logics alone are not able to prevent incorrect representations; this is because they do not come with a theory indicating what is computed by using them, just as classical arithmetic does not tell us anything about the entities …Read more
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317Ontologische Aspekte der Husserlschen PhänomenologieHusserl Studies 3 (2): 115-130. 1986.A study of the background of Husserl’s early thinking in the perceptual psychology of Carl Stumpf and of the implications of Stumpfian ideas for an understanding of Husserl’s phenomenology. Other topics treated include the ontology of part, whole and dependence; gestalt theory; and Husserl’s notion of the synthetic a priori
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272Ontologies of cellular networksScience Signalling 1 (50): 1--3. 2008.A comparison of six alternative definitions of the term 'cellular pathway' against the background of ontological realism.
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404We 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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641Ontologies for the life sciencesIn Schulze-Kremer Steffen & Smith Barry (eds.), Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, vol. 4, Wiley. 2005.Where humans can manipulate and integrate the information they receive in subtle and ever-changing ways from context to context, computers need structured and context-free background information of a sort which ontologies can help to provide. A domain ontology captures the stable, highly general and commonly accepted core knowledge for an application domain. The domain at issue here is that of the life sciences, in particular molecular biology and bioinformatics. Contemporary life science resear…Read more
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888Abstract of plenary talk Held at GIScience 2000: First International Conference on Geographic Information Science, Savannah, Georgia.
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210Ontological representation of CDC Active Bacterial Core Surveillance Case ReportsProceedings of the Fifth International Conference on Biomedical Ontology 1327 74-77. 2014.The Center for Disease Control and Prevention’s Active Bacterial Core Surveillance (CDC ABCs) Program is a collaborative effort betweeen the CDC, state health departments, laboratories, and universities to track invasive bacterial pathogens of particular importance to public health [1]. The year-end surveillance reports produced by this program help to shape public policy and coordinate responses to emerging infectious diseases over time. The ABCs case report form (CRF) data represents an excell…Read more
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146Oggetti fiatRivista di Estetica 42 (2). 2002.Extended entities have boundaries of two different sorts: those that do, and those that do not correspond to physical discontinuities. Call the first sort (coastlines, the surface of your nose) bona fide boundaries; and the second (the boundary of Montana, the boundary separating your upper from your lower torso) fiat boundaries. Fiat boundaries are found especially in the geographic realm, but are involved wherever language carves out portions of reality in ways which do not reflect physical di…Read more
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224OmniSearch: a semantic search system based on the Ontology for MIcroRNA Target Gene Interaction dataJournal of Biomedical Semantics 7 (1): 1. 2016.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 a…Read more
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134In previous work on biomedical ontologies we showed how the provision of formal definitions for relations such as is_a and part_of can support new types of auto-mated reasoning about biomedical phenomena. We here extend this approach to the transformation_of characteristic of pathologies.
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548On 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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223Ontobull 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 & C. G. Dean (eds.), Evolving Knowledge in Natural Science and Artificial Intelligence, Pitman Publishing. 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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393Novel 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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656National 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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224Methodology 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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259A 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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249OBCS: 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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239Formalisms 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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779Finding 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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341Informatics: 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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216The 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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3614In Defense of Truth: Skepticism, Morality, and The MatrixIn William 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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201Despite 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
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 |