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  1. Saliva Ontology: An Ontology-Based Framework for a Salivaomics Knowledge Base.Jiye Ai, Barry Smith & David Wong - 2010 - BMC Bioinformatics 11 (1):302.
    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-based controlled vocabulary of terms and relations dedicated to the salivaomics (...)
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  • The Ontology for Biomedical Investigations.Anita Bandrowski, Ryan Brinkman, Mathias Brochhausen, Matthew H. Brush, Bill Bug, Marcus C. Chibucos, Kevin Clancy, Mélanie Courtot, Dirk Derom, Michel Dumontier, Liju Fan, Jennifer Fostel, Gilberto Fragoso, Frank Gibson, Alejandra Gonzalez-Beltran, Melissa A. Haendel, Yongqun He, Mervi Heiskanen, Tina Hernandez-Boussard, Mark Jensen, Yu Lin, Allyson L. Lister, Phillip Lord, James Malone, Elisabetta Manduchi, Monnie McGee, Norman Morrison, James A. Overton, Helen Parkinson, Bjoern Peters, Philippe Rocca-Serra, Alan Ruttenberg, Susanna-Assunta Sansone, Richard H. Scheuermann, Daniel Schober, Barry Smith, Larisa N. Soldatova, Christian J. Stoeckert, Chris F. Taylor, Carlo Torniai, Jessica A. Turner, Randi Vita, Patricia L. Whetzel & Jie Zheng - 2016 - PLoS ONE 11 (4):e0154556.
    The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to (...)
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  • Applications of the ACGT Master Ontology on Cancer.Mathias Brochhausen, Gabriele Weiler, Luis Martín, Cristian Cocos, Holger Stenzhorn, Norbert Graf, Martin Dörr, Manolis Tsiknakis & Barry Smith - 2008 - In R. Meersman & P. Herrero (eds.), Proceedings of 4th International IFIP Workshop On Semantic Web and Web Semantics (OTM 2008: Workshops), LNCS 5333. pp. 1046–1055.
    In this paper we present applications of the ACGT Master Ontology (MO) which is a new terminology resource for a transnational network providing data exchange in oncology, emphasizing the integration of both clinical and molecular data. The development of a new ontology was necessary due to problems with existing biomedical ontologies in oncology. The ACGT MO is a test case for the application of best practices in ontology development. This paper provides an overview of the application of the ontology within (...)
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  • Applied Ontology: An Introduction.Katherine Munn & Barry Smith (eds.) - 2008 - Frankfurt: ontos.
    Ontology is the philosophical discipline which aims to understand how things in the world are divided into categories and how these categories are related together. This is exactly what information scientists aim for in creating structured, automated representations, called 'ontologies,' for managing information in fields such as science, government, industry, and healthcare. Currently, these systems are designed in a variety of different ways, so they cannot share data with one another. They are often idiosyncratically structured, accessible only to those who (...)
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  • The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses.Laurel Cooper, Ramona Walls, Justin Elser, Maria A. Gandolfo, Dennis W. Stevenson, Barry Smith & Others - 2013 - Plant and Cell Physiology 54 (2):1-23..
    The Plant Ontology (PO; http://www.plantontology.org/) is a publicly-available, collaborative effort to develop and maintain a controlled, structured vocabulary (“ontology”) of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of the PO has been expanded (...)
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  • On Carcinomas and Other Pathological Entities.Barry Smith, Anand Kumar, Werner Ceusters & Cornelius Rosse - 2005 - Comparative and Functional Genomics 6 (7/8):379–387.
    Tumors, abscesses, cysts, scars, fractures are familiar types of what we shall call pathological continuant entities. The instances of such types exist always in or on anatomical structures, which thereby become transformed into pathological anatomical structures of corresponding types: a fractured tibia, a blistered thumb, a carcinomatous colon. In previous work on biomedical ontologies we showed how the provision of formal definitions for relations such as is_a, part_of and transformation_of can facilitate the integration of such ontologies in ways which have (...)
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  • Barry Smith an Sich.Gerald J. Erion & Gloria Zúñiga Y. Postigo (eds.) - 2017 - Cosmos + Taxis.
    Festschrift in Honor of Barry Smith on the occasion of his 65th Birthday. Published as issue 4:4 of the journal Cosmos + Taxis: Studies in Emergent Order and Organization. Includes contributions by Wolfgang Grassl, Nicola Guarino, John T. Kearns, Rudolf Lüthe, Luc Schneider, Peter Simons, Wojciech Żełaniec, and Jan Woleński.
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  • Establishing and Harmonizing Ontologies in an Interdisciplinary Health Care and Clinical Research Environment.Barry Smith & Mathias Brochhausen - 2008 - Studies in Health, Technology and Informatics 134:219-234.
    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 paradigm in (...)
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  • Persistence and Ontological Pluralism.Pierre Grenon & Barry Smith - 2008 - In Christian Kanzian (ed.), Persistence. Ontos. pp. 33-48.
    We aim to provide the ontological grounds for an adequate account of persistence. We defend a perspectivalist, or moderate pluralist, position, according to which some aspects of reality can be accounted for in ontological terms only via partial and mutually complementary ontologies, each one of which captures some relevant aspect of reality. Our thesis here is that this is precisely the sort of ontological account that is needed for the understanding of persistence, specifically an account involving two independent ontologies, one (...)
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  • BioTop: An Upper Domain Ontology for the Life sciencesA Description of its Current Structure, Contents and Interfaces to OBO Ontologies.Elena Beisswanger, Stefan Schulz, Holger Stenzhorn & Udo Hahn - 2008 - Applied Ontology 3 (4):205-212.
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  • Overcoming the Ontology Enrichment Bottleneck with Quick Term Templates.Philippe Rocca-Serra, Alan Ruttenberg, Martin J. O'Connor, Patricia L. Whetzel, Daniel Schober, Jay Greenbaum, Mélanie Courtot, Ryan R. Brinkman, Susanna Assunta Sansone & Richard Scheuermann - 2011 - Applied Ontology 6 (1):13-22.
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  • Flexibility and Utility of the Cell Cycle Ontology.Vladimir Mironov, Erick Antezana, Mikel Egaña, Ward Blondé, Bernard De Baets, Martin Kuiper & Robert Stevens - 2011 - Applied Ontology 6 (3):247-261.
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  • MIREOT: The Minimum Information to Reference an External Ontology Term.Mélanie Courtot, Frank Gibson, Allyson L. Lister, James Malone, Daniel Schober, Ryan R. Brinkman & Alan Ruttenberg - 2011 - Applied Ontology 6 (1):23-33.
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  • Referent Tracking: The Problem of Negative Findings.Werner Ceusters, Peter Elkin & Barry Smith - 2006 - Studies in Health Technology and Informatics 124:741-46.
    The paradigm of referent tracking is based on a realist presupposition which rejects so-called negative entities (congenital absent nipple, and the like) as spurious. How, then, can a referent tracking-based Electronic Health Record deal with what are standardly called ‘negative findings’? To answer this question we carried out an analysis of some 748 sentences drawn from patient charts and containing some form of negation. Our analysis shows that to deal with these sentences we need to introduce a new ontological relationship (...)
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  • A Terminological and Ontological Analysis of the NCI Thesaurus.Werner Ceusters, Barry Smith & Louis Goldberg - 2005 - Methods of Information in Medicine 44 (4):498-507.
    We performed a qualitative analysis of the Thesaurus in order to assess its conformity with principles of good practice in terminology and ontology design. We used both the on-line browsable version of the Thesaurus and its OWL-representation (version 04.08b, released on August 2, 2004), measuring each in light of the requirements put forward in relevant ISO terminology standards and in light of ontological principles advanced in the recent literature. Version 04.08b of the NCI Thesaurus suffers from the same broad range (...)
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  • Foundation for the Electronic Health Record: An Ontological Analysis of the HL7 Reference Information Model.Lowell Vizenor, Barry Smith & Werner Ceusters - 2004 - In IFOMIS Reports. Saarbrücken: IFOMIS. pp. 1-14.
    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 healthcare information and knowledge needs to rest (...)
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  • Referent Tracking for Corporate Memories.Werner Ceusters & Barry Smith - 2007 - In Peter Rittgen (ed.), Handbook of Ontologies for Business Interaction. Idea Group Publishing. pp. 34-46.
    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 objective. We discuss how (...)
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  • Bioinformatics Advances in Saliva Diagnostics.Ji-Ye Ai, Barry Smith & David T. W. Wong - 2012 - International Journal of Oral Science 4 (2):85--87.
    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 informatics advances in saliva (...)
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  • An Evolutionary Approach to the Representation of Adverse Events.Werner Ceusters, Maria Capolupo, Barry Smith & Georges De Moor - 2009 - Studies in Health Technology and Informatics 150:537-541.
    One way to detect, monitor and prevent adverse events with the help of Information Technology is by using ontologies capable of representing three levels of reality: what is the case, what is believed about reality, and what is represented. We report on how Basic Formal Ontology and Referent Tracking exhibit this capability and how they are used to develop an adverse event ontology and related data annotation scheme for the European ReMINE project.
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  • Biomedizinische Ontologien für die Praxis.M. Brochhausen & Barry Smith - 2009 - European Journal for Biomedical Informatics 1.
    Hintergrund: Biomedizinische Ontologien existieren unter anderem zur Integration von klinischen und experimentellen Daten. Um dies zu erreichen ist es erforderlich, dass die fraglichen Ontologien von einer großen Zahl von Benutzern zur Annotation von Daten verwendet werden. Wie können Ontologien das erforderliche Maß an Benutzerfreundlichkeit, Zuverlässigkeit, Kosteneffektivität und Domänenabdeckung erreichen, um weitreichende Akzeptanz herbeizuführen? -/- Material und Methoden: Wir konzentrieren uns auf zwei unterschiedliche Strategien, die zurzeit hierbei verfolgt werden. Eine davon wird von SNOMED CT im Bereich der Medizin vertreten, die (...)
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  • The Evaluation of Ontologies: Editorial Review Vs. Democratic Ranking.Barry Smith - 2008 - In Proceedings of InterOntology (Tokyo, Japan, 26-27 February 2008),. Tokyo: Keio University Press. pp. 127-138.
    Increasingly, the high throughput technologies used by biomedical researchers are bringing about a situation in which large bodies of data are being described using controlled structured vocabularies—also known as ontologies—in order to support the integration and analysis of this data. Annotation of data by means of ontologies is already contributing in significant ways to the cumulation of scientific knowledge and, prospectively, to the applicability of cross-domain algorithmic reasoning in support of scientific advance. This very success, however, has led to a (...)
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  • Ontologies for the Life Sciences.Steffen Schulze-Kremer & Barry Smith - 2005 - In Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, vol. 4. Wiley.
    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 research includes components drawn from physics, chemistry, mathematics, medicine (...)
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  • Proposed Actions Are No Actions: Re-Modelling an Ontology Design Pattern with a Realist Top-Level Ontology.D. Seddig-Raufie, L. Jansen, S. Schulz, D. Schober & M. Boeker - 2012 - Journal of Biomedical Semantics 3 (2).
    Background -/- Ontology Design Patterns (ODPs) are representational artifacts devised to offer solutions for recurring ontology design problems. They promise to enhance the ontology building process in terms of flexibility, re-usability and expansion, and to make the result of ontology engineering more predictable. In this paper, we analyze ODP repositories and investigate their relation with upper-level ontologies. In particular, we compare the BioTop upper ontology to the Action ODP from the NeOn an ODP repository. In view of the differences in (...)
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  • Introduction: What is Ontology For.Katherine Munn - 2008 - In Munn Katherine & Smith Barry (eds.), Applied Ontology: An Introduction. Walter de Gruyter. pp. 7-19.
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  • Ontology of Psychological Attributes on Color Emotions.Keiichi Muramatsu, Tatsuo Togawa, Kazuaki Kojima & Tatsunori Matsui - 2015 - Transactions of the Japanese Society for Artificial Intelligence 30 (1):47-60.
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