Results for 'applied ontology'

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  1. Applied Ontology: Focusing on Content.Nicola Guarino & Mark A. Musen - 2005 - Applied ontology 1 (1):1-5.
    In a world that is overflowing with journals and other outlets for scientific publication, the appearance of any new periodical requires some justification. There are already more journals than we can read and more conferences than we can attend. In the case of applied Ontology, we believe that the creation of anew journal not only is completely justifiable, it is downright exciting. For too long, workers in computer science have assumed that content comes for free. “Theory” in computer (...)
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  2. 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 (...)
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  3. Analytic Metaphysics Versus Naturalized Metaphysics: The Relevance of Applied Ontology.Baptiste Le Bihan & Adrien Barton - 2021 - Erkenntnis 86 (1):21-37.
    The relevance of analytic metaphysics has come under criticism: Ladyman & Ross, for instance, have suggested do discontinue the field. French & McKenzie have argued in defense of analytic metaphysics that it develops tools that could turn out to be useful for philosophy of physics. In this article, we show first that this heuristic defense of metaphysics can be extended to the scientific field of applied ontology, which uses constructs from analytic metaphysics. Second, we elaborate on a parallel (...)
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  4. Applied Ontology: A New Discipline is Born.B. Smith - 1998 - Philosophy Today 12 (29):5-6.
    The discipline of applied ethics already has a certain familiarity in the Anglo-Saxon world, above all through the work of Peter Singer. Applied ethics uses the tools of moral philosophy to resolve practical problems of the sort which arise, for example, in the running of hospitals. In the University at Buffalo (New York) there was organized on April 24-25 1998 the world's first conference on a new, sister discipline, the discipline of applied ontology. Applied ontologists (...)
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  5. Classifying Processes: An Essay in Applied Ontology.Barry Smith - 2012 - Ratio 25 (4):463-488.
    We begin by describing recent developments in the burgeoning discipline of applied ontology, focusing especially on the ways ontologies are providing a means for the consistent representation of scientific data. We then introduce Basic Formal Ontology (BFO), a top-level ontology that is serving as domain-neutral framework for the development of lower level ontologies in many specialist disciplines, above all in biology and medicine. BFO is a bicategorial ontology, embracing both three-dimensionalist (continuant) and four-dimensionalist (occurrent) perspectives (...)
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  6. Biodynamic Ontology: Applying BFO in the Biomedical Domain.Barry Smith, Pierre Grenon & Louis Goldberg - 2004 - Studies in Health and Technology Informatics 102:20–38.
    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 (...)
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  7. Mapping the Patient’s Experience: An Applied Ontological Framework for Phenomenological Psychopathology.Rasmus Rosenberg Larsen & Janna Hastings - 2020 - Phenomenology and Mind 18:200-219.
    Mental health research faces a suite of unresolved challenges that have contributed to a stagnation of research efforts and treatment innovation. One such challenge is how to reliably and validly account for the subjective side of patient symptomatology, that is, the patient’s inner experiences or patient phenomenology. Providing a structured, standardised semantics for patient phenomenology would enable future research in novel directions. In this contribution, we aim at initiating a standardized approach to patient phenomenology by sketching a tentative formalisation within (...)
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  8. Applying the Realism-Based Ontology-Versioning Method for Tracking Changes in the Basic Formal Ontology.Selja Seppälä, Barry Smith & Werner Ceusters - 2014 - In P. Garbacz & O. Kutz (eds.), Formal Ontology in Information Systems (FOIS 2014). IOS Press. pp. 227-240.
    Changes in an upper level ontology have obvious conse-quences for the domain ontologies that use it at lower levels. It is therefore crucial to document the changes made between successive versions of ontologies of this kind. We describe and apply a method for tracking, explaining and measuring changes between successive versions of upper level ontologies such as the Basic Formal Ontology (BFO). The proposed change-tracking method extends earlier work on Realism-Based Ontology Versioning (RBOV) and Evolutionary Terminology Auditing (...)
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  9. Building Ontologies with Basic Formal Ontology.Robert Arp, Barry Smith & Andrew D. Spear - 2015 - Cambridge, MA: MIT Press.
    In the era of “big data,” science is increasingly information driven, and the potential for computers to store, manage, and integrate massive amounts of data has given rise to such new disciplinary fields as biomedical informatics. Applied ontology offers a strategy for the organization of scientific information in computer-tractable form, drawing on concepts not only from computer and information science but also from linguistics, logic, and philosophy. This book provides an introduction to the field of applied (...) that is of particular relevance to biomedicine, covering theoretical components of ontologies, best practices for ontology design, and examples of biomedical ontologies in use. After defining an ontology as a representation of the types of entities in a given domain, the book distinguishes between different kinds of ontologies and taxonomies, and shows how applied ontology draws on more traditional ideas from metaphysics. It presents the core features of the Basic Formal Ontology (BFO), now used by over one hundred ontology projects around the world, and offers examples of domain ontologies that utilize BFO. The book also describes Web Ontology Language (OWL), a common framework for Semantic Web technologies. Throughout, the book provides concrete recommendations for the design and construction of domain ontologies. (shrink)
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  10. Ontology.Barry Smith - 2003 - In Luciano Floridi (ed.), Blackwell Guide to the Philosophy of Computing and Information. Oxford: Blackwell. pp. 155-166.
    Ontology as a branch of philosophy is the science of what is, of the kinds and structures of objects, properties, events, processes and relations in every area of reality. ‘Ontology’ in this sense is often used by philosophers as a synonym of ‘metaphysics’ (a label meaning literally: ‘what comes after the Physics’), a term used by early students of Aristotle to refer to what Aristotle himself called ‘first philosophy’. But in recent years, in a development hardly noticed by (...)
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  11. Ontology and Metaontology: A Contemporary Guide.Francesco Berto & Matteo Plebani - 2015 - Bloomsbury Academic.
    'Ontology and Metaontology: A Contemporary Guide' is a clear and accessible survey of ontology, focussing on the most recent trends in the discipline. -/- Divided into parts, the first half characterizes metaontology: the discourse on the methodology of ontological inquiry, covering the main concepts, tools, and methods of the discipline, exploring the notions of being and existence, ontological commitment, paraphrase strategies, fictionalist strategies, and other metaontological questions. The second half considers a series of case studies, introducing and familiarizing (...)
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  12. 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 (...)
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  13. The Ontology of Bohmian Mechanics.M. Esfeld, D. Lazarovici, Mario Hubert & D. Durr - 2014 - British Journal for the Philosophy of Science 65 (4):773-796.
    The paper points out that the modern formulation of Bohm’s quantum theory known as Bohmian mechanics is committed only to particles’ positions and a law of motion. We explain how this view can avoid the open questions that the traditional view faces according to which Bohm’s theory is committed to a wave-function that is a physical entity over and above the particles, although it is defined on configuration space instead of three-dimensional space. We then enquire into the status of the (...)
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  14. Primitive Ontology in a Nutshell.Valia Allori - 2015 - International Journal of Quantum Foundations 1 (2):107-122.
    The aim of this paper is to summarize a particular approach of doing metaphysics through physics - the primitive ontology approach. The idea is that any fundamental physical theory has a well-defined architecture, to the foundation of which there is the primitive ontology, which represents matter. According to the framework provided by this approach when applied to quantum mechanics, the wave function is not suitable to represent matter. Rather, the wave function has a nomological character, given that (...)
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  15. Ontology: Towards a New Synthesis.Barry Smith & Chris Welty - 2001 - In Formal Ontology in Information Systems. New York: ACM Press.
    This introduction to the second international conference on Formal Ontology and Information Systems presents a brief history of ontology as a discipline spanning the boundaries of philosophy and information science. We sketch some of the reasons for the growth of ontology in the information science field, and offer a preliminary stocktaking of how the term ‘ontology’ is currently used. We conclude by suggesting some grounds for optimism as concerns the future collaboration between philosophical ontologists and information (...)
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  16. Ontological Pluralism and Notational Variance.Bruno Whittle - 2020 - Oxford Studies in Metaphysics 12:58-72.
    Ontological pluralism is the view that there are different ways to exist. It is a position with deep roots in the history of philosophy, and in which there has been a recent resurgence of interest. In contemporary presentations, it is stated in terms of fundamental languages: as the view that such languages contain more than one quantifier. For example, one ranging over abstract objects, and another over concrete ones. A natural worry, however, is that the languages proposed by the pluralist (...)
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  17. Ontological Individualism Reconsidered.Brian Epstein - 2009 - Synthese 166 (1):187-213.
    The thesis of methodological individualism in social science is commonly divided into two different claims—explanatory individualism and ontological individualism. Ontological individualism is the thesis that facts about individuals exhaustively determine social facts. Initially taken to be a claim about the identity of groups with sets of individuals or their properties, ontological individualism has more recently been understood as a global supervenience claim. While explanatory individualism has remained controversial, ontological individualism thus understood is almost universally accepted. In this paper I argue (...)
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  18. Ontology-Based Fusion of Sensor Data and Natural Language.Erik Thomsen & Barry Smith - 2018 - Applied Ontology 13 (4):295-333.
    We describe a prototype ontology-driven information system (ODIS) that exploits what we call Portion of Reality (POR) representations. The system takes both sensor data and natural language text as inputs and composes on this basis logically structured POR assertions. The goal of our prototype is to represent both natural language and sensor data within a single framework that is able to support both axiomatic reasoning and computation. In addition, the framework should be capable of discovering and representing new kinds (...)
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  19. Ontology as Product-Service System: Lessons Learned From GO, BFO and DOLCE.Barry Smith - 2019 - In Proceedings of the 10th International Conference on Biomedical Ontology (ICBO), Buffalo, NY.
    This paper defends a view of the Gene Ontology (GO) and of Basic Formal Ontology (BFO) as examples of what the manufacturing industry calls product-service systems. This means that they are products (the ontologies) bundled with a range of ontology services such as updates, training, help desk, and permanent identifiers. The paper argues that GO and BFO are contrasted in this respect with DOLCE, which approximates more closely to a scientific theory or a scientific publication. The paper (...)
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  20. Ontological Realism: A Methodology for Coordinated Evolution of Scientific Ontologies.Barry Smith & Werner Ceusters - 2010 - Applied ontology 5 (3):139-188.
    Since 2002 we have been testing and refining a methodology for ontology development that is now being used by multiple groups of researchers in different life science domains. Gary Merrill, in a recent paper in this journal, describes some of the reasons why this methodology has been found attractive by researchers in the biological and biomedical sciences. At the same time he assails the methodology on philosophical grounds, focusing specifically on our recommendation that ontologies developed for scientific purposes should (...)
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  21. Functions in Basic Formal Ontology.Andrew D. Spear, Werner Ceusters & Barry Smith - 2016 - Applied ontology 11 (2):103-128.
    The notion of function is indispensable to our understanding of distinctions such as that between being broken and being in working order (for artifacts) and between being diseased and being healthy (for organisms). A clear account of the ontology of functions and functioning is thus an important desideratum for any top-level ontology intended for application to domains such as engineering or medicine. The benefit of using top-level ontologies in applied ontology can only be realized when each (...)
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  22.  87
    The Ontology of the Gene Ontology.Barry Smith, Jennifer Williams & Steffen Schulze-Kremer - 2003 - In AMIA 2003 Symposium Proceedings. Washington, DC: AMIA. pp. 609-613.
    The rapidly increasing wealth of genomic data has driven the development of tools to assist in the task of representing and processing information about genes, their products and their functions. One of the most important of these tools is the Gene Ontology (GO), which is being developed in tandem with work on a variety of bioinformatics databases. An examination of the structure of GO, however, reveals a number of problems, which we believe can be resolved by taking account of (...)
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  23. An Ontological Approach to Representing the Product Life Cycle.J. Neil Otte, Dimitris Kiritsi, Munira Mohd Ali, Ruoyu Yang, Binbin Zhang, Ron Rudnicki, Rahul Rai & Barry Smith - 2019 - Applied Ontology 14 (2):1-19.
    The ability to access and share data is key to optimizing and streamlining any industrial production process. Unfortunately, the manufacturing industry is stymied by a lack of interoperability among the systems by which data are produced and managed, and this is true both within and across organizations. In this paper, we describe our work to address this problem through the creation of a suite of modular ontologies representing the product life cycle and its successive phases, from design to end of (...)
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  24. Levels: Descriptive, Explanatory, and Ontological.Christian List - 2019 - Noûs 53 (4):852-883.
    Scientists and philosophers frequently speak about levels of description, levels of explanation, and ontological levels. In this paper, I propose a unified framework for modelling levels. I give a general definition of a system of levels and show that it can accommodate descriptive, explanatory, and ontological notions of levels. I further illustrate the usefulness of this framework by applying it to some salient philosophical questions: (1) Is there a linear hierarchy of levels, with a fundamental level at the bottom? And (...)
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  25. The Ontology of Group Agency.Daniele Porello, Emanuele Bottazzi & Roberta Ferrario - 2014 - In Pawel Garbacz & Oliver Kutz (eds.), Formal Ontology in Information Systems - Proceedings of the Eighth International Conference, {FOIS} 2014, September, 22-25, 2014, Rio de Janeiro, Brazil. pp. 183--196.
    We present an ontological analysis of the notion of group agency developed by Christian List and Philip Pettit. We focus on this notion as it allows us to neatly distinguish groups, organizations, corporations – to which we may ascribe agency – from mere aggregates of individuals. We develop a module for group agency within a foundational ontology and we apply it to organizations.
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  26. Ontology and Values Anchor Indigenous and Grey Nomenclatures: A Case Study in Lichen Naming Practices Among the Samí, Sherpa, Scots, and Okanagan.Catherine Kendig - 2020 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 84:101340.
    Ethnobotanical research provides ample justification for comparing diverse biological nomenclatures and exploring ways that retain alternative naming practices. However, how (and whether) comparison of nomenclatures is possible remains a subject of discussion. The comparison of diverse nomenclatural practices introduces a suite of epistemic and ontological difficulties and considerations. Different nomenclatures may depend on whether the communities using them rely on formalized naming conventions; cultural or spiritual valuations; or worldviews. Because of this, some argue that the different naming practices may not (...)
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  27. Ontological Dependence, Spatial Location, and Part Structure.Friederike Moltmann - 2019 - In Roberta Ferrario, Stefano Borgo, Laure Vieu & Claudio Masolo (eds.), Festschrift for Nicola Guarino. Amsterdam: IOS Publications.
    This paper discusses attributively limited concrete objects such as disturbances (holes, folds, scratches etc), tropes, and attitudinal objects, which lack the sort of spatial location or part structures expected of them as concrete objects. The paper proposes an account in terms of (quasi-Fregean) abstraction, which has so far been applied only to abstract objects.
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  28. Ontology-Based Error Detection in SNOMED-CT.Werner Ceusters, Barry Smith, Anand Kumar & Christoffel Dhaen - 2004 - Proceedings of Medinfo 2004:482-6.
    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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  29.  96
    On the Ontology of Functions.Stefano Borgo, Riichiro Mizoguchi & Barry Smith - 2011 - Applied Ontology 6 (2):99-104.
    This special issue of Applied Ontology is devoted to the foundation, the comparison and the application of functional theories in all areas, with particular attention to the biological and engineering domains. It includes theoretical and technical contributions related to the description, characterization, and application of functions.
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  30. An Ontological Architecture for Orbital Debris Data.Robert J. Rovetto - 2015 - Earth Science Informatics 9 (1):67-82.
    The orbital debris problem presents an opportunity for inter-agency and international cooperation toward the mutually beneficial goals of debris prevention, mitigation, remediation, and improved space situational awareness (SSA). Achieving these goals requires sharing orbital debris and other SSA data. Toward this, I present an ontological architecture for the orbital debris and broader SSA domain, taking steps in the creation of an orbital debris ontology (ODO). The purpose of this ontological system is to (I) represent general orbital debris and SSA (...)
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  31.  76
    Formal Approaches to the Ontological Argument.Ricardo Silvestre & Jean-Yves Beziau - 2018 - Journal of Applied Logics 5 (7):1433-1440.
    This paper introduces the special issue on Formal Approaches to the Ontological Argument of the Journal of Applied Logics (College Publications). The issue contains the following articles: Formal Approaches to the Ontological Argument, by Ricardo Sousa Silvestre and Jean-Yves Béziau; A Brief Critical Introduction to the Ontological Argument and its Formalization: Anselm, Gaunilo, Descartes, Leibniz and Kant, by Ricardo Sousa Silvestre; A Mechanically Assisted Examination of Begging the Question in Anselm’s Ontological Argument, by John Rushby; A Tractarian Resolution to (...)
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  32. The 2006 Upper Ontology Summit Joint Communiqué.Leo Obrst, Patrick Cassidy, Steve Ray, Barry Smith, Dagobert Soergel, Matthew West & Peter Yim - 2006 - Applied Ontology 1 (2):203-211.
    On March 14-15, 2006, at the US National Institute of Standards and Technology (NIST) in Gaithersburg, MD there took place the first Upper Ontology Summit (UOS). This was a convening of custodians of several prominent upper ontologies, key technology participants, and interested other parties, with the purpose of finding a means to relate the different ontologies to each other. The result is reflected in a joint communiqué, directed to the larger ontology community and the general public, and expressing (...)
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  33. Ontology Based Annotation of Contextualized Vital Signs.Goldfain Albert, Xu Min, Bona Jonathan & Barry Smith - 2013 - In Proceedings of the Fourth International Conference on Biomedical Ontology (ICBO). Montreal: pp. 28-33.
    Representing 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 represent the patient’s kinetic state at the time of measurement. The annotation system is (...)
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  34. SNAP and SPAN: Towards Dynamic Spatial Ontology.Pierre Grenon & Barry Smith - 2004 - Spatial Cognition and Computation 4 (1):69–103.
    We propose a modular ontology of the dynamic features of reality. This amounts, on the one hand, to a purely spatial ontology supporting snapshot views of the world at successive instants of time and, on the other hand, to a purely spatiotemporal ontology of change and process. We argue that dynamic spatial ontology must combine these two distinct types of inventory of the entities and relationships in reality, and we provide characterizations of spatiotemporal reasoning in the (...)
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  35. Representing Mental Functioning: Ontologies for Mental Health and Disease.Janna Hastings, Werner Ceusters, Mark Jensen, Kevin Mulligan & Barry Smith - 2012 - In Towards an Ontology of Mental Functioning (ICBO Workshop), Proceeedings of the Third International Conference on Biomedical Ontology.
    Mental and behavioral disorders represent a significant portion of the public health burden in all countries. The human cost of these disorders is immense, yet treatment options for sufferers are currently limited, with many patients failing to respond sufficiently to available interventions and drugs. High quality ontologies facilitate data aggregation and comparison across different disciplines, and may therefore speed up the translation of primary research into novel therapeutics. Realism-based ontologies describe entities in reality and the relationships between them in such (...)
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  36. Fictionalism in Ontology.Achille C. Varzi - 2013 - In Carola Barbero, Maurizio Ferraris & Alberto Voltolini (eds.), From Fictionalism to Realism. Cambridge Scholars Press. pp. 133–151.
    Fictionalism in ontology is a mixed bag. Here I focus on three main variants—which I label after the names of Pascal, Berkeley, and Hume—and consider their relative strengths and weaknesses. The first variant is just a version of the epistemic Wager, applied across the board. The second variant builds instead on the fact that ordinary language is not ontologically transparent; we speak with the vulgar, but deep down we think with the learned. Finally, on the Humean variant it’s (...)
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  37. Counterfactuals of Ontological Dependence.Sam Baron - forthcoming - Journal of the American Philosophical Association.
    A great deal has been written about 'would' counterfactuals of causal dependence. Comparatively little has been said regarding 'would' counterfactuals of ontological dependence. The standard Lewis-Stalnaker semantics is inadequate for handling such counterfactuals. That's because some of these counterfactuals are counterpossibles, and the standard Lewis-Stalnaker semantics trivializes for counterpossibles. Fortunately, there is a straightforward extension of the Lewis-Stalnaker semantics available that handles counterpossibles: simply take Lewis's closeness relation that orders possible worlds and unleash it across impossible worlds. To apply the (...)
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  38. Assessing Ontologies: The Question of Human Origins and Its Ethical Significance.Daniel Cohnitz & Barry Smith - 2003 - In E. Runggaldier & C. Kanzian (eds.), Persons: An Interdisciplinary Approach. öbv&hpt. pp. 243--259.
    In their paper “Sixteen Days” Barry Smith and Berit Brogaard try to answer the question: when does a human being begin to exist? In this paper we will address some methodological issues connected with this exercise in ontology. We shall begin by sketching the argument of “Sixteen Days”. We shall then attempt to characterize what is special about the ontological realism of “Sixteen Days” as contrasted to the linguistic constructivism which represents the more dominant current in contemporary analytic philosophy. (...)
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  39. Ontology For Europe's Space Situational Awareness Program.Robert J. Rovetto - 2017 - In T. Flohrer & F. Schmitz (eds.), Proceedings of the 7th European Conference on Space Debris. Darmstadt, Germany: European Space Agency.
    This paper presents an ontology architecture concept for the European Space Agency‘s (ESA) Space Situational Awareness (SSA) Program. It incorporates the author‘s domain ontology, The Space Situational Awareness Ontology and related ontology work. I summarize computational ontology, discuss the segments of ESA SSA, and introduce an option for a modular ontology framework reflecting the divisionsof the SSA program. Among other things, ontologies are used for data sharing and integration. By applying ontology to ESA (...)
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  40. Mistakes in Medical Ontologies: Where Do They Come From and How Can They Be Detected?Werner Ceusters, Barry Smith, Anand Kumar & Christoffel Dhaen - 2004 - Studies in Health and Technology Informatics 102:145-164.
    We present the details of a methodology for quality assurance in large medical terminologies and describe three algorithms that can help terminology developers and users to identify potential mistakes. The methodology is based in part on linguistic criteria and in part on logical and ontological principles governing sound classifications. We conclude by outlining the results of applying the methodology in the form of a taxonomy different types of errors and potential errors detected in SNOMED-CT.
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  41. Existence as a Real Property: The Ontology of Meinongianism.Francesco Berto - 2012 - Synthèse Library, Springer.
    This book is both an introduction to and a research work on Meinongianism. “Meinongianism” is taken here, in accordance with the common philosophical jargon, as a general label for a set of theories of existence – probably the most basic notion of ontology. As an introduction, the book provides the first comprehensive survey and guide to Meinongianism and non-standard theories of existence in all their main forms. As a research work, the book exposes and develops the most up-to-date Meinongian (...)
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  42. An Improved Ontological Representation of Dendritic Cells as a Paradigm for All Cell Types.Anna Maria Masci, Cecilia N. Arighi, Alexander D. Diehl, Anne E. Liebermann, Chris Mungall, Richard H. Scheuermann, Barry Smith & Lindsay Cowell - 2009 - BMC Bioinformatics 10 (1):70.
    Recent increases in the volume and diversity of life science data and information and an increasing emphasis on data sharing and interoperability have resulted in the creation of a large number of biological ontologies, including the Cell Ontology (CL), designed to provide a standardized representation of cell types for data annotation. Ontologies have been shown to have significant benefits for computational analyses of large data sets and for automated reasoning applications, leading to organized attempts to improve the structure and (...)
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  43. Development of a Manufacturing Ontology for Functionally Graded Materials.Francesco Furini, Rahul Rai, Barry Smith, Georgio Colombo & Venkat Krovi - 2016 - In Proceedings of International Design Engineering Technical Conferences & Computers and Information in Engineering Conference (IDETC/CIE).
    The development of manufacturing technologies for new materials involves the generation of a large and continually evolving volume of information. The analysis, integration and management of such large volumes of data, typically stored in multiple independently developed databases, creates significant challenges for practitioners. There is a critical need especially for open-sharing of data pertaining to engineering design which together with effective decision support tools can enable innovation. We believe that ontology applied to engineering (OE) represents a viable strategy (...)
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  44. On Classifying Material Entities in Basic Formal Ontology.Barry Smith - 2012 - In Interdisciplinary Ontology: Proceedings of the Third Interdisciplinary Ontology Meeting. Keio University Press. pp. 1-13.
    Basic Formal Ontology was created in 2002 as an upper-level ontology to support the creation of consistent lower-level ontologies, initially in the subdomains of biomedical research, now also in other areas, including defense and security. BFO is currently undergoing revisions in preparation for the release of BFO version 2.0. We summarize some of the proposed revisions in what follows, focusing on BFO’s treatment of material entities, and specifically of the category object.
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  45. The Ontology of Biological and Clinical Statistics (OBCS) for Standardized and Reproducible Statistical Analysis.Jie Zheng, Marcelline R. Harris, Anna Maria Masci, Lin Yu, Alfred Hero, Barry Smith & Yongqun He - 2016 - Journal of Biomedical Semantics 7 (53).
    Statistics play a critical role in biological and clinical research. However, most reports of scientific results in the published literature make it difficult for the reader to reproduce the statistical analyses performed in achieving those results because they provide inadequate documentation of the statistical tests and algorithms applied. The Ontology of Biological and Clinical Statistics (OBCS) is put forward here as a step towards solving this problem. Terms in OBCS, including ‘data collection’, ‘data transformation in statistics’, ‘data visualization’, (...)
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  46. An Improved Ontological Representation of Dendritic Cells as a Paradigm for All Cell Types.Masci Anna Maria, N. Arighi Cecilia, D. Diehl Alexander, E. Lieberman Anne, Mungall Chris, H. Scheuermann Richard, Barry Smith & G. Cowell Lindsay - 2009 - BMC Bioinformatics 10 (1):70.
    The Cell Ontology (CL) is designed to provide a standardized representation of cell types for data annotation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL’s utility for cross-species data integration. To address this problem, we developed a method for the ontological representation of cells and applied this method to (...)
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  47. The National Center for Biomedical Ontology.Mark A. Musen, Natalya F. Noy, Nigam H. Shah, Patricia L. Whetzel, Christopher G. Chute, Margaret-Anne Story & Barry Smith - 2012 - Journal of the American Medical Informatics Association 19 (2):190-195.
    The National Center for Biomedical Ontology is now in its seventh year. The goals of this National Center for Biomedical Computing are to: create and maintain a repository of biomedical ontologies and terminologies; build tools and web services to enable the use of ontologies and terminologies in clinical and translational research; educate their trainees and the scientific community broadly about biomedical ontology and ontology-based technology and best practices; and collaborate with a variety of groups who develop and (...)
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  48.  82
    An Ontology for Carcinoma Classification for Clinical Bioinformatics.Anand Kumar, Yum Lina Yip, Barry Smith, Dirk Marwede & Daniel Novotny - 2005 - Studies in Health Technology and Informatics 116 (1):635-640.
    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 theory for addressing these issues in a (...)
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  49. A Formal Ontology of Artefacts.Gilles Kassel - 2010 - Applied Ontology 5 (3):223-246.
    This article presents a formal ontology which accounts for the general nature of artefacts. The objective is to help structure application ontologies in areas where specific artefacts are present - in other words, virtually any area of activity. The conceptualization relies on recent philosophical and psychological research on artefacts, having resulted in a largely consensual theoretical basis. Furthermore, this ontology of artefacts extends the foundational DOLCE ontology and supplements its axiomatization. The conceptual primitives are as follows: artificial (...)
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  50. In Pursuit of the Functional Definition of a Mind: The Inevitability of the Language Ontology.Vitalii Shymko - 2018 - Psycholinguistics 23 (1):327-346.
    In this article, the results of conceptualization of the definition of mind as an object of interdisciplinary applied research are described. The purpose of the theoretical analysis is to generate a methodological discourse suitable for a functional understanding of the mind in the context of the problem of natural language processing as one of the components of developments in the field of artificial intelligence. The conceptual discourse was realized with the help of the author's method of structural-ontological analysis, and (...)
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