Results for 'Basic Formal Ontology'

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  1. 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 ontology that (...)
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  2. 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 of (...)
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  3. Basic Formal Ontology for Bioinformatics.Barry Smith, Anand Kumar & Thomas Bittner - 2005 - IFOMIS Reports.
    Two senses of ‘ontology’ can be distinguished in the current literature. First is the sense favored by information scientists, who view ontologies as software implementations designed to capture in some formal way the consensus conceptualization shared by those working on information systems or databases in a given domain. [Gruber 1993] Second is the sense favored by philosophers, who regard ontologies as theories of different types of entities (objects, processes, relations, functions) [Smith 2003]. Where information systems ontologists seek to (...)
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  4. Function, Role and Disposition in Basic Formal Ontology.Robert Arp & Barry Smith - 2008 - Proceedings of Bio-Ontologies Workshop, Intelligent Systems for Molecular Biology (ISMB), Toronto.
    Numerous research groups are now utilizing Basic Formal Ontology as an upper-level framework to assist in the organization and integration of biomedical information. This paper provides elucidation of the three existing BFO subcategories of realizable entity, namely function, role, and disposition. It proposes one further sub-category of tendency, and considers the merits of recognizing two sub-categories of function for domain ontologies, namely, artifactual and biological function. The motivation is to help advance the coherent ontological treatment of functions, (...)
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  5. 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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  6. An Axiomatisation of Basic Formal Ontology with Projection Functions.Kerry Trentelman, Alan Ruttenberg & Barry Smith - 2010 - In Kerry Taylor (ed.), Advances in Ontologies, Proceedings of the Sixth Australasian Ontology Workshop. University of Adelaide. pp. 71-80.
    This paper proposes a reformulation of the treatment of boundaries, at parts and aggregates of entities in Basic Formal Ontology. These are currently treated as mutually exclusive, which is inadequate for biological representation since some entities may simultaneously be at parts, boundaries and/or aggregates. We introduce functions which map entities to their boundaries, at parts or aggregations. We make use of time, space and spacetime projection functions which, along the way, allow us to develop a simple temporal (...)
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  7. Normalizing Medical Ontologies Using Basic Formal Ontology.Thomas Bittner & Barry Smith - 2004 - In K. Versorgung & V. Forschung (eds.), Ubiquitäre Information (Proceedings of GMDS 2004). Videel OHG. pp. 199-201.
    Description Logics are nowadays widely accepted as formalisms which provide reasoning facilities which allow us to discover inconsistencies in ontologies in an automatic fashion. Where ontologies are developed in modular fashion, they allow changes in one module to propogated through the system of ontologies automatically in a way which helps to maintain consistency and stability. For this feature to be utilized effectively, however, requires that domain ontologies be represented in a normalized form.
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  8. A First-Order Logic Formalization of the Industrial Ontology Foundry Signature Using Basic Formal Ontology.Barry Smith, Farhad Ameri, Hyunmin Cheong, Dimitris Kiritsis, Dusan Sormaz, Chris Will & J. Neil Otte - 2019 - In Proceedings of the Joint Ontology Workshops (JOWO), Graz.
    Basic Formal Ontology (BFO) is a top-level ontology used in hundreds of active projects in scientific and other domains. BFO has been selected to serve as top-level ontology in the Industrial Ontologies Foundry (IOF), an initiative to create a suite of ontologies to support digital manufacturing on the part of representatives from a number of branches of the advanced manufacturing industries. We here present a first draft set of axioms and definitions of an IOF upper (...)
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  9. Interoperability of Disparate Engineering Domain Ontologies Using Basic Formal Ontology.Thomas J. Hagedorn, Barry Smith, Sundar Krishnamurty & Ian R. Grosse - 2019 - Journal of Engineering Design 31.
    As engineering applications require management of ever larger volumes of data, ontologies offer the potential to capture, manage, and augment data with the capability for automated reasoning and semantic querying. Unfortunately, considerable barriers hinder wider deployment of ontologies in engineering. Key among these is lack of a shared top-level ontology to unify and organise disparate aspects of the field and coordinate co-development of orthogonal ontologies. As a result, many engineering ontologies are limited to their scope, and functionally difficult to (...)
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  10. 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 (...)
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  11. Basic Concepts of Formal Ontology.Barry Smith - 1998 - In Nicola Guarino (ed.), Formal Ontology in Information Systems. IOS Press. pp. 19-28.
    The term ‘formal ontology’ was first used by the philosopher Edmund Husserl in his Logical Investigations to signify the study of those formal structures and relations – above all relations of part and whole – which are exemplified in the subject-matters of the different material sciences. We follow Husserl in presenting the basic concepts of formal ontology as falling into three groups: the theory of part and whole, the theory of dependence, and the theory (...)
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    BFO: Basic Formal Ontology1.J. Neil Otte, John Beverley & Alan Ruttenberg - 2022 - Applied ontology 17 (1):17-43.
    Basic Formal Ontology is a top-level ontology consisting of thirty-six classes, designed to support information integration, retrieval, and analysis across all domains of scientific investigation, presently employed in over 350 ontology projects around the world. BFO is a genuine top-level ontology, containing no terms particular to material domains, such as physics, medicine, or psychology. In this paper, we demonstrate how a series of cases illustrating common types of change may be represented by universals, defined (...)
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    Caracteristica-Actividad. See Part-Whole Relation/Steps-Activity Causal Relation Certainty In. See Certainty.Basic Formal Ontology - 2010 - In Alain Auger & Caroline Barrière (eds.), Probing Semantic Relations: Exploration and Identification in Specialized Texts. John Benjamins. pp. 149.
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  14. Formal Ontology for Biomedical Knowledge Systems Integration.J. M. Fielding, J. Simon & Barry Smith - 2004 - Proceedings of Euromise:12-17.
    The central hypothesis of the collaboration between Language and Computing (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is that the methodology and conceptual rigor of a philosophically inspired formal ontology will greatly benefit software application ontologies. To this end LinKBase®, L&C’s ontology, which is designed to integrate and reason across various external databases simultaneously, has been submitted to the conceptual demands of IFOMIS’s Basic Formal Ontology (BFO). With (...)
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  15. Formal Ontology for Natural Language Processing and the Integration of Biomedical Databases.Jonathan Simon, James M. Fielding, Mariana C. Dos Santos & Barry Smith - 2005 - International Journal of Medical Informatics 75 (3-4):224-231.
    The central hypothesis of the collaboration between Language and Computing (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is that the methodology and conceptual rigor of a philosophically inspired formal ontology greatly benefits application ontologies. To this end r®, L&C’s ontology, which is designed to integrate and reason across various external databases simultaneously, has been submitted to the conceptual demands of IFOMIS’s Basic Formal Ontology (BFO). With this project (...)
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  16.  65
    Some Formal Ontological Relations.E. J. Lowe - 2004 - Dialectica 58 (3):297–316.
    Some formal ontological relations are identified, in the context of an account of ontological categorization. It is argued that neither formal ontological relations nor ontological categories should themselves be regarded as elements of being, but that this does not undermine the claim of formal ontology to be a purely objective science. It is also argued that some formal ontological relations, like some ontological categories, are more basic than others. A four‐category ontology is proposed, (...)
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  17.  61
    A Formal Ontological Theory Based on Timeless Events.Gustavo Romero - 2016 - Philosophia 44 (2):607-622.
    I offer a formal ontological theory where the basic building blocks of the world are timeless events. The composition of events results in processes. Spacetime emerges as the system of all events. Things are construed as bundles of processes. I maintain that such a view is in accord with General Relativity and offers interesting prospects for the foundations of classical and quantum gravity.
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  18. Representing Concepts in Formal Ontologies: Compositionality Vs. Typicality Effects".Marcello Frixione & Antonio Lieto - 2012 - Logic and Logical Philosophy 21 (4):391-414.
    The problem of concept representation is relevant for many sub-fields of cognitive research, including psychology and philosophy, as well as artificial intelligence. In particular, in recent years it has received a great deal of attention within the field of knowledge representation, due to its relevance for both knowledge engineering as well as ontology-based technologies. However, the notion of a concept itself turns out to be highly disputed and problematic. In our opinion, one of the causes of this state of (...)
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  19.  8
    Some Formal Ontological Relations.E. J. Lowe - 2004 - Dialectica 58 (3):297-316.
    Some formal ontological relations are identified, in the context of an account of ontological categorization. It is argued that neither formal ontological relations nor ontological categories should themselves be regarded as elements of being, but that this does not undermine the claim of formal ontology to be a purely objective science. It is also argued that some formal ontological relations, like some ontological categories, are more basic than others. A four‐category ontology is proposed, (...)
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  20.  6
    GFO: The General Formal Ontology.Frank Loebe, Patryk Burek & Heinrich Herre - 2022 - Applied ontology 17 (1):71-106.
    The General Formal Ontology is a top-level ontology that is being developed at the University of Leipzig since 1999. Besides introducing some of the basic principles of the ontology, we expound axiomatic fragments of its formalization and present ontological models of several use cases. GFO is a top-level ontology that integrates objects and processes into a unified framework, in a way that differs significantly from other ontologies. Another unique selling feature of GFO is its (...)
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    Who Cares About Axiomatization? Representation, Invariance, and Formal Ontologies.R. Ferrario - 2006 - Epistemologia 29 (2):323-342.
    The philosophy of science of Patrick Suppes is centered on two important notions that are part of the title of his recent book (Suppes 2002): Representation and Invariance. Representation is important because when we embrace a theory we implicitly choose a way to represent the phenomenon we are studying. Invariance is important because, since invariants are the only things that are constant in a theory, in a way they give the “objective” meaning of that theory. Every scientific theory gives a (...)
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    Effects of Guideline-Based Training on the Quality of Formal Ontologies: A Randomized Controlled Trial.M. Boeker, L. Jansen, J. Röhl, N. Grewe, D. Seddig-Raufie & S. Schulz - 2013 - PLoS ONE 1.
    BACKGROUND -/- The importance of ontologies in the biomedical domain is generally recognized. However, their quality is often too poor for large-scale use in critical applications, at least partially due to insufficient training of ontology developers. -/- OBJECTIVE -/- To show the efficacy of guideline-based ontology development training on the performance of ontology developers. The hypothesis was that students who received training on top-level ontologies and design patterns perform better than those who only received training in the (...)
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  23. Why is It No Longer Possible to Build a Formal Ontology as a Mereotopology?Martina Properzi - 2019 - In The Philosophy of Aristotle. Atene, Grecia:
    This brief paper aims to underline which are the philosophical limits of mereotopology, when one takes it as a basic unitary theoretical framework for formal ontology. Mereotopology is a first-order theory of the relations among wholes, parts and the boundaries between parts, that combines mereological and topological concepts. Nowadays, with the expression “formal ontology” one intends either the computational (engineering) version, or the philosophical (categorial) one. It is important, then, to avoid terminological confusions. The main (...)
     
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  24. Biomedical Ontologies.Barry Smith - forthcoming - In Peter Elkin (ed.), Terminology, Ontology and their Implementations. Springer Nature Switzerland AG.
    We begin at the beginning, with an outline of Aristotle’s views on ontology and with a discussion of the influence of these views on Linnaeus. We move from there to consider the data standardization initiatives launched in the 19th century, and then turn to investigate how the idea of computational ontologies developed in the AI and knowledge representation communities in the closing decades of the 20th century. We show how aspects of this idea, particularly those relating to the use (...)
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  25. 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 (...)
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    Formal Reconstructions of St. Anselm’s Ontological Argument.Esther Ramharter & Günther Eder - 2015 - Synthese 192 (9):2795-2825.
    In this paper, we discuss formal reconstructions of Anselm’s ontological argument. We first present a number of requirements that any successful reconstruction should meet. We then offer a detailed preparatory study of the basic concepts involved in Anselm’s argument. Next, we present our own reconstructions—one in modal logic and one in classical logic—and compare them with each other and with existing reconstructions from the reviewed literature. Finally, we try to show why and how one can gain a better (...)
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  27. 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. (...)
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  28. Constructing Formal Semantics From an Ontological Perspective. The Case of Second-Order Logics.Thibaut Giraud - 2014 - Synthese 191 (10):2115-2145.
    In a first part, I defend that formal semantics can be used as a guide to ontological commitment. Thus, if one endorses an ontological view \(O\) and wants to interpret a formal language \(L\) , a thorough understanding of the relation between semantics and ontology will help us to construct a semantics for \(L\) in such a way that its ontological commitment will be in perfect accordance with \(O\) . Basically, that is what I call constructing (...) semantics from an ontological perspective. In the rest of the paper, I develop rigorously and put into practice such a method, especially concerning the interpretation of second-order quantification. I will define the notion of ontological framework: it is a set-theoretical structure from which one can construct semantics whose ontological commitments correspond exactly to a given ontological view. I will define five ontological frameworks corresponding respectively to: (i) predicate nominalism, (ii) resemblance nominalism, (iii) armstrongian realism, (iv) platonic realism, and (v) tropism. From those different frameworks, I will construct different semantics for first-order and second-order languages. Notably I will present different kinds of nominalist semantics for second-order languages, showing thus that we can perfectly quantify over properties and relations while being ontologically committed only to individuals. I will show in what extent those semantics differ from each other; it will make clear how the disagreements between the ontological views extend from ontology to logic, and thus why endorsing an ontological view should have an impact on the kind of logic one should use. (shrink)
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  29. 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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  30. LinkSuite™: Software Tools for Formally Robust Ontology-Based Data and Information Integration.Werner Ceusters, Barry Smith & James Matthew Fielding - 2004 - In Proceedings of DILS 2004 (Data Integration in the Life Sciences), (Lecture Notes in Bioinformatics, 2994). Springer. pp. 1-16.
    The integration of information resources in the life sciences is one of the most challenging problems facing bioinformatics today. We describe how Language and Computing nv, originally a developer of ontology-based natural language understanding systems for the healthcare domain, is developing a framework for the integration of structured data with unstructured information contained in natural language texts. L&C’s LinkSuite™ combines the flexibility of a modular software architecture with an ontology based on rigorous philosophical and logical principles that is (...)
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  31. 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) (...)
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  32. Trouble Up at T’Ontological Mill: An Inconclusive Dialog.Peter Simons - 2017 - Cosmos + Taxis 4 (4):64-66.
    Grenon and Smith (2004) propose a framework for the ontology of things in space and time involving and invoking the distinction between continuants and occurrents, which has become a key element of Basic Formal Ontology (BFO). The terminology of SNAP (from “snapshot:” state of a continuant at a time) and SPAN (how an occurrent develops over an interval or timespan) occurs in that paper’s title. While any commonsense ontology will have a place for both continuants (...)
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  33. 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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  34. A Visual Representation of Part-Whole Relationships in BFO-Conformant Ontologies.Jose M. Parente de Oliveira & Barry Smith - 2017 - In Á Rocha, A. M. Correia, H. Adeli, L. P. Reis & S. Costanzo (eds.), Recent Advances in Information Systems and Technologies (Advances in Intelligent Systems and Computing, 569). New York: Springer. pp. 184-194.
    In the visual representation of ontologies, in particular of part-whole relationships, 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, and we propose instead a new representation of part-whole structures for ontologies, and describe the results of experiments designed to show the effectiveness of this new proposal especially as concerns reduction of visual complexity. The proposal is developed to serve visualization of ontologies conformant to the (...)
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  35. Foundation for a Realist Ontology of Cognitive Processes.David Kasmier, David Limbaugh & Barry Smith - 2019 - In Proceedings of the International Conference on Biomedical Ontology (ICBO), University at Buffalo, NY.
    What follows is a first step towards an ontology of conscious mental processes. We provide a theoretical foundation and characterization of conscious mental processes based on a realist theory of intentionality and using BFO as our top-level ontology. We distinguish three components of intentional mental process: character, directedness, and objective referent, and describe several features of the process character and directedness significant to defining and classifying mental processes. We arrive at the definition of representational mental process as a (...)
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  36. 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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  37. 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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  38. CTO: A Community-Based Clinical Trial Ontology and Its Applications in PubChemRDF and SCAIViewH.Asiyah Yu Lin, Stephan Gebel, Qingliang Leon Li, Sumit Madan, Johannes Darms, Evan Bolton, Barry Smith, Martin Hofmann-Apitius, Yongqun Oliver He & Alpha Tom Kodamullil - 2021 - Proceedings of the 11th International Conference on Biomedical Ontologies (ICBO) and 10th Workshop on Ontologies and Data in Life Sciences (ODLS).
    Driven by the use cases of PubChemRDF and SCAIView, we have developed a first community-based clinical trial ontology (CTO) by following the OBO Foundry principles. CTO uses the Basic Formal Ontology (BFO) as the top level ontology and reuses many terms from existing ontologies. CTO has also defined many clinical trial-specific terms. The general CTO design pattern is based on the PICO framework together with two applications. First, the PubChemRDF use case demonstrates how a drug (...)
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  39. Foundations for a Realist Ontology of Mental Disease.Werner Ceusters & Barry Smith - 2010 - Journal of Biomedical Semantics 1 (10):1-23.
    While classifications of mental disorders have existed for over one hundred years, it still remains unspecified what terms such as 'mental disorder', 'disease' and 'illness' might actually denote. While ontologies have been called in aid to address this shortfall since the GALEN project of the early 1990s, most attempts thus far have sought to provide a formal description of the structure of some pre-existing terminology or classification, rather than of the corresponding structures and processes on the side of the (...)
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  40. 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’, ‘statistical (...)
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  41. Ontological Theory for Ontological Engineering: Biomedical Systems Information Integration.James M. Fielding, Jonathan Simon, Werner Ceusters & Barry Smith - 2004 - In Proceedings of the Ninth International Conference on the Principles of Knowledge Representation and Reasoning (KR2004), Whistler, BC, 2-5 June 2004. AMIA. pp. 114–120.
    Software application ontologies have the potential to become the keystone in state-of-the-art information management techniques. It is expected that these ontologies will support the sort of reasoning power required to navigate large and complex terminologies correctly and efficiently. Yet, there is one problem in particular that continues to stand in our way. As these terminological structures increase in size and complexity, and the drive to integrate them inevitably swells, it is clear that the level of consistency required for such navigation (...)
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  42. Endurants and Perdurants in Directly Depicting Ontologies.Thomas Bittner, Maureen Donnelly & Barry Smith - 2004 - AI Communications 13 (4):247–258.
    We propose an ontological theory that is powerful enough to describe both complex spatio-temporal processes and the enduring entities that participate therein. For this purpose we introduce the notion a directly depicting ontology. Directly depicting ontologies are based on relatively simple languages and fall into two major categories: ontologies of type SPAN and ontologies of type SNAP. These represent two complementary perspectives on reality and employ distinct though compatible systems of categories. A SNAP (snapshot) ontology comprehends enduring entities (...)
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  43. Peer Review Report: Ontologies Relevant to Behaviour Change Interventions, Version 3.Robert M. Kelly, David Limbaugh & Barry Smith - 2021 - Human Behaviour Change Project.
    In the present review we focus on what we take to be some remaining issues with the Behaviour Change Intervention Ontology (BCIO). We are in full agreement with the authors’ endorsement of the principles of best practice for ontology development In particular, we agree that an ontology should be “logically consistent and having a clear structures [sic], preferably a well-organised hierarchical structure,” and that “Maximising the new ontology’s interoperability with existing ontologies by reusing entities from existing (...)
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  44. Granular Spatio-Temporal Ontologies.Thomas Bittner & Barry Smith - 2003 - In AAAI Symposium: Foundations and Applications of Spatio-Temporal Reasoning (FASTR). pp. 12-17.
    We propose an ontological theory that is powerful enough to describe both complex spatio-temporal processes (occurrents) and the enduring entities (continuants) that participate therein. The theory is divided into two major categories of sub-theories: (sub-) theories of type SPAN and (sub-)theories of type SNAP. These theories represent two complementary perspectives on reality and result in distinct though compatible systems of categories. In SNAP we have enduring entities such as substances, qualities, roles, functions; in SPAN we have perduring entities such as (...)
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  45.  95
    An Ontological Approach to Enhancing Information Sharing in Disaster Response.Linda Elmhadhbi, Mohamed-Hedi Karray, Bernard Archimède, J. Neil Otte & Barry Smith - 2021 - Information 12 (10).
    Managing complex disaster situations is a challenging task because of the large number of actors involved and the critical nature of the events themselves. In particular, the different terminologies and technical vocabularies that are being exchanged among Emergency Responders may lead to misunderstandings. Maintaining a shared semantics for exchanged data is a major challenge. To help to overcome these issues, we elaborate a modular suite of ontologies called POLARISCO that formalizes the complex knowledge of the ERs. Such a shared vocabulary (...)
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  46. Toward an Ontology of Commercial Exchange.Jonathan Vajda, Eric Merrell & Barry Smith - 2019 - In Proceedings of the Joint Ontology Workshops (JOWO), Graz.
    In this paper we propose an Ontology of Commercial Exchange (OCE) based on Basic Formal Ontology. OCE is designed for re-use in the Industrial Ontologies Foundry (IOF) and in other ontologies addressing different aspects of human social behavior involving purchasing, selling, marketing, and so forth. We first evaluate some of the design patterns used in the Financial Industry Business Ontology (FIBO) and Product Types Ontology (PTO). We then propose terms and definitions that we believe (...)
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  47. Capabilities.Eric Merrell, David Limbaugh, Peter Koch & Barry Smith - manuscript
    We propose a definition of capability as a class intermediate between function and disposition as the latter are defined in Basic Formal Ontology (BFO). A disposition inheres in a material entity and is realized in a certain kind of process. An example is the disposition of a glass to break when struck, which is realized when it shatters. A function is a disposition which is (simply put) the rationale for the existence of its bearer. To say for (...)
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  48. Ontology for the Intelligence Analyst.Barry Smith - 2012 - CrossTalk 14 (Nov/Dec):18-25.
    As available intelligence data and information expand in both quantity and variety, new techniques must be deployed for search and analytics. One technique involves the semantic enhancement of data through the creation of what are called ‘ontologies’ or ‘controlled vocabularies.’ When multiple different bodies of heterogeneous data are tagged by means of terms from common ontologies, then these data become linked together in ways which allow more effective retrieval and integration. We describe a simple case study to show how these (...)
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  49. 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 for (...)
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  50. SNAPVis and SPANVis: Ontologies for Recognizing Variable Vista Spatial Environments.Tiansi Dong - 2004 - In International Conference on Spatial Cognition. Springer. pp. 344-365.
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