Results for 'upper-level ontology'

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  1.  43
    GOL: Toward an Axiomatized Upper-Level Ontology. IMISE Report.Wolfgang Degen, Barbary Haller, Heinrich Herre & Barry Smith - 2001 - In IMISE Report. Leipzig: IMISE.
    Every domain-specific ontology must use as a framework some upper-level ontology which describes the most general domain-independent categories of reality. In the present paper we sketch a new type of upper-level ontology, and we outline an associated knowledge modelling language called GOL – for: General Ontological Language. It turns out that the upper-level ontology underlying well-known standard modelling languages such as KIF, F-Logic and CycL is restricted to the ontology of sets. In (...)
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  2. 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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  3. 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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  4. 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 ontology (...)
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  5. GOL: A General Ontological Language.Wolfgang Degen, Barbara Heller, Heinrich Herre & Barry Smith - 2001 - In Chris Welty & Barry Smith (eds.), Formal Ontology in Information Systems (FOIS). New York: ACM Press. pp. 34-46.
    Every domain-specific ontology must use as a framework some upper-level ontology which describes the most general, domain-independent categories of reality. In the present paper we sketch a new type of upper-level ontology, which is intended to be the basis of a knowledge modelling language GOL (for: 'General Ontological Language'). It turns out that the upper- level ontology underlying standard modelling languages such as KIF, F-Logic and CycL is restricted to the ontology of sets. (...)
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  6. 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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  7. Against Idiosyncrasy in Ontology Development.Barry Smith - 2006 - In B. Bennett & C. Fellbaum (eds.), Formal Ontology in Information Systems (FOIS). Amsterdam: IOS Press. pp. 15-26.
    The world of ontology development is full of mysteries. Recently, ISO Standard 15926 (“Lifecycle Integration of Process Plant Data Including Oil and Gas Production Facilities”), a data model initially designed to support the integration and handover of large engineering artefacts, has been proposed by its principal custodian for general use as an upper level ontology. As we shall discover, ISO 15926 is, when examined in light of this proposal, marked by a series of quite astonishing defects, which may (...)
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  8. 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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  9. 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, roles, (...)
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  10.  23
    An Overview of the BFO - Basic Formal Ontology - and Its Applicability for Satellite Systems.Adolfo Americano Brandão & Geilson Loureiro - 2020 - In Franciele Braga Machado Tullio & Lucio Mauro Braga Machado (eds.), Ampliação e Aprofundamento de Conhecimentos nas Áreas das Engenharias,. Ponta Grossa, Brazil: Atena Editora. pp. 30-38.
    This work aims to present an overview of the top-level ontology BFO - Basic Formal Ontology - and its applicability for Satellite Systems. As an upper level ontology, the BFO was designed to be extended, providing the basis for the specification of detailed representational artifacts about scientific information domains. These aspects and the challenges of satellite systems complexity and large size compose a suitable scenario for the creation of a specialized dialect to improve efficiency and accuracy when (...)
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  11. 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 theory.
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  12. 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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  13. 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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  14. A Horse is a Horse, of Course, of Course, but What About Horseness?Necip Fikri Alican - 2015 - In Debra Nails & Harold Tarrant (eds.), Second Sailing: Alternative Perspectives on Plato. Helsinki: Societas Scientiarum Fennica. pp. 307–324.
    Plato is commonly considered a metaphysical dualist conceiving of a world of Forms separate from the world of particulars in which we live. This paper explores the motivation for postulating that second world as opposed to making do with the one we have. The main objective is to demonstrate that and how everything, Forms and all, can instead fit into the same world. The approach is exploratory, as there can be no proof in the standard sense. The debate between explaining (...)
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  15. Rethought Forms: How Do They Work?Necip Fikri Alican - 2014 - Arctos: Acta Philologica Fennica 48: 25–55.
    This paper is a critical evaluation of Holger Thesleff’s thinking on Plato’s Forms, especially of his “rethinking” of the matter, as he puts it in the title of his most recent contribution. It lays out a broadly sympathetic perspective through dialectical engagement with the main lines of his interpretation and reconstruction of Plato’s world. The aim is to launch the formal academic reception of that reconstruction (rethinking), which Thesleff cautiously and modestly presents as a “proposal” — his teaser to elicit (...)
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  16. Ontology of the False State: On the Relation Between Critical Theory, Social Philosophy, and Social Ontology.Italo Testa - 2015 - Journal of Social Ontology 1 (2):271-300.
    In this paper I will argue that critical theory needs to make its socio-ontological commitments explicit, whilst on the other hand I will posit that contemporary social ontology needs to amend its formalistic approach by embodying a critical theory perspective. In the first part of my paper I will discuss how the question was posed in Horkheimer’s essays of the 1930s, which leave open two options: (1) a constructive inclusion of social ontology within social philosophy, or else (2) (...)
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  17. Social Space and the Ontology of Recognition.Italo Testa - 2011 - In Heikki Ikäheimo Arto Laitinen (ed.), Recognition and Social Ontology. Brill Books (pp. 287-308).
    In this paper recognition is taken to be a question of social ontology, regarding the very constitution of the social space of interaction. I concentrate on the question of whether certain aspects of the theory of recognition can be translated into the terms of a socio-ontological paradigm: to do so, I make reference to some conceptual tools derived from John Searle's social ontology and Robert Brandom's normative pragmatics. My strategy consists in showing that recognitive phenomena cannot be isolated (...)
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  18.  77
    Dispositions and the Infectious Disease Ontology.Albert Goldfain, Barry Smith & Lindsay Cowell - 2010 - In Formal Ontology in Information Systems: Proceedings of the Sixth International Conference (FOIS). IOS Press. pp. 400-413.
    This paper addresses the use of dispositions in the Infectious Disease Ontology (IDO). IDO is an ontology constructed according to the principles of the Open Biomedical Ontology (OBO) Foundry and uses the Basic Formal Ontology (BFO) as an upper ontology. After providing a brief introduction to disposition types in BFO and IDO, we discuss three general techniques for representing combinations of dispositions under the headings blocking dispositions, complementary dispositions, and collective dispositions. Motivating examples for each (...)
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  19. 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 within (...)
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  20. From Ontology of Interaction to Semiotics of Education.Eetu Pikkarainen - 2013 - In K. Tirri, E. Hanhimäki & E. Kuusisto (eds.), Interaction in Educational Domains. Sense Publishers. pp. 51-62.
    In this article I try to show that the most deep level ontology can have rich meaning for our understanding of such practical and everyday phenomena as education and interaction. With this deep level ontology I mean the problem of universals. Starting from famous traditional stances of realism and nominalism, which both are for the modern theories of growth and Bildung, I continue to the third and more recently developed ontological theory, trope theory according to which the properties (...)
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  21.  16
    Archeology of Consciousness ↔ The Ontological Basification of Mathematics (Knowledge) ↔ The Nature of Consciousness. [REVIEW]Vladimir Rogozhin - manuscript
    A condensed summary of the adventures of ideas (1990-2020). Methodology of evolutionary-phenomenological constitution of Consciousness. Vector (BeVector) of Consciousness. Consciousness is a qualitative vector quantity. Vector of Consciousness as a synthesizing category, eidos-prototecton, intentional meta-observer. The development of the ideas of Pierre Teilhard de Chardin, Brentano, Husserl, Bergson, Florensky, Losev, Mamardashvili, Nalimov. Dialectic of Eidos and Logos. "Curve line" of the Consciousness Vector from space and time. The lower and upper sides of the "abyss of being". The existential tension of (...)
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  22. 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 developed (...)
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  23. Towards a Reference Terminology for Ontology Research and Development in the Biomedical Domain.Barry Smith, Waclaw Kusnierczyk, Daniel Schober, & Werner Ceusters - 2006 - In Proceedings of KR-MED, CEUR, vol. 222. pp. 57-65.
    Ontology is a burgeoning field, involving researchers from the computer science, philosophy, data and software engineering, logic, linguistics, and terminology domains. Many ontology-related terms with precise meanings in one of these domains have different meanings in others. Our purpose here is to initiate a path towards disambiguation of such terms. We draw primarily on the literature of biomedical informatics, not least because the problems caused by unclear or ambiguous use of terms have been there most thoroughly addressed. We (...)
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  24. 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 we aim to move (...)
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  25. A Proposal for a Dualistic Ontology of Art.Simon Fokt - 2013 - Sztuka I Filozofia (42):29-47.
    While pluralism in ontology of art improves on various monistic views, through its eclectic approach it lost a lot of their simplicity, parsimony, unity and intuitiveness. The dualistic theory presented in this paper offers an alternative – it shares the advantages of the monistic views while retaining the wide scope of pluralism, and thus should be preferred for methodological reasons. On this view all artworks are at the same time abstract universals which are called recipes, and particular physical objects (...)
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  26. CARO: The Common Anatomy Reference Ontology.Melissa Haendel, Fabian Neuhaus, David Osumi-Sutherland, Paula M. Mabee, José L. V. Mejino Jr, Chris J. Mungall & Barry Smith - 2008 - In Anatomy Ontologies for Bioinformatics: Principles and Practice. Springer. pp. 327-349.
    The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies. CARO has a structural axis of classification based on the top-level nodes of the Foundational Model of Anatomy. CARO will complement the developmental process sub-ontology of the GO Biological Process ontology, using it to ensure the coherent treatment of developmental stages, and to provide a common framework for the (...)
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  27.  69
    What Do Identifiers in HL7 Identify? An Essay in the Ontology of Identity.Werner Ceusters & Barry Smith - 2009 - In Mitsu Okada (ed.), Proceedings of InterOntology (Tokyo, Japan, February 27-March 1, 2009). Tokyo: Keio University Press. pp. 77-86.
    Health Level 7 (HL7) is an organization seeking to provide universal standards for the exchange of healthcare information. In a document entitled ‘HL7 Version 3 Standard: Data Types’, the HL7 organization advances descriptions of data types recom- mended for use as identifiers. We will argue that the descriptions supplied provide insufficient guidance as to what exactly the entities are which these data types uniquely identify. Are they real things, such as persons or pieces of equipment? Or are they representations of (...)
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  28.  80
    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 this, we aim to (...)
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  29.  68
    The Plant Ontology: A Common Reference Ontology for Plants.L. Walls Ramona, D. Cooper Laurel, Elser Justin, W. Stevenson Dennis, Barry Smith, Mungall Chris, A. Gandolfo Maria & Jaiswal Pankaj - 2010 - In Proceedings of the Workshop on Bio-Ontologies, ISMB, Boston, July, 2010.
    The Plant Ontology (PO) (http://www.plantontology.org) (Jaiswal et al., 2005; Avraham et al., 2008) was designed to facilitate cross-database querying and to foster consistent use of plant-specific terminology in annotation. As new data are generated from the ever-expanding list of plant genome projects, the need for a consistent, cross-taxon vocabulary has grown. To meet this need, the PO is being expanded to represent all plants. This is the first ontology designed to encompass anatomical structures as well as growth and (...)
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  30. 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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  31. Dispositions and Processes in the Emotion Ontology.Janna Hastings, Werner Ceusters, Barry Smith & Kevin Mulligan - 2011 - In Proceedings of the 2nd International Conference on Biomedical Ontology. CEUR Workshop Proceedings. pp. 71-78.
    Affective science conducts interdisciplinary research into the emotions and other affective phenomena. Currently, such research is hampered by the lack of common definitions of te rms used to describe, categorise and report both individual emotional experiences and the results of scientific investigations of such experiences. High quality ontologies provide formal definitions for types of entities in reality and for the relationships between such entities, definitions which can be used to disambiguate and unify data across different disciplines. Heretofore, there has been (...)
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  32.  30
    Enriching the Functionally Graded Materials (FGM) Ontology for Digital Manufacturing.Munira Mohd Ali, Ruoyu Yang, Binbin Zhang, Francesco Furini, Rahul Rai, J. Neil Otte & Barry Smith - 2020 - International Journal of Production Research:1-18.
    Functionally graded materials (FGMs) have been used in many different kinds of applications in recent years and have attracted significant research attention. However, we do not yet have a commonly accepted way of representing the various aspects of FGMs. Lack of standardised vocabulary creates obstacles to the extraction of useful information relating to pertinent aspects of different applications. A standard resource is needed for describing various elements of FGMs, including existing applications, manufacturing techniques, and material characteristics. This motivated the creation (...)
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  33. Can Physics Ever Be Complete If There is No Fundamental Level in Nature?Markus Schrenk - 2009 - Dialectica 63 (2):205-208.
    In their recent book Every Thing Must Go, Ladyman and Ross claim: (i) Physics is analytically complete since it is the only science that cannot be left incomplete. (ii) There might not be an ontologically fundamental level. (iii) We should not admit anything into our ontology unless it has explanatory and predictive utility. In this discussion note I aim to show that the ontological commitment in implies that the completeness of no science can be achieved where no fundamental level (...)
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  34.  75
    Methodology and Ontology in Microbiome Research.John Huss - 2014 - Biological Theory 9 (4):392-400.
    Research on the human microbiome has gen- erated a staggering amount of sequence data, revealing variation in microbial diversity at the community, species (or phylotype), and genomic levels. In order to make this complexity more manageable and easier to interpret, new units—the metagenome, core microbiome, and entero- type—have been introduced in the scientific literature. Here, I argue that analytical tools and exploratory statisti- cal methods, coupled with a translational imperative, are the primary drivers of this new ontology. By reducing (...)
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  35. Primitive Ontology and the Classical World.Valia Allori - 2016 - In R. Kastner, J. Jeknic-Dugic & G. Jaroszkiewicz (eds.), Quantum Structural Studies: Classical Emergence from the Quantum Level. World Scientific. pp. 175-199.
    In this paper I present the common structure of quantum theories with a primitive ontology, and discuss in what sense the classical world emerges from quantum theories as understood in this framework. In addition, I argue that the primitive ontology approach is better at answering this question than the rival wave function ontology approach or any other approach in which the classical world is nonreductively ‘emergent:’ even if the classical limit within this framework needs to be fully (...)
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  36. Kind Instantiation and Kind Change - A Problem for Four-Category Ontology.Markku Keinänen & Jani Hakkarainen - 2017 - Studia Neoaristotelica 14 (2):139-165.
    In Lowe’s Four-Category Ontology, instantiation is a basic formal ontological relation between particulars (objects, modes) and their kinds (kinds, attributes). Therefore, instantiation must be considered as a metaphysically necessary relation, which also rules out the metaphysical possibility of kind change. Nevertheless, according to Lowe, objects obtain their identity conditions in a more general level than specific natural kinds, which allows for kind change. There also seems to be actual examples of kind change. The advocate of Four-Category Ontology is (...)
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  37.  48
    Protein Ontology: Enhancing and Scaling Up the Representation of Protein Entities.Darren A. Natale, Cecilia N. Arighi, Judith A. Blake, Jonathan Bona, Chuming Chen, Sheng-Chih Chen, Karen R. Christie, Julie Cowart, Peter D'Eustachio, Alexander D. Diehl, Harold J. Drabkin, William D. Duncan, Hongzhan Huang, Jia Ren, Karen Ross & Alan Ruttenberg - 2017 - Nucleic Acids Research 45 (D1):D339-D346.
    The Protein Ontology (PRO; http://purl.obolibrary.org/obo/pr) formally defines and describes taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced from a given gene; and protein-containing complexes. PRO thus serves as a tool for referencing protein entities at any level of specificity. To enhance this ability, and to facilitate the comparison of such entities described in different resources, we developed a standardized representation of proteoforms using UniProtKB as a sequence reference and PSI-MOD as a post-translational (...)
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  38. TGF-Beta Signaling Proteins and the Protein Ontology.Arighi Cecilia, Liu Hongfang, Natale Darren, Barker Winona, Drabkin Harold, Blake Judith, Barry Smith & Wu Cathy - 2009 - BMC Bioinformatics 10 (Suppl 5):S3.
    The Protein Ontology (PRO) is designed as a formal and principled Open Biomedical Ontologies (OBO) Foundry ontology for proteins. The components of PRO extend from a classification of proteins on the basis of evolutionary relationships at the homeomorphic level to the representation of the multiple protein forms of a gene, including those resulting from alternative splicing, cleavage and/or posttranslational modifications. Focusing specifically on the TGF-beta signaling proteins, we describe the building, curation, usage and dissemination of PRO. PRO provides (...)
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  39. Protein Ontology: A Controlled Structured Network of Protein Entities.A. Natale Darren, N. Arighi Cecilia, A. Blake Judith, J. Bult Carol, R. Christie Karen, Cowart Julie, D’Eustachio Peter, D. Diehl Alexander, J. Drabkin Harold, Helfer Olivia, Barry Smith & Others - 2013 - Nucleic Acids Research 42 (1):D415-21..
    The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO (...)
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  40. Objects and Their Environments: From Aristotle to Ecological Ontology.Barry Smith - 2001 - In Andrew U. Frank, Jonathan Raper & Jean-Paul Cheylan (eds.), The Life and Motion of Socio-Economic Units. London: Taylor & Francis. pp. 79-97.
    What follows is a contribution to the theory of space and of spatial objects. It takes as its starting point the philosophical subfield of ontology, which can be defined as the science of what is: of the various types and categories of objects and relations in all realms of being. More specifically, it begins with ideas set forth by Aristotle in his Categories and Metaphysics, two works which constitute the first great contributions to ontological science. Because Aristotle’s ontological ideas (...)
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  41.  88
    A Method for Re-Engineering a Thesaurus Into an Ontology.D. Kless, L. Jansen, J. Lindenthal & J. Wiebensohn - 2012 - In Maureen Donnelly & Giancarlo Guizzardi (eds.), Formal Ontology and Information Systems. IOS. pp. 133-146.
    The construction of complex ontologies can be facilitated by adapting existing vocabularies. There is little clarity and in fact little consensus as to what modifications of vocabularies are necessary in order to re-engineer them into ontologies. In this paper we present a method that provides clear steps to follow when re-engineering a thesaurus. The method makes use of top-level ontologies and was derived from the structural differences between thesauri and ontologies as well as from best practices in modeling, some of (...)
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  42.  54
    Ontology-Based Integration of Medical Coding Systems and Electronic Patient Records.W. Ceusters, Barry Smith & G. De Moor - 2004 - IFOMIS Reports.
    In the last two decades we have witnessed considerable efforts directed towards making electronic healthcare records comparable and interoperable through advances in record architectures and (bio)medical terminologies and coding systems. Deep semantic issues in general, and ontology in particular, have received some interest from the research communities. However, with the exception of work on so-called ‘controlled vocabularies’, ontology has thus far played little role in work on standardization. The prime focus has been rather the rapid population of terminologies (...)
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  43.  47
    Physics and Ontology - or The 'Ontology-Ladenness' of Epistemology and the 'Scientific Realism'-Debate.Rudolf Lindpointner - manuscript
    The question of what ontological insights can be gained from the knowledge of physics (keyword: ontic structural realism) cannot obviously be separated from the view of physics as a science from an epistemological perspective. This is also visible in the debate about 'scientific realism'. This debate makes it evident, in the form of the importance of perception as a criterion for the assertion of existence in relation to the 'theoretical entities' of physics, that epistemology itself is 'ontologically laden'. This is (...)
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  44. 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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  45. The Ontology of Epistemology.Barry Smith - 1987 - Reports in Philosophy 11:57-66.
    Ingarden’s puzzle is: how can we come to know what is essentially involved in an act of knowing? As starting point he takes what he holds to be a particular good candidate example of such an act, namely an act of perceiving an apple. Here we have act and object standing in a certain first-level relation to each other. We now in a second level act of reflection, make this first-level relation into an object, and strive to apprehend this object (...)
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  46. Permanent Generic Relatedness and Silent Change.Niels Grewe, Ludger Jansen & Barry Smith - 2016 - In Formal Ontology and Information Systems. CEUR, Vol. 1060. pp. 1-5.
    Given the assertion of a relation between two types, like: “Epidermis has part some Keratinocyte”, we define silent change as any kind of change of the instance-relata of the relation in question that does not change the truth-value of the respective type-level assertion. Such assertions are notoriously difficult to model in OWL 2. To address this problem, we distinguish different modes of type-level relatedness giving rise to this problem and describe a conservative extension to the BFO top-level ontology that (...)
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  47. Ontological Foundations of Competition.Tiago Prince Sales, Daniele Porello, Nicola Guarino, Giancarlo Guizzardi & John Mylopoulos - 2018 - In Stefano Borgo, Pascal Hitzler & Oliver Kutz (eds.), Formal Ontology in Information Systems: Proceedings of the 10th International Conference (FOIS 2018). Amsterdam: IOS Press. pp. 96-112.
    It is widely recognized that accurately identifying and classifying competitors is a challenge for many companies and entrepreneurs. Nonetheless, it is a paramount activity which provide valuable insights that affect a wide range of strategic decisions. One of the main challenges in competitor identification lies in the complex nature of the competitive relationships that arise in business envi- ronments. These have been extensively investigate over the years, which lead to a plethora of competition theories and frameworks. Still, the concept of (...)
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  48.  58
    Is Distributed Cognition Group Level Cognition?Kirk Ludwig - 2015 - Journal of Social Ontology 1 (2):189-224.
    This paper shows that recent arguments from group problem solving and task performance to emergent group level cognition that rest on the social parity and related principles are invalid or question begging. The paper shows that standard attributions of problem solving or task performance to groups require only multiple agents of the outcome, not a group agent over and above its members, whether or not any individual member of the group could have accomplished the task independently.
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  49. 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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  50.  34
    Review Of: Ontologies Relevant to Behaviour Change Interventions.Robert M. Kelly, David Limbaugh & Barry Smith - 2020 - Human Behaviour Change Project.
    In “Ontologies Relevant to behaviour change interventions: A Method for their Development” Wright, et al. outline a step by step process for building ontologies of behaviour modification – what the authors call the Refined Ontology Developmental Method (RODM) – and demonstrate its use in the development of the Behaviour Change Intervention Ontology (BCIO). RODM is based on the principles of good ontology building used by the Open Biomedical Ontology (OBO) Foundry in addition to those outlined in (...)
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