Results for 'Constituent ontology'

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  1. Bare Particulars and Constituent Ontology.Robert K. Garcia - 2014 - Acta Analytica 29 (2):149-159.
    My general aim in this paper is to shed light on the controversial concept of a bare particular. I do so by arguing that bare particulars are best understood in terms of the individuative work they do within the framework of a realist constituent ontology. I argue that outside such a framework, it is not clear that the notion of a bare particular is either motivated or coherent. This is suggested by reflection on standard objections to bare particulars. (...)
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  2. On Substances, Accidents and Universals: In Defence of a Constituent Ontology.Barry Smith - 1997 - Philosophical Papers 26 (1):105-127.
    The essay constructs an ontological theory designed to capture the categories instantiated in those portions or levels of reality which are captured in our common sense conceptual scheme. It takes as its starting point an Aristotelian ontology of “substances” and “accidents”, which are treated via the instruments of mereology and topology. The theory recognizes not only individual parts of substances and accidents, including the internal and external boundaries of these, but also universal parts, such as the “humanity” which is (...)
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  3. Nominalist Constituent Ontologies: A Development and Critique.Robert K. Garcia - 2009 - Dissertation, University of Notre Dame
    In this dissertation I consider the merits of certain nominalist accounts of phenomena related to the character of ordinary objects. What these accounts have in common is the fact that none of them is an error theory about standard cases of predication and none of them deploys God or uniquely theistic resources in its explanatory framework. -/- The aim of the dissertation is to answer the following questions: -/- • What is the best nominalist account on offer? • How might (...)
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  4. Bundle Theory’s Black Box: Gap Challenges for the Bundle Theory of Substance.Robert Garcia - 2014 - Philosophia 42 (1):115-126.
    My aim in this article is to contribute to the larger project of assessing the relative merits of different theories of substance. An important preliminary step in this project is assessing the explanatory resources of one main theory of substance, the so-called bundle theory. This article works towards such an assessment. I identify and explain three distinct explanatory challenges an adequate bundle theory must meet. Each points to a putative explanatory gap, so I call them the Gap Challenges. I consider (...)
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  5. What Does It Mean for Something to Exist?Lajos L. Brons - 2013 - The Science of Mind 51 (1):53-74.
    (First paragraph.) Ontology is often described as the inquiry into what exists, but there is some disagreement among (meta-) ontologists about what “existence” means and whether there are different kinds or senses of “existence” or just one; that is, whether “existence” is equivocal or univocal. Furthermore, there is a growing number of philosophers (many of whom take inspiration from Aristotle’s metaphysical writings) who argue that ontology should not be concerned so much with what exists, but with what is (...)
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  6. The Infectious Disease Ontology in the Age of COVID-19.Shane Babcock, Lindsay G. Cowell, John Beverley & Barry Smith - 2020 - In OSF Preprints. Center for Open Science.
    The Infectious Disease Ontology (IDO) is a suite of interoperable ontology modules that aims to provide coverage of all aspects of the infectious disease domain, including biomedical research, clinical care, and public health. IDO Core is designed to be a disease and pathogen neutral ontology, covering just those types of entities and relations that are relevant to infectious diseases generally. IDO Core is then extended by a collection of ontology modules focusing on specific diseases and pathogens. (...)
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  7. Bare Particulars and Exemplifcation.Timothy Pickavance - 2014 - American Philosophical Quarterly 51 (2):95-108.
    Bare particulars tend to get a bad rap. But often, the arguments lodged against bare particulars seem to miss important aspects of the theoretical context of bare particulars. In particular, these arguments fail to situate bare particulars within a constituent ontology with substrates, and thus fail to appreciate an important consequence of that context: the need for two types of exemplification. In this paper, I do three things. First, I motivate and describe the need, given bare particulars, for (...)
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  8. 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 will improve (...)
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  9. 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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  10. 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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  11. 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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  12. 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 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 provides a (...)
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  13. The Ontology of Words: Realism, Nominalism, and Eliminativism.James Miller - 2020 - Philosophy Compass 15 (7).
    What are words? What makes two token words tokens of the same word-type? Are words abstract entities, or are they (merely) collections of tokens? The ontology of words tries to provide answers to these, and related questions. This article provides an overview of some of the most prominent views proposed in the literature, with a particular focus on the debate between type-realist, nominalist, and eliminativist ontologies of words.
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  14. Analytic Metaphysics Versus Naturalized Metaphysics: The Relevance of Applied Ontology.Baptiste Le Bihan & Adrien Barton - 2018 - Erkenntnis:1-17.
    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 by (...)
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  15. 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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  16. 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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  17.  50
    Levels of Ontology and Natural Language: The Case of the Ontology of Parts and Wholes.Friederike Moltmann - forthcoming - In James Miller (ed.), The Language of Ontology. Oxford University Press.
    It is common in contemporary metaphysics to distinguish two levels of ontology: the ontology of ordinary objects and the ontology of fundamental reality. This papers argues that natural language reflects not only the ontology of ordinary objects, but also a language-driven ontology, which is involved in the mass-count distinction and part-structure-sensitive semantic selection, as well as perhaps the light ontology of pleonastic entities. The paper recasts my older theory of situated part structures without situations, (...)
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  18. Aboutness: Towards Foundations for the Information Artifact Ontology.Werner Ceusters & Barry Smith - 2015 - In Proceedings of the Sixth International Conference on Biomedical Ontology (ICBO). CEUR vol. 1515. pp. 1-5.
    The Information Artifact Ontology (IAO) was created to serve as a domain‐neutral resource for the representation of types of information content entities (ICEs) such as documents, data‐bases, and digital im‐ages. We identify a series of problems with the current version of the IAO and suggest solutions designed to advance our understanding of the relations between ICEs and associated cognitive representations in the minds of human subjects. This requires embedding IAO in a larger framework of ontologies, including most importantly the (...)
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  19. 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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  20.  87
    Logic and Ontology of Language.Urszula Wybraniec-Skardowska - 2019 - In Bartłomiej Skowron (ed.), Contemporary Polish Ontology. Berlin/Boston: DE GRUYTER, MOUTON. pp. 109-132.
    The main purpose of the paper is to outline the formal-logical, general theory of language treated as a particular ontological being. The theory itself is called the ontology of language, because it is motivated by the fact that the language plays a special role: it reflects ontology and ontology reflects the world. Language expressions are considered to have a dual ontological status. They are understood as either concretes, that is tokens – material, physical objects, or types – (...)
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  21. 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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  22. Towards an Ontology of Pain.Barry Smith, Werner Ceusters, Louis J. Goldberg & Richard Ohrbach - 2011 - In Proceedings of the Conference on Ontology and Analytical Metaphysics. Keio University Press.
    We present an ontology of pain and of other pain-related phenomena, building on the definition of pain provided by the International Association for the Study of Pain (IASP). Our strategy is to identify an evolutionarily basic canonical pain phenomenon, involving unpleasant sensory and emotional experience based causally in localized tissue damage that is concordant with that experience. We then show how different variant cases of this canonical pain phenomenon can be distinguished, including pain that is elevated relative to peripheral (...)
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  23. Questions of Ontology.Kathrin Koslicki - 2015 - In Stephan Blatti & Sandra Lapointe (eds.), Ontology After Carnap. Oxford University Press.
    Following W.V. Quine’s lead, many metaphysicians consider ontology to be concerned primarily with existential questions of the form, “What is there?”. Moreover, if the position advanced by Rudolf Carnap, in his seminal essay, “Empiricism, Semantics, and Ontology ”, is correct, then many of these existential ontological questions ought to be classified as either trivially answerable or as “pseudo-questions”. One may justifiably wonder, however, whether the Quinean and Carnapian perspective on ontology really does justice to many of the (...)
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  24. 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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  25.  86
    Recognition and Social Ontology: An Introduction.Heikki Ikäheimo & Arto Laitinen - 2011 - In Heikki Ikäheimo & Arto Laitinen (eds.), Recognition and Social Ontology. Leiden: Brill. pp. 1-24.
    A substantial article length introduction to a collection on social ontology and mutual recognition.
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  26.  79
    The Ontology-Epistemology Divide: A Case Study in Medical Terminology.OIivier Bodenreider, Barry Smith & Anita Burgun - 2004 - In Achille Varzi & Laure Vieu (eds.), Formal Ontology in Information Systems. Proceedings of the Third International Conference (FOIS 2004). IOS Press.
    Medical terminology collects and organizes the many different kinds of terms employed in the biomedical domain both by practitioners and also in the course of biomedical research. In addition to serving as labels for biomedical classes, these names reflect the organizational principles of biomedical vocabularies and ontologies. Some names represent invariant features (classes, universals) of biomedical reality (i.e., they are a matter for ontology). Other names, however, convey also how this reality is perceived, measured, and understood by health professionals (...)
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  27. 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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  28. A Product Life Cycle Ontology for Additive Manufacturing.Munira Mohd Ali, Rahul Rai, J. Neil Otte & Barry Smith - 2019 - Computers in Industry 105:191-203.
    The manufacturing industry is evolving rapidly, becoming more complex, more interconnected, and more geographically distributed. Competitive pressure and diversity of consumer demand are driving manufacturing companies to rely more and more on improved knowledge management practices. As a result, multiple software systems are being created to support the integration of data across the product life cycle. Unfortunately, these systems manifest a low degree of interoperability, and this creates problems, for instance when different enterprises or different branches of an enterprise interact. (...)
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  29.  95
    Ontology and Cognitive Outcomes (Preprint).David Limbaugh, David Kasmier, Ronald Rudnicki, James Llinas & Barry Smith - 2020 - In arXiv.
    The intelligence community relies on human-machine-based analytic strategies that 1) access and integrate vast amounts of information from disparate sources, 2) continuously process this information, so that, 3) a maximally comprehensive understanding of world actors and their behaviors can be developed and updated. Herein we describe an approach to utilizing outcomes-based learning (OBL) to support these efforts that is based on an ontology of the cognitive processes performed by intelligence analysts.
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  30. Duality and Ontology.Baptiste Le Bihan & James Read - 2018 - Philosophy Compass 13 (12):e12555.
    A ‘duality’ is a formal mapping between the spaces of solutions of two empirically equivalent theories. In recent times, dualities have been found to be pervasive in string theory and quantum field theory. Naïvely interpreted, duality-related theories appear to make very different ontological claims about the world—differing in e.g. space-time structure, fundamental ontology, and mereological structure. In light of this, duality-related theories raise questions familiar from discussions of underdetermination in the philosophy of science: in the presence of dual theories, (...)
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  31. 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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  32. 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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  33. A Plant Disease Extension of the Infectious Disease Ontology.Ramona Walls, Barry Smith, Elser Justin, Goldfain Albert & W. Stevenson Dennis - 2012 - In Proceedings of the Third International Conference on Biomedical Ontology (CEUR 897). pp. 1-5.
    Plants from a handful of species provide the primary source of food for all people, yet this source is vulnerable to multiple stressors, such as disease, drought, and nutrient deficiency. With rapid population growth and climate uncertainty, the need to produce crops that can tolerate or resist plant stressors is more crucial than ever. Traditional plant breeding methods may not be sufficient to overcome this challenge, and methods such as highOthroughput sequencing and automated scoring of phenotypes can provide significant new (...)
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  34. 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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  35.  40
    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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  36.  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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  37. Annotating Affective Neuroscience Data with the Emotion Ontology.Janna Hastings, Werner Ceusters, Kevin Mulligan & Barry Smith - 2012 - In Third International Conference on Biomedical Ontology. ICBO. pp. 1-5.
    The Emotion Ontology is an ontology covering all aspects of emotional and affective mental functioning. It is being developed following the principles of the OBO Foundry and Ontological Realism. This means that in compiling the ontology, we emphasize the importance of the nature of the entities in reality that the ontology is describing. One of the ways in which realism-based ontologies are being successfully used within biomedical science is in the annotation of scientific research results in (...)
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  38.  59
    OBCS: The Ontology of Biological and Clinical Statistics.Jie Zheng, Marcelline R. Harris, Anna Maria Masci, Yu Lin, Alfred Hero, Barry Smith & Yongqun He - 2014 - Proceedings of the Fifth International Conference on Biomedical Ontology 1327:65.
    Statistics play a critical role in biological and clinical research. To promote logically consistent representation and classification of statistical entities, we have developed the Ontology of Biological and Clinical Statistics (OBCS). OBCS extends the Ontology of Biomedical Investigations (OBI), an OBO Foundry ontology supported by some 20 communities. Currently, OBCS contains 686 terms, including 381 classes imported from OBI and 147 classes specific to OBCS. The goal of this paper is to present OBCS for community critique and (...)
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  39. 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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  40.  85
    Ontology Summit 2008 Communiqué: Towards an Open Ontology Repository.Leo Obrst, Mark Musen, Barry Smith, Fabian Neuhaus, Frank Olken, Mike Gruninger, M. Raymond, Patrick Hayes & Raj Sharma - 2008 - In Ontology Summit 2008. cim3.
    Each annual Ontology Summit initiative makes a statement appropriate to each Summit’s theme as part of our general advocacy designed to bring ontology science and engineering into the mainstream. The theme this year is "Towards an Open Ontology Repository". This communiqué represents the joint position of those who were engaged in the year's summit discourse on an Open Ontology Repository (OOR) and of those who endorse below. In this discussion, we have agreed that an "ontology (...)
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  41. 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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  42.  51
    Representing Disease Courses: An Application of the Neurological Disease Ontology to Multiple Sclerosis Typology.Mark Jensen, Alexander P. Cox, Barry Smith & Alexander Diehl - 2013 - In Proceedings of the Fourth International Conference on Biomedical Ontology (ICBO), CEUR, vol. 1060.
    The Neurological Disease Ontology (ND) is being developed to provide a comprehensive framework for the representation of neurological diseases (Diehl et al., 2013). ND utilizes the model established by the Ontology for General Medical Science (OGMS) for the representation of entities in medicine and disease (Scheuermann et al., 2009). The goal of ND is to include information for each disease concerning its molecular, genetic, and environmental origins, the processes involved in its etiology and realization, as well as its (...)
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  43.  77
    Protein-Centric Connection of Biomedical Knowledge: Protein Ontology Research and Annotation Tools.Cecilia N. Arighi, Darren A. Natale, Judith A. Blake, Carol J. Bult, Michael Caudy, Alexander D. Diehl, Harold J. Drabkin, Peter D'Eustachio, Alexei Evsikov, Hongzhan Huang, Barry Smith & Others - 2011 - In Proceedings of the 2nd International Conference on Biomedical Ontology. Buffalo, NY: NCOR. pp. 285-287.
    The Protein Ontology (PRO) web resource provides an integrative framework for protein-centric exploration and enables specific and precise annotation of proteins and protein complexes based on PRO. Functionalities include: browsing, searching and retrieving, terms, displaying selected terms in OBO or OWL format, and supporting URIs. In addition, the PRO website offers multiple ways for the user to request, submit, or modify terms and/or annotation. We will demonstrate the use of these tools for protein research and annotation.
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  44.  57
    Towards a Body Fluids Ontology: A Unified Application Ontology for Basic and Translational Science.Jiye Ai, Mauricio Barcellos Almeida, André Queiroz De Andrade, Alan Ruttenberg, David Tai Wai Wong & Barry Smith - 2011 - Second International Conference on Biomedical Ontology , Buffalo, Ny 833:227-229.
    We describe the rationale for an application ontology covering the domain of human body fluids that is designed to facilitate representation, reuse, sharing and integration of diagnostic, physiological, and biochemical data, We briefly review the Blood Ontology (BLO), Saliva Ontology (SALO) and Kidney and Urinary Pathway Ontology (KUPO) initiatives. We discuss the methods employed in each, and address the project of using them as starting point for a unified body fluids ontology resource. We conclude with (...)
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  45.  48
    Ontobull and BFOConvert: Web-Based Programs to Support Automatic Ontology Conversion.Ong Edison: Xiang, Zheng Jie, Barry Smith & He Yongqun - 2016 - Proceedings of the Joint International Conference on Biological Ontology and Biocreative 1747.
    When a widely reused ontology appears in a new version which is not compatible with older versions, the ontologies reusing it need to be updated accordingly. Ontobull has been developed to automatically update ontologies with new term IRI(s) and associated metadata to take account of such version changes. To use the Ontobull web interface a user is required to (i) upload one or more ontology OWL source files; (ii) input an ontology term IRI mapping; and (where needed) (...)
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  46. 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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  47. 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 its (...)
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  48. What is Ontology? A Dialogue.Uriah Kriegel - 2019 - Think 18 (53):49-65.
    This dialogue presents a substantive account of the nature and aim of ontology.Export citation.
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  49.  96
    Organisms, activity, and being: on the substance of process ontology.Christopher J. Austin - 2020 - European Journal for Philosophy of Science 10 (2):1-21.
    According to contemporary ‘process ontology’, organisms are best conceptualised as spatio-temporally extended entities whose mereological composition is fundamentally contingent and whose essence consists in changeability. In contrast to the Aristotelian precepts of classical ‘substance ontology’, from the four-dimensional perspective of this framework, the identity of an organism is grounded not in certain collections of privileged properties, or features which it could not fail to possess, but in the succession of diachronic relations by which it persists, or ‘perdures’ as (...)
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  50.  28
    CIDO, a Community-Based Ontology for Coronavirus Disease Knowledge and Data Integration, Sharing, and Analysis.Oliver He, John Beverley, Gilbert S. Omenn, Barry Smith, Brian Athey, Luonan Chen, Xiaolin Yang, Junguk Hur, Hsin-hui Huang, Anthony Huffman, Yingtong Liu, Yang Wang, Edison Ong & Hong Yu - 2020 - Scientific Data 181 (7):5.
    Ontologies, as the term is used in informatics, are structured vocabularies comprised of human- and computer-interpretable terms and relations that represent entities and relationships. Within informatics fields, ontologies play an important role in knowledge and data standardization, representation, integra- tion, sharing and analysis. They have also become a foundation of artificial intelligence (AI) research. In what follows, we outline the Coronavirus Infectious Disease Ontology (CIDO), which covers multiple areas in the domain of coronavirus diseases, including etiology, transmission, epidemiology, pathogenesis, (...)
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