Results for 'Plant Ontology'

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  1.  40
    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 (...)
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  2.  81
    A Plant Disease Extension of the Infectious Disease Ontology.Ramona Walls, Barry Smith, Elser Justin, Goldfain Albert & W. Stevenson Dennis - 2012 - In Proceeedings 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 (...)
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  3. The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses.Laurel Cooper, Ramona Walls, Justin Elser, Maria A. Gandolfo, Dennis W. Stevenson, Barry Smith & Others - 2013 - Plant and Cell Physiology 54 (2):1-23..
    The Plant Ontology (PO; http://www.plantontology.org/) is a publicly-available, collaborative effort to develop and maintain a controlled, structured vocabulary (“ontology”) of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, (...)
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  4.  81
    The Planteome Database: An Integrated Resource for Reference Ontologies, Plant Genomics and Phenomics.Laurel Cooper, Austin Meier, Marie-Angélique Laporte, Justin L. Elser, Chris Mungall, Brandon T. Sinn, Dario Cavaliere, Seth Carbon, Nathan A. Dunn, Barry Smith, Botong Qu, Justin Preece, Eugene Zhang, Sinisa Todorovic, Georgios Gkoutos, John H. Doonan, Dennis W. Stevenson, Elizabeth Arnaud & Pankaj Jaiswal - 2018 - Nucleic Acids Research 46 (D1):D1168–D1180.
    The Planteome project provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology, and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and (...)
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  5. Ontologies as Integrative Tools for Plant Science.Ramona Walls, Balaji Athreya, Laurel Cooper, Justin Elser, Maria A. Gandolfo, Pankaj Jaiswal, Christopher J. Mungall, Justin Preece, Stefan Rensing, Barry Smith & Dennis W. Stevenson - 2012 - American Journal of Botany 99 (8):1263–1275.
    Bio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. They are a key component of the Semantic Web. This paper provides background on what bio-ontologies are, why they are relevant to botany, and the principles of ontology development. It includes an overview of ontologies and related resources that are relevant to (...)
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  6. 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 (...)
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  7. 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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  8. 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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  9. 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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  10. Ontology (Science).Barry Smith - 2003 - In Carola Eschenbach & Michael Grüninger (eds.), Formal Ontology in Information Systems. Oxford: IOS Press. pp. 21-35.
    Increasingly, in data-intensive areas of the life sciences, experimental results are being described in algorithmically useful ways with the help of ontologies. Such ontologies are authored and maintained by scientists to support the retrieval, integration and analysis of their data. The proposition to be defended here is that ontologies of this type – the Gene Ontology (GO) being the most conspicuous example – are a part of science. Initial evidence for the truth of this proposition (which some will find (...)
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  11. 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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  12. What is Ontology? A Dialogue.Uriah Kriegel - forthcoming - Think.
    This dialogue presents a substantive account of the nature and aim of ontology.
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  13. 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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  14. Functions in Basic Formal Ontology.Andrew 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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  15. 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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  16. 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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  17. 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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  18. 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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  19. 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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  20. 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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  21. 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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  22.  38
    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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  23.  44
    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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  24. 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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  25.  38
    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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  26.  60
    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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  27.  29
    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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  28.  26
    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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  29.  93
    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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  30.  22
    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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  31.  16
    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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  32.  51
    Plant Seedlings Classification Using Deep Learning.Belal A. M. Ashqar, Bassem S. Abu-Nasser & Samy S. Abu-Naser - 2019 - International Journal of Academic Information Systems Research (IJAISR) 3 (1):7-14.
    Agriculture is very important to human continued existence and remains a key driver of many economies worldwide, especially in underdeveloped and developing economies. There is an increasing demand for food and cash crops, due to the increasing in world population and the challenges enforced by climate modifications, there is an urgent need to increase plant production while reducing costs. Preceding instrument vision methods established for selective weeding have confronted with major challenges for trustworthy and precise weed recognition. In this (...)
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  33.  36
    Quine, Ontology, and Physicalism.Frederique Janssen-Lauret - 2019 - In Robert Sinclair (ed.), Science and Sensibilia by W.V. Quine: The 1980 Immanuel Kant Lectures. Basingstoke: Palgrave Macmillan. pp. 181-204.
    Quine's views on ontology and naturalism are well-known but rarely considered in tandem. According to my interpretation the connection between them is vital. I read Quine as a global epistemic structuralist. Quine thought we only ever know objects qua solutions to puzzles about significant intersections in observations. Objects are always accessed descriptively, via their roles in our best theory. Quine's Kant lectures contain an early version of epistemic structuralism with uncharacteristic remarks about the mental. Here Quine embraces mitigated anomalous (...)
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  34. 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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  35. The Relevance of Philosophical Ontology to Information and Computer Science.Barry Smith - 2014 - In Ruth Hagengruber & Uwe Riss (eds.), Philosophy, Computing and Information Science. Chatto & Pickering. pp. 75-83.
    The discipline of ontology has enjoyed a checkered history since 1606, with a significant expansion in recent years. We focus here on those developments in the recent history of philosophy which are most relevant to the understanding of the increased acceptance of ontology, and especially of realist ontology, as a valuable method also outside the discipline of philosophy.
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  36. Easy Ontology, Application Conditions and Infinite Regress.Andrew Brenner - 2018 - Analysis 78 (4):605-614.
    In a number of recent publications Thomasson has defended a deflationary approach to ontological disputes, according to which ontological disputes are relatively easy to settle, by either conceptual analysis, or conceptual analysis in conjunction with empirical investigation. Thomasson’s “easy” approach to ontology is intended to derail many prominent ontological disputes. In this paper I present an objection to Thomasson’s approach to ontology. Thomasson’s approach to existence assertions means that she is committed to the view that application conditions associated (...)
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  37. Debunking Rationalist Defenses of Common-Sense Ontology: An Empirical Approach.Robert Osborne - 2016 - Review of Philosophy and Psychology 7 (1):197-221.
    Debunking arguments typically attempt to show that a set of beliefs or other intensional mental states bear no appropriate explanatory connection to the facts they purport to be about. That is, a debunking argument will attempt to show that beliefs about p are not held because of the facts about p. Such beliefs, if true, would then only be accidentally so. Thus, their causal origins constitute an undermining defeater. Debunking arguments arise in various philosophical domains, targeting beliefs about morality, the (...)
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  38. 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, and (...)
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  39. 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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  40. 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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  41. The Ontology of Organisms: Mechanistic Modules or Patterned Processes?Christopher Austin - 2016 - Biology and Philosophy 31 (5):639-662.
    Though the realm of biology has long been under the philosophical rule of the mechanistic magisterium, recent years have seen a surprisingly steady rise in the usurping prowess of process ontology. According to its proponents, theoretical advances in the contemporary science of evo-devo have afforded that ontology a particularly powerful claim to the throne: in that increasingly empirically confirmed discipline, emergently autonomous, higher-order entities are the reigning explanantia. If we are to accept the election of evo-devo as our (...)
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  42. 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. However, (...)
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  43. Natural Language Ontology.Friederike Moltmann - 2017 - Oxford Encyclopedia of Linguistics.
    The aim of natural language ontology is to uncover the ontological categories and structures that are implicit in the use of natural language, that is, that a speaker accepts when using a language. This article aims to clarify what exactly the subject matter of natural language ontology is, what sorts of linguistic data it should take into account, how natural language ontology relates to other branches of metaphysics, in what ways natural language ontology is important, and (...)
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  44. 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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  45.  51
    Ontology as Transcendental Philosophy.Huaping Lu-Adler - 2018 - In Courtney Fugate (ed.), Kant’s Lectures on Metaphysics: A Critical Guide. Cambridge: Cambridge University Press. pp. 53-73.
    How does the critical Kant view ontology? There is no shared scholarly answer to this question. Norbert Hinske sees in the Critique of Pure Reason a “farewell to ontology,” albeit one that took Kant long to bid (Hinske 2009). Karl Ameriks has found evidence in Kant’s metaphysics lectures from the critical period that he “was unwilling to break away fully from traditional ontology” (Ameriks 1992: 272). Gualtiero Lorini argues that a decisive break with the tradition of (...) is essential to Kant’s critical reform of metaphysics, as is reflected in his shift from “ontology” to “transcendental philosophy,” two notions that Lorini takes to be related by mere “analogy” (Lorini 2015). I agree with Lorini that a thorough reform of ontology is a pivotal part of Kant’s critical plan for metaphysics and that ontology somehow “survives within the critical philosophy” (Lorini 2015: 76). To make this case, however, I deem it important to identify “ontology” and “transcendental philosophy” in the sense of extensional equivalence. While we can detect this identification in Kant’s writings, only from his metaphysics lectures can we get a full sense of its historical and philosophical significance. In this chapter I focus on how it represents a definitive turn from as well as notable continuity with traditional treatments of ontology, particularly the Wolffian one. (shrink)
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  46. Modal Ontology and Generalized Quantifiers.Peter Fritz - 2013 - Journal of Philosophical Logic 42 (4):643-678.
    Timothy Williamson has argued that in the debate on modal ontology, the familiar distinction between actualism and possibilism should be replaced by a distinction between positions he calls contingentism and necessitism. He has also argued in favor of necessitism, using results on quantified modal logic with plurally interpreted second-order quantifiers showing that necessitists can draw distinctions contingentists cannot draw. Some of these results are similar to well-known results on the relative expressivity of quantified modal logics with so-called inner and (...)
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  47. Reiner Schürmann and Cornelius Castoriadis Between Ontology and Praxis.John Krummel - 2013 - Anarchist Developments in Cultural Studies 2013 (2).
    Every metaphysic, according to Reiner Schürmann, involves the positing of a first principle for thinking and doing whereby the world becomes intelligible and masterable. What happens when such rules or norms no longer have the power they previously had? According to Cornelius Castoriadis, the world makes sense through institutions of imaginary significations. What happens when we discover that these significations and institutions truly are imaginary, without ground? Both thinkers begin their ontologies by acknowledging a radical finitude that threatens to destroy (...)
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  48. Cognitive Ontology in Flux: The Possibility of Protean Brains.Daniel D. Hutto, Anco Peeters & Miguel Segundo Ortin - 2017 - Philosophical Explorations 20 (2):209-223.
    This paper motivates taking seriously the possibility that brains are basically protean: that they make use of neural structures in inventive, on-the-fly improvisations to suit circumstance and context. Accordingly, we should not always expect cognition to divide into functionally stable neural parts and pieces. We begin by reviewing recent work in cognitive ontology that highlights the inadequacy of traditional neuroscientific approaches when it comes to divining the function and structure of cognition. Cathy J. Price and Karl J. Friston, and (...)
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  49. An Ontology of Affordances.John T. Sanders - 1997 - Ecological Psychology 9 (1):97-112.
    I argue that the most promising approach to understanding J.J. Gibson's "affordances" takes affordances themselves as ontological primitives, instead of treating them as dispositional properties of more primitive things, events, surfaces, or substances. These latter are best treated as coalescences of affordances present in the environment (or "coalescences of use-potential," as in Sanders (1994) and Hilditch (1995)). On this view, even the ecological approach's stress on the complementary organism/environment pair is seen as expressing a particular affordance relation between the world (...)
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  50. Non-Existent Objects and Epistemological Ontology.William J. Rapaport - 1985 - Grazer Philosophische Studien 25:61-95.
    This essay examines the role of non-existent objects in "epistemological ontology" — the study of the entities that make thinking possible. An earlier revision of Meinong's Theory of Objects is reviewed, Meinong's notions of Quasisein and Außersein are discussed, and a theory of Meinongian objects as "combinatorially possible" entities is presented.
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