Results for 'RNA ontology'

974 found
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  1. The Non-Coding RNA Ontology : a comprehensive resource for the unification of non-coding RNA biology.Huang Jingshan, Eilbeck Karen, Barry Smith, A. Blake Judith, Dou Dejing, Huang Weili, A. Natale Darren, Ruttenberg Alan, Huan Jun & T. Zimmermann Michael - 2016 - Journal of Biomedical Semantics 7 (1).
    In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for (...)
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  2. The development of non-coding RNA ontology.Jingshan Huang, Karen Eilbeck, Barry Smith, Judith Blake, Deijing Dou, Weili Huang, Darren Natale, Alan Ruttenberg, Jun Huan, Michael Zimmermann, Guoqian Jiang, Yu Lin, Bin Wu, Harrison Strachan, Nisansa de Silva & Mohan Vamsi Kasukurthi - 2016 - International Journal of Data Mining and Bioinformatics 15 (3):214--232.
    Identification of non-coding RNAs (ncRNAs) has been significantly improved over the past decade. On the other hand, semantic annotation of ncRNA data is facing critical challenges due to the lack of a comprehensive ontology to serve as common data elements and data exchange standards in the field. We developed the Non-Coding RNA Ontology (NCRO) to handle this situation. By providing a formally defined ncRNA controlled vocabulary, the NCRO aims to fill a specific and highly needed niche in semantic (...)
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  3. A domain ontology for the non-coding RNA field.Jingshan Huang, Karen Eilbeck, Judith A. Blake, Dejing Dou, Darren A. Natale, Alan Ruttenberg, Barry Smith, Michael T. Zimmermann, Guoqian Jiang & Yu Lin - 2015 - In Huang Jingshan, Eilbeck Karen, Blake Judith A., Dou Dejing, Natale Darren A., Ruttenberg Alan, Smith Barry, Zimmermann Michael T., Jiang Guoqian & Lin Yu (eds.), IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM 2015). pp. 621-624.
    Identification of non-coding RNAs (ncRNAs) has been significantly enhanced due to the rapid advancement in sequencing technologies. On the other hand, semantic annotation of ncRNA data lag behind their identification, and there is a great need to effectively integrate discovery from relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a precisely defined ncRNA controlled vocabulary, which can fill a specific and highly needed niche in unification of ncRNA biology.
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  4. OmniSearch: a semantic search system based on the Ontology for MIcroRNA Target Gene Interaction data.Huang Jingshan, Gutierrez Fernando, J. Strachan Harrison, Dou Dejing, Huang Weili, A. Blake Judith, Barry Smith, Eilbeck Karen, A. Natale Darren & Lin Yu - 2016 - Journal of Biomedical Semantics 7 (1):1.
    In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for (...)
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  5. 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, the scope of the PO (...)
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  6. Quasispecies Productivity.Guenther Witzany - 2024 - The Science of Nature (Naturwissenschaften) 111:11.
    Abstract The quasispecies theory is a helpful concept in the explanation of RNA virus evolution and behaviour, with a relevant impact on methods used to fight viral diseases. It has undergone some adaptations to integrate new empirical data, especially the non-deterministic nature of mutagenesis, and the variety of behavioural motifs in cooperation, competition, communication, innovation, integration, and exaptation. Also, the consortial structure of quasispecies with complementary roles of memory genomes of minority populations better fits the empirical data than did the (...)
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  7. A semantic approach for knowledge capture of microRNA-target gene interactions.Jingshan Huang, Fernando Gutierrez, Dejing Dou, Judith A. Blake, Karen Eilbeck, Darren A. Natale, Barry Smith, Yu Lin, Xiaowei Wang & Zixing Liu - 2015 - In Jingshan Huang, Fernando Gutierrez, Dejing Dou, Judith A. Blake, Karen Eilbeck, Darren A. Natale, Barry Smith, Yu Lin, Xiaowei Wang & Zixing Liu (eds.), IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM 2015),. pp. 975-982.
    Research has indicated that microRNAs (miRNAs), a special class of non-coding RNAs (ncRNAs), can perform important roles in different biological and pathological processes. miRNAs’ functions are realized by regulating their respective target genes (targets). It is thus critical to identify and analyze miRNA-target interactions for a better understanding and delineation of miRNAs’ functions. However, conventional knowledge discovery and acquisition methods have many limitations. Fortunately, semantic technologies that are based on domain ontologies can render great assistance in this regard. In our (...)
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  8. Arthur M. Diamond, Jr., Openness to Creative Destruction Sustaining Innovative Dynamism. Oxford: Oxford UP, 2019. [REVIEW]Kelly Kate Evans - 2021 - Journal of Value Inquiry 57 (3):581-592.
    The Pfizer-BioNTech coronavirus vaccine is 90 percent effective in protecting against COVID-19. It would not have been possible without the tireless effort of Professor Katalin Karikó, a scientific innovator fitting the mold of dynamic inventor Arthur Diamond presents in his book, Openness to Creative Destruction Sustaining Innovative Dynamism. Not only did Professor Karikó persist in her beliefs in the therapeutic potential of synthetic messenger RNA over the course of four decades, but she did so despite the criticisms of other scientists (...)
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  9. The question of ontology.Kit Fine - 2009 - In Ryan Wasserman, David Manley & David Chalmers (eds.), Metametaphysics: New Essays on the Foundations of Ontology. Oxford, England: Oxford University Press. pp. 157--177.
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  10. The GRW Flash Theory: A Relativistic Quantum Ontology of Matter in Space-Time?Michael Esfeld & Nicolas Gisin - 2014 - Philosophy of Science 81 (2):248-264.
    John Bell proposed an ontology for the GRW modification of quantum mechanics in terms of flashes occurring at space- time points. This article spells out the motivation for this ontology, inquires into the status of the wave function in it, critically examines the claim of its being Lorentz invariant, and considers whether it is a parsimonious but nevertheless physically adequate ontology.
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  11. Fundamental Quantification and the Language of the Ontology Room.Daniel Z. Korman - 2013 - Noûs 49 (2):298-321.
    Nihilism is the thesis that no composite objects exist. Some ontologists have advocated abandoning nihilism in favor of deep nihilism, the thesis that composites do not existO, where to existO is to be in the domain of the most fundamental quantifier. By shifting from an existential to an existentialO thesis, the deep nihilist seems to secure all the benefits of a composite-free ontology without running afoul of ordinary belief in the existence of composites. I argue that, while there are (...)
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  12. That is life: communicating RNA networks from viruses and cells in continuous interaction.Guenther Witzany - 2019 - Annals of the New York Academy of Sciences:1-16.
    All the conserved detailed results of evolution stored in DNA must be read, transcribed, and translated via an RNAmediated process. This is required for the development and growth of each individual cell. Thus, all known living organisms fundamentally depend on these RNA-mediated processes. In most cases, they are interconnected with other RNAs and their associated protein complexes and function in a strictly coordinated hierarchy of temporal and spatial steps (i.e., an RNA network). Clearly, all cellular life as we know it (...)
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  13. What is Individualism in Social Ontology? Ontological Individualism vs. Anchor Individualism.Brian Epstein - 2014 - In Julie Zahle & Finn Collin (eds.), Rethinking the Individualism-Holism Debate. Cham: Springer.
    Individualists about social ontology hold that social facts are “built out of” facts about individuals. In this paper, I argue that there are two distinct kinds of individualism about social ontology, two different ways individual people might be the metaphysical “builders” of the social world. The familiar kind is ontological individualism. This is the thesis that social facts supervene on, or are exhaustively grounded by, facts about individual people. What I call anchor individualism is the alternative thesis that (...)
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  14. Introduction: What is Ontology for?Katherine Munn - 2008 - In Katherine Munn & Barry Smith (eds.), Applied Ontology: An Introduction. Frankfurt: ontos. pp. 7-19.
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  15. Variance Theses in Ontology and Metaethics.Matti Eklund - 2019 - In Alexis Burgess, Herman Cappelen & David Plunkett (eds.), Conceptual Engineering and Conceptual Ethics. New York, USA: Oxford University Press.
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  16. RNA’s Role in the Origins of Life: An Agentic ‘Manager’, or Recipient of ‘Off-loaded’ Constraints?John E. Stewart - 2021 - Biosemiotics 14 (3):643-650.
    In his Target Article, Terrence Deacon develops simple models that assist in understanding the role of RNA in the origins of life. However, his models fail to adequately represent an important evolutionary dynamic. Central to this dynamic is the selection that impinges on RNA molecules in the context of their association with proto-metabolisms. This selection shapes the role of RNA in the emergence of life. When this evolutionary dynamic is appropriately taken into account, it predicts a role for RNA that (...)
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  17. Ontological physicalism and property pluralism: Why they are incompatible.Robert Francescotti - 2000 - Pacific Philosophical Quarterly 81 (4):349-362.
    To earn the title “ontological physicalist,” one must endorse an entailment thesis of the following sort: the physical properties that are had, together with the causal laws, determine which higher-level properties are had. I argue that if this thesis is to capture all that is essential to physicalist intuitions, the relevant set of causal laws must be restricted to purely physical laws. But then it follows that higher-level properties are physical properties. The conclusion is that one cannot consistently be an (...)
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  18.  62
    Language and deontology in social ontology.Luca Forgione - 2024 - Mechané 7:55-70.
    In his book Documentality, Ferraris imagines a wedding scenario where all participants have Alzheimer. The ceremony proceeds as normal, and by its end, a new husband and wife exist. However, the next morning, the spouses forget everything. This scenario underscores the importance of writing in Ferraris’ theory. A recorded document, such as a marriage certificate, could confirm their marriage. Ferraris’ approach to documentality and social ontology illustrates that if the discovery of this document occurred after the death of the (...)
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  19. 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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  20. The Reality of Brands: Towards an Ontology of Marketing.Wolfgang Grassl - 1999 - American Journal of Economics and Sociology 58:313-360.
    The ontology of marketing, particularly the question of what products and brands are, is still largely unexplored. The ontological status of brands hinges on their relationship with products. Idealists about brands see perceptual or cognitive acts of consumers grouped under the heading ‘brand awareness’ or ‘brand image’ as constitutive for the existence of brands so that, in their view, tools of the marketing mix can influence relevant mental dispositions and attitudes. Brand realists, on the other hand, reject the view (...)
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  21. Cambridge social ontology: an interview with Tony Lawson.Tony Lawson & C. Tyler DesRoches - 2009 - Erasmus Journal for Philosophy and Economics 2 (1):100.
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  22. Review, What Is, and What Is in Itself: A Systematic Ontology.Craig Warmke - 2024 - Philosophical Review 133 (4):415-419.
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  23. Emerging into the rainforest: Emergence and special science ontology.Alexander Franklin & Katie Robertson - 2024 - European Journal for Philosophy of Science 14 (4):1-26.
    Scientific realists don’t standardly discriminate between, say, biology and fundamental physics when deciding whether the evidence and explanatory power warrant the inclusion of new entities in our ontology. As such, scientific realists are committed to a lush rainforest of special science kinds (Ross, 2000). Viruses certainly inhabit this rainforest – their explanatory power is overwhelming – but viruses’ properties can be explained from the bottom up: reductive explanations involving amino acids are generally available. However, reduction has often been taken (...)
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  24. Bohmian mechanics without wave function ontology.Albert Solé - 2013 - Studies in History and Philosophy of Science Part B: Studies in History and Philosophy of Modern Physics 44 (4):365-378.
    In this paper, I critically assess different interpretations of Bohmian mechanics that are not committed to an ontology based on the wave function being an actual physical object that inhabits configuration space. More specifically, my aim is to explore the connection between the denial of configuration space realism and another interpretive debate that is specific to Bohmian mechanics: the quantum potential versus guidance approaches. Whereas defenders of the quantum potential approach to the theory claim that Bohmian mechanics is better (...)
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  25. Searle and De Soto: The New Ontology of the Social World.Barry Smith - 2008 - In Barry Smith, David M. Mark & Isaac Ehrlich (eds.), The Mystery of Capital and the Construction of Social Reality. Open Court. pp. 35-51.
    Consider a game of blind chess between two chess masters that is recorded in some standard chess notation. The recording is a representation of the game. But what is the game itself? This question is, we believe, central to the entire domain of social ontology. We argue that the recorded game is a special sort of quasi-abstract pattern, something that is: (i) like abstract entities such as numbers or forms, in that it is both nonphysical and nonpsychological; but at (...)
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  26. Eleaticism and Socratic Dialectic: On Ontology, Philosophical Inquiry, and Estimations of Worth in Plato’s Parmenides, Sophist and Statesman.Jens Kristian Larsen - 2019 - Études Platoniciennes 19 (19).
    The Parmenides poses the question for what entities there are Forms, and the criticism of Forms it contains is commonly supposed to document an ontological reorientation in Plato. According to this reading, Forms no longer express the excellence of a given entity and a Socratic, ethical perspective on life, but come to resemble concepts, or what concepts designate, and are meant to explain nature as a whole. Plato’s conception of dialectic, it is further suggested, consequently changes into a value-neutral method (...)
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  27. A Spatio-Temporal Ontology for Geographic Information Integration.Thomas Bittner & Barry Smith - 2009 - International Journal for Geographical Information Science 23 (6):765-798.
    This paper presents an axiomatic formalization of a theory of top-level relations between three categories of entities: individuals, universals, and collections. We deal with a variety of relations between entities in these categories, including the sub-universal relation among universals and the parthood relation among individuals, as well as cross-categorial relations such as instantiation and membership. We show that an adequate understanding of the formal properties of such relations – in particular their behavior with respect to time – is critical for (...)
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  28. Metabolism Instead of Machine: Towards an Ontology of Hybrids.Julia Rijssenbeek, Vincent Blok & Zoë Robaey - 2022 - Philosophy and Technology 35 (3):1-23.
    The emerging field of synthetic biology aims to engineer novel biological entities. The envisioned future bio-based economy builds largely on “cell factories”: organisms that have been metabolically engineered to sustainably produce substances for human ends. In this paper, we argue that synthetic biology’s goal of creating efficient production vessels for industrial applications implies a set of ontological assumptions according to which living organisms are machines. Traditionally, a machine is understood as a technological, isolated and controllable production unit consisting of parts. (...)
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  29. Dispositions and Processes in the Emotion Ontology.Janna Hastings, Werner Ceusters, Barry Smith & Kevin Mulligan - 2011 - In Landgrebe Jobst & Smith Barry (eds.), Proceedings of the 2nd International Conference on Biomedical Ontology. CEUR, vol. 833. 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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  30. The substance of Brentano's ontology.Barry Smith - 1987 - Topoi 6 (1):39-49.
    This paper is a study of Brentano’s ontology, and more specifically of his theory of substance and accident as put forward toward the end of his life in the materials collected together as the Kategorienlehre or Theory of Categories. Here Brentano presents an auditious (re-)interpretation of Aristotle’s theory of substance and accidence. We show that on the Brentano initially defends, it is space which serves as the single substance upon which all other entities depend as accidents of space. In (...)
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  31. Relationalism about mechanics based on a minimalist ontology of matter.Antonio Vassallo, Dirk-André Deckert & Michael Esfeld - 2016 - European Journal for Philosophy of Science:1-20.
    This paper elaborates on relationalism about space and time as motivated by a minimalist ontology of the physical world: there are only matter points that are individuated by the distance relations among them, with these relations changing. We assess two strategies to combine this ontology with physics, using classical mechanics as example: the Humean strategy adopts the standard, non-relationalist physical theories as they stand and interprets their formal apparatus as the means of bookkeeping of the change of the (...)
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  32. Properties and dispositions: Some metaphysical remarks on quantum ontology.Mauro Dorato - 2006 - American Institute of Physics (1):139-157.
    After some suggestions about how to clarify the confused metaphysical distinctions between dispositional and non-dispositional or categorical properties, I review some of the main interpretations of QM in order to show that – with the relevant exception of Bohm’s minimalist interpretation – quantum ontology is irreducibly dispositional. Such an irreducible character of dispositions must be explained differently in different interpretations, but the reducibility of the contextual properties in the case of Bohmian mechanics is guaranteed by the fact that the (...)
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  33. Review of Social Goodness: On the Ontology of Social Norms, by Charlotte Witt. [REVIEW]Daniel Kelly & Katherine Ritchie - forthcoming - Mind.
    Charlotte Witt covers a remarkable amount of ground in this concise and elegantly written book. Coming in at under 150 pages, she artfully weaves together Aristotle’s theory of functions with contemporary work on cultural transmission and apprenticeship, ideas about self-creation with theories of aspiration and transformative experience, and reflections on the relationships among social norms and games with thoughts about social roles and the nature of hierarchy. At the heart of it is an elaboration and defense of a thoroughly externalist (...)
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  34. 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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  35. Category Theory and the Ontology of Śūnyatā.Posina Venkata Rayudu & Sisir Roy - 2024 - In Peter Gobets & Robert Lawrence Kuhn (eds.), The Origin and Significance of Zero: An Interdisciplinary Perspective. Leiden: Brill. pp. 450-478.
    Notions such as śūnyatā, catuṣkoṭi, and Indra's net, which figure prominently in Buddhist philosophy, are difficult to readily accommodate within our ordinary thinking about everyday objects. Famous Buddhist scholar Nāgārjuna considered two levels of reality: one called conventional reality, and the other ultimate reality. Within this framework, śūnyatā refers to the claim that at the ultimate level objects are devoid of essence or "intrinsic properties", but are interdependent by virtue of their relations to other objects. Catuṣkoṭi refers to the claim (...)
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  36. Acting for Others: Moral Ontology in Simone de Beauvoir's Pyrrhus and Cineas.Tove Pettersen - 2010 - Simone de Beauvoir Studies 26 (2009-2010):18-27.
    There are prominent resemblances between issues addressed by Simone de Beauvoir in her early essay on moral philosophy, Pyrrhus and Cineas (1944), and issues attracting the attention of contemporary feminist ethicists, especially those concerned with the ethics of care. They include a focus on relationships, interaction, and mutual dependency. Both emphasize concrete ethical challenges rooted in everyday life, such as those affecting parents and children. Both are critical of the level of abstraction and insensitivity to the situation of the moral (...)
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  37.  74
    Summary by an AI of the article The Ontology of Knowledge, Logic, Arithmetic, Set Theory, and Geometry.Jean-Louis Boucon - 2024 - Academia.
    The text “The Ontology of Knowledge, Logic, Arithmetic, Set Theory, and Geometry” by Jean-Louis Boucon explores a deeply philosophical interpretation of knowledge, its logical structure, and the foundational elements of mathematical and scientific reasoning. -/- Here’s an overview condensed by an AI of the key themes and ideas, summarized into a quite general conceptual structure. These two pages are instructive on their own, but their main purpose is to facilitate the reading of the entire article, allowing the reader to (...)
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  38. The Logic of Biological Classification and the Foundations of Biomedical Ontology.Barry Smith - 2009 - In C. Glymour, D. Westerstahl & W. Wang (eds.), Logic, Methodology and Philosophy of Science. Proceedings of the 13th International Congress. King’s College. pp. 505-520.
    Biomedical research is increasingly a matter of the navigation through large computerized information resources deriving from functional genomics or from the biochemistry of disease pathways. To make such navigation possible, controlled vocabularies are needed in terms of which data from different sources can be unified. One of the most influential developments in this regard is the so-called Gene Ontology, which consists of controlled vocabularies of terms used by biologists to describe cellular constituents, biological processes and molecular functions, organized into (...)
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  39. (1 other version)From Locke to Materialism: Empiricism, the Brain and the Stirrings of Ontology.Charles Wolfe - 2018 - In A. L. Rey S. Bodenmann (ed.), 18th-Century Empiricism and the Sciences.
    My topic is the materialist appropriation of empiricism – as conveyed in the ‘minimal credo’ nihil est in intellectu quod non fuerit in sensu (which interestingly is not just a phrase repeated from Hobbes and Locke to Diderot, but is also a medical phrase, used by Harvey, Mandeville and others). That is, canonical empiricists like Locke go out of their way to state that their project to investigate and articulate the ‘logic of ideas’ is not a scientific project: “I shall (...)
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  40. The Mandatory Ontology of Robot Responsibility.Marc Champagne - 2021 - Cambridge Quarterly of Healthcare Ethics 30 (3):448–454.
    Do we suddenly become justified in treating robots like humans by positing new notions like “artificial moral agency” and “artificial moral responsibility”? I answer no. Or, to be more precise, I argue that such notions may become philosophically acceptable only after crucial metaphysical issues have been addressed. My main claim, in sum, is that “artificial moral responsibility” betokens moral responsibility to the same degree that a “fake orgasm” betokens an orgasm.
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  41.  94
    Expansiveness, objectivity, and actuality in affection: Nicolai hartmann’s theory of person, its position in his ontology of intellectual being and its relation to phenomenology.Moritz von Kalckreuth - 2019 - HORIZON. Studies in Phenomenology 8 (1):211-229.
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  42. The ImmPort Antibody Ontology.William Duncan, Travis Allen, Jonathan Bona, Olivia Helfer, Barry Smith, Alan Ruttenberg & Alexander D. Diehl - 2016 - Proceedings of the International Conference on Biological Ontology 1747.
    Monoclonal antibodies are essential biomedical research and clinical reagents that are produced by companies and research laboratories. The NIAID ImmPort (Immunology Database and Analysis Portal) resource provides a long-term, sustainable data warehouse for immunological data generated by NIAID, DAIT and DMID funded investigators for data archiving and re-use. A variety of immunological data is generated using techniques that rely upon monoclonal antibody reagents, including flow cytometry, immunofluorescence, and ELISA. In order to facilitate querying, integration, and reuse of data, standardized terminology (...)
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  43. The Unified Medical Language System and the Gene Ontology: Some critical reflections.Anand Kumar & Barry Smith - 2003 - In A. Günter, R. Kruse & B. Neumann (eds.), KI 2003: Advances in Artificial Intelligence. Berlin: Springer. pp. 135-148.
    The Unified Medical Language System and the Gene Ontology are among the most widely used terminology resources in the biomedical domain. However, when we evaluate them in the light of simple principles for wellconstructed ontologies we find a number of characteristic inadequacies. Employing the theory of granular partitions, a new approach to the understanding of ontologies and of the relationships ontologies bear to instances in reality, we provide an application of this theory in relation to an example drawn from (...)
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  44. (1 other version)Vital anti-mathematicism and the ontology of the emerging life sciences: from Mandeville to Diderot.Charles T. Wolfe - 2017 - Synthese:1-22.
    Intellectual history still quite commonly distinguishes between the episode we know as the Scientific Revolution, and its successor era, the Enlightenment, in terms of the calculatory and quantifying zeal of the former—the age of mechanics—and the rather scientifically lackadaisical mood of the latter, more concerned with freedom, public space and aesthetics. It is possible to challenge this distinction in a variety of ways, but the approach I examine here, in which the focus on an emerging scientific field or cluster of (...)
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  45. Social Goodness: The Ontology of Social Norms. BY CHARLOTTE WITT (New York: Oxford University Press, 2023. Pp. xi + 145. Price £ 54.). [REVIEW]Luca Moretti - forthcoming - Philosophical Quarterly 75 (1):341-343.
    Charlotte Witt's finely crafted book offers an original and powerful account of social role normativity––the normativity of norms associated with social ro.
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  46. The Economic World View: Studies in the Ontology of Economics.Uskali Mäki (ed.) - 2001 - New York: Cambridge University Press.
    The beliefs of economists are not solely determined by empirical evidence in direct relation to the theories and models they hold. Economists hold 'ontological presuppositions', fundamental ideas about the nature of being which direct their thinking about economic behaviour. In this volume, leading philosophers and economists examine these hidden presuppositions, searching for a 'world view' of economics. What properties are attributed to human individuals in economic theories, and which are excluded? Does economic man exist? Do markets have an essence? Do (...)
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  47. 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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  48. 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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  49. Psychiatric Euthanasia and the Ontology of Mental Disorder.Hane Htut Maung - 2020 - Journal of Applied Philosophy 38 (1):136-154.
    In the Netherlands and Belgium, it is lawful for voluntary euthanasia to be offered on the grounds of psychiatric suffering. A recent case that has sparked much debate is that of Aurelia Brouwers, who was helped to die in the Netherlands on account of her suffering from borderline personality disorder. It is sometimes claimed that whether or not a mentally ill person’s wish to die is valid hinges on whether or not that wish is a symptom of the person’s mental (...)
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  50. (1 other version)The green and the blue: a new political ontology for a mature information society.Luciano Floridi - 2020 - Philosophisches Jahrbuch 127 (2):307–⁠338.
    Today, in any mature information society, we live neither online nor offline but on life, that is, we increasingly live in that special space that is both analogue and digital, both online and offline. Imagine someone asking whether the water is fresh or salty in the estuary where the river meets the sea. That someone has not understood the special nature of the place. Our information society is that place. And our technologies are perfectly evolved to take advantage of it, (...)
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