Results for 'Glen A. Smith'

962 found
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  1. Time at the Depth of the World.Glen A. Mazis - 2010 - In Kascha Semonovitch Neal DeRoo (ed.), Merleau-Ponty at the Limits of Art, Religion, and Perception. Continuum. pp. 120--146.
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  2. Earthbodies: rediscovering our planetary senses.Glen A. Mazis - 2002 - Albany, NY: State University of New York Press.
    Earthbodies describes how our bodies are open circuits to a sensual magic and planetary care that when closed off leads to disastrous detours, such as illness, ...
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  3. A New Approach to Sortre's Theory of Emotions.Glen A. Mazis - 1983 - Philosophy Today 27 (3):183-199.
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  4. The Semantic Theory of Truth: Field’s Incompleteness Objection.Glen A. Hoffmann - 2007 - Philosophia 35 (2):161-170.
    According to Field’s influential incompleteness objection, Tarski’s semantic theory of truth is unsatisfactory since the definition that forms its basis is incomplete in two distinct senses: (1) it is physicalistically inadequate, and for this reason, (2) it is conceptually deficient. In this paper, I defend the semantic theory of truth against the incompleteness objection by conceding (1) but rejecting (2). After arguing that Davidson and McDowell’s reply to the incompleteness objection fails to pass muster, I argue that, within the constraints (...)
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  5. La Chair et L'Imaginaire: The Developing Role of the Imagination in Merleau-Ponty's Philosophy.Glen A. Mazis - 1988 - Philosophy Today (1):30-42.
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  6. Cyborg Life: The In-Between of Humans and Machines.Glen A. Mazis - 2008 - PhaenEx 3 (2):14-36.
    Cyborgs are ongoing becomings of a doubly “in-between” temporality of humans and machines. Materially made from components of both sorts of beings, cyborgs gain increasing function through an interweaving in which each alters the other, from the level of “neural plasticity” to software updates to emotional breakthroughs of which both are a part. One sort of temporal in-between is of the progressive unfolding of a deepening becoming as “not-one-not-two” and the other is a “doubling back” of time into itself in (...)
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  7. Merleau Ponty, Inhabitation and the Emotions.Glen A. Mazis - 1989 - In Henry Pietersma (ed.), Merleau-Ponty: Critical Essays, Current Continental Research. Lanham, MD: Upa.
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  8. Merleau Ponty and the 'Syntax in Depth': Semiotics and Language as 'Another Less Heavy, More Transparent Body'.Glen A. Mazis - 1990 - In Recent Developments in Theory and History: The Semiotic Web 1990.
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  9. Interdyscyplinarne perspektywy rozwoju, integracji i zastosowań ontologii poznawczych.Joanna Hastings, Gwen A. Frishkoff, Barry Smith, Mark Jensen, Russell A. Poldrack, Jane Lomax, Anita Bandrowski, Fahim Imam, Jessica A. Turner & Maryann E. Martone - 2016 - Avant: Trends in Interdisciplinary Studies 7 (3):101-117.
    We discuss recent progress in the development of cognitive ontologies and summarize three challenges in the coordinated development and application of these resources. Challenge 1 is to adopt a standardized definition for cognitive processes. We describe three possibilities and recommend one that is consistent with the standard view in cognitive and biomedical sciences. Challenge 2 is harmonization. Gaps and conflicts in representation must be resolved so that these resources can be combined for mark-up and interpretation of multi-modal data. Finally, Challenge (...)
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  10. Towards Interoperability of Biomedical Ontologies.Musen Mark, A. Schroeder, Michael Smith & Barry - 2008 - Schloss Dagstuhl: Leibniz-Zentrum für Informatik.
    Report on Dagstuhl Seminar 07132, Schloss Dagstuhl, March 27-30 , 2007.
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  11. 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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  12. 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 the (...)
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  13. 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 Attribute Ontology, and others. The project also provides (...)
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  14. National Center for Biomedical Ontology: Advancing biomedicine through structured organization of scientific knowledge.Daniel L. Rubin, Suzanna E. Lewis, Chris J. Mungall, Misra Sima, Westerfield Monte, Ashburner Michael, Christopher G. Chute, Ida Sim, Harold Solbrig, M. A. Storey, Barry Smith, John D. Richter, Natasha Noy & Mark A. Musen - 2006 - Omics: A Journal of Integrative Biology 10 (2):185-198.
    The National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) to create (...)
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  15. Commentaries on David Hodgson's "a plain person's free will".Graham Cairns-Smith, Thomas W. Clark, Ravi Gomatam, Robert H. Kane, Nicholas Maxwell, J. J. C. Smart, Sean A. Spence & Henry P. Stapp - 2005 - Journal of Consciousness Studies 12 (1):20-75.
    REMARKS ON EVOLUTION AND TIME-SCALES, Graham Cairns-Smith; HODGSON'S BLACK BOX, Thomas Clark; DO HODGSON'S PROPOSITIONS UNIQUELY CHARACTERIZE FREE WILL?, Ravi Gomatam; WHAT SHOULD WE RETAIN FROM A PLAIN PERSON'S CONCEPT OF FREE WILL?, Gilberto Gomes; ISOLATING DISPARATE CHALLENGES TO HODGSON'S ACCOUNT OF FREE WILL, Liberty Jaswal; FREE AGENCY AND LAWS OF NATURE, Robert Kane; SCIENCE VERSUS REALIZATION OF VALUE, NOT DETERMINISM VERSUS CHOICE, Nicholas Maxwell; COMMENTS ON HODGSON, J.J.C. Smart; THE VIEW FROM WITHIN, Sean Spence; COMMENTARY ON HODGSON, Henry (...)
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  16. Infallible A Priori Self-Justifying Propositions.Glen Hoffmann - 2012 - Croatian Journal of Philosophy 12 (1):55-68.
    On rationalist infallibilism, a wide range of both (i) analytic and (ii) synthetic a priori propositions can be infallibly justified, i.e., justified in a way that is truth-entailing. In this paper, I examine the second thesis of rationalist infallibilism, what might be called ‘synthetic a priori infallibilism’. Exploring the seemingly only potentially plausible species of synthetic a priori infallibility, I reject the infallible justification of so-called self-justifying propositions.
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  17. Two kinds of a priori infallibility.Glen Hoffmann - 2011 - Synthese 181 (2):241-253.
    On rationalist infallibilism, a wide range of both (i) analytic and (ii) synthetic a priori propositions can be infallibly justified (or absolutely warranted), i.e., justified to a degree that entails their truth and precludes their falsity. Though rationalist infallibilism is indisputably running its course, adherence to at least one of the two species of infallible a priori justification refuses to disappear from mainstream epistemology. Among others, Putnam (1978) still professes the a priori infallibility of some category (i) propositions, while Burge (...)
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  18. Chaos Theory and Merleau-Ponty's Ontology: Beyond the Dead Father's Paralysis towards a Dynamic and Fragile Materiality.Glen Mazis - 1999 - In Olkowski And Morely (ed.), Merleau-Ponty: Interiority and Exteriority, Psychic Life and the World. Suny Press. pp. 217--241.
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  19. A Dilemma for the Weak Deflationist about Truth.Glen Hoffmann - 2007 - Sorites 18:129-137.
    The weak deflationist about truth is committed to two theses: one conceptual, the other ontological. On the conceptual thesis (what might be called a ‘triviality thesis’), the content of the truth predicate is exhausted by its involvement in some version of the ‘truth-schema’. On the ontological thesis, truth is a deflated property of truth bearers. In this paper, I focus on weak deflationism’s ontological thesis, arguing that it generates an instability in its view of truth: the view threatens to collapse (...)
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  20. A unified theory of truth and reference.Barry Smith & Berit Brogaard - 2000 - Logique Et Analyse 43 (169-170):49–93.
    The truthmaker theory rests on the thesis that the link between a true judgment and that in the world to which it corresponds is not a one-to-one but rather a one-to-many relation. An analogous thesis in relation to the link between a singular term and that in the world to which it refers is already widely accepted. This is the thesis to the effect that singular reference is marked by vagueness of a sort that is best understood in supervaluationist terms. (...)
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  21. Ontology of language, with applications to demographic data.S. Clint Dowland, Barry Smith, Matthew A. Diller, Jobst Landgrebe & William R. Hogan - 2023 - Applied ontology 18 (3):239-262.
    Here we present what we believe is a novel account of what languages are, along with an axiomatically rich representation of languages and language-related data that is based on this account. We propose an account of languages as aggregates of dispositions distributed across aggregates of persons, and in doing so we address linguistic competences and the processes that realize them. This paves the way for representing additional types of language-related entities. Like demographic data of other sorts, data about languages may (...)
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  22. Protein Ontology: A controlled structured network of protein entities.A. Natale Darren, N. Arighi Cecilia, A. Blake Judith, J. Bult Carol, R. Christie Karen, Cowart Julie, D’Eustachio Peter, D. Diehl Alexander, J. Drabkin Harold, Helfer Olivia, Barry Smith & Others - 2013 - Nucleic Acids Research 42 (1):D415-21..
    The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO relates to (...)
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  23. 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 Walls Ramona L., Cooper Laurel D., Justin Elser, Stevenson Dennis W., Smith Barry, Chris Mungall, Gandolfo Maria A. & Pankaj Jaiswal (eds.), Proceedings of the Workshop on Bio-Ontologies, ISMB, Boston, July, 2010.
    The Plant Ontology (PO) (http://www.plantontology.org) (Jaiswal et al., 2005; Avraham et al., 2008) was designed to facilitate cross-database querying and to foster consistent use of plant-specific terminology in annotation. As new data are generated from the ever-expanding list of plant genome projects, the need for a consistent, cross-taxon vocabulary has grown. To meet this need, the PO is being expanded to represent all plants. This is the first ontology designed to encompass anatomical structures as well as growth and developmental stages (...)
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  24. A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology.Yongqun He, Hong Yu, Anthony Huffman, Asiyah Yu Lin, Darren A. Natale, John Beverley, Ling Zheng, Yehoshua Perl, Zhigang Wang, Yingtong Liu, Edison Ong, Yang Wang, Philip Huang, Long Tran, Jinyang Du, Zalan Shah, Easheta Shah, Roshan Desai, Hsin-hui Huang, Yujia Tian, Eric Merrell, William D. Duncan, Sivaram Arabandi, Lynn M. Schriml, Jie Zheng, Anna Maria Masci, Liwei Wang, Hongfang Liu, Fatima Zohra Smaili, Robert Hoehndorf, Zoë May Pendlington, Paola Roncaglia, Xianwei Ye, Jiangan Xie, Yi-Wei Tang, Xiaolin Yang, Suyuan Peng, Luxia Zhang, Luonan Chen, Junguk Hur, Gilbert S. Omenn, Brian Athey & Barry Smith - 2022 - Journal of Biomedical Semantics 13 (1):25.
    The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of developing effective and safe vaccines and drugs and to better understand coronaviruses and associated disease mechenisms it is necessary to integrate the large and exponentially growing body of heterogeneous coronavirus data. Ontologies play an important role in standard-based knowledge and data representation, integration, sharing, and analysis. Accordingly, we initiated the (...)
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  25. Human Ethics as a Violence Towards Animals: The Demonized Wolf.Glen Mazis - 2011 - Spaziofilosofico, 3:291-304.
    This essay discusses how our traditional ethics may harbor assumptions that place humans in a position in which overt violence towards animals is an almost inevitable outcome since their formulation involves violence towards ourselves and our animal fellows in our cutting our embodied ties with them. The essay explores Derrida’s Animal that Therefore, I Am, in its detailing of the two discourses within European intellectual history of those who felt they were “above” animals and were not addressed by them versus (...)
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  26. Infinitism and epistemic normativity.Adam C. Podlaskowski & Joshua A. Smith - 2011 - Synthese 178 (3):515-527.
    Klein’s account of epistemic justification, infinitism, supplies a novel solution to the regress problem. We argue that concentrating on the normative aspect of justification exposes a number of unpalatable consequences for infinitism, all of which warrant rejecting the position. As an intermediary step, we develop a stronger version of the ‘finite minds’ objection.
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  27. A Critical Exploration of Principlism.Glen Cordha - 2 - Dissertation, University of Liverpool
    Beauchamp and Childress created the ‘four principle’ approach to help clinicians analyse and resolve ethical dilemmas they may encounter when working. In this project, I will consider whether autonomy ought to have a privileged position within the four principles and if the four principles can apply outside the medical sphere.
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  28. 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 the (...)
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  29. The Minimalist Theory of Truth: Challenges and Concerns.Glen Hoffmann - 2010 - Philosophy Compass 5 (10):938-949.
    Minimalism is currently the received deflationary theory of truth. On minimalism, truth is a transparent concept and a deflated property of truth bearers. In this paper, I situate minimalism within current deflationary debate about truth by contrasting it with its main alternative―the redundancy theory of truth. I also outline three of the primary challenges facing minimalism, its formulation, explanatory adequacy and stability, and draw some lessons for the soundness of its conception of truth.
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  30. Probabilistic Regresses and the Availability Problem for Infinitism.Adam C. Podlaskowski & Joshua A. Smith - 2014 - Metaphilosophy 45 (2):211-220.
    Recent work by Peijnenburg, Atkinson, and Herzberg suggests that infinitists who accept a probabilistic construal of justification can overcome significant challenges to their position by attending to mathematical treatments of infinite probabilistic regresses. In this essay, it is argued that care must be taken when assessing the significance of these formal results. Though valuable lessons can be drawn from these mathematical exercises (many of which are not disputed here), the essay argues that it is entirely unclear that the form of (...)
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  31. Framework for a protein ontology.Darren A. Natale, Cecilia N. Arighi, Winona Barker, Judith Blake, Ti-Cheng Chang, Zhangzhi Hu, Hongfang Liu, Barry Smith & Cathy H. Wu - 2007 - BMC Bioinformatics 8 (Suppl 9):S1.
    Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies—one that describes the protein entities themselves and their relationships. We have designed a PRotein Ontology (PRO) (...)
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  32. Gene Ontology annotations: What they mean and where they come from.David P. Hill, Barry Smith, Monica S. McAndrews-Hill & Judith A. Blake - 2008 - BMC Bioinformatics 9 (5):1-9.
    The computational genomics community has come increasingly to rely on the methodology of creating annotations of scientific literature using terms from controlled structured vocabularies such as the Gene Ontology (GO). We here address the question of what such annotations signify and of how they are created by working biologists. Our goal is to promote a better understanding of how the results of experiments are captured in annotations in the hope that this will lead to better representations of biological reality through (...)
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  33. Literature and Life.Gilles Deleuze, Daniel W. Smith & Michael A. Greco - 1997 - Critical Inquiry 23 (2):225-230.
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  34. Truth, Superassertability, and Conceivability.Glen Hoffmann - 2008 - Journal of Value Inquiry 42 (3):287-299.
    The superassertability theory of truth, inspired by Crispin Wright (1992, 2003), holds that a statement is true if and only if it is superassertable in the following sense: it possesses warrant that cannot be defeated by any improvement of our information. While initially promising, the superassertability theory of truth is vulnerable to a persistent difficulty highlighted by James Van Cleve (1996) and Terrence Horgan (1995) but not properly fleshed out: it is formally illegitimate in a similar sense that unsophisticated epistemic (...)
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  35. Nativism: In Defense of the Representational Interpretation.Glen Hoffmann - 2009 - Croatian Journal of Philosophy 9 (3):303-315.
    Linguistic competence, in general terms, involves the ability to learn, understand, and speak a language. The nativist view in the philosophy of linguistics holds that the principal foundation of linguistic competence is an innate faculty of linguistic cognition. In this paper, close scrutiny is given to nativism's fundamental commitments in the area of metaphysics. In the course of this exploration it is argued that any minimally defensible variety of nativism is, for better or worse, married to two theses: linguistic competence (...)
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  36. Adam Smith's political philosophy: the invisible hand and spontaneous order.Craig Smith - 2006 - New York: Routledge.
    When Adam Smith published his celebrated writings on economics and moral philosophy he famously referred to the operation of an invisible hand. Adam Smith's Political Philosophy makes visible the invisible hand by examining its significance in Smith's political philosophy and relating it to similar concepts used by other philosophers, revealing a distinctive approach to social theory that stresses the significance of the unintended consequences of human action. This book introduces greater conceptual clarity to the discussion of the (...)
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  37. Anselmian Defense of Hell.T. Parker Haratine & Kevin A. Smith - 2024 - TheoLogica: An International Journal for Philosophy of Religion and Philosophical Theology 8 (1).
    This article constructively retrieves St. Anselm of Canterbury’s theory of retributive justice and provides a defense of what can be called the retributive model of hell. In the first part of this article, we develop the place of retributive punishment in Anselm’s thinking and discuss how and when retributive punishment is a good thing. In the second part, we apply Anselm’s thinking on retributive justice to the problem of hell and provide a defense of how hell, defined as a state (...)
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  38. Benefiting from Failures to Address Climate Change.Holly Lawford-Smith - 2014 - Journal of Applied Philosophy 31 (4):392-404.
    The politics of climate change is marked by the fact that countries are dragging their heels in doing what they ought to do; namely, creating a binding global treaty, and fulfilling the duties assigned to each of them under it. Many different agents are culpable in this failure. But we can imagine a stylised version of the climate change case, in which no agents are culpable: if the bad effects of climate change were triggered only by crossing a particular threshold, (...)
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  39. 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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  40. Staging an encounter between anthropology and philosophy: Hits and misses in the work of Michael Jackson.James K. A. Smith - 2017 - Reviews in Anthropology 46 (4):151-163.
    This review essay assesses Michael Jackson’s ongoing project of staging an encounter between anthropology and philosophy in two books: Lifeworlds (2013) and As Wide as the World Is Wise (2016). Considering his philosophical enrichment of ethnographic theory and method, this essay addresses foundational questions about the prospects and practices of interdisciplinary engagement. It also suggests future avenues for continued dialogue between philosophy and anthropology.
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  41. The National Center for Biomedical Ontology.Mark A. Musen, Natalya F. Noy, Nigam H. Shah, Patricia L. Whetzel, Christopher G. Chute, Margaret-Anne Story & Barry Smith - 2012 - Journal of the American Medical Informatics Association 19 (2):190-195.
    The National Center for Biomedical Ontology is now in its seventh year. The goals of this National Center for Biomedical Computing are to: create and maintain a repository of biomedical ontologies and terminologies; build tools and web services to enable the use of ontologies and terminologies in clinical and translational research; educate their trainees and the scientific community broadly about biomedical ontology and ontology-based technology and best practices; and collaborate with a variety of groups who develop and use ontologies and (...)
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  42. Six questions on the construction of ontologies in biomedicine.Anand Kumar, A. Burgun, W. Ceusters, J. Cimino, J. Davis, P. Elkin, I. Kalet, A. Rector, J. Rice, J. Rogers, Barry Smith & Others - 2005 - Report of the AMIA Working Group on Formal Biomedical Knowledge Representation 1.
    (Report assembled for the Workshop of the AMIA Working Group on Formal Biomedical Knowledge Representation in connection with AMIA Symposium, Washington DC, 2005.) Best practices in ontology building for biomedicine have been frequently discussed in recent years. However there is a range of seemingly disparate views represented by experts in the field. These views not only reflect the different uses to which ontologies are put, but also the experiences and disciplinary background of these experts themselves. We asked six questions related (...)
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  43. Debate: Ideal Theory—A Reply to Valentini.Holly Lawford-Smith - 2009 - Journal of Political Philosophy 18 (3):357-368.
    In her ‘On the apparent paradox of ideal theory’, Laura Valentini combines three supposedly plausible premises to derive the paradoxical result that ideal theory is both unable to, and indispensable for, guiding action. Her strategy is to undermine one of the three premises by arguing that there are good and bad kinds of ideal theory, and only the bad kinds are vulnerable to the strongest version of their opponents’ attack. By undermining one of the three premises she releases ideal theorists (...)
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  44. The Protein Ontology: A structured representation of protein forms and complexes.Darren Natale, Cecilia N. Arighi, Winona C. Barker, Judith A. Blake, Carol J. Bult, Michael Caudy, Harold J. Drabkin, Peter D’Eustachio, Alexei V. Evsikov, Hongzhan Huang, Jules Nchoutmboube, Natalia V. Roberts, Barry Smith, Jian Zhang & Cathy H. Wu - 2011 - Nucleic Acids Research 39 (1):D539-D545.
    The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of protein (...)
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  45. Unethical Consumption & Obligations to Signal.Holly Lawford-Smith - 2015 - Ethics and International Affairs 29 (3):315-330.
    Many of the items that humans consume are produced in ways that involve serious harms to persons. Familiar examples include the harms involved in the extraction and trade of conflict minerals (e.g. coltan, diamonds), the acquisition and import of non- fair trade produce (e.g. coffee, chocolate, bananas, rice), and the manufacture of goods in sweatshops (e.g. clothing, sporting equipment). In addition, consumption of certain goods (significantly fossil fuels and the products of the agricultural industry) involves harm to the environment, to (...)
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  46. The World of Wolves: Lessons about the Sacredness of the Surround, Belonging, and the Silent Dialogue of Interdependence and Death, and Speciocide.Glen Mazis - 2008 - Environmental Philosophy 5 (2):69-92.
    This essay details wolves’ sense of their surround in terms of how wolves’ perceptual acuities, motor abilities, daily habits, overriding concerns, network of intimate social bonds and relationship to prey gives them a unique sense of space, time, belonging with other wolves, memorial sense, imaginative capacities, dominant emotions (of affection, play, loyalty, hunger, etc.), communicative avenues, partnership with other creatures, and key role in ecological thriving. Wolves are seen to live within a vast sense of aroundness and closeness to aspects (...)
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  47. 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 an (...)
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  48. Difference-Making and Individuals' Climate-Related Obligations.Holly Lawford-Smith - 2016 - In Clare Heyward & Dominic Roser (eds.), Climate Justice in a Non-Ideal World. Oxford University Press UK. pp. 64-82.
    Climate change appears to be a classic aggregation problem, in which billions of individuals perform actions none of which seem to be morally wrong taken in isolation, and yet which combine to drive the global concentration of greenhouse gases (GHGs) ever higher toward environmental (and humanitarian) catastrophe. When an individual can choose between actions that will emit differing amounts of GHGs―such as to choose a vegan rather than carnivorous meal, to ride a bike to work rather than drive a car, (...)
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  49. Measuring the Consequences of Rules: Holly M. Smith.Holly M. Smith - 2010 - Utilitas 22 (4):413-433.
    Recently two distinct forms of rule-utilitarianism have been introduced that differ on how to measure the consequences of rules. Brad Hooker advocates fixed-rate rule-utilitarianism, while Michael Ridge advocates variable-rate rule-utilitarianism. I argue that both of these are inferior to a new proposal, optimum-rate rule-utilitarianism. According to optimum-rate rule-utilitarianism, an ideal code is the code whose optimum acceptance level is no lower than that of any alternative code. I then argue that all three forms of rule-utilitarianism fall prey to two fatal (...)
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  50. Developing the Quantitative Histopathology Image Ontology : A case study using the hot spot detection problem.Metin Gurcan, Tomaszewski N., Overton John, A. James, Scott Doyle, Alan Ruttenberg & Barry Smith - 2017 - Journal of Biomedical Informatics 66:129-135.
    Interoperability across data sets is a key challenge for quantitative histopathological imaging. There is a need for an ontology that can support effective merging of pathological image data with associated clinical and demographic data. To foster organized, cross-disciplinary, information-driven collaborations in the pathological imaging field, we propose to develop an ontology to represent imaging data and methods used in pathological imaging and analysis, and call it Quantitative Histopathological Imaging Ontology – QHIO. We apply QHIO to breast cancer hot-spot detection with (...)
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