Results for 'Thomas H. Smith'

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Thomas H. Smith
University of Manchester
  1. 'Shared Agency', Gilbert, and Deep Continuity.Thomas H. Smith - 2015 - Journal of Social Ontology 1 (1):49-57.
    I compare Bratman’s theory with Gilbert’s. I draw attention to their similarities, query Bratman’s claim that his theory is the more parsimonious, and point to one theoretical advantage of Gilbert’s theory.
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  2. 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, (...)
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  3. The Incarceration of Wildness: Wilderness Areas as Prisons.Thomas H. Birch - 1990 - Environmental Ethics 12 (1):3-26.
    Even with the very best intentions , Western culture’s approach to wilderness and wildness, the otherness of nature, tends to be one of imperialistic domination and appropriation. Nevertheless, in spite of Western culture’s attempt to gain total control over nature by imprisoning wildness in wilderness areas, which are meant to be merely controlled “simulations” of wildness, a real wildness, a real otherness, can still be found in wilderness reserves . This wildness can serve as the literal ground for the subversion (...)
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  4. 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 extend (...)
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  5. Nietzsche's Ethics of Character: A Study of Nietzsche's Ethics and its Place in the History of Moral Thinking.Thomas H. Brobjer - 1999 - Journal of Nietzsche Studies 17:73-77.
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  6. Distributive Justice as an Ethical Principle for Autonomous Vehicle Behavior Beyond Hazard Scenarios.Manuel Dietrich & Thomas H. Weisswange - 2019 - Ethics and Information Technology 21 (3):227-239.
    Through modern driver assistant systems, algorithmic decisions already have a significant impact on the behavior of vehicles in everyday traffic. This will become even more prominent in the near future considering the development of autonomous driving functionality. The need to consider ethical principles in the design of such systems is generally acknowledged. However, scope, principles and strategies for their implementations are not yet clear. Most of the current discussions concentrate on situations of unavoidable crashes in which the life of human (...)
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  7. A Taxonomy of Granular Partitions.Thomas E. Bittner & Barry Smith - 2001 - In Daniel Montello (ed.), Spatial Information Theory. Foundations of Geographic Information Science. Berlin: Springer. pp. 28-43.
    In this paper we propose a formal theory of partitions (ways of dividing up or sorting or mapping reality) and we show how the theory can be applied in the geospatial domain. We characterize partitions at two levels: as systems of cells (theory A), and in terms of their projective relation to reality (theory B). We lay down conditions of well-formedness for partitions and we define what it means for partitions to project truly onto reality. We continue by classifying well-formed (...)
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  8.  25
    Three Normative Models of Work.Nicholas H. Smith - 2012 - In Nicholas H. Smith & Jean-Philippe Deranty (eds.), New Philosophies of Labour: Work and the Social Bond. Brill. pp. 181-206.
    I suggest that the post-Hegelian tradition presents us with three contrasting normative models of work. According to the first model, the core norms of work are those of means-ends rationality. In this model, the modern world of work is constitutively a matter of deploying the most effective means to bring about given ends. The rational kernel of modern work, the core norm that has shaped its development, is on this view instrumental reason, and this very same normative core, in the (...)
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  9.  12
    Expressivism in Brandom and Taylor.Nicholas H. Smith - 2010 - In James Williams, James Chase, Jack Reynolds & Edwin Mares (eds.), Postanalytic and Metacontinental: Crossing Philosophical Divides. Continuum. pp. 145--156.
    I begin by picking up on Brandom’s suggestion that expressivism follows American pragmatism in seeking to advance the cause of the Enlightenment. This provides us with a first point of contrast with Taylor’s understanding of expressivism, since Taylor takes expressivism to be inseparably bound up with the Romantic critique of the Enlightenment and as fundamentally opposed to Enlightenment naturalism. I then distinguish two features of what we ordinarily mean by the term ‘expression’, one of which provides an intuitive basis for (...)
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  10. An Improved Ontological Representation of Dendritic Cells as a Paradigm for All Cell Types.Masci Anna Maria, N. Arighi Cecilia, D. Diehl Alexander, E. Lieberman Anne, Mungall Chris, H. Scheuermann Richard, Barry Smith & G. Cowell Lindsay - 2009 - BMC Bioinformatics 10 (1):70.
    The Cell Ontology (CL) is designed to provide a standardized representation of cell types for data annotation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL’s utility for cross-species data integration. To address this problem, we developed a method for the ontological representation of cells and applied this method to develop a (...)
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  11. An Improved Ontological Representation of Dendritic Cells as a Paradigm for All Cell Types.Anna Maria Masci, Cecilia N. Arighi, Alexander D. Diehl, Anne E. Liebermann, Chris Mungall, Richard H. Scheuermann, Barry Smith & Lindsay Cowell - 2009 - BMC Bioinformatics 10 (1):70.
    Recent increases in the volume and diversity of life science data and information and an increasing emphasis on data sharing and interoperability have resulted in the creation of a large number of biological ontologies, including the Cell Ontology (CL), designed to provide a standardized representation of cell types for data annotation. Ontologies have been shown to have significant benefits for computational analyses of large data sets and for automated reasoning applications, leading to organized attempts to improve the structure and formal (...)
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  12.  25
    Recognition, Culture and Economy : Honneth’s Debate with Fraser.Nicholas H. Smith - 2011 - In Danielle Petherbridge (ed.), Axel Honneth: Critical Essays with a Reply by Axel Honneth. Leiden: Brill. pp. 321-344.
    Although the contrast between ‘economy’ and culture’ that structures the Fraser-Honneth debate derives ultimately from Weber, it has a more proximate ancestry in Habermas’ work. I begin by glancing back at Habermas’ formulation, not just because its background role in shaping the current debate has not been properly acknowledged (though I believe that is the case), but because Fraser and Honneth’s original responses to it provide a nice segue into their current positions. After briefly reviewing what those responses were, I (...)
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  13. Adam Smith on Morality and Self-Interest.Thomas R. Wells - 2013 - In Christoph Luetge (ed.), Handbook of the Philosophical Foundations of Business Ethics. Dordrecht, Netherlands: Springer. pp. 281--296.
    Adam Smith is respected as the father of contemporary economics for his work on systemizing classical economics as an independent field of study in The Wealth of Nations. But he was also a significant moral philosopher of the Scottish Enlightenment, with its characteristic concern for integrating sentiments and rationality. This article considers Adam Smith as a key moral philosopher of commercial society whose critical reflection upon the particular ethical challenges posed by the new pressures and possibilities of commercial (...)
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  14. Adam Smith’s Bourgeois Virtues in Competition.Thomas Wells & Johan Graafland - 2012 - Business Ethics Quarterly 22 (2):319-350.
    Whether or not capitalism is compatible with ethics is a long standing dispute. We take up an approach to virtue ethics inspired by Adam Smith and consider how market competition influences the virtues most associated with modern commercial society. Up to a point, competition nurtures and supports such virtues as prudence, temperance, civility, industriousness and honesty. But there are also various mechanisms by which competition can have deleterious effects on the institutions and incentives necessary for sustaining even these most (...)
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  15. A Theory of Granular Partitions.Thomas Bittner & Barry Smith - 2003 - In M. Duckham, M. F. Goodchild & M. F. Worboys (eds.), Foundations of Geographic Information Science. London: Taylor & Francis. pp. 117-151.
    We have a variety of different ways of dividing up, classifying, mapping, sorting and listing the objects in reality. The theory of granular partitions presented here seeks to provide a general and unified basis for understanding such phenomena in formal terms that is more realistic than existing alternatives. Our theory has two orthogonal parts: the first is a theory of classification; it provides an account of partitions as cells and subcells; the second is a theory of reference or intentionality; it (...)
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  16. Individuals, Universals, Collections: On the Foundational Relations of Ontology.Thomas Bittner, Maureen Donnelly & Barry Smith - 2004 - In Achille Varzi Laure Vieu (ed.), ”, Formal Ontology in Information Systems. Proceedings of the Third International Conference. IOS Press. pp. 37–48.
    This paper provides an axiomatic formalization of a theory of foundational relations between three categories of entities: individuals, universals, and collections. We deal with a variety of relations between entities in these categories, including the is-a relation among universals and the part-of relation among individuals as well as cross-category relations such as instance-of, member-of, and partition-of. We show that an adequate understanding of the formal properties of such relations – in particular their behavior with respect to time – is critical (...)
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  17. Gregory E. Kaebnick and Thomas H. Murray, Eds., Synthetic Biology and Morality: Artificial Life and the Bounds of Nature: The MIT Press, Cambridge, Mass., 2013, 214 Pp. ISBN: 978-0-262-01939-2, $21.00. [REVIEW]Mahesh Ananth - 2016 - Journal of Value Inquiry 50 (1):241-248.
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  18. Endurants and Perdurants in Directly Depicting Ontologies.Thomas Bittner, Maureen Donnelly & Barry Smith - 2004 - AI Communications 13 (4):247–258.
    We propose an ontological theory that is powerful enough to describe both complex spatio-temporal processes and the enduring entities that participate therein. For this purpose we introduce the notion a directly depicting ontology. Directly depicting ontologies are based on relatively simple languages and fall into two major categories: ontologies of type SPAN and ontologies of type SNAP. These represent two complementary perspectives on reality and employ distinct though compatible systems of categories. A SNAP (snapshot) ontology comprehends enduring entities such as (...)
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  19. 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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  20.  26
    Introduction : A Recognition-Theoretical Research Programme in the Social Sciences.Nicholas H. Smith - 2012 - In Shane O'Neill & Nicholas H. Smith (eds.), Recognition Theory as Social Research: Investigating the Dynamics of Social Conflict. Palgrave MacMillan. pp. 1-18.
    A summary of the main features of a 'recognition-theoretic' research program in the social sciences and a brief account of how it promises to advance on rival research programs in the social sciences.
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  21.  23
    Language, Work and Hermeneutics.Nicholas H. Smith - 2011 - In Gadamer’s Hermeneutics and the Art of Conversation. LIT Verlag. pp. 201-220.
    The essay reflects on Gadamer’s ambiguous legacy for the philosophy of work. On the one hand, there are times when Gadamer reproduces the problematic distinction between language and labor which short-circuits the very idea of a hermeneutics of work. This is particularly evident in Gadamer’s reflections on technique and craftsmanship in the central sections of Truth and Method, as well as in his descriptions of the “art” of dialogue and the tasks of hermeneutics that separate them emphatically them from the (...)
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  22.  25
    Work as a Sphere of Norms, Paradoxes, and Ideologies of Recognition.Nicholas H. Smith - 2012 - In Shane O'Neill & Nicholas H. Smith (eds.), Recognition Theory as Social Research: Investigating the Dynamics of Social Conflict. Palgrave MacMillan. pp. 87-108.
    An analysis of how the sphere of work can be considered to instantiate norms of recognition, even when those norms give rise to paradoxes and ideologies surrounding how work ought to be done and the goods at stake in it.
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  23. Granular Partitions and Vagueness.Thomas Bittner & Barry Smith - 2003 - In Chris Welty & Barry Smith (eds.), Formal Ontology in Information Systems (FOIS). New York, USA: ACM Press. pp. 309-320.
    There are some who defend a view of vagueness according to which there are intrinsically vague objects or attributes in reality. Here, in contrast, we defend a view of vagueness as a semantic property of names and predicates. All entities are crisp, on this view, but there are, for each vague name, multiple portions of reality that are equally good candidates for being its referent, and, for each vague predicate, multiple classes of objects that are equally good candidates for being (...)
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  24. Vague Reference and Approximating Judgements.Thomas Bittner & Barry Smith - 2003 - Spatial Cognition and Computation 3 (2):137–156.
    We propose a new account of vagueness and approximation in terms of the theory of granular partitions. We distinguish different kinds of crisp and non-crisp granular partitions and we describe the relations between them, concentrating especially on spatial examples. We describe the practice whereby subjects use regular grid-like reference partitions as a means for tempering the vagueness of their judgments, and we demonstrate how the theory of reference partitions can yield a natural account of this practice, which is referred to (...)
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  25. ImmPort, Toward Repurposing of Open Access Immunological Assay Data for Translational and Clinical Research.Sanchita Bhattacharya, Patrick Dunn, Cristel Thomas, Barry Smith, Henry Schaefer, Jieming Chen, Zicheng Hu, Kelly Zalocusky, Ravi Shankar & Shai Shen-Orr - 2018 - Scientific Data 5:180015.
    Immunology researchers are beginning to explore the possibilities of reproducibility, reuse and secondary analyses of immunology data. Open-access datasets are being applied in the validation of the methods used in the original studies, leveraging studies for meta-analysis, or generating new hypotheses. To promote these goals, the ImmPort data repository was created for the broader research community to explore the wide spectrum of clinical and basic research data and associated findings. The ImmPort ecosystem consists of four components–Private Data, Shared Data, Data (...)
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  26.  20
    Arendt's Anti-Humanism of Labour.Nicholas H. Smith - 2019 - European Journal of Social Theory 2 (22):175-190.
    The aim of this article is to situate Arendt’s account of labour as a critical response to humanisms of labour, or put otherwise, to situate it as an anti-humanism of labour. It compares Arendt’s account of labour with that of the most prominent humanist theorist of labour at the time of the composition of The Human Condition: Georges Friedmann. Arendt’s and Friedmann’s accounts of labour are compared specifically with respect to the range of capacities, social relations, and possibilities of fulfilment (...)
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  27. Toward an Ontological Treatment of Disease and Diagnosis.Richard H. Scheuermann, Werner Ceusters & Barry Smith - 2009 - In Proceedings of the 2009 AMIA Summit on Translational Bioinformatics. American Medical Informatics Association.
    Many existing biomedical vocabulary standards rest on incomplete, inconsistent or confused accounts of basic terms pertaining to diseases, diagnoses, and clinical phenotypes. Here we outline what we believe to be a logically and biologically coherent framework for the representation of such entities and of the relations between them. We defend a view of disease as involving in every case some physical basis within the organism that bears a disposition toward the execution of pathological processes. We present our view in the (...)
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  28.  86
    Formal Ontologies of Space and Time. IFOMIS Report.Thomas Bittner & Barry Smith - 2003 - In IFOMIS Report.
    We propose an ontological theory that is powerful enough to describe both complex spatio-temporal processes (occurrents) and the enduring entities (continuants) that participate in such processes. For this purpose we distinguish between meta-ontology and token ontologies. Token ontologies fall into two major categories: ontologies of type SPAN and ontologies of type SNAP. These represent two complementary perspectives on reality and result in distinct though compatible systems of categories. The meta-ontological level then describes the relationships between the different token ontologies. In (...)
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  29.  59
    Directly Depicting Granular Ontologies.Thomas Bittner & Barry Smith - 2004 - In IFOMIS Reports. pp. 117--151.
    Published in extended form as "Endurants and Perdurants in Directly Depicting Ontologies", -/- We propose an ontological theory that is powerful enough to describe both complex spatio-temporal processes and the enduring entities that participate in such processes. For this purpose we distinguish between ontologies and metaontology. Ontologies are based on very simple directly depicting languages and fall into two major categories: ontologies of type SPAN and ontologies of type SNAP. These represent two complementary perspectives on reality and result in distinct (...)
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  30.  84
    A Unified Theory of Granularity, Vagueness and Approximation.Thomas Bittner & Barry Smith - 2001 - In COSIT Workshop on Spatial Vagueness, Uncertainty and Granularity. pp. 39.
    Abstract: We propose a view of vagueness as a semantic property of names and predicates. All entities are crisp, on this semantic view, but there are, for each vague name, multiple portions of reality that are equally good candidates for being its referent, and, for each vague predicate, multiple classes of objects that are equally good candidates for being its extension. We provide a new formulation of these ideas in terms of a theory of granular partitions. We show that this (...)
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  31.  66
    Introduction to Foucault Studies (April 2014), Special Issue on Foucault and Deleuze.Nicolae Morar, Thomas Nail & Daniel W. Smith - 2014 - Foucault Studies 17:4-10.
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  32. The Ontology for Biomedical Investigations.Anita Bandrowski, Ryan Brinkman, Mathias Brochhausen, Matthew H. Brush, Bill Bug, Marcus C. Chibucos, Kevin Clancy, Mélanie Courtot, Dirk Derom, Michel Dumontier, Liju Fan, Jennifer Fostel, Gilberto Fragoso, Frank Gibson, Alejandra Gonzalez-Beltran, Melissa A. Haendel, Yongqun He, Mervi Heiskanen, Tina Hernandez-Boussard, Mark Jensen, Yu Lin, Allyson L. Lister, Phillip Lord, James Malone, Elisabetta Manduchi, Monnie McGee, Norman Morrison, James A. Overton, Helen Parkinson, Bjoern Peters, Philippe Rocca-Serra, Alan Ruttenberg, Susanna-Assunta Sansone, Richard H. Scheuermann, Daniel Schober, Barry Smith, Larisa N. Soldatova, Christian J. Stoeckert, Chris F. Taylor, Carlo Torniai, Jessica A. Turner, Randi Vita, Patricia L. Whetzel & Jie Zheng - 2016 - PLoS ONE 11 (4):e0154556.
    The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to (...)
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  33. Normalizing Medical Ontologies Using Basic Formal Ontology.Thomas Bittner & Barry Smith - 2004 - In K. Versorgung & V. Forschung (eds.), Ubiquitäre Information (Proceedings of GMDS 2004). Videel OHG. pp. 199-201.
    Description Logics are nowadays widely accepted as formalisms which provide reasoning facilities which allow us to discover inconsistencies in ontologies in an automatic fashion. Where ontologies are developed in modular fashion, they allow changes in one module to propogated through the system of ontologies automatically in a way which helps to maintain consistency and stability. For this feature to be utilized effectively, however, requires that domain ontologies be represented in a normalized form.
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  34. Granular Spatio-Temporal Ontologies.Thomas Bittner & Barry Smith - 2003 - In AAAI Symposium: Foundations and Applications of Spatio-Temporal Reasoning (FASTR). pp. 12-17.
    We propose an ontological theory that is powerful enough to describe both complex spatio-temporal processes (occurrents) and the enduring entities (continuants) that participate therein. The theory is divided into two major categories of sub-theories: (sub-) theories of type SPAN and (sub-)theories of type SNAP. These theories represent two complementary perspectives on reality and result in distinct though compatible systems of categories. In SNAP we have enduring entities such as substances, qualities, roles, functions; in SPAN we have perduring entities such as (...)
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  35. Basic Formal Ontology for Bioinformatics.Barry Smith, Anand Kumar & Thomas Bittner - 2005 - IFOMIS Reports.
    Two senses of ‘ontology’ can be distinguished in the current literature. First is the sense favored by information scientists, who view ontologies as software implementations designed to capture in some formal way the consensus conceptualization shared by those working on information systems or databases in a given domain. [Gruber 1993] Second is the sense favored by philosophers, who regard ontologies as theories of different types of entities (objects, processes, relations, functions) [Smith 2003]. Where information systems ontologists seek to maximize (...)
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  36.  31
    The Logic of Systems of Granular Partitions.Thomas Bittner, Barry Smith & Maureen Donnelly - 2005 - IFOMIS Reports.
    The theory of granular partitions is designed to capture in a formal framework important aspects of the selective character of common-sense views of reality. It comprehends not merely the ways in which we can view reality by conceiving its objects as gathered together not merely into sets, but also into wholes of various kinds, partitioned into parts at various levels of granularity. We here represent granular partitions as triples consisting of a rooted tree structure as first component, a domain satisfying (...)
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  37. 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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  38.  18
    Basic Income, Social Freedom and the Fabric of Justice.Nicholas H. Smith - 2019 - Critical Review of International Social and Political Philosophy.
    This paper examines the justice of unconditional basic income (UBI) through the lens of the Hegel-inspired recognition-theory of justice. As explained in the first part of the paper, this theory takes everyday social roles to be the primary subject-matter of the theory of justice, and it takes justice in these roles to be a matter of the kind of freedom that is available through their performance, namely ‘social’ freedom. The paper then identifies the key criteria of social freedom. The extent (...)
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  39. Patient Understanding of Benefits, Risks, and Alternatives to Screening Colonoscopy.Peter H. Schwartz, Elizabeth Edenberg, Patrick R. Barrett, Susan M. Perkins, Eric M. Meslin & Thomas F. Imperiale - 2013 - Family Medicine 45 (2):83-89.
    While several tests and strategies are recommended for colorectal cancer (CRC) screening, studies suggest that primary care providers often recommend colonoscopy without providing information about its risks or alternatives. These observations raise concerns about the quality of informed consent for screening colonoscopy.
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  40. Promoting Coherent Minimum Reporting Guidelines for Biological and Biomedical Investigations: The MIBBI Project.Chris F. Taylor, Dawn Field, Susanna-Assunta Sansone, Jan Aerts, Rolf Apweiler, Michael Ashburner, Catherine A. Ball, Pierre-Alain Binz, Molly Bogue, Tim Booth, Alvis Brazma, Ryan R. Brinkman, Adam Michael Clark, Eric W. Deutsch, Oliver Fiehn, Jennifer Fostel, Peter Ghazal, Frank Gibson, Tanya Gray, Graeme Grimes, John M. Hancock, Nigel W. Hardy, Henning Hermjakob, Randall K. Julian, Matthew Kane, Carsten Kettner, Christopher Kinsinger, Eugene Kolker, Martin Kuiper, Nicolas Le Novere, Jim Leebens-Mack, Suzanna E. Lewis, Phillip Lord, Ann-Marie Mallon, Nishanth Marthandan, Hiroshi Masuya, Ruth McNally, Alexander Mehrle, Norman Morrison, Sandra Orchard, John Quackenbush, James M. Reecy, Donald G. Robertson, Philippe Rocca-Serra, Henry Rodriguez, Heiko Rosenfelder, Javier Santoyo-Lopez, Richard H. Scheuermann, Daniel Schober, Barry Smith & Jason Snape - 2008 - Nature Biotechnology 26 (8):889-896.
    Throughout the biological and biomedical sciences there is a growing need for, prescriptive ‘minimum information’ (MI) checklists specifying the key information to include when reporting experimental results are beginning to find favor with experimentalists, analysts, publishers and funders alike. Such checklists aim to ensure that methods, data, analyses and results are described to a level sufficient to support the unambiguous interpretation, sophisticated search, reanalysis and experimental corroboration and reuse of data sets, facilitating the extraction of maximum value from data sets (...)
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  41. 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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  42. Heyting Mereology as a Framework for Spatial Reasoning.Thomas Mormann - 2013 - Axiomathes 23 (1):137- 164.
    In this paper it is shown that Heyting and Co-Heyting mereological systems provide a convenient conceptual framework for spatial reasoning, in which spatial concepts such as connectedness, interior parts, (exterior) contact, and boundary can be defined in a natural and intuitively appealing way. This fact refutes the wide-spread contention that mereology cannot deal with the more advanced aspects of spatial reasoning and therefore has to be enhanced by further non-mereological concepts to overcome its congenital limitations. The allegedly unmereological concept of (...)
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  43.  24
    Achtung in Kant and Smith.Michael H. Walschots - forthcoming - Kant-Studien.
    Although it is clear that Kant read Adam Smith’s ‘Theory of Moral Sentiments’ (TMS) soon after it was translated into German in 1770, work remains to be done in order to determine whether or not Smith had a lasting influence on Kant’s moral philosophy, and in what way. One of Kant’s main reasons for reading Smith would have been the latter’s careful analysis of the passions and human motivation and in this paper I illustrate a fairly substantial, (...)
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  44. Elements of Speech Act Theory in the Work of Thomas Reid.Karl Schuhmann & Barry Smith - 1990 - History of Philosophy Quarterly 7 (1):47 - 66.
    Historical research has recently made it clear that, prior to Austin and Searle, the phenomenologist Adolf Reinach (1884-1917) developed a full-fledged theory of speech acts under the heading of what he called "social acts". He we consider a second instance of a speech act theory avant la lettre, which is to be found in the common sense philosophy of Thomas Reid (1710-1796). Reid’s s work, in contrast to that of Reinach, lacks both a unified approach and the detailed analyses (...)
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  45.  30
    A Strategy for Origins of Life Research. [REVIEW]Caleb Scharf, Nathaniel Virgo, H. James Cleaves Ii, Masashi Aono, Nathanael Aubert-Kato, Arsev Aydinoglu, Ana Barahona, Laura M. Barge, Steven A. Benner, Martin Biehl, Ramon Brasser, Christopher J. Butch, Kuhan Chandru, Leroy Cronin, Sebastian Danielache, Jakob Fischer, John Hernlund, Piet Hut, Takashi Ikegami, Jun Kimura, Kensei Kobayashi, Carlos Mariscal, Shawn McGlynn, Bryce Menard, Norman Packard, Robert Pascal, Juli Pereto, Sudha Rajamani, Lana Sinapayen, Eric Smith, Christopher Switzer, Ken Takai, Feng Tian, Yuichiro Ueno, Mary Voytek, Olaf Witkowski & Hikaru Yabuta - 2015 - Astrobiology 15:1031-1042.
    Aworkshop was held August 26–28, 2015, by the Earth- Life Science Institute (ELSI) Origins Network (EON, see Appendix I) at the Tokyo Institute of Technology. This meeting gathered a diverse group of around 40 scholars researching the origins of life (OoL) from various perspectives with the intent to find common ground, identify key questions and investigations for progress, and guide EON by suggesting a roadmap of activities. Specific challenges that the attendees were encouraged to address included the following: What key (...)
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  46. 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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  47. "Socratic Moral Psychology". By Thomas C. Brickhouse and Nicholas D. Smith. Cambridge: Cambridge University Press, 2010. Pp. Vii + 276. $85.00 (Hardback). ISBN 978-0-521-19843-1. [REVIEW]J. Clerk Shaw - 2012 - Ancient Philosophy 32 (1):181-185.
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  48.  96
    VO: Vaccine Ontology.Yongqun He, Lindsay Cowell, Alexander D. Diehl, H. L. Mobley, Bjoern Peters, Alan Ruttenberg, Richard H. Scheuermann, Ryan R. Brinkman, Melanie Courtot, Chris Mungall, Barry Smith & Others - 2009 - In ICBO 2009: Proceedings of the First International Conference on Biomedical Ontology. Buffalo:
    Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced vaccine (...)
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  49. Bioportal: Ontologies and Integrated Data Resources at the Click of the Mouse.L. Whetzel Patricia, H. Shah Nigam, F. Noy Natalya, Dai Benjamin, Dorf Michael, Griffith Nicholas, Jonquet Clement, Youn Cherie, Callendar Chris, Coulet Adrien, Barry Smith, Chris Chute & Mark Musen - 2011 - In Proceedings of the 2nd International Conference on Biomedical Ontology, Buffalo, NY. pp. 292-293.
    BioPortal is a Web portal that provides access to a library of biomedical ontologies and terminologies developed in OWL, RDF(S), OBO format, Protégé frames, and Rich Release Format. BioPortal functionality, driven by a service-oriented architecture, includes the ability to browse, search and visualize ontologies (Figure 1). The Web interface also facilitates community-based participation in the evaluation and evolution of ontology content.
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  50. Informatics: The Fuel for Pharmacometric Analysis.H. Grasela Thaddeus, Fiedler-Kelly Jill, Cirincione Brenda, Hitchcock Darcy, Reitz Kathleen, Sardella Susanne & Barry Smith - 2007 - AAPS Journal 9 (1):E84--E91.
    The current informal practice of pharmacometrics as a combination art and science makes it hard to appreciate the role that informatics can and should play in the future of the discipline and to comprehend the gaps that exist because of its absence. The development of pharmacometric informatics has important implications for expediting decision making and for improving the reliability of decisions made in model-based development. We argue that well-defined informatics for pharmacometrics can lead to much needed improvements in the efficiency, (...)
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