Results for 'Norman Kemp Smith'

940 found
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  1. The Environment Ontology: Contextualising biological and biomedical entities.Pier Luigi Buttigieg, Norman Morrison, Barry Smith, Christopher J. Mungall & Suzanna E. Lewis - 2013 - Journal of Biomedical Semantics 4 (43):1-9.
    As biological and biomedical research increasingly reference the environmental context of the biological entities under study, the need for formalisation and standardisation of environment descriptors is growing. The Environment Ontology (ENVO) is a community-led, open project which seeks to provide an ontology for specifying a wide range of environments relevant to multiple life science disciplines and, through an open participation model, to accommodate the terminological requirements of all those needing to annotate data using ontology classes. This paper summarises ENVO’s motivation, (...)
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  2. 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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  3. 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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  4. 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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  5. Fisiologia do Ciclo Estral dos Animais Domésticos.Emanuel Isaque Cordeiro da Silva -
    FISIOLOGIA DO CICLO ESTRAL DOS ANIMAIS -/- Departamento de Zootecnia – UFRPE Embrapa Semiárido e IPA -/- • _____OBJETIVO -/- O cio ou estro é a fase reprodutiva dos animais, onde as fêmeas apresentam receptividade sexual seguida de ovulação. Para tanto, é necessário entender a fisiologia do estro para a realização do manejo reprodutivo dos animais. Em geral, as fêmeas manifestam comportamentos fora do comum quando estão ciclando, tais comportamentos devem ser observados para que não percam o pico de ovulação (...)
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  6. Comportamento Sexual dos Animais Domésticos.Emanuel Isaque Cordeiro Da Silva -
    COMPORTAMENTO SEXUAL DOS ANIMAIS OBJETIVO O estudante explicará a conduta sexual de fêmeas e machos de diferentes espécies domésticas para detectar a fase de receptividade sexual, com a finalidade de programar de maneira adequada a monta ou a inseminação artificial. A observação da conduta sexual dos animais é indispensável para o sucesso da estação reprodutiva em uma determinada propriedade. Logo, o estudante obterá o alicerce necessário sobre os pontos teóricos e práticos a serem observados para a seleção dos animais aptos (...)
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  7. Type distinctions of reason and Hume’s Separability Principle.Hsueh Qu - 2019 - British Journal for the History of Philosophy 28 (1):90-111.
    Commentators such as Kemp Smith (1941), Mendelbaum (1974), and Bricke (1980) have taken the distinctions of reason to pose either a counterexample to or a limitation of scope on the Separability Principle. This has been convincingly addressed by various accounts such as Garrett (1997), Hoffman (2011), and Baxter (2011). However, I argue in this paper that there are two notions of ‘distinction of reason’, one between particular instantiations (token distinctions of reason) and one between general ideas (type distinctions (...)
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  8. Is 'the monstrous thesis' truly Cartesian?Rodrigo González - 2017 - Discusiones Filosóficas 18 (30):15-33.
    According to Kemp Smith, Descartes believed that animals were devoid of feelings and sensations. This is the so-called ‘monstrous thesis,’ which I explore here in light of two Cartesian approaches to animals. Firstly, I examine their original treatment in function of Descartes’ early metaphysical approach, i.e., all natural phenomena are to be elucidated in terms of mental scrutiny. As pain would only exist in the understanding, and animals have neither understanding nor souls, Descartes held that they did not (...)
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  9. The Title Principle (Or Lack Thereof) in the Enquiry.Hsueh Qu - 2016 - History of Philosophy Quarterly 33 (3):257-274.
    The Title Principle is seen by a number of commentators as crucial to Hume’s resolution of skeptical doubts in THN 1.4.7, thus providing an answer to Kemp Smith’s (1941) famous worry regarding the tension between Hume’s skepticism and his naturalism. However, I will argue that in the Enquiry, Hume rejects both the Title Principle and the role of the passions in his epistemology. Those who think that neither the Title Principle nor the passions play a significant role in (...)
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  10. Hume's Epistemology: The State of the Question.Hsueh M. Qu - 2019 - Southern Journal of Philosophy 57 (3):301-323.
    This article surveys the state of the literature on Hume’s epistemology, focusing on treatments of what has come to be known as the ‘Kemp Smith problem’, that is, the problem of reconciling Hume’s scepticism with his naturalism. It first surveys the literature on this issue with regard to the Treatise, moving on to briefly compare the Treatise and the Enquiry in virtue of their epistemological frameworks, before finally examining the literature with regard to the first Enquiry.
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  11. Hume on Substance: A Critique of Locke.Donald L. M. Baxter - 2014 - In Paul Lodge & Tom Stoneham (eds.), Locke and Leibniz on Substance. New York: Routledge. pp. 45-62.
    The ancient theory of substance and accident is supposed to make sense of complex unities in a way that respects both their unity and their complexity. On Hume’s view such complex unities are only fictitiously unities. This result follows from his thoroughgoing critique of the theory of substance. I will characterize the theory Hume is critiquing as it is presented in Locke, presupposing what Bennett calls the “Leibnizian interpretation.” Locke uses the word ‘substance’ in two senses. Call substance in the (...)
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  12. Bayle, Hume y los molinos de viento.Andrés Páez - 2000 - Ideas Y Valores 49 (113):29-44.
    El análisis de los conceptos de espacio y tiempo es generalmente considerado uno de los aspectos menos satisfactorios de la obra de Hume. Kemp Smith ha demostrado que en esta sección del Tratado Hume estaba respondiendo a los argumentos que Pierre Bayle había utilizado para probar que el razonamiento humano siempre termina refutándose a sí mismo. En este ensayo expongo las falacias en los argumentos de Bayle, las cuales están basadas en una comprensión inadecuada del concepto de extensión. (...)
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  13. Hume's Methodology and the Science of Human Nature.Vadim V. Vasilyev - 2013 - History of Philosophy Yearbook 2012:62-115.
    In this paper I try to explain a strange omission in Hume’s methodological descriptions in his first Enquiry. In the course of this explanation I reveal a kind of rationalistic tendency of the latter work. It seems to contrast with “experimental method” of his early Treatise of Human Nature, but, as I show that there is no discrepancy between the actual methods of both works, I make an attempt to explain the change in Hume’s characterization of his own methods. This (...)
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  14. Stroud's Humean Skepticism.Michael Morales - 2010 - Southwest Philosophical Studies 32:93-97.
    In “The Constraints of Hume’s Naturalism” Barry Stroud takes on the task of looking at Hume’s negative and positive accounts of induction in conjunction. Stroud goes about doing this so that we might walk away with “a more general lesson about naturalism, at least when it is indulged in for philosophical purposes”. Given the boldness of Stroud’s quote from above there should be some explicit talk of this general lesson about naturalism outside of Hume’s, but there is none that is (...)
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  15. Integration of Intelligence Data through Semantic Enhancement.David Salmen, Tatiana Malyuta, Alan Hansen, Shaun Cronen & Barry Smith - 2011 - In David Salmen, Tatiana Malyuta, Alan Hansen, Shaun Cronen & Barry Smith (eds.), Integration of Intelligence Data through Semantic Enhancement. CEUR, Vol. 808.
    We describe a strategy for integration of data that is based on the idea of semantic enhancement. The strategy promises a number of benefits: it can be applied incrementally; it creates minimal barriers to the incorporation of new data into the semantically enhanced system; it preserves the existing data (including any existing data-semantics) in their original form (thus all provenance information is retained, and no heavy preprocessing is required); and it embraces the full spectrum of data sources, types, models, and (...)
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  16. (1 other version)The Good in Boethius’ De hebdomadibus.Dan Kemp - 2023 - History of Philosophy Quarterly 40 (3):202-221.
    The De hebdomadibus (DH) of Boethius presents a problem with the idea that ordinary finite substances are good and then proposes a solution to the problem. Careful reconstruction of Boethius’ arguments reveals that his solution relies on an account of finite goodness that he does not make explicit. Moreover, accounts of finite goodness that commentators have supplied to the DH should be rejected. Instead, the account of finite goodness given in book III of the Consolatio successfully resolves the problem raised (...)
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  17. Created Goodness and the Goodness of God: Divine Ideas and the Possibility of Creaturely Value.Dan Kemp - 2022 - Religious Studies 58 (3):534-546.
    Traditional theism says that the goodness of everything comes from God. Moreover, the goodness of something intrinsically valuable can only come from what has it. Many conclude from these two claims that no creatures have intrinsic value if traditional theism is true. I argue that the exemplarist theory of the divine ideas gives the theist a way out. According to exemplarism, God creates everything according to ideas that are about himself, and so everything resembles God. Since God is wholly good (...)
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  18. The Artistic Expression of Feeling.Gary Kemp - 2020 - Philosophia 49 (1):315-332.
    In the past 60 years or so, the philosophical subject of artistic expression has generally been handled as an inquiry into the artistic expression of emotion. In my view this has led to a distortion of the relevant territory, to the artistic expression of feeling’s too often being overlooked. I explicate the emotion-feeling distinction in modern terms, and urge that the expression of feeling is too central to be waived off as outside the proper philosophical subject of artistic expression. Restricting (...)
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  19. Warranted Diagnosis.David Limbaugh, David Kasmier, Werner Ceusters & Barry Smith - 2019 - In David Limbaugh, David Kasmier, Werner Ceusters & Barry Smith (eds.), Proceedings of the International Conference on Biomedical Ontology (ICBO), Buffalo, NY. Buffalo: pp. 1-10.
    A diagnostic process is an investigative process that takes a clinical picture as input and outputs a diagnosis. We propose a method for distinguishing diagnoses that are warranted from those that are not, based on the cognitive processes of which they are the outputs. Processes designed and vetted to reliably produce correct diagnoses will output what we shall call ‘warranted diagnoses’. The latter are diagnoses that should be trusted even if they later turn out to have been wrong. Our work (...)
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  20. An Ontological Approach to Representing the Product Life Cycle.J. Neil Otte, Dimitris Kiritsi, Munira Mohd Ali, Ruoyu Yang, Binbin Zhang, Ron Rudnicki, Rahul Rai & Barry Smith - 2019 - Applied ontology 14 (2):1-19.
    The ability to access and share data is key to optimizing and streamlining any industrial production process. Unfortunately, the manufacturing industry is stymied by a lack of interoperability among the systems by which data are produced and managed, and this is true both within and across organizations. In this paper, we describe our work to address this problem through the creation of a suite of modular ontologies representing the product life cycle and its successive phases, from design to end of (...)
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  21. A Product Life Cycle Ontology for Additive Manufacturing.Munira Mohd Ali, Rahul Rai, J. Neil Otte & Barry Smith - 2019 - Computers in Industry 105:191-203.
    The manufacturing industry is evolving rapidly, becoming more complex, more interconnected, and more geographically distributed. Competitive pressure and diversity of consumer demand are driving manufacturing companies to rely more and more on improved knowledge management practices. As a result, multiple software systems are being created to support the integration of data across the product life cycle. Unfortunately, these systems manifest a low degree of interoperability, and this creates problems, for instance when different enterprises or different branches of an enterprise interact. (...)
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  22. 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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  23. More Than Provocative, Less Than Scientific: A Commentary on the Editorial Decision to Publish Cofnas (2020).Rasmus Rosenberg Larsen, Helen De Cruz, Jonathan Kaplan, Agustín Fuentes, Massimo Pigliucci, Jonathan Marks, Mark Alfano, David Smith & Lauren Schroeder - manuscript
    We are addressing this letter to the editors of Philosophical Psychology after reading an article they decided to publish in the recent vol. 33, issue 1. The article is by Nathan Cofnas and is entitled “Research on group differences in intelligence: A defense of free inquiry” (2020). The purpose of our letter is not to invite Cofnas’s contribution into a broader dialogue, but to respectfully voice our concerns about the decision to publish the manuscript, which, in our opinion, fails to (...)
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  24. Revisiting Kant’s Deduction of Taste.Ryan S. Kemp - forthcoming - History of Philosophy Quarterly.
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  25. Biography of Barry Smith.Sandra Smith - 2017 - Cosmos + Taxis 4 (4):4-5.
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  26. On an Alleged Case of Propaganda: Reply to McKinnon.Sophie R. Allen, Elizabeth Finneron-Burns, Mary Leng, Holly Lawford-Smith, Jane Clare Jones, Rebecca Reilly-Cooper & R. J. Simpson - manuscript
    In her recent paper ‘The Epistemology of Propaganda’ Rachel McKinnon discusses what she refers to as ‘TERF propaganda’. We take issue with three points in her paper. The first is her rejection of the claim that ‘TERF’ is a misogynistic slur. The second is the examples she presents as commitments of so-called ‘TERFs’, in order to establish that radical (and gender critical) feminists rely on a flawed ideology. The third is her claim that standpoint epistemology can be used to establish (...)
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  27. Diagnostic Criteria for Temporomandibular Disorders (DC/TMD) for clinical and research applications.Eric Schiffman, Richard Ohrbach, E. Truelove, Edmond Truelove, John Look, Gary Anderson, Werner Ceusters, Barry Smith & Others - 2014 - Journal of Oral and Facial Pain and Headache 28 (1):6-27.
    Aims: The Research Diagnostic Criteria for Temporomandi¬bular Disorders (RDC/TMD) Axis I diagnostic algorithms were demonstrated to be reliable but below target sensitivity and specificity. Empirical data supported Axis I algorithm revisions that were valid. Axis II instruments were shown to be both reliable and valid. An international consensus workshop was convened to obtain recommendations and finalization of new Axis I diagnostic algorithms and new Axis II instruments. Methods: A comprehensive search of published TMD diagnostic literature was followed by review and (...)
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  28. 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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  29. Vantagens e limitações das ontologias formais na área biomédica.Stefan Schulz, Holger Stenzhorn, Martin Boeker & Barry Smith - 2009 - RECIIS: Revista Electronica de Comunicacao Informacao, Inovacao Em Saude 3 (1).
    Propomos uma tipologia dos artefatos de representação para as áreas de saúde e ciências biológicas, e a associação dessa tipologia com diferentes tipos de ontologia formal e lógica, chegando a conclusões quanto aos pontos fortes e limitações da ontologia de diferentes tipos de recursos lógicos, enquanto mantemos o foco na lógica descritiva. Consideramos quatro tipos de representação de área: (i) representação léxico-semântica, (ii) representação de tipos de entidades, (iii) representação de conhecimento prévio, e (iv) representação de indivíduos. Defendemos uma clara (...)
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  30. Constructing a lattice of Infectious Disease Ontologies from a Staphylococcus aureus isolate repository.Albert Goldfain, Lindsay G. Cowell & Barry Smith - 2012 - In Goldfain Albert, Cowell Lindsay G. & Smith Barry (eds.), Proceeedings of the Third International Conference on Biomedical Ontology (CEUR 897).
    A repository of clinically associated Staphylococcus aureus (Sa) isolates is used to semi‐automatically generate a set of application ontologies for specific subfamilies of Sa‐related disease. Each such application ontology is compatible with the Infectious Disease Ontology (IDO) and uses resources from the Open Biomedical Ontology (OBO) Foundry. The set of application ontologies forms a lattice structure beneath the IDO‐Core and IDO‐extension reference ontologies. We show how this lattice can be used to define a strategy for the construction of a new (...)
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  31. From meta-processes to conscious access: Evidence from children's metalinguistic and repair data.Annette Karmiloff-Smith - 1986 - Cognition 23 (2):95-147.
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  32. Mental Capabilities.Eric Merrell, David Limbaugh, Alex Anderson & Barry Smith - 2019 - In David Kasmier, David Limbaugh & Barry Smith (eds.), Proceedings of the International Conference on Biomedical Ontology (ICBO), University at Buffalo, NY.
    We propose capability as a universal or type intermediate between function and disposition. A capability is, broadly speaking, a disposition that is of a type whose instances can be evaluated on the basis of how well they are realized. A function, on the view we are proposing, is a capability the possession of which is the rationale for the existence of its bearer. To say for example that a water pump has the function to pump water is to say that (...)
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  33. Pushing Wittgenstein and Quine Closer Together.Gary Kemp - 2014 - Journal for the History of Analytical Philosophy 2 (10).
    As against the view represented here by Peter Hacker and John Canfield, I urge that the philosophies of Quine and Wittgenstein can be reconciled. Both replace the orthodox view of language as resting on reference: Quine with the notion of linguistic disposition, Wittgenstein with the notions of grammar and forms of life. I argue that Wittgenstein's insistence, in the rule-following discussion, that at bottom these are matters of practice, of ‘what we do’, is not only compatible in a rough sort (...)
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  34. The Innateness Charge: Conception and Belief for Reid and Hume.Catherine Kemp - 2000 - Reid Studies 3 (2):43.
    Hume's notion of conception is closer to Reid's than Reid realizes and may lie behind Hume's charge in the letter to Hugh Blair (1762) that Reid's philosophy "leads us back to innate ideas".
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  35. Creating a Controlled Vocabulary for the Ethics of Human Research: Towards a biomedical ethics ontology.David Koepsell, Robert Arp, Jennifer Fostel & Barry Smith - 2009 - Journal of Empirical Research on Human Research Ethics 4 (1):43-58.
    Ontologies describe reality in specific domains in ways that can bridge various disciplines and languages. They allow easier access and integration of information that is collected by different groups. Ontologies are currently used in the biomedical sciences, geography, and law. A Biomedical Ethics Ontology would benefit members of ethics committees who deal with protocols and consent forms spanning numerous fields of inquiry. There already exists the Ontology for Biomedical Investigations (OBI); the proposed BMEO would interoperate with OBI, creating a powerful (...)
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  36. The Plant Ontology facilitates comparisons of plant development stages across species.Ramona Lynn Walls, Laurel Cooper, Justin Lee Elser, Maria Alejandra Gandolfo, Christopher J. Mungall, Barry Smith, Dennis William Stevenson & Pankaj Jaiswal - 2019 - Frontiers in Plant Science 10.
    The Plant Ontology (PO) is a community resource consisting of standardized terms, definitions, and logical relations describing plant structures and development stages, augmented by a large database of annotations from genomic and phenomic studies. This paper describes the structure of the ontology and the design principles we used in constructing PO terms for plant development stages. It also provides details of the methodology and rationale behind our revision and expansion of the PO to cover development stages for all plants, particularly (...)
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  37. Ontology based annotation of contextualized vital signs.Goldfain Albert, Xu Min, Bona Jonathan & Barry Smith - 2013 - In Albert Goldfain, Min Xu, Jonathan Bona & Smith Barry (eds.), Proceedings of the Fourth International Conference on Biomedical Ontology (ICBO). pp. 28-33.
    Representing the kinetic state of a patient (posture, motion, and activity) during vital sign measurement is an important part of continuous monitoring applications, especially remote monitoring applications. In contextualized vital sign representation, the measurement result is presented in conjunction with salient measurement context metadata. We present an automated annotation system for vital sign measurements that uses ontologies from the Open Biomedical Ontology Foundry (OBO Foundry) to represent the patient’s kinetic state at the time of measurement. The annotation system is applied (...)
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  38. 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 Whetzel Patricia L., Shah Nigam H., Noy Natalya F., Benjamin Dai, Michael Dorf, Nicholas Griffith, Clement Jonquet, Cherie Youn, Chris Callendar, Adrien Coulet, Smith Barry, Chute Chris & Musen Mark (eds.), 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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  39. Applications of the ACGT Master Ontology on Cancer.Mathias Brochhausen, Gabriele Weiler, Luis Martín, Cristian Cocos, Holger Stenzhorn, Norbert Graf, Martin Dörr, Manolis Tsiknakis & Barry Smith - 2008 - In Meersman R. & Herrero P. (eds.), Proceedings of 4th International IFIP Workshop On Semantic Web and Web Semantics (OTM 2008: Workshops), LNCS 5333. pp. 1046–1055.
    In this paper we present applications of the ACGT Master Ontology (MO) which is a new terminology resource for a transnational network providing data exchange in oncology, emphasizing the integration of both clinical and molecular data. The development of a new ontology was necessary due to problems with existing biomedical ontologies in oncology. The ACGT MO is a test case for the application of best practices in ontology development. This paper provides an overview of the application of the ontology within (...)
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  40. 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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  41. Clinical ontologies interfacing the real world.Stefan Schulz, Holger Stenzhorn, Martin Boeker, Rüdiger Klar & Barry Smith - 2007 - In Schulz Stefan, Stenzhorn Holger, Boeker Martin, Klar Rüdiger & Smith Barry (eds.), Third International Conference on Semantic Technologies (i-semantics 2007), Graz, Austria. pp. 356-363..
    The desideratum of semantic interoperability has been intensively discussed in medical informatics circles in recent years. Originally, experts assumed that this issue could be sufficiently addressed by insisting simply on the application of shared clinical terminologies or clinical information models. However, the use of the term ‘ontology’ has been steadily increasing more recently. We discuss criteria for distinguishing clinical ontologies from clinical terminologies and information models. Then, we briefly present the role clinical ontologies play in two multicentric research projects. Finally, (...)
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  42. OBCS: The Ontology of Biological and Clinical Statistics.Jie Zheng, Marcelline R. Harris, Anna Maria Masci, Yu Lin, Alfred Hero, Barry Smith & Yongqun He - 2014 - Proceedings of the Fifth International Conference on Biomedical Ontology 1327:65.
    Statistics play a critical role in biological and clinical research. To promote logically consistent representation and classification of statistical entities, we have developed the Ontology of Biological and Clinical Statistics (OBCS). OBCS extends the Ontology of Biomedical Investigations (OBI), an OBO Foundry ontology supported by some 20 communities. Currently, OBCS contains 686 terms, including 381 classes imported from OBI and 147 classes specific to OBCS. The goal of this paper is to present OBCS for community critique and to describe a (...)
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  43. Trump's Inducement of America's Banality of Evil.Norman K. Swazo - manuscript
    When political philosopher Hannah Arendt introduced the concept of ‘banality of evil’ she did so in reference to the actions of Germans who appropriated the doctrines of National Socialism “thoughtlessly” and without obvious intentions to do evil. But, Arendt’s description of this phenomenon entails that such banality can be found even in a democracy such as the USA. The relation of law and morality must therefore be unambiguous to defend the rule of law against the rule of men. However, a (...)
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  44. Ontology-based knowledge representation of experiment metadata in biological data mining.Scheuermann Richard, Kong Megan, Dahlke Carl, Cai Jennifer, Lee Jamie, Qian Yu, Squires Burke, Dunn Patrick, Wiser Jeff, Hagler Herb, Herb Hagler, Barry Smith & David Karp - 2009 - In Chen Jake & Lonardi Stefano (eds.), Biological Data Mining. Chapman Hall / Taylor and Francis. pp. 529-559.
    According to the PubMed resource from the U.S. National Library of Medicine, over 750,000 scientific articles have been published in the ~5000 biomedical journals worldwide in the year 2007 alone. The vast majority of these publications include results from hypothesis-driven experimentation in overlapping biomedical research domains. Unfortunately, the sheer volume of information being generated by the biomedical research enterprise has made it virtually impossible for investigators to stay aware of the latest findings in their domain of interest, let alone to (...)
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  45. The “Unguarding” (Vehrwahrlosung) of Human Life in Biotechnology: Thinking Essentially with Heidegger.Norman K. Swazo - manuscript
    Philosopher Martin Heidegger’s writing on the essence of technology has often been seen as too abstract even though he illustrated his concerns with reference to technological developments of his day. While most in the immediate post-World War 2 period judged thermonuclear weaponry to be the most obvious technological threat to the future of humanity, Heidegger instead considered developments in the biological sciences to be more so. In the discussion presented here, Heidegger’s thinking is related to developments in biotechnology, specifically assisted (...)
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  46. Clinical data wrangling using Ontological Realism and Referent Tracking.Werner Ceusters, Chiun Yu Hsu & Barry Smith - 2014 - In Ceusters Werner, Hsu Chiun Yu & Smith Barry (eds.), Proceedings of the Fifth International Conference on Biomedical Ontology (ICBO), Houston, 2014, (CEUR, 1327). pp. 27-32.
    Ontological realism aims at the development of high quality ontologies that faithfully represent what is general in reality and to use these ontologies to render heterogeneous data collections comparable. To achieve this second goal for clinical research datasets presupposes not merely (1) that the requisite ontologies already exist, but also (2) that the datasets in question are faithful to reality in the dual sense that (a) they denote only particulars and relationships between particulars that do in fact exist and (b) (...)
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  47. 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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  48. 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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  49. Novel sequence feature variant type analysis of the HLA genetic association in systemic sclerosis.R. Karp David, Marthandan Nishanth, G. E. Marsh Steven, Ahn Chul, C. Arnett Frank, S. DeLuca David, D. Diehl Alexander, Dunivin Raymond, Eilbeck Karen, Feolo Michael & Barry Smith - 2009 - Human Molecular Genetics 19 (4):707-719.
    Significant associations have been found between specific human leukocyte antigen (HLA) alleles and organ transplant rejection, autoimmune disease development, and the response to infection. Traditional searches for disease associations have conventionally measured risk associated with the presence of individual HLA alleles. However, given the high level of HLA polymorphism, the pattern of amino acid variability, and the fact that most of the HLA variation occurs at functionally important sites, it may be that a combination of variable amino acid sites shared (...)
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  50. OntONeo: The Obstetric and Neonatal Ontology.Fernanda Farinelli, Mauricio Almeida, Peter Elkin & Barry Smith - 2016 - In Farinelli Fernanda, Almeida Mauricio, Elkin Peter & Barry Smith (eds.), Dealing with elements of medical encounters: An approach based on ontological realism. CEUR, vol. 1747.
    This paper presents the Obstetric and Neonatal Ontology (OntONeo). This ontology has been created to provide a consensus representation of salient electronic health record (EHR) data and to serve interoperability of the associated data and information systems. More generally, it will serve interoperability of clinical and translational data, for example deriving from genomics disciplines and from clinical trials. Interoperability of EHR data is important to ensuring continuity of care during the prenatal and postnatal periods for both mother and child. As (...)
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