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  1. added 2018-09-20
    Justifying Public Health Surveillance: Basic Interests, Unreasonable Exercise, and Privacy.Alan Rubel - 2012 - Kennedy Institute of Ethics Journal 22 (1):1-33.
    Surveillance plays a crucial role in public health, and for obvious reasons conflicts with individual privacy. This paper argues that the predominant approach to the conflict is problematic, and then offers an alternative. It outlines a Basic Interests Approach to public health measures, and the Unreasonable Exercise Argument, which sets forth conditions under which individuals may justifiably exercise individual privacy claims that conflict with public health goals. The view articulated is compatible with a broad range conceptions of the value of (...)
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  2. added 2018-08-30
    On Defining Bruxism.W. Ceusters & B. Smith - 2018 - Studies in Health Technology and Informatics 247:551-555.
    In a series of recent publications, orofacial researchers have debated the question of how ‘bruxism’ should be defined for the purposes of accurate diagnosis and reliable clinical research. Following the principles of realism-based ontology, we performed an analysis of the arguments involved. This revealed that the disagreements rested primarily on inconsistent use of terms, so that issues of ontology were thus obfuscated by shortfalls in terminology. In this paper, we demonstrate how bruxism terminology can be improved by paying attention to (...)
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  3. added 2018-05-18
    A Sartrean Account of Mental Health.Jelena Krgovic - 2017 - Theoria: Beograd 60:17-31.
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  4. added 2018-03-30
    Bridging the Gap Between Medical and Bioinformatics: An Ontological Case Study in Colon Carcinoma.Anand Kumar, Yum Lina Yip, Barry Smith & Pierre Grenon - 2006 - Computers in Biology and Medicine 36 (7):694--711.
    Ontological principles are needed in order to bridge the gap between medical and biological information in a robust and computable fashion. This is essential in order to draw inferences across the levels of granularity which span medicine and biology, an example of which include the understanding of the roles of tumor markers in the development and progress of carcinoma. Such information integration is also important for the integration of genomics information with the information contained in the electronic patient records in (...)
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  5. added 2018-03-30
    Oncology Ontology in the NCI Thesaurus.Anand Kumar & Barry Smith - 2005 - Artificial Intelligence in Medicine:213-220.
    The National Cancer Institute’s Thesaurus (NCIT) has been created with the goal of providing a controlled vocabulary which can be used by specialists in the various sub-domains of oncology. It is intended to be used for purposes of annotation in ways designed to ensure the integration of data and information deriving from these various sub-domains, and thus to support more powerful cross-domain inferences. In order to evaluate its suitability for this purpose, we examined the NCIT’s treatment of the kinds of (...)
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  6. added 2017-12-11
    Malaria Diagnosis and the Plasmodium Life Cycle: The BFO Perspective.Werner Ceusters & Barry Smith - 2010 - In Interdisciplinary Ontology. Proceedings of the Third Interdisciplinary Ontology Meeting. Tokyo: Keio University Press. pp. 25-34.
    Definitive diagnosis of malaria requires the demonstration through laboratory tests of the presence within the patient of malaria parasites or their components. Since malaria parasites can be present even in the absence of malaria manifestations, and since symptoms of malaria can be manifested even in the absence of malaria parasites, malaria diagnosis raises important issues for the adequate understanding of disease, etiology and diagnosis. One approach to the resolution of these issues adopts a realist view, according to which the needed (...)
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  7. added 2017-12-08
    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 R. Meersman & P. Herrero (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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  8. added 2017-12-01
    A Plant Disease Extension of the Infectious Disease Ontology.Ramona Walls, Barry Smith, Elser Justin, Goldfain Albert & W. Stevenson Dennis - 2012 - In Proceeedings of the Third International Conference on Biomedical Ontology (CEUR 897). pp. 1-5.
    Plants from a handful of species provide the primary source of food for all people, yet this source is vulnerable to multiple stressors, such as disease, drought, and nutrient deficiency. With rapid population growth and climate uncertainty, the need to produce crops that can tolerate or resist plant stressors is more crucial than ever. Traditional plant breeding methods may not be sufficient to overcome this challenge, and methods such as highOthroughput sequencing and automated scoring of phenotypes can provide significant new (...)
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  9. added 2017-11-24
    Ontological Representation of CDC Active Bacterial Core Surveillance Case Reports.Albert Goldfain, Barry Smith & Lindsay G. Cowell - 2014 - Proceedings of the Fifth International Conference on Biomedical Ontology 1327:74-77.
    The Center for Disease Control and Prevention’s Active Bacterial Core Surveillance (CDC ABCs) Program is a collaborative effort betweeen the CDC, state health departments, laboratories, and universities to track invasive bacterial pathogens of particular importance to public health [1]. The year-end surveillance reports produced by this program help to shape public policy and coordinate responses to emerging infectious diseases over time. The ABCs case report form (CRF) data represents an excellent opportunity for data reuse beyond the original surveillance purposes.
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  10. added 2017-11-13
    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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  11. added 2017-11-13
    Constructing a Lattice of Infectious Disease Ontologies From a Staphylococcus Aureus Isolate Repository.Albert Goldfain, Lindsay G. Cowell & Barry Smith - 2012 - In 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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  12. added 2017-11-09
    On the Proper Treatment of Pathologies in Biomedical Ontologies.Barry Smith & Anand Kumar - 2005 - In Proceedings of the Bio-Ontologies Workshop, Intelligent Systems for Molecular Biology (ISMB 2005). Detroit: pp. 22-23.
    In previous work on biomedical ontologies we showed how the provision of formal definitions for relations such as is_a and part_of can support new types of auto-mated reasoning about biomedical phenomena. We here extend this approach to the transformation_of characteristic of pathologies.
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  13. added 2017-11-02
    Representing Disease Courses: An Application of the Neurological Disease Ontology to Multiple Sclerosis Typology.Mark Jensen, Alexander P. Cox, Barry Smith & Alexander Diehl - 2013 - In Proceedings of the Fourth International Conference on Biomedical Ontology (ICBO), CEUR, vol. 1060.
    The Neurological Disease Ontology (ND) is being developed to provide a comprehensive framework for the representation of neurological diseases (Diehl et al., 2013). ND utilizes the model established by the Ontology for General Medical Science (OGMS) for the representation of entities in medicine and disease (Scheuermann et al., 2009). The goal of ND is to include information for each disease concerning its molecular, genetic, and environmental origins, the processes involved in its etiology and realization, as well as its clinical presentation (...)
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  14. added 2017-10-29
    Mistakes in Medical Ontologies: Where Do They Come From and How Can They Be Detected?Werner Ceusters, Barry Smith, Anand Kumar & Christoffel Dhaen - 2004 - Studies in Health and Technology Informatics 102:145-164.
    We present the details of a methodology for quality assurance in large medical terminologies and describe three algorithms that can help terminology developers and users to identify potential mistakes. The methodology is based in part on linguistic criteria and in part on logical and ontological principles governing sound classifications. We conclude by outlining the results of applying the methodology in the form of a taxonomy different types of errors and potential errors detected in SNOMED-CT.
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  15. added 2017-07-24
    Decision and Discovery in Defining “Disease”.Peter H. Schwartz - 2007 - In Harold Kincaid & Jennifer McKitrick (eds.), Establishing medical reality: Methodological and metaphysical issues in philosophy of medicine. Dordrecht: Springer. pp. 47-63.
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  16. added 2017-07-14
    Risk and Disease.Peter H. Schwartz - 2008 - Perspectives in Biology and Medicine 51 (3):320-334.
    The way that diseases such as high blood pressure (hypertension), high cholesterol, and diabetes are defined is closely tied to ideas about modifiable risk. In particular, the threshold for diagnosing each of these conditions is set at the level where future risk of disease can be reduced by lowering the relevant parameter (of blood pressure, low-density lipoprotein, or blood glucose, respectively). In this article, I make the case that these criteria, and those for diagnosing and treating other “risk-based diseases,” reflect (...)
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  17. added 2017-05-13
    Functions in Basic Formal Ontology.Andrew Spear, Werner Ceusters & Barry Smith - 2016 - Applied Ontology 11 (2):103-128.
    The notion of function is indispensable to our understanding of distinctions such as that between being broken and being in working order (for artifacts) and between being diseased and being healthy (for organisms). A clear account of the ontology of functions and functioning is thus an important desideratum for any top-level ontology intended for application to domains such as engineering or medicine. The benefit of using top-level ontologies in applied ontology can only be realized when each of the categories identified (...)
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  18. added 2017-02-15
    Reframing the Disease Debate and Defending the Biostatistical Theory.Peter H. Schwartz - 2014 - Journal of Medicine and Philosophy 39 (6):572-589.
    Similarly to other accounts of disease, Christopher Boorse’s Biostatistical Theory (BST) is generally presented and considered as conceptual analysis, that is, as making claims about the meaning of currently used concepts. But conceptual analysis has been convincingly critiqued as relying on problematic assumptions about the existence, meaning, and use of concepts. Because of these problems, accounts of disease and health should be evaluated not as claims about current meaning, I argue, but instead as proposals about how to define and use (...)
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  19. added 2017-02-10
    The Functional Sense of Mechanism.Justin Garson - 2013 - Philosophy of Science 80 (3):317-333.
    This article presents a distinct sense of ‘mechanism’, which I call the functional sense of mechanism. According to this sense, mechanisms serve functions, and this fact places substantive restrictions on the kinds of system activities ‘for which’ there can be a mechanism. On this view, there are no mechanisms for pathology; pathologies result from disrupting mechanisms for functions. Second, on this sense, natural selection is probably not a mechanism for evolution because it does not serve a function. After distinguishing this (...)
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  20. added 2016-10-07
    Big Data, Epistemology and Causality: Knowledge in and Knowledge Out in EXPOsOMICS.Stefano Canali - 2016 - Big Data and Society 3 (2).
    Recently, it has been argued that the use of Big Data transforms the sciences, making data-driven research possible and studying causality redundant. In this paper, I focus on the claim on causal knowledge by examining the Big Data project EXPOsOMICS, whose research is funded by the European Commission and considered capable of improving our understanding of the relation between exposure and disease. While EXPOsOMICS may seem the perfect exemplification of the data-driven view, I show how causal knowledge is necessary for (...)
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  21. added 2016-09-22
    Ethical Dilemma for a Medical Resident: A Case Study Analysis.Marvin J. H. Lee, Ana Maheshwari & Peter A. Clark - 2016 - Internet Journal of Infectious Diseases 15 (1).
    Ebola is a deadly disease with no cure; there is no vaccine developed yet. Many died during the 2014 outbreak in West Africa, and many healthcare professionals went to the virus infected area to treat the patients while placing their lives in danger. Not every medical professional placed in the field is a fully trained specialist, and sometimes one or two under-trained doctors are in charge of the entire clinic with some nurses and operating technicians. When unexpected outbreaks of the (...)
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  22. added 2016-07-21
    Effectiveness of Medical Interventions.Jacob Stegenga - 2015 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 54:34-44.
    To be effective, a medical intervention must improve one's health by targeting a disease. The concept of disease, though, is controversial. Among the leading accounts of disease-naturalism, normativism, hybridism, and eliminativism-I defend a version of hybridism. A hybrid account of disease holds that for a state to be a disease that state must both (i) have a constitutive causal basis and (ii) cause harm. The dual requirement of hybridism entails that a medical intervention, to be deemed effective, must target either (...)
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  23. added 2016-05-05
    Ontologies, Disorders and Prototypes.Cristina Amoretti, Marcello Frixione, Antonio Lieto & Greta Adamo - 2016 - In Proceedings of IACAP 2016.
    As it emerged from philosophical analyses and cognitive research, most concepts exhibit typicality effects, and resist to the efforts of defining them in terms of necessary and sufficient conditions. This holds also in the case of many medical concepts. This is a problem for the design of computer science ontologies, since knowledge representation formalisms commonly adopted in this field (such as, in the first place, the Web Ontology Language - OWL) do not allow for the representation of concepts in terms (...)
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  24. added 2014-09-24
    Is Obesity a Public Health Problem?Jonny Anomaly - 2012 - Public Health Ethics 5 (3):216-221.
    It is often claimed that there is an obesity epidemic in affluent countries, and that obesity is one of the most serious public health threats in the developed world. I will argue that obesity is not an 'epidemic' in any useful sense of the word, and that classifying it as a public health problem requires us to make fairly controversial moral and empirical assumptions. While evidence suggests that the prevalence of obesity is on the rise, and that obesity can lead (...)
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  25. added 2014-06-21
    What is an Epidemic?: Currents in Contemporary Bioethics.Jonny Anomaly - 2014 - Journal of Law, Medicine and Ethics 42 (3):389-391.
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  26. added 2014-06-10
    On the Classification of Diseases.Benjamin Smart - 2014 - Theoretical Medicine and Bioethics 35 (4):251-269.
    Identifying the necessary and sufficient conditions for individuating and classifying diseases is a matter of great importance in the fields of law, ethics, epidemiology, and of course, medicine. In this paper, I first propose a means of achieving this goal, ensuring that no two distinct disease-types could correctly be ascribed to the same disease-token. I then posit a metaphysical ontology of diseases—that is, I give an account of what a disease is. This is essential to providing the most effective means (...)
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  27. added 2014-04-17
    Unifying Diseases From a Genetic Point of View: The Example of the Genetic Theory of Infectious Diseases.Marie Darrason - 2013 - Theoretical Medicine and Bioethics 34 (4):327-344.
    In the contemporary biomedical literature, every disease is considered genetic. This extension of the concept of genetic disease is usually interpreted either in a trivial or genocentrist sense, but it is never taken seriously as the expression of a genetic theory of disease. However, a group of French researchers defend the idea of a genetic theory of infectious diseases. By identifying four common genetic mechanisms (Mendelian predisposition to multiple infections, Mendelian predisposition to one infection, and major gene and polygenic predispositions), (...)
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  28. added 2014-04-13
    The Preoccupation with Death.Rodrigo Laera - 2013 - Problemata: Revista Internacional de Filosofía 4 (1):110-133.
    Against the epicurean position, the rationality about the preoccupation with death is discussed by the present paper. For this purpose two elemental thesis are proposed. The first one supports that it is rational to worry about death before dying because we conceive the idea of a discourse in which the impossibility of interfere in the world to satisfy our pending goals is lamented. The second thesis is that death afflicts any prejudice only to whom wonders about it, because this question (...)
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  29. added 2014-02-26
    Religious Conservatives and Safe Sex: Reconciliation by Nonpublic Reason.Robert S. Taylor - 2014 - American Political Thought 3 (2):322-340.
    Religious conservatives in the U.S. have frequently opposed public-health measures designed to combat STDs among minors, such as sex education, condom distribution, and HPV vaccination. Using Rawls’s method of conjecture, I will clear up what I take to be a misunderstanding on the part of religious conservatives: even if we grant their premises regarding the nature and source of sexual norms, the wide-ranging authority of parents to enforce these norms against their minor children, and the potential sexual-disinhibition effects of the (...)
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  30. added 2014-01-19
    The Neurological Disease Ontology.Mark Jensen, Alexander P. Cox, Naveed Chaudhry, Marcus Ng, Donat Sule, William Duncan, Patrick Ray, Bianca Weinstock-Guttman, Barry Smith, Alan Ruttenberg, Kinga Szigeti & Alexander D. Diehl - 2013 - Journal of Biomedical Semantics 4 (42).
    We are developing the Neurological Disease Ontology (ND) to provide a framework to enable representation of aspects of neurological diseases that are relevant to their treatment and study. ND is a representational tool that addresses the need for unambiguous annotation, storage, and retrieval of data associated with the treatment and study of neurological diseases. ND is being developed in compliance with the Open Biomedical Ontology Foundry principles and builds upon the paradigm established by the Ontology for General Medical Science (OGMS) (...)
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  31. added 2013-10-31
    Pragmatism and the Definition of the Idea of Disease.Maurilio Lovatti - manuscript
    The purpose of this paper is to support the idea that pragmatism is still a productive resource for the study of health and disease. Combining the results of thermodynamic theories with evolutionism, some said that the biological structures selected by evolution are perfect to maximize the conservation of energy; as a consequence, they tend to reduce the entropy in the organism. Thus, a process can be defined as pathological if it increases the entropy, which means a diminished efficiency of the (...)
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  32. added 2013-10-04
    A Strategy for Improving and Integrating Biomedical Ontologies.Cornelius Rosse, Anand Kumar, Jose L. V. Mejino, Daniel L. Cook, Landon T. Detwiler & Barry Smith - 2005 - In Proceedings of the Annual Symposium of the American Medical Informatics Association. AMIA. pp. 639-643.
    The integration of biomedical terminologies is indispensable to the process of information integration. When terminologies are linked merely through the alignment of their leaf terms, however, differences in context and ontological structure are ignored. Making use of the SNAP and SPAN ontologies, we show how three reference domain ontologies can be integrated at a higher level, through what we shall call the OBR framework (for: Ontology of Biomedical Reality). OBR is designed to facilitate inference across the boundaries of domain ontologies (...)
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  33. added 2013-07-05
    Towards an Ontological Representation of Resistance: The Case of MRSA.Albert Goldfain, Barry Smith & Lindsay G. Cowell - 2011 - Journal of Biomedical Informatics 44 (1):35-41.
    This paper addresses a family of issues surrounding the biological phenomenon of resistance and its representation in realist ontologies. The treatments of resistance terms in various existing ontologies are examined and found to be either overly narrow, internally inconsistent, or otherwise problematic. We propose a more coherent characterization of resistance in terms of what we shall call blocking dispositions, which are collections of mutually coordinated dispositions which are of such a sort that they cannot undergo simultaneous realization within a single (...)
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  34. added 2013-06-24
    Rethinking Health: Healthy or Healthier Than?S. Andrew Schroeder - 2013 - British Journal for the Philosophy of Science 64 (1):131-159.
    Theorists of health have, to this point, focused exclusively on trying to define a state—health—that an organism might be in. I argue that they have overlooked the possibility of a comparativist theory of health, which would begin by defining a relation—healthier than—that holds between two organisms or two possible states of the same organism. I show that a comparativist approach to health has a number of attractive features, and has important implications for philosophers of medicine, bioethicists, health economists, and policy (...)
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