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  1. Joseph Agassi (1996). Prescriptions for Responsible Psychiatry. In William T. O'Donohue & Richard F. Kitchener (eds.), The Philosophy of Psychology. Sage Publications. 339.
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  2. Robert S. Avens (1982). Heidegger and Archetypal Psychology.
    Heidegger's notion of dasein, Understood as the pre-Conceptual togetherness of man and world, Is deepened by going back to the "beginnings" of this togetherness in the imaginal (archaic) psyche, Which archetypal psychology, Founded by james hillman, Envisions--In the wake of the platonic tradition--As part of the "anima mundi". As a result the phenomenological call "back to the things themselves" is redefined in the sense of "back to the images themselves." imagination in its fully creative import is seen as equivalent to (...)
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  3. Mostafa Bachar (forthcoming). Modeling the Cardiovascular-Respiratory Control System: Data, Model Analysis, and Parameter Estimation. Acta Biotheoretica.
    Several key areas in modeling the cardiovascular and respiratory control systems are reviewed and examples are given which reflect the research state of the art in these areas. Attention is given to the interrelated issues of data collection, experimental design, and model application including model development and analysis. Examples are given of current clinical problems which can be examined via modeling, and important issues related to model adaptation to the clinical setting.
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  4. Thomas Bittner & Barry Smith (2004). Normalizing Medical Ontologies Using Basic Formal Ontology. In Proceedings of GMDS 2004.
    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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  5. OIivier Bodenreider, Barry Smith & Anita Burgun (2004). The Ontology-Epistemology Divide: A Case Study in Medical Terminology. In Achille Varzi & Laure Vieu (eds.), Formal Ontology in Information Systems. Proceedings of the Third International Conference (FOIS 2004),. IOS Press.
    Medical terminology collects and organizes the many different kinds of terms employed in the biomedical domain both by practitioners and also in the course of biomedical research. In addition to serving as labels for biomedical classes, these names reflect the organizational principles of biomedical vocabularies and ontologies. Some names represent invariant features (classes, universals) of biomedical reality (i.e., they are a matter for ontology). Other names, however, convey also how this reality is perceived, measured, and understood by health professionals (i.e., (...)
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  6. James J. Bono (1990). Reform and the Languages of Renaissance Theoretical Medicine: Harvey Versus Fernel. [REVIEW] Journal of the History of Biology 23 (3):341 - 387.
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  7. Jenifer Booth (2013). Towards a Pre-Modern Psychaitry. Palgrave Macmillan.
    Responding to the work of previous critics of psychiatry, who have associated its undue dominance with both a modern scientific paradigm and political factors, I put forward a theoretical challenge based on MacIntyre`s work on Aquinas and Aristotle, but adding the museum and assembly as conceptual thinking tools. -/- MacIntyre`s work on practices, tradition-constituted enquiry, Marxist ideology and Kuhn are all used in putting forward a pre-modern view of knowledge. The feminist philosophy of Luce Irigaray widens the project to include (...)
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  8. Alex Broadbent (2011). Defining Neglected Disease. BioSocieties 6 (1):51-70.
    In this article I seek to say what it is for something to count as a neglected disease. I argue that neglect should be defined in terms of efforts at prevention, mitigation and cure, and not solely in terms of research dollars per disability-adjusted life-year. I further argue that the trend towards multifactorialism and risk factor thinking in modern epidemiology has lent credibility to the erroneous view that the primary problem with neglected diseases is a lack of research. A more (...)
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  9. Alex Broadbent (2011). Inferring Causation in Epidemiology: Mechanisms, Black Boxes, and Contrasts. In Phyllis McKay Illari, Federica Russo & Jon Williamson (eds.), Causality in the Sciences. Oxford University Press. 45--69.
    This chapter explores the idea that causal inference is warranted if and only if the mechanism underlying the inferred causal association is identified. This mechanistic stance is discernible in the epidemiological literature, and in the strategies adopted by epidemiologists seeking to establish causal hypotheses. But the exact opposite methodology is also discernible, the black box stance, which asserts that epidemiologists can and should make causal inferences on the basis of their evidence, without worrying about the mechanisms that might underlie their (...)
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  10. Sylvia Burrow (2012). On The Cutting Edge: Ethical Responsiveness to Cesarean Section Rates. American Journal of Bioethics 12 (7):44-52.
    Cesarean delivery rates have been steadily increasing worldwide. In response, many countries have introduced target goals to reduce rates. But a focus on target goals fails to address practices embedded in standards of care that encourage, rather than discourage, cesarean sections. Obstetrical standards of care normalize use of technology, creating an imperative to use technology during labor and birth. A technological imperative is implicated in rising cesarean rates if physicians or patients fear refusing use of technology. Reproductive autonomy is at (...)
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  11. Olio Center (1987). Mary B. Mahowald Sex-Role Stereotypes In Medicine. Hypatia 2 (2).
  12. Werner Ceusters, Peter Elkin & Barry Smith (2006). Referent Tracking: The Problem of Negative Findings. Studies in Health Technology and Informatics 124:741-46.
    The paradigm of referent tracking is based on a realist presupposition which rejects so-called negative entities (congenital absent nipple, and the like) as spurious. How, then, can a referent tracking-based Electronic Health Record deal with what are standardly called ‘negative findings’? To answer this question we carried out an analysis of some 748 sentences drawn from patient charts and containing some form of negation. Our analysis shows that to deal with these sentences we need to introduce a new ontological relationship (...)
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  13. Werner Ceusters & Barry Smith (2010). Foundations for a Realist Ontology of Mental Disease. Journal of Biomedical Semantics 1 (10):1-23.
    While classifications of mental disorders have existed for over one hundred years, it still remains unspecified what terms such as 'mental disorder', 'disease' and 'illness' might actually denote. While ontologies have been called in aid to address this shortfall since the GALEN project of the early 1990s, most attempts thus far have sought to provide a formal description of the structure of some pre-existing terminology or classification, rather than of the corresponding structures and processes on the side of the patient. (...)
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  14. Werner Ceusters & Barry Smith (2010). Malaria Diagnosis and the Plasmodium Life Cycle: The BFO Perspective. In Interdisciplinary Ontology. Proceedings of the Third Interdisciplinary Ontology Meeting. Keio University Press.
    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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  15. Werner Ceusters & Barry Smith (2006). A Realism-Based Approach to the Evolution of Biomedical Ontologies. In Proceedings of the Annual AMIA Symposium. AMIA.
    We present a novel methodology for calculating the improvements obtained in successive versions of biomedical ontologies. The theory takes into account changes both in reality itself and in our understanding of this reality. The successful application of the theory rests on the willingness of ontology authors to document changes they make by following a number of simple rules. The theory provides a pathway by which ontology authoring can become a science rather than an art, following principles analogous to those that (...)
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  16. Werner Ceusters & Barry Smith (2006). Strategies for Referent Tracking in Electronic Health Records. Journal of Biomedical Informatics 39 (3):362-378.
    The goal of referent tracking is to create an ever-growing pool of data relating to the entities existing in concrete spatiotemporal reality. In the context of Electronic Healthcare Records (EHRs) the relevant concrete entities are not only particular patients but also their parts, diseases, therapies, lesions, and so forth, insofar as these are salient to diagnosis and treatment. Within a referent tracking system, all such entities are referred to directly and explicitly, something which cannot be achieved when familiar concept-based systems (...)
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  17. James A. Coffman (2005). On Reductionism, Organicism, Somatic Mutations and Cancer. Bioessays 27 (4):459-459.
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  18. Megan Delehanty (2010). Why Images? Medicine Studies 2 (3):161-173.
    Given that many imaging technologies in biology and medicine are non-optical and generate data that is essentially numerical, it is a striking feature of these technologies that the data generated using them are most frequently displayed in the form of semi-naturalistic, photograph-like images. In this paper, I claim that three factors underlie this: (1) historical preferences, (2) the rhetorical power of images, and (3) the cognitive accessibility of data presented in the form of images. The third of these can be (...)
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  19. Frank Dikotter (1996). Sex, Culture and Modernity in China Medical Science and the Construction of Sexual Identities in the Early Republican Period. History and Philosophy of the Life Sciences 18 (2):241.
  20. Anastassia Elefteriadis & Mirko D. Grmek (1995). Die Struktur der hippocratischen Theorie der Medizin. History and Philosophy of the Life Sciences 17 (1):173.
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  21. James M. Fielding, Jonathan Simon, Werner Ceusters & Barry Smith (2004). Ontological Theory for Ontological Engineering: Biomedical Systems Information Integration. In Proceedings of the Ninth International Conference on the Principles of Knowledge Representation and Reasoning. AMIA.
    Software application ontologies have the potential to become the keystone in state-of-the-art information management techniques. It is expected that these ontologies will support the sort of reasoning power required to navigate large and complex terminologies correctly and efficiently. Yet, there is one problem in particular that continues to stand in our way. As these terminological structures increase in size and complexity, and the drive to integrate them inevitably swells, it is clear that the level of consistency required for such navigation (...)
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  22. Irving B. Fritz (1988). The Banting and Best Department of Medical Research at the University of Toronto. Bioessays 9 (2-3):92-97.
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  23. A. Garzya (2002). Alfrieda Et Jackie Pigeaud, Les Textes Medicaux Latins Comme Litterature. History and Philosophy of the Life Sciences 23 (2):297-297.
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  24. Maya J. Goldenberg (2006). On Evidence and Evidence-Based Medicine: Lessons From the Philosophy of Science. Social Science and Medicine 62 (11):2621-2632.
    The evidence-based medicine (EBM) movement is touted as a new paradigm in medical education and practice, a description that carries with it an enthusiasm for science that has not been seen since logical positivism flourished (circa 1920–1950). At the same time, the term ‘‘evidence-based medicine’’ has a ring of obviousness to it, as few physicians, one suspects, would claim that they do not attempt to base their clinical decision-making on available evidence. However, the apparent obviousness of EBM can and should (...)
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  25. Janna Hastings, Nicolas Le Novère, Werner Ceusters, Kevin Mulligan & Barry Smith (2012). Wanting What We Don’T Want to Want: Representing Addiction in Interoperable Bio-Ontologies. In Proceeedings of the Third International Conference on Biomedical Ontology. CEUR.
    Ontologies are being developed throughout the biomedical sciences to address standardization, integration, classification and reasoning needs against the background of an increasingly data-driven research paradigm. In particular, ontologies facilitate the translation of basic research into benefits for the patient by making research results more discoverable and by facilitating knowledge transfer across disciplinary boundaries. Addressing and adequately treating mental illness is one of our most pressing public health challenges. Primary research across multiple disciplines such as psychology, psychiatry, biology, neuroscience and pharmacology (...)
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  26. Daniel J. Kevles (1993). Renato Dulbecco and the New Animal Virology: Medicine, Methods, and Molecules. [REVIEW] Journal of the History of Biology 26 (3):409 - 442.
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  27. Maria Kronfeldner (2009). Genetic Determinism and the Innate-Acquired Distinction. Medicine Studies 1 (2):167-181.
    This article illustrates in which sense genetic determinism is still part of the contemporary interactionist consensus in medicine. Three dimensions of this consensus are discussed: kinds of causes, a continuum of traits ranging from monogenetic diseases to car accidents, and different kinds of determination due to different norms of reaction. On this basis, this article explicates in which sense the interactionist consensus presupposes the innate?acquired distinction. After a descriptive Part 1, Part 2 reviews why the innate?acquired distinction is under attack (...)
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  28. Anand Kumar & Barry Smith (2007). The Ontology of Processes and Functions: A Study of the International Classification of Functioning, Disability and Health. In Sharing Knowledge through the ICF: 13th Annual North American WHO Collaborating Center Conference on the ICF, Niagara Falls, June 7, 2007. North American WHO Collaborating Center.
    The International Classification of Functioning, Disability and Health provides a classification of human bodily functions, which, while exhibiting non-conformance to many formal ontological principles, provides an insight into which basic functions such a classification should include. Its evaluation is an important first step towards such an adequate ontology of this domain. Presented at the 13th Annual North American WHO Collaborating Center Conference on the ICF, 2007.
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  29. Chiara Lepora & Joseph Millum (2011). The Tortured Patient: A Medical Dilemma. Hastings Center Report 41 (3):38-47.
    Torture is unethical and usually counterproductive. It is prohibited by international and national laws. Yet it persists: according to Amnesty International, torture is widespread in more than a third of countries. Physicians and other medical professionals are frequently asked to assist with torture. -/- Medical complicity in torture, like other forms of involvement, is prohibited both by international law and by codes of professional ethics. However, when the victims of torture are also patients in need of treatment, doctors can find (...)
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  30. I. Löwy (2002). ['Intervening is Representing': Medical Campaigns That Helped Identify the Prevalence of Hookworm]. History and Philosophy of the Life Sciences 25 (3):337-362.
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  31. Mary B. Mahowald (1987). Sex-Role Stereotypes in Medicine. Hypatia 2 (2):21 - 38.
    I argue for compatibility between feminism and medicine by developing a model of the physician-other relationship which is essentially egalitarian. This entails rejection of (a) a paternalistic model which reinforces sex-role stereotypes, (b) a maternalistic model which exclusively emphasizes patient autonomy, and (c) a model which focuses on the physician's conscience. The model I propose (parentalism) captures the complexity and dynamism of the physician-other relationship, by stressing mutuality in respect for autonomy and regard for each other's interests.
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  32. Jane Maienschein (2009). Controlling Life: From Jacques Loeb to Regenerative Medicine. [REVIEW] Journal of the History of Biology 42 (2):215 - 230.
    In his 1987 book "Controlling Life: Jacques Loeb and the Engineering Ideal in Biology", Philip Pauly presented his readers with the biologist Jacques Loeb and his role in developing an emphasis on control of life processes. Loeb's work on artificial parthenogenesis, for example, provided an example of bioengineering at work. This paper revisits Pauly's study of Loeb and explores the way current research in regenerative medicine reflects the same tradition. A history of regeneration research reveals patterns of thinking and research (...)
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  33. Wallace F. Marshall (2012). Organelle Size Control Systems: From Cell Geometry to Organelle‐Directed Medicine. Bioessays 34 (9):721-724.
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  34. J. Andrew Mendelsohn (2002). 'Like All That Lives': Biology, Medicine and Bacteria in the Age of Pasteur and Koch * *In Memory of Gerry Geison, Great Teacher, Scholar, and Friend. History and Philosophy of the Life Sciences 24 (1):3-36.
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  35. Nestor Micheli Morales (2009). Psychological and Ideological Aspects of Human Cloning: A Transition to a Transhumanist Psychology. Journal of Evolution and Technology 20.
    The prospect of replication of human beings through genetic manipulation has engendered one of the most controversial debates about reproduction in our society. Ideology is clearly influencing the direction of research and legislation on human cloning, which may present one of the greatest existential challenges to the meaning of creation. In this article, I argue that, in view of the possibility that human cloning and other emerging technologies could enhance physical and cognitive abilities, there is a need for a different (...)
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  36. Katherine Munn & Barry Smith (eds.) (2008). Applied Ontology: An Introduction. ontos.
    Ontology is the philosophical discipline which aims to understand how things in the world are divided into categories and how these categories are related together. This is exactly what information scientists aim for in creating structured, automated representations, called 'ontologies,' for managing information in fields such as science, government, industry, and healthcare. Currently, these systems are designed in a variety of different ways, so they cannot share data with one another. They are often idiosyncratically structured, accessible only to those who (...)
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  37. Guangjin Pan, Tao Wang, Hongjie Yao & Duanqing Pei (2012). Somatic Cell Reprogramming for Regenerative Medicine: SCNT Vs. iPS Cells. Bioessays 34 (6):472-476.
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  38. Arlene I. Ramsingh, Nora Chapman & Steven Tracy (1997). Coxsackieviruses and Diabetes. Bioessays 19 (9):793-800.
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  39. Cornelius Rosse, Anand Kumar, Jose L. V. Mejino, Daniel L. Cook, Landon T. Detwiler & Barry Smith (2005). A Strategy for Improving and Integrating Biomedical Ontologies. In Proceedings of the Annual Symposium of the American Medical Informatics Association. AMIA.
    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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  40. Leif E. Sander (2012). Improved Vaccines Through Targeted Manipulation of the Body's Immunological Risk‐Assessment? Bioessays 34 (10):876-884.
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  41. Richard H. Scheuermann, Werner Ceusters & Barry Smith (2009). Toward an Ontological Treatment of Disease and Diagnosis. 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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  42. David Shaw (2010). Homeopathy Is Where the Harm Is: Five Unethical Effects of Funding Unscientific Remedies. Journal of Medical Ethics 36 (3):130-131.
    Homeopathic medicine is based on the two principles that “like cures like” and that the potency of substances increases in proportion to their dilution. In November 2009 the UK Parliament’s Science and Technology Committee heard evidence on homeopathy, with several witnesses arguing that homeopathic practice is “unethical, unreliable, and pointless”. Although this increasing scepticism about the merits of homeopathy is to be welcomed, the unethical effects of funding homeopathy on the NHS are even further-reaching than has been acknowledged.
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  43. Susan Sherwin (2014). Remembering Sue Campbell: An Introduction. Hypatia 29 (2):474-475.
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  44. Susan Sherwin (2001). Diagnosis: Difference: The Moral Authority of Medicine (Review). Hypatia 16 (3):172-176.
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  45. Barry Smith (2010). Putting Biomedical Ontologies to Work. Methods of Information in Medicine, 2010 Feb 5;49 49 (2):135-40.
    Biomedical ontologies exist to serve integration of clinical and experimental data, and it is critical to their success that they be put to widespread use in the annotation of data. How, then, can ontologies achieve the sort of user-friendliness, reliability, cost-effectiveness, and breadth of coverage that is necessary to ensure extensive usage? Methods: Our focus here is on two different sets of answers to these questions that have been proposed, on the one hand in medicine, by the SNOMED CT community, (...)
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  46. Barry Smith (2005). Wüsteria. Studies in Health Technology and Informatic 116:647–652.
    The last two decades have seen considerable efforts directed towards making Electronic Health Records interoperable through improvements in medical ontologies, terminologies and coding systems. Unfortunately, these efforts have been hampered by a number of influential ideas inherited from the work of Eugen Wüster, the father of terminology standardization and the founder of ISO TC 37. We here survey Wüster’s ideas – which see terminology work as being focused on the classification of concepts in people’s minds – and we argue that (...)
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  47. Barry Smith, Michael Ashburner, Cornelius Rosse, Jonathan Bard, William Bug, Werner Ceusters, Louis J. Goldberg, Karen Eilbeck, Amelia Ireland, Mungall Christopher J., Neocles Leontis & et al (2007). The OBO Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration. Nature Biotechnology 25 (11):1251-1255.
    The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or ‘ontologies’. Unfortunately, the very success of this approach has led to a proliferation of ontologies which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium has set in train a strategy to overcome this problem. Existing (...)
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  48. Barry Smith & Mathias Brochhausen (2008). Establishing and Harmonizing Ontologies in an Interdisciplinary Health Care and Clinical Research Environment. Studies in Health, Technology and Informatics 134:219-234.
    Ontologies are being ever more commonly used in biomedical informatics and we provide a survey of some of these uses, and of the relations between ontologies and other terminology resources. In order for ontologies to become truly useful, two objectives must be met. First, ways must be found for the transparent evaluation of ontologies. Second, existing ontologies need to be harmonised. We argue that one key foundation for both ontology evaluation and harmonisation is the adoption of a realist paradigm in (...)
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  49. Barry Smith & Cornelius Rosse (2004). The Role of Foundational Relations in the Alignment of Biomedical Ontologies. In Medinfo. IOS Press.
    The Foundational Model of Anatomy (FMA) symbolically represents the structural organization of the human body from the macromolecular to the macroscopic levels, with the goal of providing a robust and consistent scheme for classifying anatomical entities that is designed to serve as a reference ontology in biomedical informatics. Here we articulate the need for formally clarifying the is-a and part-of relations in the FMA and similar ontology and terminology systems. We diagnose certain characteristic errors in the treatment of these relations (...)
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  50. Bartlomiej Swiatczak, Maria Rescigno & Irun Cohen (2011). Systemic Features of Immune Recognition in the Gut. Microbes and Infection 13:983-991.
    The immune system, to protect the body, must discriminate between the pathogenic and non-pathogenic microbes and respond to them in different ways. How the mucosal immune system manages to make this distinction is poorly understood. We suggest here that the distinction between pathogenic and non-pathogenic microbes is made by an integrated system rather than by single types of cells or single types of receptors; a systems biology approach is needed to understand immune recognition.
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