Results for 'clinical ontologies'

597 found
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  1. Clinical Ontologies Interfacing the Real World.Stefan Schulz, Holger Stenzhorn, Martin Boeker, Rüdiger Klar & Barry Smith - 2007 - In Third International Conference on Semantic Technologies (i-semantics 2007), Graz, Austria. Graz: 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 (...)
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  2. Context-Based Task Ontologies for Clinical Guidelines.Anand Kumar, Paolo Ciccarese, Barry Smith & Matteo Piazza - 2004 - In D. Pisanelli (ed.), Ontologies in Medicine: Proceedings of the Workshop on Medical Ontologies, Rome October 2003 (Studies in Health and Technology Informatics, 102). Amsterdam: IOS Press. pp. 81-94.
    Evidence-based medicine relies on the execution of clinical practice guidelines and protocols. A great deal of of effort has been invested in the development of various tools which automate the representation and execution of the recommendations contained within such guidelines and protocols by creating Computer Interpretable Guideline Models (CIGMs). Context-based task ontologies (CTOs), based on standard terminology systems like UMLS, form one of the core components of such a model. We have created DAML+OIL-based CTOs for the tasks mentioned (...)
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  3. Adapting Clinical Ontologies in Real-World Environments.Holger Stenzhorn, Stefan Schulz, Martin Boeker & Barry Smith - 2008 - Journal of Universal Computer Science 14 (22):3767-3780.
    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 (...)
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  4. Establishing and Harmonizing Ontologies in an Interdisciplinary Health Care and Clinical Research Environment.Barry Smith & Mathias Brochhausen - 2008 - 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 (...)
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  5.  61
    Guest Editorial: Ontologies for Clinical and Translational Research.Barry Smith & Richard H. Scheuermann - 2011 - Journal of Biomedical Informatics 44 (1):3--7.
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  6.  60
    Enhancing GO for the Sake of Clinical Bioinformatics.Anand Kumar & Barry Smith - 2004 - Proceedings of the Bio-Ontologies Workshop , Glasgow 133.
    Recent work on the quality assurance of the Gene Ontology (GO, Gene Ontology Consortium 2004) from the perspective of both linguistic and ontological organization has made it clear that GO lacks the kind of formalism needed to support logic-based reasoning. At the same time it is no less clear that GO has proven itself to be an excellent terminological resource that can serve to combine together a variety of biomedical database and information systems. Given the strengths of GO, it is (...)
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  7. Ontology for Task-Based Clinical Guidelines and the Theory of Granular Partitions.Anand Kumar & Barry Smith - 2003 - In Proceedings of 9th Conference on Artificial Intelligence in Medicine Europe (AIME 2003). Berlin: Springer. pp. 71-75.
    The theory of granular partitions (TGP) is a new approach to the understanding of ontologies and other classificatory systems. The paper explores the use of this new theory in the treatment of task-based clinical guidelines as a means for better understanding the relations between different clinical tasks, both within the framework of a single guideline and between related guidelines. We used as our starting point a DAML+OIL-based ontology for the WHO guideline for hypertension management, comparing this with (...)
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  8. Putting Biomedical Ontologies to Work.Barry Smith & Mathias Brochhausen - 2010 - Methods of Information in Medicine 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 (...)
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  9.  69
    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 (...)
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  10.  63
    Clinical Data Wrangling Using Ontological Realism and Referent Tracking.Werner Ceusters, Chiun Yu Hsu & Barry Smith - 2014 - In 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 (...)
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  11. Biomedical Imaging Ontologies: A Survey and Proposal for Future Work.Barry Smith, Sivaram Arabandi, Mathias Brochhausen, Michael Calhoun, Paolo Ciccarese, Scott Doyle, Bernard Gibaud, Ilya Goldberg, Charles E. Kahn Jr, James Overton, John Tomaszewski & Metin Gurcan - 2015 - Journal of Pathology Informatics 6 (37):37.
    Ontology is one strategy for promoting interoperability of heterogeneous data through consistent tagging. An ontology is a controlled structured vocabulary consisting of general terms (such as “cell” or “image” or “tissue” or “microscope”) that form the basis for such tagging. These terms are designed to represent the types of entities in the domain of reality that the ontology has been devised to capture; the terms are provided with logical defi nitions thereby also supporting reasoning over the tagged data. Aim: This (...)
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  12.  92
    Ontologies for the Study of Neurological Disease.Alexander P. Cox, Mark Jensen, William Duncan, Bianca Weinstock-Guttman, Kinga Szigeti, Alan Ruttenberg, Barry Smith & Alexander D. Diehl - 2012 - In Towards an Ontology of Mental Functioning (ICBO Workshop), Third International Conference on Biomedical Ontology. Graz:
    We have begun work on two separate but related ontologies for the study of neurological diseases. The first, the Neurological Disease Ontology (ND), is intended to provide a set of controlled, logically connected classes to describe the range of neurological diseases and their associated signs and symptoms, assessments, diagnoses, and interventions that are encountered in the course of clinical practice. ND is built as an extension of the Ontology for General Medical Sciences — a high-level candidate OBO Foundry (...)
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  13.  67
    A Unified Framework for Biomedical Terminologies and Ontologies.Werner Ceusters & Barry Smith - 2010 - Studies in Health Technology and Informatics 160:1050-1054.
    The goal of the OBO (Open Biomedical Ontologies) Foundry initiative is to create and maintain an evolving collection of non-overlapping interoperable ontologies that will offer unambiguous representations of the types of entities in biological and biomedical reality. These ontologies are designed to serve non-redundant annotation of data and scientific text. To achieve these ends, the Foundry imposes strict requirements upon the ontologies eligible for inclusion. While these requirements are not met by most existing biomedical terminologies, the (...)
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  14. The Ontology of Biological and Clinical Statistics (OBCS) for Standardized and Reproducible Statistical Analysis.Jie Zheng, Marcelline R. Harris, Anna Maria Masci, Lin Yu, Alfred Hero, Barry Smith & Yongqun He - 2016 - Journal of Biomedical Semantics 7 (53).
    Statistics play a critical role in biological and clinical research. However, most reports of scientific results in the published literature make it difficult for the reader to reproduce the statistical analyses performed in achieving those results because they provide inadequate documentation of the statistical tests and algorithms applied. The Ontology of Biological and Clinical Statistics (OBCS) is put forward here as a step towards solving this problem. Terms in OBCS, including ‘data collection’, ‘data transformation in statistics’, ‘data visualization’, (...)
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  15.  54
    An Ontology for Carcinoma Classification for Clinical Bioinformatics.Anand Kumar, Yum Lina Yip, Barry Smith, Dirk Marwede & Daniel Novotny - 2005 - Studies in Health Technology and Informatics 116 (1):635-640.
    There are a number of existing classifications and staging schemes for carcinomas, one of the most frequently used being the TNM classification. Such classifications represent classes of entities which exist at various anatomical levels of granularity. We argue that in order to apply such representations to the Electronic Health Records one needs sound ontologies which take into consideration the diversity of the domains which are involved in clinical bioinformatics. Here we outline a formal theory for addressing these issues (...)
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  16.  59
    A General Framework for Implementation of Clinical Guidelines by Healthcare Organizations.A. Kumar, Barry Smith, D. M. Pisanelli, A. Gangemi & M. Stefanelli - 2003 - In D. M. Pisanelli (ed.), Ontologies in Medicine: Proceedings of the Workshop on Medical Ontologies (Rome October 2003). Amsterdam: IOS Press. pp. 95-107.
    The paper presents the outlines of an ontology of plans and guidelines, which is then used as the basis for a framework for implementing guideline-based systems for the management of workflow in health care organizations. The framework has a number of special features, above all in that it enables us to represent in formal terms assignments of work-items both to individuals and to teams and to tailor guideline to specific contexts of application in health care organizations. It is designed also (...)
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  17. The Infectious Disease Ontology in the Age of COVID-19.Shane Babcock, Lindsay G. Cowell, John Beverley & Barry Smith - 2020 - In OSF Preprints. Center for Open Science.
    The Infectious Disease Ontology (IDO) is a suite of interoperable ontology modules that aims to provide coverage of all aspects of the infectious disease domain, including biomedical research, clinical care, and public health. IDO Core is designed to be a disease and pathogen neutral ontology, covering just those types of entities and relations that are relevant to infectious diseases generally. IDO Core is then extended by a collection of ontology modules focusing on specific diseases and pathogens. In this paper (...)
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  18. The Role of Ontologies for Sustainable, Semantically Interoperable and Trustworthy EHR Solutions.Bernd Blobel, Dipak Kalra, Marc Koehn, Ken Lunn, Peter Pharow, Pekka Ruotsalainen, Stefan Schulz & Barry Smith - 2009 - Studies in Health Technology and Informatics 150:953-957.
    As health systems around the world turn towards highly distributed, specialized and cooperative structures to increase quality and safety of care as well as efficiency and efficacy of delivery processes, there is a growing need for supporting communication and collaboration of all parties involved with advanced ICT solutions. The Electronic Health Record (EHR) provides the information platform which is maturing towards the eHealth core application. To meet the requirements for sustainable, semantically interoperable, and trustworthy EHR solutions, different standards and different (...)
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  19. Infectious Disease Ontology.Lindsay Grey Cowell & Barry Smith - 2009 - In Infectious Disease Informatics. New York: Springer New York. pp. 373-395.
    Technological developments have resulted in tremendous increases in the volume and diversity of the data and information that must be processed in the course of biomedical and clinical research and practice. Researchers are at the same time under ever greater pressure to share data and to take steps to ensure that data resources are interoperable. The use of ontologies to annotate data has proven successful in supporting these goals and in providing new possibilities for the automated processing of (...)
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  20. 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 (...)
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  21.  71
    ARGOS Policy Brief on Semantic Interoperability.Dipak Kalra, Mark Musen, Barry Smith & Werner Ceusters - 2011 - Studies in Health Technology and Informatics 170 (1):1-15.
    Semantic interoperability requires the use of standards, not only for Electronic Health Record (EHR) data to be transferred and structurally mapped into a receiving repository, but also for the clinical content of the EHR to be interpreted in conformity with the original meanings intended by its authors. Accurate and complete clinical documentation, faithful to the patient’s situation, and interoperability between systems, require widespread and dependable access to published and maintained collections of coherent and quality-assured semantic resources, including models (...)
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  22. Rhetoric and Argumentation: How Clinical Practice Guidelines Think.Jonathan Fuller - 2013 - Journal of Evaluation in Clinical Practice 19 (3):433-441.
    Introduction: Clinical practice guidelines (CPGs) are an important source of justification for clinical decisions in modern evidence-based practice. Yet, we have given little attention to how they argue their evidence. In particular, how do CPGs argue for treatment with long-term medications that are increasingly prescribed to older patients? Approach and rationale: I selected six disease-specific guidelines recommending treatment with five of the medication classes most commonly prescribed for seniors in Ontario, Canada. I considered the stated aims of these (...)
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  23.  38
    Towards Interoperability of Biomedical Ontologies - Report Number 07132.Mark Musen, Michael Schroeder & Barry Smith - 2008 - In Towards Interoperability of Biomedical Ontologies. Schloss Dagstuhl-Leibniz-Zentrum Fuer Informatik.
    The meeting focused on uses of ontologies, with a special focus on spatial ontologies, in addressing the ever increasing needs faced by biology and medicine to cope with ever expanding quantities of data. To provide effective solutions computers need to integrate data deriving from myriad heterogeneous sources by bringing the data together within a single framework. The meeting brought together leaders in the field of what are called "top-level ontologies" to address this issue, and to establish strategies (...)
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  24.  31
    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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  25.  61
    Ontologies for Space and Ground Systems.Barry Smith - 2020 - In Ground System Architectures Workshop. Los Angeles, CA: GSAW. pp. 1-3.
    We will survey a range of ontologies relevant to space and ground system domains. The ontologies form part of the Common Core Ontology ecosystem (CCO) developed under the IARPA KDD initiative. We focus specifically on the Space Domain Ontologies, a suite of ontologies to support space situational awareness, including the Spacecraft Mission Ontology, Spacecraft Ontology, Space Event Ontology and Space Object Ontology.
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  26. What Health Care Providers Know: A Taxonomy of Clinical Disagreements.Daniel Groll - 2011 - Hastings Center Report 41 (5):27-36.
    When, if ever, can healthcare provider's lay claim to knowing what is best for their patients? In this paper, I offer a taxonomy of clinical disagreements. The taxonomy, I argue, reveals that healthcare providers often can lay claim to knowing what is best for their patients, but that oftentimes, they cannot do so *as* healthcare providers.
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  27. The Industrial Ontologies Foundry Proof-of-Concept Project.Evan Wallace, Dimitris Kiritsis, Barry Smith & Chris Will - 2018 - In Ilkyeong Moon, Gyu M. Lee, Jinwoo Park, Dimitris Kiritsis & Gregor von Cieminski (eds.), Advances in Production Management Systems. Smart Manufacturing for Industry 4.0. IFIP. pp. 402-409.
    The current industrial revolution is said to be driven by the digitization that exploits connected information across all aspects of manufacturing. Standards have been recognized as an important enabler. Ontology-based information standard may provide benefits not offered by current information standards. Although there have been ontologies developed in the industrial manufacturing domain, they have been fragmented and inconsistent, and little has received a standard status. With successes in developing coherent ontologies in the biological, biomedical, and financial domains, an (...)
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  28. Consent in Clinical Research.Collin O'Neil - 2018 - In Andreas Müller & Peter Schaber (eds.), The Routledge Handbook of the Ethics of Consent. New York, USA: Routledge. pp. 297-310.
    This article addresses two areas of continuing controversy about consent in clinical research: the question of when consent to low risk research is necessary, and the question of when consent to research is valid. The article identifies a number of considerations relevant to determining whether consent is necessary, chief of which is whether the study would involve subjects in ways that would (otherwise) infringe their rights. When consent is necessary, there is a further question of under what conditions consent (...)
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  29. Clinical Research: Should Patients Pay to Play?Ezekiel J. Emanuel, Steven Joffe, Christine Grady, David Wendler & Govind Persad - 2015 - Science Translational Medicine 7 (298):298ps16.
    We argue that charging people to participate in research is likely to undermine the fundamental ethical bases of clinical research, especially the principles of social value, scientific validity, and fair subject selection.
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  30. The Prediction of Future Behavior: The Empty Promises of Expert Clinical and Actuarial Testimony.Andrés Páez - 2016 - Teoria Jurídica Contemporânea 1 (1):75-101.
    Testimony about the future dangerousness of a person has become a central staple of many judicial processes. In settings such as bail, sentencing, and parole decisions, in rulings about the civil confinement of the mentally ill, and in custody decisions in a context of domestic violence, the assessment of a person’s propensity towards physical or sexual violence is regarded as a deciding factor. These assessments can be based on two forms of expert testimony: actuarial or clinical. The purpose of (...)
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  31. Failures in Clinical Trials in the European Union: Lessons From the Polish Experience.Marcin Waligora - 2013 - Science and Engineering Ethics 19 (3):1087-1098.
    When discussing the safety of research subjects, including their exploitation and vulnerability as well as failures in clinical research, recent commentators have focused mostly on countries with low or middle-income economies. High-income countries are seen as relatively safe and well-regulated. This article presents irregularities in clinical trials in an EU member state, Poland, which were revealed by the Supreme Audit Office of Poland (the NIK). Despite adopting many European Union regulations, including European Commission directives concerning Good Clinical (...)
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  32. The National Center for Biomedical Ontology.Mark A. Musen, Natalya F. Noy, Nigam H. Shah, Patricia L. Whetzel, Christopher G. Chute, Margaret-Anne Story & Barry Smith - 2012 - Journal of the American Medical Informatics Association 19 (2):190-195.
    The National Center for Biomedical Ontology is now in its seventh year. The goals of this National Center for Biomedical Computing are to: create and maintain a repository of biomedical ontologies and terminologies; build tools and web services to enable the use of ontologies and terminologies in clinical and translational research; educate their trainees and the scientific community broadly about biomedical ontology and ontology-based technology and best practices; and collaborate with a variety of groups who develop and (...)
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  33. Ontologies for the Life Sciences.Steffen Schulze-Kremer & Barry Smith - 2005 - In Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, vol. 4. Wiley.
    Where humans can manipulate and integrate the information they receive in subtle and ever-changing ways from context to context, computers need structured and context-free background information of a sort which ontologies can help to provide. A domain ontology captures the stable, highly general and commonly accepted core knowledge for an application domain. The domain at issue here is that of the life sciences, in particular molecular biology and bioinformatics. Contemporary life science research includes components drawn from physics, chemistry, mathematics, (...)
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  34. Vital Sign Ontology.Albert Goldfain, Barry Smith, Sivaram Arabandi, Mathias Brochhausen & William R. Hogan - 2011 - In Proceedings of the Workshop on Bio-Ontologies, ISMB, Vienna, June 2011. Vienna: pp. 71-74.
    We introduce the Vital Sign Ontology (VSO), an extension of the Ontology for General Medical Science (OGMS) that covers the consensus human vital signs: blood pressure, body temperature, respiratory rate, and pulse rate. VSO provides a controlled structured vocabulary for describing vital sign measurement data, the processes of measuring vital signs, and the anatomical entities participating in such measurements. VSO is implemented in OWL-DL and follows OBO Foundry guidelines and best practices. If properly developed and extended, we believe the VSO (...)
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  35. ImmPort, Toward Repurposing of Open Access Immunological Assay Data for Translational and Clinical Research.Sanchita Bhattacharya, Patrick Dunn, Cristel Thomas, Barry Smith, Henry Schaefer, Jieming Chen, Zicheng Hu, Kelly Zalocusky, Ravi Shankar & Shai Shen-Orr - 2018 - Scientific Data 5:180015.
    Immunology researchers are beginning to explore the possibilities of reproducibility, reuse and secondary analyses of immunology data. Open-access datasets are being applied in the validation of the methods used in the original studies, leveraging studies for meta-analysis, or generating new hypotheses. To promote these goals, the ImmPort data repository was created for the broader research community to explore the wide spectrum of clinical and basic research data and associated findings. The ImmPort ecosystem consists of four components–Private Data, Shared Data, (...)
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  36. Bioportal: Ontologies and Integrated Data Resources at the Click of the Mouse.L. Whetzel Patricia, H. Shah Nigam, F. Noy Natalya, Dai Benjamin, Dorf Michael, Griffith Nicholas, Jonquet Clement, Youn Cherie, Callendar Chris, Coulet Adrien, Barry Smith, Chris Chute & Mark Musen - 2011 - In Proceedings of the 2nd International Conference on Biomedical Ontology, Buffalo, NY. pp. 292-293.
    BioPortal is a Web portal that provides access to a library of biomedical ontologies and terminologies developed in OWL, RDF(S), OBO format, Protégé frames, and Rich Release Format. BioPortal functionality, driven by a service-oriented architecture, includes the ability to browse, search and visualize ontologies (Figure 1). The Web interface also facilitates community-based participation in the evaluation and evolution of ontology content.
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  37. A Taxonomy of Multinational Ethical and Methodological Standards for Clinical Trials of Therapeutic Interventions.C. M. Ashton, N. P. Wray, A. F. Jarman, J. M. Kolman, D. M. Wenner & B. A. Brody - 2011 - Journal of Medical Ethics 37 (6):368-373.
    Background If trials of therapeutic interventions are to serve society's interests, they must be of high methodological quality and must satisfy moral commitments to human subjects. The authors set out to develop a clinical - trials compendium in which standards for the ethical treatment of human subjects are integrated with standards for research methods. Methods The authors rank-ordered the world's nations and chose the 31 with >700 active trials as of 24 July 2008. Governmental and other authoritative entities of (...)
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  38. OAE: The Ontology of Adverse Events.Yongqun He, Sirarat Sarntivijai, Yu Lin, Zuoshuang Xiang, Abra Guo, Shelley Zhang, Desikan Jagannathan, Luca Toldo, Cui Tao & Barry Smith - 2014 - Journal of Biomedical Semantics 5 (29):1-13.
    A medical intervention is a medical procedure or application intended to relieve or prevent illness or injury. Examples of medical interventions include vaccination and drug administration. After a medical intervention, adverse events (AEs) may occur which lie outside the intended consequences of the intervention. The representation and analysis of AEs are critical to the improvement of public health. Description: The Ontology of Adverse Events (OAE), previously named Adverse Event Ontology (AEO), is a community-driven ontology developed to standardize and integrate data (...)
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  39. 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 (...)
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  40. Quality Control for Terms and Definitions in Ontologies and Taxonomies.Jacob Köhler, Katherine Munn, Alexander Rüegg, Andre Skusa & Barry Smith - 2006 - BMC Bioinformatics 7 (212):1-12.
    Background: Ontologies and taxonomies are among the most important computational resources for molecular biology and bioinformatics. A series of recent papers has shown that the Gene Ontology (GO), the most prominent taxonomic resource in these fields, is marked by flaws of certain characteristic types, which flow from a failure to address basic ontological principles. As yet, no methods have been proposed which would allow ontology curators to pinpoint flawed terms or definitions in ontologies in a systematic way. Results: (...)
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  41. OntONeo: The Obstetric and Neonatal Ontology.Fernanda Farinelli, Mauricio Almeida, Peter Elkin & Barry Smith - 2016 - In Dealing with elements of medical encounters: An approach based on ontological realism. Aachen: 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 (...)
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  42.  85
    Modeling the Invention of a New Inference Rule: The Case of ‘Randomized Clinical Trial’ as an Argument Scheme for Medical Science.Jodi Schneider & Sally Jackson - 2018 - Argument and Computation 9 (2):77-89.
    A background assumption of this paper is that the repertoire of inference schemes available to humanity is not fixed, but subject to change as new schemes are invented or refined and as old ones are obsolesced or abandoned. This is particularly visible in areas like health and environmental sciences, where enormous societal investment has been made in finding ways to reach more dependable conclusions. Computational modeling of argumentation, at least for the discourse in expert fields, will require the possibility of (...)
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  43.  72
    A Unified Framework for Building Ontological Theories with Application and Testing in the Field of Clinical Trials.Heller Barbara, Herre Heinrich & Barry Smith - 2001 - In IFOMIS Reports. Leipzig: University of Leipzig.
    The objective of this research programme is to contribute to the establishment of the emerging science of Formal Ontology in Information Systems via a collaborative project involving researchers from a range of disciplines including philosophy, logic, computer science, linguistics, and the medical sciences. The re­searchers will work together on the construction of a unified formal ontology, which means: a general framework for the construction of ontological theories in specific domains. The framework will be constructed using the axiomatic-deductive method of modern (...)
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  44.  52
    Formalizing UMLS Relations Using Semantic Partitions in the Context of a Task-Based Clinical Guidelines Model.Anand Kumar, Matteo Piazza, Barry Smith, Silvana Quaglini & Mario Stefanelli - 2004 - In IFOMIS Reports. Saarbrücken: IFOMIS.
    An important part of the Unified Medical Language System (UMLS) is its Semantic Network, consisting of 134 Semantic Types connected to each other by edges formed by one or more of 54 distinct Relation Types. This Network is however for many purposes overcomplex, and various groups have thus made attempts at simplification. Here we take this work further by simplifying the relations which involve the three Semantic Types – Diagnostic Procedure, Laboratory Procedure and Therapeutic or Preventive Procedure. We define operators (...)
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  45.  49
    Biomedical Terminologies and Ontologies: Enabling Biomedical Semantic Interoperability and Standards in Europe.Bernard de Bono, Mathias Brochhausen, Sybo Dijkstra, Dipak Kalra, Stephan Keifer & Barry Smith - 2009 - In European Large-Scale Action on Electronic Health.
    In the management of biomedical data, vocabularies such as ontologies and terminologies (O/Ts) are used for (i) domain knowledge representation and (ii) interoperability. The knowledge representation role supports the automated reasoning on, and analysis of, data annotated with O/Ts. At an interoperability level, the use of a communal vocabulary standard for a particular domain is essential for large data repositories and information management systems to communicate consistently with one other. Consequently, the interoperability benefit of selecting a particular O/T as (...)
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  46.  48
    Non Classical Concept Representation and Reasoning in Formal Ontologies.Antonio Lieto - 2012 - Dissertation, Università Degli Studi di Salerno
    Formal ontologies are nowadays widely considered a standard tool for knowledge representation and reasoning in the Semantic Web. In this context, they are expected to play an important role in helping automated processes to access information. Namely: they are expected to provide a formal structure able to explicate the relationships between different concepts/terms, thus allowing intelligent agents to interpret, correctly, the semantics of the web resources improving the performances of the search technologies. Here we take into account a problem (...)
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  47. Augmented Ontologies or How to Philosophize with a Digital Hammer.Stefano Gualeni - 2014 - Philosophy and Technology 27 (2):177-199.
    Could a person ever transcend what it is like to be in the world as a human being? Could we ever know what it is like to be other creatures? Questions about the overcoming of a human perspective are not uncommon in the history of philosophy. In the last century, those very interrogatives were notably raised by American philosopher Thomas Nagel in the context of philosophy of mind. In his 1974 essay What is it Like to Be a Bat?, Nagel (...)
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  48.  46
    Clinical Guidelines as Plans: An Ontological Theory.Anand Kumar, Barry Smith, Domenica Pisanelli, Aldo Gangemi & Mario Stefanelli - 2006 - Methods of Information in Medicine 45 (2):204-210.
    Clinical guidelines are special types of plans realized by collective agents. We provide an ontological theory of such plans that is designed to support the construction of a framework in which guideline-based information systems can be employed in the management of workflow in health care organizations. The framework we propose allows us to represent in formal terms how clinical guidelines are realized through the actions of are realized through the actions of individuals organized into teams. We provide various (...)
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  49.  40
    Implementing Clinical Guidelines in an Organizational Setup.Anand Kumar, Barry Smith, Mario Stefanelli, Silvana Quaglini & Matteo Piazza - 2003 - In Proceedings of the Workshop on Model-Based and Qualitative Reasoning in Biomedicine, AIME . pp. 39-44.
    Outcomes research in healthcare has been a topic much addressed in recent years. Efforts in this direction have been supplemented by work in the areas of guidelines for clinical practice and computer-interpretable workflow and careflow models.In what follows we present the outlines of a framework for understanding the relations between organizations, guidelines, individual patients and patient-related functions. The derived framework provides a means to extract the knowledge contained in the guideline text at different granularities, in ways that can help (...)
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  50. Translating Trial Results in Clinical Practice: The Risk GP Model.Jonathan Fuller & Luis J. Flores - 2016 - Journal of Cardiovascular Translational Research 9:167-168.
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