Results for 'informatics'

73 found
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  1. Genome Informatics: The Role of DNA in Cellular Computations.James A. Shapiro - 2006 - Biological Theory 1 (3):288-301.
    Cells are cognitive entities possessing great computational power. DNA serves as a multivalent information storage medium for these computations at various time scales. Information is stored in sequences, epigenetic modifications, and rapidly changing nucleoprotein complexes. Because DNA must operate through complexes formed with other molecules in the cell, genome functions are inherently interactive and involve two-way communication with various cellular compartments. Both coding sequences and repetitive sequences contribute to the hierarchical systemic organization of the genome. By virtue of nucleoprotein complexes, (...)
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  2. Biomedical Informatics and Granularity.Anand Kumar & Barry Smith - 2004 - Comparative and Functional Genomics 5 (6-7):501-508.
    An explicit formal-ontological representation of entities existing at multiple levels of granularity is an urgent requirement for biomedical information processing. We discuss some fundamental principles which can form a basis for such a representation. We also comment on some of the implicit treatments of granularity in currently available ontologies and terminologies (GO, FMA, SNOMED CT).
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  3.  62
    Informatics: Science or Téchne?Tito Palmeiro - 2016 - O Que Nos Faz Pensar 25:88-97.
    Informatics is generally understood as a “new technology” and is therewith discussed according to technological aspects such as speed, data retrieval, information control and so on. Its widespread use from home appliances to enterprises and universities is not the result of a clear-cut analysis of its inner possibilities but is rather dependent on all sorts of ideological promises of unlimited progress. We will discuss the theoretical definition of informatics proposed in 1936 by Alan Turing in order to show (...)
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  4. Informatics: The Fuel for Pharmacometric Analysis.H. Grasela Thaddeus, Fiedler-Kelly Jill, Cirincione Brenda, Hitchcock Darcy, Reitz Kathleen, Sardella Susanne & Barry Smith - 2007 - AAPS Journal 9 (1):E84--E91.
    The current informal practice of pharmacometrics as a combination art and science makes it hard to appreciate the role that informatics can and should play in the future of the discipline and to comprehend the gaps that exist because of its absence. The development of pharmacometric informatics has important implications for expediting decision making and for improving the reliability of decisions made in model-based development. We argue that well-defined informatics for pharmacometrics can lead to much needed improvements (...)
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  5. Discussion of “Biomedical Informatics: We Are What We Publish”.Geissbuhler Antoine, W. E. Hammond, A. Hasman, R. Hussein, R. Koppel, C. A. Kulikowski, V. Maojo, F. Martin-Sanchez, P. W. Moorman, Moura La, F. G. De Quiros, M. J. Schuemle, Barry Smith & J. Talmon - 2013 - Methods of Information in Medicine 52 (6):547-562.
    This article is part of a For-Discussion-Section of Methods of Information in Medicine about the paper "Biomedical Informatics: We Are What We Publish", written by Peter L. Elkin, Steven H. Brown, and Graham Wright. It is introduced by an editorial. This article contains the combined commentaries invited to independently comment on the Elkin et al. paper. In subsequent issues the discussion can continue through letters to the editor.
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  6. Semantics and Metaphysics in Informatics: Toward an Ontology of Tasks (a Reply to Lenartowicz Et Al. 2010, Towards an Ontology of Cognitive Control).Carrie Figdor - 2011 - Topics in Cognitive Science 3 (2):222-226.
    This article clarifies three principles that should guide the development of any cognitive ontology. First, that an adequate cognitive ontology depends essentially on an adequate task ontology; second, that the goal of developing a cognitive ontology is independent of the goal of finding neural implementations of the processes referred to in the ontology; and third, that cognitive ontologies are neutral regarding the metaphysical relationship between cognitive and neural processes.
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  7. Giving Patients Granular Control of Personal Health Information: Using an Ethics ‘Points to Consider’ to Inform Informatics System Designers.Eric M. Meslin, Sheri A. Alpert, Aaron E. Carroll, Jere D. Odell, William M. Tierney & Peter H. Schwartz - 2013 - International Journal of Medical Informatics 82:1136-1143.
    Objective: There are benefits and risks of giving patients more granular control of their personal health information in electronic health record (EHR) systems. When designing EHR systems and policies, informaticists and system developers must balance these benefits and risks. Ethical considerations should be an explicit part of this balancing. Our objective was to develop a structured ethics framework to accomplish this. -/- Methods: We reviewed existing literature on the ethical and policy issues, developed an ethics framework called a “Points to (...)
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  8.  76
    Ontology as the Core Discipline of Biomedical Informatics: Legacies of the Past and Recommendations for the Future Direction of Research.Barry Smith & Werner Ceusters - 2007 - In Gordana Dodig Crnkovic & Susan Stuart (eds.), Computation, Information, Cognition: The Nexus and the Liminal. Cambridge Scholars Publishing. pp. 104-122.
    The automatic integration of rapidly expanding information resources in the life sciences is one of the most challenging goals facing biomedical research today. Controlled vocabularies, terminologies, and coding systems play an important role in realizing this goal, by making it possible to draw together information from heterogeneous sources – for example pertaining to genes and proteins, drugs and diseases – secure in the knowledge that the same terms will also represent the same entities on all occasions of use. In the (...)
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  9. Towards Industrial Strength Philosophy: How Analytical Ontology Can Help Medical Informatics.Barry Smith & Werner Ceusters - 2003 - Interdisciplinary Science Reviews 28 (2):106–111.
    Initially the problems of data integration, for example in the field of medicine, were resolved in case by case fashion. Pairs of databases were cross-calibrated by hand, rather as if one were translating from French into Hebrew. As the numbers and complexity of database systems increased, the idea arose of streamlining these efforts by constructing one single benchmark taxonomy, as it were a central switchboard, into which all of the various classification systems would need to be translated only once. By (...)
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  10. Ontology and the Future of Dental Research Informatics.Barry Smith, Louis J. Goldberg, Alan Ruttenberg & Michael Glick - 2010 - Journal of the American Dental Association 141 (10):1173-75.
    How do we find what is clinically significant in the swarms of data being generated by today’s diagnostic technologies? As electronic records become ever more prevalent – and digital imaging and genomic, proteomic, salivaomics, metabalomics, pharmacogenomics, phenomics and transcriptomics techniques become commonplace – fdifferent clinical and biological disciplines are facing up to the need to put their data houses in order to avoid the consequences of an uncontrolled explosion of different ways of describing information. We describe a new strategy to (...)
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  11.  81
    A Review Paper on Scope of Big Data Analysis in Heath Informatics.Kazi Md Shahiduzzaman, Lusekelo Kibona & Hassana Ganame - 2018 - International Journal of Engineering and Information Systems (IJEAIS) 2 (5):1-8.
    Abstract— The term Health Informatics represent a huge volume of data that is collected from different source of health sector. Because of its’ diversity in nature, quite a big number of attributes, numerous amount data, health informatics can be considered as Big Data. Therefore, different techniques used for analyzing Big Data will also fit for Health Informatics. In recent years, implementation of Data Mining on Health Informatics brings a lot of fruitful outcomes that improve the overall (...)
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  12. Doctor of Philosophy Thesis in Military Informatics (OpenPhD ) : Lethal Autonomy of Weapons is Designed and/or Recessive.Nyagudi Nyagudi Musandu - 2016-12-09 - Dissertation, OpenPhD (#Openphd) E.G. Wikiversity Https://En.Wikiversity.Org/Wiki/Doctor_of_Philosophy , Etc.
    My original contribution to knowledge is : Any weapon that exhibits intended and/or untended lethal autonomy in targeting and interdiction – does so by way of design and/or recessive flaw(s) in its systems of control – any such weapon is capable of war-fighting and other battle-space interaction in a manner that its Human Commander does not anticipate. Even with the complexity of Lethal Autonomy issues there is nothing particular to gain from being a low-tech Military. Lethal autonomous weapons are therefore (...)
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  13. The Role of Foundational Relations in the Alignment of Biomedical Ontologies.Barry Smith & Cornelius Rosse - 2004 - In M. Fieschi, E. Coiera & Y.-C. J. Li (eds.), Medinfo. IOS Press. pp. 444-448.
    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 (...)
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  14. 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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  15. Quem ou o que pensa? Uma busca de aportes para questões filosóficas suscitadas pela revolução informática atual.Lamartine De Hollanda Cavalcanti Neto - 2020 - Dissertation, Universidade Federal de São Paulo
    Taking as an assumption the existence of an informatics revolution nowadays and that the examination of studies and debates related to it may allow the identification of questions of a philosophical nature, the present study aims to identify and formulate some of these questions, as well as to investigate whether the historical controversy about monopsychism, which occurred at the University of Paris in 1270, can be considered a theoretical framework capable of providing contributions to these philosophical questions. The answer (...)
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  16.  95
    Using Philosophy to Improve the Coherence and Interoperability of Applications Ontologies: A Field Report on the Collaboration of IFOMIS and L&C.Jonathan Simon, James Matthew Fielding & Barry Smith - 2004 - In Proceedings of the First Workshop on Philosophy and Informatics. Deutsches Forschungs­zentrum für künstliche Intelligenz, Cologne: 2004 (CEUR Workshop Proceedings 112). pp. 65-72.
    The collaboration of Language and Computing nv (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is guided by the hypothesis that quality constraints on ontologies for software ap-plication purposes closely parallel the constraints salient to the design of sound philosophical theories. The extent of this parallel has been poorly appreciated in the informatics community, and it turns out that importing the benefits of phi-losophical insight and methodology into application domains yields a variety of improvements. L&C’s (...)
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  17.  27
    More About Ontology: Response.Barry Smith, Louis Goldberg, Michael Glick & Alan Ruttenberg - 2011 - Journal of the American Dental Association 142 (3):252-254.
    Letter commenting on the paper -/- Barry Smith, Louis J. Goldberg, Alan Ruttenberg & Michael Glick, "Ontology and the Future of Dental Research Informatics", Journal of the American Dental Association 141 2010;(10):1173-75 -/- with responses by the authors of the paper.
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  18. 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):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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  19. Building Ontologies with Basic Formal Ontology.Robert Arp, Barry Smith & Andrew D. Spear - 2015 - Cambridge, MA: MIT Press.
    In the era of “big data,” science is increasingly information driven, and the potential for computers to store, manage, and integrate massive amounts of data has given rise to such new disciplinary fields as biomedical informatics. Applied ontology offers a strategy for the organization of scientific information in computer-tractable form, drawing on concepts not only from computer and information science but also from linguistics, logic, and philosophy. This book provides an introduction to the field of applied ontology that is (...)
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  20. 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 SNOMED CT community, (...)
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  21. 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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  22.  84
    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 latter may nonetheless support (...)
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  23.  49
    Biomedical Ontologies.Barry Smith - forthcoming - In Peter Elkin (ed.), Terminology, Ontology and their Implementations. Springer Nature Switzerland AG.
    We begin at the beginning, with an outline of Aristotle’s views on ontology and with a discussion of the influence of these views on Linnaeus. We move from there to consider the data standardization initiatives launched in the 19th century, and then turn to investigate how the idea of computational ontologies developed in the AI and knowledge representation communities in the closing decades of the 20th century. We show how aspects of this idea, particularly those relating to the use of (...)
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  24.  97
    The Representation of Protein Complexes in the Protein Ontology.Carol Bult, Harold Drabkin, Alexei Evsikov, Darren Natale, Cecilia Arighi, Natalia Roberts, Alan Ruttenberg, Peter D’Eustachio, Barry Smith, Judith Blake & Cathy Wu - 2011 - BMC Bioinformatics 12 (371):1-11.
    Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified (...)
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  25.  86
    Infotality: On Living, Loving, and Dying Through Information.Joel Michael Reynolds - 2018 - American Journal of Bioethics 18 (2):33-35.
    Responding to Danaher et al. on self-tracking technologies, I argue that human lived experience is becoming increasingly mediated by generalized, statistical information, which I term our "infotality." Drawing on the work of Foucault, I argue that infotality is historically novel and best understood as the product of biopolitics, healthism, and informatics. I then critique the authors' "stance of cautious openness,” which misunderstands the aims of the technology in question and the fundamental ambiguity of the role information plays in the (...)
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  26. How Bioethics Principles Can Aid Design of Electronic Health Records to Accommodate Patient Granular Control.Eric M. Meslin & Peter H. Schwartz - 2014 - Journal of General Internal Medicine 30 (1):3-6.
    Ethics should guide the design of electronic health records (EHR), and recognized principles of bioethics can play an important role. This approach was adopted recently by a team of informaticists designing and testing a system where patients exert granular control over who views their personal health information. While this method of building ethics in from the start of the design process has significant benefits, questions remain about how useful the application of bioethics principles can be in this process, especially when (...)
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  27. Towards a Reference Terminology for Ontology Research and Development in the Biomedical Domain.Barry Smith, Waclaw Kusnierczyk, Daniel Schober, & Werner Ceusters - 2006 - In Proceedings of KR-MED, CEUR, vol. 222. pp. 57-65.
    Ontology is a burgeoning field, involving researchers from the computer science, philosophy, data and software engineering, logic, linguistics, and terminology domains. Many ontology-related terms with precise meanings in one of these domains have different meanings in others. Our purpose here is to initiate a path towards disambiguation of such terms. We draw primarily on the literature of biomedical informatics, not least because the problems caused by unclear or ambiguous use of terms have been there most thoroughly addressed. We advance (...)
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  28. Applied Ontology: Focusing on Content.Nicola Guarino & Mark A. Musen - 2005 - Applied ontology 1 (1):1-5.
    In a world that is overflowing with journals and other outlets for scientific publication, the appearance of any new periodical requires some justification. There are already more journals than we can read and more conferences than we can attend. In the case of applied Ontology, we believe that the creation of anew journal not only is completely justifiable, it is downright exciting. For too long, workers in computer science have assumed that content comes for free. “Theory” in computer science has (...)
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  29. Revising the UMLS Semantic Network.Steffen Schulze-Kremer, Barry Smith & Anand Kumar - 2004 - In MedInfo.
    The integration of standardized biomedical terminologies into a single, unified knowledge representation system has formed a key area of applied informatics research in recent years. The Unified Medical Language System (UMLS) is the most advanced and most prominent effort in this direction, bringing together within its Metathesaurus a large number of distinct source-terminologies. The UMLS Semantic Network, which is designed to support the integration of these source-terminologies, has proved to be a highly successful combination of formal coherence and broad (...)
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  30.  21
    Internet, el nuevo dios.Enrique Morata - forthcoming - Academia.Edu.
    In Spanish, on Internet as the new god of all us.
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  31. 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 play in two multicentric research projects. (...)
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  32. Global Innovations in Tourism.Sergii Sardak & A. Samoilenko S. Sardak, V. Dzhyndzhoian - 2016 - Innovative Marketing 12 (3):45 – 50.
    The article is devoted to the increasing role of tourism in the world economy. The dynamics of international tourism indicators is investigated. The main global innovations in the tourism industry are identified: the growth of tourism types; the application of qualitatively new solutions of scientific and methodological and applied character; growing of tourism influence on the society; the existence of synergistic effect in the tourist industry as a result of combination of subjects efforts at all management levels; changing of the (...)
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  33. Can Mathematics Explain the Evolution of Human Language?Guenther Witzany - 2011 - Communicative and Integrative Biology 4 (5):516-520.
    Investigation into the sequence structure of the genetic code by means of an informatic approach is a real success story. The features of human language are also the object of investigation within the realm of formal language theories. They focus on the common rules of a universal grammar that lies behind all languages and determine generation of syntactic structures. This universal grammar is a depiction of material reality, i.e., the hidden logical order of things and its relations determined by natural (...)
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  34. VO: Vaccine Ontology.Yongqun He, Lindsay Cowell, Alexander D. Diehl, H. L. Mobley, Bjoern Peters, Alan Ruttenberg, Richard H. Scheuermann, Ryan R. Brinkman, Melanie Courtot, Chris Mungall, Barry Smith & Others - 2009 - In ICBO 2009: Proceedings of the First International Conference on Biomedical Ontology. Buffalo:
    Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced vaccine (...)
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  35. Introduction to the Special Issue on The Enactive Approach to Qualitative Ontology.Andrea Pace Giannotta, Roberta Lanfredini, Nicola Liberati & Pagni Elena - 2016 - Humana.Mente - Journal of Philosophical Studies (31).
    This Special Issue is dedicated to building a bridge between different disciplines concerned in the investigation of the qualitative dimension of experience and reality. The two main objectives of the Issue can be summarized as follows: 1) to elucidate the need for a revision of categories to account for the qualitative dimension in various disciplines (that include, for example, the cognitive sciences, neurosciences, biology, linguistics, informatics, artificial intelligence, robotics, newly emerging computer technologies) in order to develop an ontology that (...)
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  36. Development of a Manufacturing Ontology for Functionally Graded Materials.Francesco Furini, Rahul Rai, Barry Smith, Georgio Colombo & Venkat Krovi - 2016 - In Proceedings of International Design Engineering Technical Conferences & Computers and Information in Engineering Conference (IDETC/CIE).
    The development of manufacturing technologies for new materials involves the generation of a large and continually evolving volume of information. The analysis, integration and management of such large volumes of data, typically stored in multiple independently developed databases, creates significant challenges for practitioners. There is a critical need especially for open-sharing of data pertaining to engineering design which together with effective decision support tools can enable innovation. We believe that ontology applied to engineering (OE) represents a viable strategy for the (...)
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  37. Is an Archaeological Contribution to the Theory of Social Science Possible? Archaeological Data and Concepts in the Dispute Between Jean-Claude Gardin and Jean-Claude Passeron.Sébastien Plutniak - 2017 - Palethnologie 9:7-21.
    The issue of the definition and position of archaeology as a discipline is examined in relation to the dispute which took place from 1980 to 2009 between the archaeologist Jean-Claude Gardin and the sociologist Jean-Claude Passeron. This case study enables us to explore the actual conceptual relationships between archaeology and the other sciences (as opposed to those wished for or prescribed). The contrasts between the positions declared by the two researchers and the rooting of their arguments in their disciplines are (...)
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  38. CIDO, a Community-Based Ontology for Coronavirus Disease Knowledge and Data Integration, Sharing, and Analysis.Oliver He, John Beverley, Gilbert S. Omenn, Barry Smith, Brian Athey, Luonan Chen, Xiaolin Yang, Junguk Hur, Hsin-hui Huang, Anthony Huffman, Yingtong Liu, Yang Wang, Edison Ong & Hong Yu - 2020 - Scientific Data 181 (7):5.
    Ontologies, as the term is used in informatics, are structured vocabularies comprised of human- and computer-interpretable terms and relations that represent entities and relationships. Within informatics fields, ontologies play an important role in knowledge and data standardization, representation, integra- tion, sharing and analysis. They have also become a foundation of artificial intelligence (AI) research. In what follows, we outline the Coronavirus Infectious Disease Ontology (CIDO), which covers multiple areas in the domain of coronavirus diseases, including etiology, transmission, epidemiology, (...)
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  39. Controlled Vocabularies in Bioinformatics: A Case Study in the Gene Ontology.Barry Smith & Anand Kumar - 2004 - Drug Discovery Today: Biosilico 2 (6):246-252.
    The automatic integration of information resources in the life sciences is one of the most challenging goals facing biomedical informatics today. Controlled vocabularies have played an important role in realizing this goal, by making it possible to draw together information from heterogeneous sources secure in the knowledge that the same terms will also represent the same entities on all occasions of use. One of the most impressive achievements in this regard is the Gene Ontology (GO), which is rapidly acquiring (...)
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  40. Applied Ontology: An Introduction.Katherine Munn & Barry Smith (eds.) - 2008 - Frankfurt: 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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  41. 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 play in two multicentric research projects. (...)
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  42. Strengths and Limitations of Formal Ontologies in the Biomedical Domain.Barry Smith - 2009 - Electronic Journal of Communication, Information and Innovation in Health 3 (1):31-45.
    We propose a typology of representational artifacts for health care and life sciences domains and associate this typology with different kinds of formal ontology and logic, drawing conclusions as to the strengths and limitations for ontology in a description logics framework. The four types of domain representation we consider are: (i) lexico-semantic representation, (ii) representation of types of entities, (iii) representations of background knowledge, and (iv) representation of individuals. We advocate a clear distinction of the four kinds of representation in (...)
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  43.  51
    Brave. Net. World: The Internet as a Disinformation Superhighway?Luciano Floridi - 1996 - The Electronic Library 14:509-514.
    This article is a modified version of a paper I gave to the conference Philosophy & Informatics - First Italian Conference on the use of ICT in philosophical disciplines, promoted by the Italian Philosophical Association (University of Rome "La Sapienza", 23-24 November, 1995).
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  44.  97
    The Ontology-Epistemology Divide: A Case Study in Medical Terminology.OIivier Bodenreider, Barry Smith & Anita Burgun - 2004 - 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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  45.  96
    基于基本形式化本体的本体构建.Robert Arp, Barry Smith & Andrew D. Spear - 2020 - Beijing: People's Medical Publishing House.
    In the era of “big data,” science is increasingly information driven, and the potential for computers to store, manage, and integrate massive amounts of data has given rise to such new disciplinary fields as biomedical informatics. Applied ontology offers a strategy for the organization of scientific information in computer-tractable form, drawing on concepts not only from computer and information science but also from linguistics, logic, and philosophy. This book provides an introduction to the field of applied ontology that is (...)
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  46.  88
    Would SNOMED CT Benefit From Realism-Based Ontology Evolution?Werner Ceusters, Kent Spackman & Barry Smith - 2007 - AMIA Annual Symposium Proceedings 2007:105-109.
    If SNOMED CT is to serve as a biomedical reference terminology, then steps must be taken to ensure comparability of information formulated using successive versions. New releases are therefore shipped with a history mechanism. We assessed the adequacy of this mechanism for its treatment of the distinction between changes occurring on the side of entities in reality and changes in our understanding thereof. We found that these two types are only partially distinguished and that a more detailed study is required (...)
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  47. Data Mining the Brain to Decode the Mind.Daniel Weiskopf - forthcoming - In Neural Mechanisms: New Challenges in the Philosophy of Neuroscience.
    In recent years, neuroscience has begun to transform itself into a “big data” enterprise with the importation of computational and statistical techniques from machine learning and informatics. In addition to their translational applications such as brain-computer interfaces and early diagnosis of neuropathology, these tools promise to advance new solutions to longstanding theoretical quandaries. Here I critically assess whether these promises will pay off, focusing on the application of multivariate pattern analysis (MVPA) to the problem of reverse inference. I argue (...)
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  48.  93
    Understanding the Human Genome Project: A Biographical Approach.Hub Zwart - 2008 - New Genetics and Society 27 (4):353 – 376.
    This article analyzes a number of recently published autobiographies by leading participants in the Human Genome Project (HGP), in order to determine to what extent they may further our understanding of the history, scientific significance and societal impact of this major research endeavor. Notably, I will focus on three publications that fall under this heading, namely The common thread by John Sulston (2002/2003), The language of God (2006) by Francis Collins and A life decoded by Craig Venter (2007).1 What may (...)
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  49. Bioinformatics Advances in Saliva Diagnostics.Ji-Ye Ai, Barry Smith & David T. W. Wong - 2012 - International Journal of Oral Science 4 (2):85--87.
    There is a need recognized by the National Institute of Dental & Craniofacial Research and the National Cancer Institute to advance basic, translational and clinical saliva research. The goal of the Salivaomics Knowledge Base (SKB) is to create a data management system and web resource constructed to support human salivaomics research. To maximize the utility of the SKB for retrieval, integration and analysis of data, we have developed the Saliva Ontology and SDxMart. This article reviews the informatics advances in (...)
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  50. 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 of a realist paradigm (...)
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