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  1. added 2020-09-25
    Life, Local Constraints and Meaning Generation. An Evolutionary Approach to Cognition (2015).Christophe Menant - manuscript
    The relations between life and cogntion have been addressed through different perspectives [Stewart 1996, Boden 2001, Bourgine and Stewart 2004, van Duijn & all 2006, Di Paolo 2009]. We would like here to address that subject by relating life to cognition through a process of meaning generation. Life emerged on earth as a far from thermodynamic equilibrium performance that had to maintain herself. Life is charactertized by a ‘stay alive’ constraint that has to be satisfied (such constraint can be included (...)
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  2. added 2020-09-21
    Semiosis and Information: Meeting the Challenge of Information Science to Post-Reductionist Biosemiotics.Arran Gare - forthcoming - Biosemiotics:1-20.
    The concept of information and its relation to biosemiotics is a major area of contention among biosemioticians. Biosemioticians influenced by von Uexküll, Sebeok, Bateson and Peirce are critical of the way the concept as developed in information science has been applied to biology, while others believe that for biosemiotics to gain acceptance it will have to embrace information science and distance biosemiotics from Peirce’s philosophical work. Here I will defend the influence of Peirce on biosemiotics, arguing that information science and (...)
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  3. added 2020-09-13
    Coordinating Coronavirus Research: The COVID-19 Infectious Disease Ontology.John Beverley, Shane Babcock, Gustavo Carvalho, Lindsay Cowell, Sebastian Duesing, Regina Hurley & Barry Smith - 2020 - Open Science Foundation Preprints.
    Rapidly, accurately and easily interpreting generated data is of fundamental concern. Ontologies – structured controlled vocabularies – support interoperability and prevent the development of data silos which undermine interoperability. The Open Biological and Biomedical Ontologies (OBO) Foundry serves to ensure ontologies remain interoperable through adherence by its members to core ontology design principles. For example, the Infectious Disease Ontology (IDO) Core includes terminological content common to investigations of all infectious diseases. Ontologies covering more specific infectious diseases in turn extend from (...)
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  4. added 2020-09-11
    The History and Philosophy of Taxonomy as an Information Science.Catherine Kendig & Joeri Witteveen - 2020 - History and Philosophy of the Life Sciences 42 (3):1-9.
    We undeniably live in an information age—as, indeed, did those who lived before us. After all, as the cultural historian Robert Darnton pointed out: ‘every age was an age of information, each in its own way’ (Darnton 2000: 1). Darnton was referring to the news media, but his insight surely also applies to the sciences. The practices of acquiring, storing, labeling, organizing, retrieving, mobilizing, and integrating data about the natural world has always been an enabling aspect of scientific work. Natural (...)
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  5. added 2020-04-29
    Information-Matter Bipolarity of the Human Organism and Its Fundamental Circuits: From Philosophy to Physics/Neurosciences-Based Modeling.Florin Gaiseanu - 2020 - Philosophy Study 10 (2):107-118.
    Starting from a philosophical perspective, which states that the living structures are actually a combination between matter and information, this article presents the results on an analysis of the bipolar information-matter structure of the human organism, distinguishing three fundamental circuits for its survival, which demonstrates and supports this statement, as a base for further development of the informational model of consciousness to a general informational model of the human organism. For this, it was examined the Informational System of the Human (...)
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  6. added 2020-04-27
    The Infectious Disease Ontology in the Age of COVID-19.Shane Babcock, Lindsay G. Cowell, John Beverley & Barry Smith - 2020 - OSF Preprints.
    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 we (...)
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  7. added 2020-04-21
    Realitätsrepräsentation: Das Ziel der Ontologie.Barry Smith - 2008 - In Ludger Jansen & Barry Smith (eds.), Biomedizinische Ontologie. Philosophie – Lebenswissenschaften - Informationstechnik. Zurich: vdf (UTB Forum). pp. 31-46.
    The development of ontologies for the purposes of data curation is an important element in modern-day data and information sciences. Unfortunately, much of the work on these applied ontologies is associated with a relativist or conceptualist point of view, according to which ontologies represent (for example) the concepts in the minds of human beings. The paper describes a series of problems with such views, and defends an alternative realist interpretation.
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  8. added 2020-03-21
    Bridging the Gap Between Medical and Bioinformatics: An Ontological Case Study in Colon Carcinoma.Anand Kumar, Yum Lina Yip, Barry Smith & Pierre Grenon - 2006 - Computers in Biology and Medicine 36 (7):694--711.
    Ontological principles are needed in order to bridge the gap between medical and biological information in a robust and computable fashion. This is essential in order to draw inferences across the levels of granularity which span medicine and biology, an example of which include the understanding of the roles of tumor markers in the development and progress of carcinoma. Such information integration is also important for the integration of genomics information with the information contained in the electronic patient records in (...)
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  9. added 2020-01-06
    OHMI: The Ontology of Host-Microbiome Interactions.Yongqun He, Haihe Wang, Jie Zheng, Daniel P. Beiting, Anna Maria Masci, Hong Yu, Kaiyong Liu, Jianmin Wu, Jeffrey L. Curtis, Barry Smith, Alexander V. Alekseyenko & Jihad S. Obeid - 2019 - Journal of Biomedical Semantics 10 (1):1-14.
    Host-microbiome interactions (HMIs) are critical for the modulation of biological processes and are associated with several diseases, and extensive HMI studies have generated large amounts of data. We propose that the logical representation of the knowledge derived from these data and the standardized representation of experimental variables and processes can foster integration of data and reproducibility of experiments and thereby further HMI knowledge discovery. A community-based Ontology of Host-Microbiome Interactions (OHMI) was developed following the OBO Foundry principles. OHMI leverages established (...)
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  10. added 2019-10-10
    Adaptive Information and Animal Behaviour: Why Motorists Stop at Red Traffic Lights.Ronald W. Templeton & James Franklin - 1992 - Evolutionary Theory 10:145-155.
    Argues that information, in the animal behaviour or evolutionary context, is correlation/covariation. The alternation of red and green traffic lights is information because it is (quite strictly) correlated with the times when it is safe to drive through the intersection; thus driving in accordance with the lights is adaptive (causative of survival). Daylength is usefully, though less strictly, correlated with the optimal time to breed. Information in the sense of covariance implies what is adaptive; if an animal can infer what (...)
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  11. added 2019-07-21
    An Improved Ontological Representation of Dendritic Cells as a Paradigm for All Cell Types.Masci Anna Maria, N. Arighi Cecilia, D. Diehl Alexander, E. Lieberman Anne, Mungall Chris, H. Scheuermann Richard, Barry Smith & G. Cowell Lindsay - 2009 - BMC Bioinformatics 10 (1):70.
    The Cell Ontology (CL) is designed to provide a standardized representation of cell types for data annotation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL’s utility for cross-species data integration. To address this problem, we developed a method for the ontological representation of cells and applied this method to develop a (...)
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  12. added 2019-05-27
    The Plant Ontology Facilitates Comparisons of Plant Development Stages Across Species.Ramona Lynn Walls, Laurel Cooper, Justin Lee Elser, Maria Alejandra Gandolfo, Christopher J. Mungall, Barry Smith, Dennis William Stevenson & Pankaj Jaiswal - 2019 - Frontiers in Plant Science 10.
    The Plant Ontology (PO) is a community resource consisting of standardized terms, definitions, and logical relations describing plant structures and development stages, augmented by a large database of annotations from genomic and phenomic studies. This paper describes the structure of the ontology and the design principles we used in constructing PO terms for plant development stages. It also provides details of the methodology and rationale behind our revision and expansion of the PO to cover development stages for all plants, particularly (...)
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  13. added 2019-02-08
    Key Levels of Biocommunication.Guenther Witzany - 2016 - In R. Seckbach & J. Gordon (eds.), Biocommunication: Sign-mediated interactions between cells and organisms. Singapore: World Scientific. pp. 37-61.
    Organisms actively compete for environmental resources. They assess their surroundings, estimate how much energy they need for particular goals, and then realize the optimum variant. They take measures to control certain environmental resources. They perceive themselves and can distinguish between “self” and “non-self.” Current empirical data on all domains of life indicate that unicellular organisms such as bacteria, archaea, giant viruses, and protozoa as well as multicellular organisms such as animals, fungi, and plants coordinate and organize their essential life functions (...)
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  14. added 2019-01-08
    Six Questions on the Construction of Ontologies in Biomedicine.Anand Kumar, A. Burgun, W. Ceusters, J. Cimino, J. Davis, P. Elkin, I. Kalet, A. Rector, J. Rice, J. Rogers, Barry Smith & Others - 2005 - Report of the AMIA Working Group on Formal Biomedical Knowledge Representation 1.
    (Report assembled for the Workshop of the AMIA Working Group on Formal Biomedical Knowledge Representation in connection with AMIA Symposium, Washington DC, 2005.) Best practices in ontology building for biomedicine have been frequently discussed in recent years. However there is a range of seemingly disparate views represented by experts in the field. These views not only reflect the different uses to which ontologies are put, but also the experiences and disciplinary background of these experts themselves. We asked six questions related (...)
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  15. added 2018-12-17
    Homesteading the Noosphere: The Ethics of Owning Biological Information.Robert R. Wadholm - 2018 - Northern Plains Ethics Journal 6 (1):47-63.
    The idea of homesteading can be extended to the realm of biological entities, to the ownership of information wherein organisms perform artifactual functions as a result of human development. Can the information of biological entities be ethically “homesteaded”: should humans (or businesses) have ownership rights over this information from the basis of mere development and possession, as in Locke’s theory of private property? I offer three non-consequentialist arguments against such homesteading: the information makeup of biological entities is not commonly owned, (...)
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  16. added 2018-11-10
    Functional Anatomy: A Taxonomic Proposal.Ingvar Johansson, Barry Smith, Katherine Dormandy [nee Munn], Kathleen Elsner, Nikoloz Tsikolia & DIrk Siebert - 2005 - Acta Biotheoretica 53 (3):153-166.
    It is argued that medical science requires a classificatory system that (a) puts functions in the taxonomic center and (b) does justice ontologically to the difference between the processes which are the realizations of functions and the objects which are their bearers. We propose formulae for constructing such a system and describe some of its benefits. The arguments are general enough to be of interest to all the life sciences.
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  17. added 2018-10-19
    Causal Specificity, Biological Possibility and Non-Parity About Genetic Causes.Marcel Weber - manuscript
    Several authors have used the notion of causal specificity in order to defend non-parity about genetic causes (Waters 2007, Woodward 2010, Weber 2017, forthcoming). Non-parity in this context is the idea that DNA and some other biomolecules that are often described as information-bearers by biologists play a unique role in life processes, an idea that has been challenged by Developmental Systems Theory (e.g., Oyama 2000). Indeed, it has proven to be quite difficult to state clearly what the alleged special role (...)
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  18. added 2018-10-19
    The Central Dogma as a Thesis of Causal Specificity.Marcel Weber - 2006 - History and Philosophy of the Life Sciences 28 (4):595-610.
    I present a reconstruction of F.H.C. Crick's two 1957 hypotheses "Sequence Hypothesis" and "Central Dogma" in terms of a contemporary philosophical theory of causation. Analyzing in particular the experimental evidence that Crick cited, I argue that these hypotheses can be understood as claims about the actual difference-making cause in protein synthesis. As these hypotheses are only true if restricted to certain nucleic acids in certain organisms, I then examine the concept of causal specificity and its potential to counter claims about (...)
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  19. added 2018-08-30
    The Planteome Database: An Integrated Resource for Reference Ontologies, Plant Genomics and Phenomics.Laurel Cooper, Austin Meier, Marie-Angélique Laporte, Justin L. Elser, Chris Mungall, Brandon T. Sinn, Dario Cavaliere, Seth Carbon, Nathan A. Dunn, Barry Smith, Botong Qu, Justin Preece, Eugene Zhang, Sinisa Todorovic, Georgios Gkoutos, John H. Doonan, Dennis W. Stevenson, Elizabeth Arnaud & Pankaj Jaiswal - 2018 - Nucleic Acids Research 46 (D1):D1168–D1180.
    The Planteome project provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology, and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others. The project also provides (...)
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  20. added 2018-08-30
    Biomedical Ontology Alignment: An Approach Based on Representation Learning.Prodromos Kolyvakis, Alexandros Kalousis, Barry Smith & Dimitris Kiritsis - 2018 - Journal of Biomedical Semantics 9 (21).
    While representation learning techniques have shown great promise in application to a number of different NLP tasks, they have had little impact on the problem of ontology matching. Unlike past work that has focused on feature engineering, we present a novel representation learning approach that is tailored to the ontology matching task. Our approach is based on embedding ontological terms in a high-dimensional Euclidean space. This embedding is derived on the basis of a novel phrase retrofitting strategy through which semantic (...)
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  21. added 2018-07-26
    La réalité du champ axiologique : cybernétique et pensée de l'information chez Raymond Ruyer [The reality of the axiological field: Cybernetics and the thinking of information in Raymond Ruyer].Philippe Gagnon - 2018 - Louvain-la-Neuve: Chromatika.
    Description courte (Électre, 2019) : Une étude d'un des principaux axes de réflexion du philosophe des sciences et de la nature Raymond Ruyer (1902-1987). À la lumière des découvertes de l'embryogenèse et en s'appuyant par ailleurs sur la théorie de l'information, il proposa une interprétation des concepts unificateurs de la cybernétique mécaniste. -/- Short Descriptor (Electre 2019): A study of one of the main axes of reflection of the French philosopher of science and of nature Raymond Ruyer (1902-1987). Relying on (...)
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  22. added 2018-07-01
    Interdyscyplinarne Perspektywy Rozwoju, Integracji I Zastosowań Ontologii Poznawczych.Joanna Hastings, Gwen A. Frishkoff, Barry Smith, Mark Jensen, Russell A. Poldrack, Jane Lomax, Anita Bandrowski, Fahim Imam, Jessica A. Turner & Maryann E. Martone - 2016 - Avant: Trends in Interdisciplinary Studies 7 (3):101-117.
    We discuss recent progress in the development of cognitive ontologies and summarize three challenges in the coordinated development and application of these resources. Challenge 1 is to adopt a standardized definition for cognitive processes. We describe three possibilities and recommend one that is consistent with the standard view in cognitive and biomedical sciences. Challenge 2 is harmonization. Gaps and conflicts in representation must be resolved so that these resources can be combined for mark-up and interpretation of multi-modal data. Finally, Challenge (...)
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  23. added 2018-06-09
    ICBO 2009: Proceedings of the First International Conference on Biomedical Ontology.Barry Smith (ed.) - 2009 - Buffalo: NCOR.
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  24. added 2018-03-30
    Oncology Ontology in the NCI Thesaurus.Anand Kumar & Barry Smith - 2005 - Artificial Intelligence in Medicine:213-220.
    The National Cancer Institute’s Thesaurus (NCIT) has been created with the goal of providing a controlled vocabulary which can be used by specialists in the various sub-domains of oncology. It is intended to be used for purposes of annotation in ways designed to ensure the integration of data and information deriving from these various sub-domains, and thus to support more powerful cross-domain inferences. In order to evaluate its suitability for this purpose, we examined the NCIT’s treatment of the kinds of (...)
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  25. added 2018-03-30
    Ontologie-basierte Qualitätssicherung medizinischer Terminologien.Barry Smith - 2004 - Kooperative Versorgung, Vernetzte Forschung, Ubiquitäre Information, Proceedings of Gmds 2004:193-195.
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  26. added 2018-03-29
    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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  27. added 2018-03-29
    Novel Sequence Feature Variant Type Analysis of the HLA Genetic Association in Systemic Sclerosis.R. Karp David, Marthandan Nishanth, G. E. Marsh Steven, Ahn Chul, C. Arnett Frank, S. DeLuca David, D. Diehl Alexander, Dunivin Raymond, Eilbeck Karen, Feolo Michael & Barry Smith - 2009 - Human Molecular Genetics 19 (4):707-719.
    Significant associations have been found between specific human leukocyte antigen (HLA) alleles and organ transplant rejection, autoimmune disease development, and the response to infection. Traditional searches for disease associations have conventionally measured risk associated with the presence of individual HLA alleles. However, given the high level of HLA polymorphism, the pattern of amino acid variability, and the fact that most of the HLA variation occurs at functionally important sites, it may be that a combination of variable amino acid sites shared (...)
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  28. added 2018-03-29
    Foundation for the Electronic Health Record: An Ontological Analysis of the HL7 Reference Information Model.Lowell Vizenor, Barry Smith & Werner Ceusters - 2004 - In IFOMIS Reports. Saarbrücken: IFOMIS. pp. 1-14.
    Despite the recent advances in information and communication technology that have increased our ability to store and circulate information, the task remains of ensuring that the right sorts of information reach the right sorts of people. In what follows we defend the thesis that efforts to develop efficient means for sharing information across healthcare systems and organizations would benefit from a careful analysis of human action in healthcare organizations, and that the communication of healthcare information and knowledge needs to rest (...)
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  29. added 2018-03-18
    Vantagens e limitações das ontologias formais na área biomédica.Stefan Schulz, Holger Stenzhorn, Martin Boeker & Barry Smith - 2009 - RECIIS: Revista Electronica de Comunicacao Informacao, Inovacao Em Saude 3 (1).
    Propomos uma tipologia dos artefatos de representação para as áreas de saúde e ciências biológicas, e a associação dessa tipologia com diferentes tipos de ontologia formal e lógica, chegando a conclusões quanto aos pontos fortes e limitações da ontologia de diferentes tipos de recursos lógicos, enquanto mantemos o foco na lógica descritiva. Consideramos quatro tipos de representação de área: (i) representação léxico-semântica, (ii) representação de tipos de entidades, (iii) representação de conhecimento prévio, e (iv) representação de indivíduos. Defendemos uma clara (...)
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  30. added 2018-03-04
    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, Data (...)
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  31. added 2018-01-20
    A Peircean Approach to ‘Information’ and its Relationship with Bateson’s and Jablonka’s Ideas.Queiroz João, Emmeche Claus & El-Hani Charbel Niño - 2008 - American Journal of Semiotics 24 (1/3):75-94.
    The Peircean semiotic approach to information that we developed in previous papers raises several new questions, and shows both similarities and differences with regard to other accounts of information. We do not intend to present here any exhaustive discussion about the relationships between our account and other approaches to information. Rather, our interest is mainly to address its relationship to ideas about information put forward by Gregory Bateson and Eva Jablonka. We conclude that all these authors offer quite broad concepts (...)
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  32. added 2018-01-19
    The Biosemiotic Approach in Biology : Theoretical Bases and Applied Models.Joao Queiroz, Claus Emmeche, Kalevi Kull & Charbel El-Hani - 2011 - In George Terzis & Robert Arp (eds.), Information and Living Systems -- Philosophical and Scientific Perspectives. MIT Press. pp. 91-130.
    Biosemiotics is a growing fi eld that investigates semiotic processes in the living realm in an attempt to combine the fi ndings of the biological sciences and semiotics. Semiotic processes are more or less what biologists have typically referred to as “ signals, ” “ codes, ”and “ information processing ”in biosystems, but these processes are here understood under the more general notion of semiosis, that is, the production, action, and interpretation of signs. Thus, biosemiotics can be seen as biology (...)
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  33. added 2018-01-19
    A Semiotic Analysis of the Genetic Information.Charbel El-Hani, Joao Queiroz & Claus Emmeche - 2006 - Semiotica - Journal of the International Association for Semiotic Studies / Revue de l'Association Internationale de Sémiotique 1 (4):1-68.
    Terms loaded with informational connotations are often employed to refer to genes and their dynamics. Indeed, genes are usually perceived by biologists as basically ‘the carriers of hereditary information.’ Nevertheless, a number of researchers consider such talk as inadequate and ‘just metaphorical,’ thus expressing a skepticism about the use of the term ‘information’ and its derivatives in biology as a natural science. First, because the meaning of that term in biology is not as precise as it is, for instance, in (...)
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  34. added 2017-12-11
    Malaria Diagnosis and the Plasmodium Life Cycle: The BFO Perspective.Werner Ceusters & Barry Smith - 2010 - In Interdisciplinary Ontology. Proceedings of the Third Interdisciplinary Ontology Meeting. Tokyo: Keio University Press. pp. 25-34.
    Definitive diagnosis of malaria requires the demonstration through laboratory tests of the presence within the patient of malaria parasites or their components. Since malaria parasites can be present even in the absence of malaria manifestations, and since symptoms of malaria can be manifested even in the absence of malaria parasites, malaria diagnosis raises important issues for the adequate understanding of disease, etiology and diagnosis. One approach to the resolution of these issues adopts a realist view, according to which the needed (...)
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  35. added 2017-12-11
    Ontological Theory for Ontological Engineering: Biomedical Systems Information Integration.James M. Fielding, Jonathan Simon, Werner Ceusters & Barry Smith - 2004 - In Proceedings of the Ninth International Conference on the Principles of Knowledge Representation and Reasoning (KR2004), Whistler, BC, 2-5 June 2004. AMIA. pp. 114–120.
    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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  36. added 2017-12-09
    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 fact exist and (b) (...)
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  37. added 2017-12-09
    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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  38. added 2017-12-09
    Biomedizinische Ontologien für die Praxis.M. Brochhausen & Barry Smith - 2009 - European Journal for Biomedical Informatics 1.
    Hintergrund: Biomedizinische Ontologien existieren unter anderem zur Integration von klinischen und experimentellen Daten. Um dies zu erreichen ist es erforderlich, dass die fraglichen Ontologien von einer großen Zahl von Benutzern zur Annotation von Daten verwendet werden. Wie können Ontologien das erforderliche Maß an Benutzerfreundlichkeit, Zuverlässigkeit, Kosteneffektivität und Domänenabdeckung erreichen, um weitreichende Akzeptanz herbeizuführen? -/- Material und Methoden: Wir konzentrieren uns auf zwei unterschiedliche Strategien, die zurzeit hierbei verfolgt werden. Eine davon wird von SNOMED CT im Bereich der Medizin vertreten, die (...)
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  39. added 2017-12-09
    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 a (...)
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  40. added 2017-12-09
    Clonal Complexes in Biomedical Ontologies.Albert Goldfain, Lindsay Cowell & Barry Smith - 2009 - In ICBO 2009: Proceedings of the First International Conference on Biomedical Ontology. pp. 168.
    An accurate classification of bacteria is essential for the proper identification of patient infections and subsequent treatment decisions. Multi-Locus Sequence Typing (MLST) is a genetic technique for bacterial classification. MLST classifications are used to cluster bacteria into clonal complexes. Importantly, clonal complexes can serve as a biological species concept for bacteria, facilitating an otherwise difficult taxonomic classification. In this paper, we argue for the inclusion of terms relating to clonal complexes in biomedical ontologies.
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  41. added 2017-12-09
    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. Finally, (...)
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  42. added 2017-12-09
    Formal Ontology for Natural Language Processing and the Integration of Biomedical Databases.Jonathan Simon, James M. Fielding, Mariana C. Dos Santos & Barry Smith - 2005 - International Journal of Medical Informatics 75 (3-4):224-231.
    The central hypothesis of the collaboration between Language and Computing (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is that the methodology and conceptual rigor of a philosophically inspired formal ontology greatly benefits application ontologies. To this end r®, L&C’s ontology, which is designed to integrate and reason across various external databases simultaneously, has been submitted to the conceptual demands of IFOMIS’s Basic Formal Ontology (BFO). With this project we aim to move beyond the level of (...)
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  43. added 2017-12-09
    Dependence Relationships Between Gene Ontology Terms Based on TIGR Gene Product Annotations.Anand Kumar, Barry Smith & Christian Borgelt - 2004 - Proceedings of the 3rd International Workshop on Computational Terminology 2004:31-38.
    The Gene Ontology is an important tool for the representation and processing of information about gene products and functions. It provides controlled vocabularies for the designations of cellular components, molecular functions, and biological processes used in the annotation of genes and gene products. These constitute three separate ontologies, of cellular components), molecular functions and biological processes, respectively. The question we address here is: how are the terms in these three separate ontologies related to each other? We use statistical methods and (...)
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  44. added 2017-12-09
    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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  45. added 2017-12-08
    An Ontology-Based Methodology for the Migration of Biomedical Terminologies to Electronic Health Records.Barry Smith & Werner Ceusters - 2005 - In Proceedings of AMIA Symposium 2005, Washington DC,. Washington, DC: AMIA. pp. 704-708.
    Biomedical terminologies are focused on what is general, Electronic Health Records (EHRs) on what is particular, and it is commonly assumed that the step from the one to the other is unproblematic. We argue that this is not so, and that, if the EHR of the future is to fulfill its promise, then the foundations of both EHR architectures and biomedical terminologies need to be reconceived. We accordingly describe a new framework for the treatment of both generals and particulars in (...)
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  46. added 2017-12-06
    An Evolutionary Approach to the Representation of Adverse Events.Werner Ceusters, Maria Capolupo, Barry Smith & Georges De Moor - 2009 - Studies in Health Technology and Informatics 150:537-541.
    One way to detect, monitor and prevent adverse events with the help of Information Technology is by using ontologies capable of representing three levels of reality: what is the case, what is believed about reality, and what is represented. We report on how Basic Formal Ontology and Referent Tracking exhibit this capability and how they are used to develop an adverse event ontology and related data annotation scheme for the European ReMINE project.
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  47. added 2017-12-01
    A Semantic Approach for Knowledge Capture of microRNA-Target Gene Interactions.Jingshan Huang, Fernando Gutierrez, Dejing Dou, Judith A. Blake, Karen Eilbeck, Darren A. Natale, Barry Smith, Yu Lin, Xiaowei Wang & Zixing Liu - 2015 - In IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM 2015),. pp. 975-982.
    Research has indicated that microRNAs (miRNAs), a special class of non-coding RNAs (ncRNAs), can perform important roles in different biological and pathological processes. miRNAs’ functions are realized by regulating their respective target genes (targets). It is thus critical to identify and analyze miRNA-target interactions for a better understanding and delineation of miRNAs’ functions. However, conventional knowledge discovery and acquisition methods have many limitations. Fortunately, semantic technologies that are based on domain ontologies can render great assistance in this regard. In our (...)
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  48. added 2017-12-01
    A Domain Ontology for the Non-Coding RNA Field.Jingshan Huang, Karen Eilbeck, Judith A. Blake, Dejing Dou, Darren A. Natale, Alan Ruttenberg, Barry Smith, Michael T. Zimmermann, Guoqian Jiang & Yu Lin - 2015 - In IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM 2015). pp. 621-624.
    Identification of non-coding RNAs (ncRNAs) has been significantly enhanced due to the rapid advancement in sequencing technologies. On the other hand, semantic annotation of ncRNA data lag behind their identification, and there is a great need to effectively integrate discovery from relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a precisely defined ncRNA controlled vocabulary, which can fill a specific and highly needed niche in unification of ncRNA biology.
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  49. added 2017-12-01
    A Plant Disease Extension of the Infectious Disease Ontology.Ramona Walls, Barry Smith, Elser Justin, Goldfain Albert & W. Stevenson Dennis - 2012 - In Proceedings of the Third International Conference on Biomedical Ontology (CEUR 897). pp. 1-5.
    Plants from a handful of species provide the primary source of food for all people, yet this source is vulnerable to multiple stressors, such as disease, drought, and nutrient deficiency. With rapid population growth and climate uncertainty, the need to produce crops that can tolerate or resist plant stressors is more crucial than ever. Traditional plant breeding methods may not be sufficient to overcome this challenge, and methods such as highOthroughput sequencing and automated scoring of phenotypes can provide significant new (...)
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  50. added 2017-12-01
    A Framework for Protein Classification.Anand Kumar & Barry Smith - 2003 - In Proceedings of the 2003 German Conference on Bioinformatics, Vol. II. pp. 55-57.
    It is widely understood that protein functions can be exhaustively described in terms of no single parameter, whether this be amino acid sequence or the three-dimensional structure of the underlying protein molecule. This means that a number of different attributes must be used to create an ontology of protein functions. Certainly much of the required information is already stored in databases such as Swiss-Prot, Protein Data Bank, SCOP and MIPS. But the latter have been developed for different purposes and the (...)
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