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  1. Improving the Quality and Utility of Electronic Health Record Data through Ontologies.Asiyah Yu Lin, Sivaram Arabandi, Thomas Beale, William Duncan, Hicks D., Hogan Amanda, R. William, Mark Jensen, Ross Koppel, Catalina Martínez-Costa, Øystein Nytrø, Jihad S. Obeid, Jose Parente de Oliveira, Alan Ruttenberg, Selja Seppälä, Barry Smith, Dagobert Soergel, Jie Zheng & Stefan Schulz - 2023 - Standards 3 (3):316–340.
    The translational research community, in general, and the Clinical and Translational Science Awards (CTSA) community, in particular, share the vision of repurposing EHRs for research that will improve the quality of clinical practice. Many members of these communities are also aware that electronic health records (EHRs) suffer limitations of data becoming poorly structured, biased, and unusable out of original context. This creates obstacles to the continuity of care, utility, quality improvement, and translational research. Analogous limitations to sharing objective data in (...)
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  2.  20
    Entscheiden und Handeln am Krankenbett. Eine Online-Simulation im Blended-Learning-Format.Sebastian Kuhn, Stefan Schulz & Susanne Michl - 2022 - Ethik in der Medizin 34 (3):407-412.
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  3. Molecular Interactions. On the Ambiguity of Ordinary Statements in Biomedical Literature.Stefan Schulz & Ludger Jansen - 2009 - Applied ontology (4):21-34.
    Statements about the behavior of biochemical entities (e.g., about the interaction between two proteins) abound in the literature on molecular biology and are increasingly becoming the targets of information extraction and text mining techniques. We show that an accurate analysis of the semantics of such statements reveals a number of ambiguities that have to be taken into account in the practice of biomedical ontology engineering: Such statements can not only be understood as event reporting statements, but also as ascriptions of (...)
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  4.  7
    Patient-centered empirical research on ethically relevant psychosocial and cultural aspects of cochlear, glaucoma and cardiovascular implants – a scoping review.Sabine Schulz, Laura Harzheim, Constanze Hübner, Mariya Lorke, Saskia Jünger & Christiane Woopen - 2023 - BMC Medical Ethics 24 (1):1-22.
    Background The significance of medical implants goes beyond technical functioning and reaches into everyday life, with consequences for individuals as well as society. Ethical aspects associated with the everyday use of implants are relevant for individuals’ lifeworlds and need to be considered in implant care and in the course of technical developments. Methods This scoping review aimed to provide a synthesis of the existing evidence regarding ethically relevant psychosocial and cultural aspects in cochlear, glaucoma and cardiovascular implants in patient-centered empirical (...)
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  5. 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. Finally, (...)
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  6.  57
    BioTop: An upper domain ontology for the life sciencesA description of its current structure, contents and interfaces to OBO ontologies.Elena Beisswanger, Stefan Schulz, Holger Stenzhorn & Udo Hahn - 2008 - Applied ontology 3 (4):205-212.
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  7.  40
    Enhanced Cardiac Perception Is Associated With Increased Susceptibility to Framing Effects.Stefan Sütterlin, Stefan M. Schulz, Theresa Stumpf, Paul Pauli & Claus Vögele - 2013 - Cognitive Science 37 (5):922-935.
    Previous studies suggest in line with dual process models that interoceptive skills affect controlled decisions via automatic or implicit processing. The “framing effect” is considered to capture implicit effects of task-irrelevant emotional stimuli on decision-making. We hypothesized that cardiac awareness, as a measure of interoceptive skills, is positively associated with susceptibility to the framing effect. Forty volunteers performed a risky-choice framing task in which the effect of loss versus gain frames on decisions based on identical information was assessed. The results (...)
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  8. 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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  9.  23
    Consolidating SNOMED CT's ontological commitment.Stefan Schulz, Ronald Cornet & Kent Spackman - 2011 - Applied ontology 6 (1):1-11.
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  10.  15
    Automatic behavioural responses to valence: Evidence that facial action is facilitated by evaluative processing.Roland Neumann, Markus Hess, Stefan Schulz & Georg Alpers - 2005 - Cognition and Emotion 19 (4):499-513.
  11. Clinical ontologies interfacing the real world.Stefan Schulz, Holger Stenzhorn, Martin Boeker, Rüdiger Klar & Barry Smith - 2007 - In Schulz Stefan, Stenzhorn Holger, Boeker Martin, Klar Rüdiger & Smith Barry (eds.), Third International Conference on Semantic Technologies (i-semantics 2007), Graz, Austria. 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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  12.  19
    Effects of Guideline-Based Training on the Quality of Formal Ontologies: A Randomized Controlled Trial.M. Boeker, L. Jansen, J. Röhl, N. Grewe, D. Seddig-Raufie & S. Schulz - 2013 - PLoS ONE 1.
    BACKGROUND -/- The importance of ontologies in the biomedical domain is generally recognized. However, their quality is often too poor for large-scale use in critical applications, at least partially due to insufficient training of ontology developers. -/- OBJECTIVE -/- To show the efficacy of guideline-based ontology development training on the performance of ontology developers. The hypothesis was that students who received training on top-level ontologies and design patterns perform better than those who only received training in the basic principles of (...)
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  13. How to Distinguish Parthood from Location in Bioontologies.Stefan Schulz, Philipp Daumke, Barry Smith & Udo Hahn - 2005 - In Stefan Schulz, Philipp Daumke, Barry Smith & Udo Hahn (eds.), Proceedings of the AMIA Symposium. American Medical Informatics Association. pp. 669-673.
    The pivotal role of the relation part-of in the description of living organisms is widely acknowledged. Organisms are open systems, which means that in contradistinction to mechanical artifacts they are characterized by a continuous flow and exchange of matter. A closer analysis of the spatial relations in biological organisms reveals that the decision as to whether a given particular is part-of a second particular or whether it is only contained-in the second particular is often controversial. We here propose a rule-based (...)
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  14.  23
    SNOMED CT and Basic Formal Ontology – convergence or contradiction between standards? The case of “clinical finding”.Stefan Schulz, James T. Case, Peter Hendler, Daniel Karlsson, Michael Lawley, Ronald Cornet, Robert Hausam, Harold Solbrig, Karim Nashar, Catalina Martínez-Costa & Yongsheng Gao - 2023 - Applied ontology 18 (3):207-237.
    Background: SNOMED CT is a large terminology system designed to represent all aspects of healthcare. Its current form and content result from decades of bottom-up evolution. Due to SNOMED CT’s formal descriptions, it can be considered an ontology. The Basic Formal Ontology (BFO) is a foundational ontology that proposes a small set of disjoint, hierarchically ordered classes, supported by relations and axioms. In contrast, as a typical top-down endeavor, BFO was designed as a foundational framework for domain ontologies in the (...)
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  15. 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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  16. Anatomical information science.Barry Smith, Jose Mejino, Stefan Schulz, Anand Kumar & Cornelius Rosse - 2005 - In A. G. Cohn & D. M. Mark (eds.), Spatial Information Theory. Springer. pp. 149-164.
    The Foundational Model of Anatomy (FMA) is a map of the human body. Like maps of other sorts – including the map-like representations we find in familiar anatomical atlases – it is a representation of a certain portion of spatial reality as it exists at a certain (idealized) instant of time. But unlike other maps, the FMA comes in the form of a sophisticated ontology of its objectdomain, comprising some 1.5 million statements of anatomical relations among some 70,000 anatomical kinds. (...)
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  17. Using cross-lingual information to cope with underspecification in formal ontologies.Werner Ceusters, Ignace Desimpel, Barry Smith & Stefan Schulz - 2003 - Studies in Health Technology and Informatics 95:391-396.
    Description logics and other formal devices are frequently used as means for preventing or detecting mistakes in ontologies. Some of these devices are also capable of inferring the existence of inter-concept relationships that have not been explicitly entered into an ontology. A prerequisite, however, is that this information can be derived from those formal definitions of concepts and relationships which are included within the ontology. In this paper, we present a novel algorithm that is able to suggest relationships among existing (...)
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  18. Lmn-2 interacts with Elf-2. On the meaning of common statements in biomedical literature.Stefan Schulz & Ludger Jansen - 2006 - In KR-MED 2006 – Biomedical Ontology in Action. Proceedings of the 2nd International Workshop on Formal Knowledge Representation. MD. pp. 37-45.
    Statements about the behavior of biological entities, e.g. about the interaction between two proteins, abound in the literature on molecular biology and are increasingly becoming the targets of information extraction and text mining techniques. We show that an accurate analysis of the semantics of such statements reveals a number of ambiguities that is necessary to take into account in the practice of biomedical ontology engineering. Several concurring formalizations are proposed. Emphasis is laid on the discussion of biological dispositions.
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  19. Proceedings of the AMIA Symposium.Stefan Schulz, Philipp Daumke, Barry Smith & Udo Hahn (eds.) - 2005 - American Medical Informatics Association.
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  20.  22
    Proposed actions are no actions: Re-modelling an ontology design pattern with a realist top-level ontology.D. Seddig-Raufie, L. Jansen, S. Schulz, D. Schober & M. Boeker - 2012 - Journal of Biomedical Semantics 3 (2).
    Background -/- Ontology Design Patterns (ODPs) are representational artifacts devised to offer solutions for recurring ontology design problems. They promise to enhance the ontology building process in terms of flexibility, re-usability and expansion, and to make the result of ontology engineering more predictable. In this paper, we analyze ODP repositories and investigate their relation with upper-level ontologies. In particular, we compare the BioTop upper ontology to the Action ODP from the NeOn an ODP repository. In view of the differences in (...)
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  21.  36
    Teaching Good Biomedical Ontology Design.D. Seddig-Raufie, M. Boeker, S. Schulz, N. Grewe, J. Röhl, L. Jansen & D. Schober - 2012 - In Ronald Cornet & Robert Stevens (eds.), International Conference for Biomedical Ontologies (ICBO 2012), KR-MED Series, Graz, Austria July 21-25, 2012.
    Background: In order to improve ontology quality, tool- and language-related tutorials are not sufficient. Care must be taken to provide optimized curricula for teaching the representational language in the context of a semantically rich upper level ontology. The constraints provided by rigid top and upper level models assure that the ontologies built are not only logically consistent but also adequately represent the domain of discourse and align to explicitly outlined ontological principles. Finally such a curriculum must take into account the (...)
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  22.  34
    Interaktives Lernen: Ethik Online im Medizinstudium.Dennis Krämer, Stefan Schulz, Joschka Haltaufderheide, Esther Braun, Matthé Scholten & Jochen Vollmann - 2021 - Ethik in der Medizin 33 (3):405-408.
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  23.  14
    Definition und Evaluation einer Guideline zur Entwicklung von qualitativ guten Ontologien.M. Boeker, S. Schulz, D. Seddig-Raufie, D. Schober, J. Röhl, N. Grewe & L. Jansen - 2013 - GMDS 2013: 58. Jahrestagung der Deutschen Gesellschaft für Medizinische Informatik, Biometrie Und Epidemiologie E.V. (GMDS). Lübeck 1.
    Ontology engineering is mainly done by domain experts who are specialists in their domain but have, if at all, limited knowledge in logics, computer science, or analytic philosophy. The literature on formal ontologies and biomedical ontologies is neither suited nor intended to serve as an educational resource that would help domain experts to become good ontologists. Existing educational resources focus rather on ontology tools and languages than on good practice. The purpose of the GoodOD guideline is to pave the road (...)
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  24. Measuring the Effect of a Guideline-based Training on Ontology Design with a Competency Questions based Evaluation Approach.M. Boeker, N. Grewe, J. Röhl, D. Schober, S. Schulz, D. Seddig-Raufie & L. Jansen - 2013 - In M. Horbach (ed.), Informatik 2013. Informatik angepasst an Mensch, Organisation und Umwelt. pp. 1783-1795.
    OBJECTIVE: (a) To measure the effect of a guideline-based training on the performance of ontology developers compared with the performance after unspecific training by a competency question based evaluation; and (b) to provide empirical evidence for the applicability of competency questions in formal ontology evaluation in general. BACKGROUND: A close connection between ontology development and ontology evaluation as quality management procedure can been attained with the use of competency questions. Competency questions are often used as a semi-formal specification of requirements (...)
     
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  25. Semantic Applications in Life Sciences. Proceedings of the 4th International Workshop on Formal Biomedical Knowledge Representation, hosted by Bio-Ontologies 2010.Ronald Cornet & Stefan Schulz (eds.) - 2011
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  26.  16
    Modelling threshold phenomena in OWL: Metabolite concentrations as evidence for disorders.J. Hastings, L. Jansen, C. Steinbeck & S. Schulz - 2011 - In Michel Dumontier & Melanie Courtot (eds.), Proceedings of the 8th International Workshop on OWL: Experiences and Directions.
    While genomic and proteomic information describe the overall cellular machinery available to an organism, the metabolic profile of an individual at a given time provides a canvas as to the current physiological state. Concentration levels of relevant metabolites vary under different conditions, in particular, in the presence or absence of different disorders. Metabolite concentrations thus mediate an important link between chemistry and biology, contributing to a systems-wide understanding of biological processes and pathways. However, there are a number of challenges in (...)
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  27.  12
    Substance concentrations as conditions for the realization of dispositions.J. Hastings, L. Jansen, Stefan Schulz & C. Steinbeck - 2011 - In Ronald Cornet & Stefan Schulz (eds.), Semantic Applications in Life Sciences. Proceedings of the 4th International Workshop on Formal Biomedical Knowledge Representation, hosted by Bio-Ontologies 2010.
    Ontologies aim to represent what is general, by means of universal statements. In contrast, dispositional predications capture knowledge about what is likely to happen if a certain set of circumstances obtain, which is crucial in investigative research such as in drug discovery and systems biology, where entities which are constitutionally dissimilar can nevertheless have similar behavior in a biological context. While such dispositional properties are increasingly included in biomedical ontologies, the circumstances under which the dispositions are realized are seldom explicitly (...)
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  28.  13
    Foreword.Boris Konev, Renate Schmidt & Stephan Schulz - 2006 - Journal of Applied Non-Classical Logics 16 (1-2):7-8.
  29.  11
    Erratum zu: Entscheiden und Handeln am Krankenbett. Eine Online-Simulation im Blended-Learning-Format.Sebastian Kuhn, Stefan Schulz & Susanne Michl - 2022 - Ethik in der Medizin 34 (3):475-476.
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  30.  13
    Case Studies in Bioethics: Dialysis for Schizophrenia: Consent & Costs.S. Charles Schulz, Daniel P. Van Kammen & John C. Fletcher - 1979 - Hastings Center Report 9 (2):10.
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  31. Die Biomedizin Im Europa- Und Völkerrecht Eine Einführung in Internationale Instrumente, Prinzipien Und Regelungen der Humangenetik.Stefan F. Schulz - 2002 - Irp.
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  32.  20
    Empirically successful computerized reasoning.Renate A. Schmidt, Geoff Sutcliffe & Stephan Schulz - 2009 - Journal of Applied Logic 7 (1):1.
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  33.  20
    Formal ontologies in biomedical knowledge representation.S. Schulz & L. Jansen - 2013 - In M.-C. Jaulent, C. U. Lehmann & B. Séroussi (eds.), Yearbook of Medical Informatics 8. pp. 132-146.
    Objectives: Medical decision support and other intelligent applications in the life sciences depend on increasing amounts of digital information. Knowledge bases as well as formal ontologies are being used to organize biomedical knowledge and data. However, these two kinds of artefacts are not always clearly distinguished. Whereas the popular RDF(S) standard provides an intuitive triple-based representation, it is semantically weak. Description logics based ontology languages like OWL-DL carry a clear-cut semantics, but they are computationally expensive, and they are often misinterpreted (...)
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  34.  10
    Rezension: Patientenwege. Die Konsiliarkorrespondenz Lorenz Heisters in der Trew-Sammlung Erlangen von Marion Maria Ruisinger.Stefan Schulz - 2010 - Berichte Zur Wissenschaftsgeschichte 33 (2):211-212.
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  35.  12
    Systematically Defined Informative Priors in Bayesian Estimation: An Empirical Application on the Transmission of Internalizing Symptoms Through Mother-Adolescent Interaction Behavior.Susanne Schulz, Mariëlle Zondervan-Zwijnenburg, Stefanie A. Nelemans, Duco Veen, Albertine J. Oldehinkel, Susan Branje & Wim Meeus - 2021 - Frontiers in Psychology 12.
    BackgroundBayesian estimation with informative priors permits updating previous findings with new data, thus generating cumulative knowledge. To reduce subjectivity in the process, the present study emphasizes how to systematically weigh and specify informative priors and highlights the use of different aggregation methods using an empirical example that examined whether observed mother-adolescent positive and negative interaction behavior mediate the associations between maternal and adolescent internalizing symptoms across early to mid-adolescence in a 3-year longitudinal multi-method design.MethodsThe sample consisted of 102 mother-adolescent dyads. (...)
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  36.  7
    How versioning of terminology systems can be supported by ontological models – a case study on TNM tumor classification.Susanne Zabka, Stefan Schulz, Oliver Brunner & Martin Boeker - forthcoming - Applied ontology:1-20.
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