Formal Methods For The Analysis Of Biomedical Ontologies

Author : Guo-Qiang Zhang
Publisher : Springer Nature
ISBN 13 : 3031121317
Total Pages : 258 pages
Book Rating : 4.19/5 ( download)

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Download or read book Formal Methods for the Analysis of Biomedical Ontologies written by Guo-Qiang Zhang and published by Springer Nature. This book was released on 2022-11-08 with total page 258 pages. Available in PDF, EPUB and Kindle. Book excerpt: The book synthesizes research on the analysis of biomedical ontologies using formal concept analysis, including through auditing, curation, and enhancement. As the evolution of biomedical ontologies almost inevitably involves manual work, formal methods are a particularly useful tool for ontological engineering and practice, particularly in uncovering unexpected "bugs" and content materials. The book first introduces simple but formalized strategies for discovering undesired and incoherent patterns in ontologies before exploring the application of formal concept analysis for semantic completeness. The book then turns to formal concept analysis, a classical approach used in the mathematical treatment of orders and lattices, as an ontological engineering principle, focusing on the structural property of ontologies with respect to its conformation to lattice or not (non-lattice). The book helpfully covers the development of more efficient algorithms for non-lattice detection and extraction required by exhaustive lattice/non-lattice analysis. The book goes on to highlight the power and utility of uncovering non-lattice structure for debugging ontologies and describes methods that leverage the linguistic information in concept names (labels) for ontological analysis. It also addresses visualization and performance evaluation issues before closing with an overview and forward-looking perspectives on the field. This book is intended for graduate students and researchers interested in biomedical ontologies and their applications. It can be a useful supplement for courses on knowledge representation and engineering and also provide readers with a reference for related scientific publications and literature to assist in identifying potential research topics. All mathematical concepts and notations used in this book can be found in standard discrete mathematics textbooks, and the appendix at the end of the book provides a list of key ontological resources, as well as annotated non-lattice and lattice examples that were discovered using the authors' methods, demonstrating how "bugs are fixed" by converting non-lattices to lattices with minimal edit changes.

Author : Tiziana Margaria
Publisher : Springer
ISBN 13 : 3662452316
Total Pages : 661 pages
Book Rating : 4.18/5 ( download)

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Download or read book Leveraging Applications of Formal Methods, Verification and Validation. Specialized Techniques and Applications written by Tiziana Margaria and published by Springer. This book was released on 2014-09-26 with total page 661 pages. Available in PDF, EPUB and Kindle. Book excerpt: The two-volume set LNCS 8802 and LNCS 8803 constitutes the refereed proceedings of the 6th International Symposium on Leveraging Applications of Formal Methods, Verification and Validation, ISoLA 2014, held in Imperial, Corfu, Greece, in October 2014. The total of 67 full papers was carefully reviewed and selected for inclusion in the proceedings. Featuring a track introduction to each section, the papers are organized in topical sections named: evolving critical systems; rigorous engineering of autonomic ensembles; automata learning; formal methods and analysis in software product line engineering; model-based code generators and compilers; engineering virtualized systems; statistical model checking; risk-based testing; medical cyber-physical systems; scientific workflows; evaluation and reproducibility of program analysis; processes and data integration in the networked healthcare; semantic heterogeneity in the formal development of complex systems. In addition, part I contains a tutorial on automata learning in practice; as well as the preliminary manifesto to the LNCS Transactions on the Foundations for Mastering Change with several position papers. Part II contains information on the industrial track and the doctoral symposium and poster session.

Author : Yamine Ait-Ameur
Publisher : Springer Nature
ISBN 13 : 9811550549
Total Pages : 345 pages
Book Rating : 4.46/5 ( download)

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Download or read book Implicit and Explicit Semantics Integration in Proof-Based Developments of Discrete Systems written by Yamine Ait-Ameur and published by Springer Nature. This book was released on 2020-07-27 with total page 345 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book addresses mechanisms for reducing model heterogeneity induced by the absence of explicit semantics expression in the formal techniques used to specify design models. More precisely, it highlights the advances in handling both implicit and explicit semantics in formal system developments, and discusses different contributions expressing different views and perceptions on the implicit and explicit semantics. The book is based on the discussions at the Shonan meeting on this topic held in 2016, and includes contributions from the participants summarising their perspectives on the problem and offering solutions. Divided into 5 parts: domain modelling, knowledge-based modelling, proof-based modelling, assurance cases, and refinement-based modelling, and offers inspiration for researchers and practitioners in the fields of formal methods, system and software engineering, domain knowledge modelling, requirement analysis, and explicit and implicit semantics of modelling languages.

Author : Tiziana Margaria
Publisher : Springer
ISBN 13 : 3662452340
Total Pages : 564 pages
Book Rating : 4.49/5 ( download)

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Download or read book Leveraging Applications of Formal Methods, Verification and Validation. Technologies for Mastering Change written by Tiziana Margaria and published by Springer. This book was released on 2014-09-26 with total page 564 pages. Available in PDF, EPUB and Kindle. Book excerpt: The two-volume set LNCS 8802 and LNCS 8803 constitutes the refereed proceedings of the 6th International Symposium on Leveraging Applications of Formal Methods, Verification and Validation, ISoLA 2014, held in Imperial, Corfu, Greece, in October 2014. The total of 67 full papers was carefully reviewed and selected for inclusion in the proceedings. Featuring a track introduction to each section, the papers are organized in topical sections named: evolving critical systems; rigorous engineering of autonomic ensembles; automata learning; formal methods and analysis in software product line engineering; model-based code generators and compilers; engineering virtualized systems; statistical model checking; risk-based testing; medical cyber-physical systems; scientific workflows; evaluation and reproducibility of program analysis; processes and data integration in the networked healthcare; semantic heterogeneity in the formal development of complex systems. In addition, part I contains a tutorial on automata learning in practice; as well as the preliminary manifesto to the LNCS Transactions on the Foundations for Mastering Change with several position papers. Part II contains information on the industrial track and the doctoral symposium and poster session.

Author : Carola Eschenbach
Publisher : IOS Press
ISBN 13 : 1586039237
Total Pages : 340 pages
Book Rating : 4.33/5 ( download)

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Download or read book Formal Ontology in Information Systems written by Carola Eschenbach and published by IOS Press. This book was released on 2008 with total page 340 pages. Available in PDF, EPUB and Kindle. Book excerpt: "Since its start ten years ago, the International Conference in Formal Ontology on Information Systems (FOIS) has explored the multiple perspectives on the notion of ontology that have arisen from such diverse research communities as philosophy, logic, computer science, cognitive science, linguistics, and various scientific domains. As ontologies have been applied in new and exciting domains such as the World Wide Web, bioinformatics, and geographical information systems, it has become evident that there is a need for ontologies that have been developed with solid theoretical foundations based on philosophical, linguistic and logical analysis. Similarly, there is also a need for theoretical research that is driven by the issues that have been raised by recent work in the more applied domains. FOIS is intended to be a forum in which to explore this interplay between the theoretical insights of formal ontology and their application to information systems and emerging semantic technologies. Themes emerging from this volume give a snapshot of current issues within the fields of formal ontology and ontological engineering, as well providing a glimpse of future research directions."--BOOK JACKET.

Author : Sébastien Ferré
Publisher : Springer Science & Business Media
ISBN 13 : 3642018149
Total Pages : 350 pages
Book Rating : 4.45/5 ( download)

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Download or read book Formal Concept Analysis written by Sébastien Ferré and published by Springer Science & Business Media. This book was released on 2009-05-12 with total page 350 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the 7th International Conference on Formal Concept Analysis, ICFCA 2009, held in Darmstadt, Germany, in May 2009. The 15 revised full papers presented were carefully reviewed and selected from 29 submissions for inclusion in the book. The papers comprise state of the art research and present new results in Formal Concept Analysis and related fields. These results range from theoretical novelties to advances in FCA-related algorithmic issues, as well as application domains of FCA such as data visualization, information retrieval, machine learning, data analysis and knowledge management.

Author : R. Ferrario
Publisher : IOS Press
ISBN 13 : 1607504588
Total Pages : 144 pages
Book Rating : 4.80/5 ( download)

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Download or read book Formal Ontologies Meet Industry written by R. Ferrario and published by IOS Press. This book was released on 2009-08-21 with total page 144 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is a collection of papers addressing the multi-shaped character of knowledge, new studies and applications in the field of ontology and semantic technology. The semantic dimension of information plays an increasingly central role in a networked, knowledge-centred economy and the need to encode information into computer systems has led to a bias towards Knowledge Engineering (KE) solutions as opposed to Knowledge Management (KM). Although the intersection between KE and KM has led to a general improvement of information systems, the overlap between these two fields has tended to eclipse interest in genuine knowledge processes. For this reason, the fourth FOMI workshop was held to coincide with the 10th European Conference of Knowledge Management (ECKM), with the explicit aim of bringing together KR and KM (sub)-communities, providing a platform for discussion of these topics. Subjects covered include: the evolution of ontologies in accordance with the evolution of the domain they are designed for; the study of the notions of functional composition and decomposition; modular ontologies for architecture; ontology infrastructure for electromagnetics; ontology of beliefs; enterprise modelling; the application of ontology-based methodologies and techniques to knowledge management issues; ontologies for standards and domain ontologies for biomedicine. The double focus on methodological and applicative issues represents the main feature of these FOMI 2009 articles. This comprehensive perspective will advance progress towards new frontiers in information systems and knowledge management, where research and development in formal ontology will play a leading role.

Author : Robert Arp
Publisher : MIT Press
ISBN 13 : 0262527812
Total Pages : 245 pages
Book Rating : 4.11/5 ( download)

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Download or read book Building Ontologies with Basic Formal Ontology written by Robert Arp and published by MIT Press. This book was released on 2015-07-31 with total page 245 pages. Available in PDF, EPUB and Kindle. Book excerpt: An introduction to the field of applied ontology with examples derived particularly from biomedicine, covering theoretical components, design practices, and practical applications. 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 of particular relevance to biomedicine, covering theoretical components of ontologies, best practices for ontology design, and examples of biomedical ontologies in use. After defining an ontology as a representation of the types of entities in a given domain, the book distinguishes between different kinds of ontologies and taxonomies, and shows how applied ontology draws on more traditional ideas from metaphysics. It presents the core features of the Basic Formal Ontology (BFO), now used by over one hundred ontology projects around the world, and offers examples of domain ontologies that utilize BFO. The book also describes Web Ontology Language (OWL), a common framework for Semantic Web technologies. Throughout, the book provides concrete recommendations for the design and construction of domain ontologies.

Author : Antony Galton
Publisher : IOS Press
ISBN 13 : 1607505347
Total Pages : 444 pages
Book Rating : 4.41/5 ( download)

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Download or read book Formal Ontology in Information Systems written by Antony Galton and published by IOS Press. This book was released on 2010 with total page 444 pages. Available in PDF, EPUB and Kindle. Book excerpt: Ontology began life in ancient times as a fundamental part of philosophical enquiry concerned with the analysis and categorisation of what exists. In recent years, the subject has taken a practical turn with the advent of complex computerised information systems which are reliant on robust and coherent representations of their subject matter. The systematisation and elaboration of such representations and their associated reasoning techniques constitute the modern discipline of formal ontology, which is now being applied to such diverse domains as artificial intelligence, computational linguistics, bioinformatics, GIS, knowledge engineering, information retrieval and the Semantic Web. Researchers in all these areas are becoming increasingly aware of the need for serious engagement with ontology, understood as a general theory of the types of entities and relations making up their respective domains of enquiry, to provide a solid foundation for their work. The conference series Formal Ontology in Information Systems (FOIS) provides a meeting point for researchers from these and other disciplines with an interest in formal ontology, where both theoretical issues and concrete applications can be explored in a spirit of genuine interdisciplinarity. This volume contains the proceedings of the sixth FOIS conference, held in Toronto, Canada, during 11-14 May 2010, including invited talks by Francis Jeffry Pelletier, John Bateman, and Alan Rector and the 28 peer-reviewed submissions selected for presentation at the conference, ranging from foundational issues to more application-oriented topics. IOS Press is an international science, technical and medical publisher of high-quality books for academics, scientists, and professionals in all fields. Some of the areas we publish in: -Biomedicine -Oncology -Artificial intelligence -Databases and information systems -Maritime engineering -Nanotechnology -Geoengineering -All aspects of physics -E-governance -E-commerce -The knowledge economy -Urban studies -Arms control -Understanding and responding to terrorism -Medical informatics -Computer Sciences

Author : R. Ferrario
Publisher : IOS Press
ISBN 13 : 1614996601
Total Pages : 392 pages
Book Rating : 4.06/5 ( download)

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Download or read book Formal Ontology in Information Systems written by R. Ferrario and published by IOS Press. This book was released on 2016-07-06 with total page 392 pages. Available in PDF, EPUB and Kindle. Book excerpt: Ontology, originally a fundamental part of philosophical enquiry, is concerned with the analysis and categorization of what exists. The advent of complex information systems which rely on robust and coherent formal representations of their subject matter has led to a renewed focus on ontological enquiry, and the systematic study of such representations are at the center of the modern discipline of formal ontology. This is now a research focus in domains as diverse as conceptual modeling, database design, software engineering, artificial intelligence, computational linguistics, the life sciences, bioinformatics, geographic information science, knowledge engineering, information retrieval and the semantic web. This book presents the proceedings of the 9th edition of the Formal Ontology in Information Systems conference (FOIS 2016) held in Annecy, France, in July 2016. It contains the 25 full papers delivered at the conference (an acceptance rate of 30.9% for the main track), as well as the abstracts of the 3 keynotes by Gilberto Câmara, Stephen Mumford and Friederike Moltmann. The remainder of the book is divided into the sections: Foundations; Space, Time and Change; Cognition, Language and Semantics; Empiricism and Measurement; Ontology for Engineering; Biomedical Ontologies; and Ontology of Social Reality. The domains addressed by the papers include geography, biomedicine, economics, social reality and engineering, and the book will be of interest to all those working in these fields, as well as to anybody with an interest in formal ontology.