Bio Ontologies
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Introduction To Bio Ontologies
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Author : Peter N. Robinson
language : en
Publisher: CRC Press
Release Date : 2011-06-22
Introduction To Bio Ontologies written by Peter N. Robinson and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2011-06-22 with Computers categories.
Introduction to Bio-Ontologies explores the computational background of ontologies. Emphasizing computational and algorithmic issues surrounding bio-ontologies, this self-contained text helps readers understand ontological algorithms and their applications. The first part of the book defines ontology and bio-ontologies. It also explains the importance of mathematical logic for understanding concepts of inference in bio-ontologies, discusses the probability and statistics topics necessary for understanding ontology algorithms, and describes ontology languages, including OBO (the preeminent language for bio-ontologies), RDF, RDFS, and OWL. The second part covers significant bio-ontologies and their applications. The book presents the Gene Ontology; upper-level ontologies, such as the Basic Formal Ontology and the Relation Ontology; and current bio-ontologies, including several anatomy ontologies, Chemical Entities of Biological Interest, Sequence Ontology, Mammalian Phenotype Ontology, and Human Phenotype Ontology. The third part of the text introduces the major graph-based algorithms for bio-ontologies. The authors discuss how these algorithms are used in overrepresentation analysis, model-based procedures, semantic similarity analysis, and Bayesian networks for molecular biology and biomedical applications. With a focus on computational reasoning topics, the final part describes the ontology languages of the Semantic Web and their applications for inference. It covers the formal semantics of RDF and RDFS, OWL inference rules, a key inference algorithm, the SPARQL query language, and the state of the art for querying OWL ontologies. Web Resource Software and data designed to complement material in the text are available on the book’s website: http://bio-ontologies-book.org The site provides the R Robo package developed for the book, along with a compressed archive of data and ontology files used in some of the exercises. It also offers teaching/presentation slides and links to other relevant websites. This book provides readers with the foundation to use ontologies as a starting point for new bioinformatics research projects or to support current molecular genetics research projects. By supplying a self-contained introduction to OBO ontologies and the Semantic Web, it bridges the gap between both fields and helps readers see what each can contribute to the analysis and understanding of biomedical data.
Bio Ontologies
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Author : Bijan Parsia
language : en
Publisher: Wiley
Release Date : 2013-03-25
Bio Ontologies written by Bijan Parsia and has been published by Wiley this book supported file pdf, txt, epub, kindle and other format this book has been release on 2013-03-25 with Medical categories.
This invaluable book covers the opportunities and challenges in building HCLS ontologies and looks at state of the art and future opportunities. Primarily focused on OWL2, the most popular ontology language, it utilizes case studies to help illustrate lessons learned through concrete examples. The definitive guide for the design and use of expressive bio-ontologies compatible with the rapidly evolving Semantic Web, this book will be the go-to resource for practicing professionals and researchers in the field.
Biological Ontologies And Semantic Biology
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Author : John Hancock
language : en
Publisher: Frontiers Media SA
Release Date : 2014-10-03
Biological Ontologies And Semantic Biology written by John Hancock and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014-10-03 with Biotechnology categories.
As the amount of biological information and its diversity accumulates massively there is a critical need to facilitate the integration of this data to allow new and unexpected conclusions to be drawn from it. The Semantic Web is a new wave of web- based technologies that allows the linking of data between diverse data sets via standardised data formats (“big data”). Semantic Biology is the application of semantic web technology in the biological domain (including medical and health informatics). The Special Topic encompasses papers in this very broad area, including not only ontologies (development and applications), but also text mining, data integration and data analysis making use of the technologies of the Semantic Web. Ontologies are a critical requirement for such integration as they allow conclusions drawn about biological experiments, or descriptions of biological entities, to be understandable and integratable despite being contained in different databases and analysed by different software systems. Ontologies are the standard structures used in biology, and more broadly in computer science, to hold standardized terminologies for particular domains of knowledge. Ontologies consist of sets of standard terms, which are defined and may have synonyms for ease of searching and to accommodate different usages by different communities. These terms are linked by standard relationships, such as “is_a” (an eye “is_a” sense organ) or “part_of” (an eye is “part_of” a head). By linking terms in this way, more detailed, or granular, terms can be linked to broader terms, allowing computation to be carried out that takes these relationships into account.
Data Mining In Biomedicine Using Ontologies
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Author : Mihail Popescu
language : en
Publisher: Artech House
Release Date : 2009
Data Mining In Biomedicine Using Ontologies written by Mihail Popescu and has been published by Artech House this book supported file pdf, txt, epub, kindle and other format this book has been release on 2009 with Medical categories.
Presently, a growing number of ontologies are being built and used for annotating data in biomedical research. Thanks to the tremendous amount of data being generated, ontologies are now being used in numerous ways, including connecting different databases, refining search capabilities, interpreting experimental/clinical data, and inferring knowledge. This cutting-edge resource introduces you to latest developments in bio-ontologies. The book provides you with the theoretical foundations and examples of ontologies, as well as applications of ontologies in biomedicine, from molecular levels to clinical levels. You also find details on technological infrastructure for bio-ontologies. This comprehensive, one-stop volume presents a wide range of practical bio-ontology information, offering you detailed guidance in the clustering of biological data, protein classification, gene and pathway prediction, and text mining. More than 160 illustrations support key topics throughout the book.
Data Centric Biology
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Author : Sabina Leonelli
language : en
Publisher: University of Chicago Press
Release Date : 2016-11-18
Data Centric Biology written by Sabina Leonelli and has been published by University of Chicago Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016-11-18 with Science categories.
In recent decades, there has been a major shift in the way researchers process and understand scientific data. Digital access to data has revolutionized ways of doing science in the biological and biomedical fields, leading to a data-intensive approach to research that uses innovative methods to produce, store, distribute, and interpret huge amounts of data. In Data-Centric Biology, Sabina Leonelli probes the implications of these advancements and confronts the questions they pose. Are we witnessing the rise of an entirely new scientific epistemology? If so, how does that alter the way we study and understand life—including ourselves? Leonelli is the first scholar to use a study of contemporary data-intensive science to provide a philosophical analysis of the epistemology of data. In analyzing the rise, internal dynamics, and potential impact of data-centric biology, she draws on scholarship across diverse fields of science and the humanities—as well as her own original empirical material—to pinpoint the conditions under which digitally available data can further our understanding of life. Bridging the divide between historians, sociologists, and philosophers of science, Data-Centric Biology offers a nuanced account of an issue that is of fundamental importance to our understanding of contemporary scientific practices.
Ontologies For Bioinformatics
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Author : Kenneth Baclawski
language : en
Publisher:
Release Date : 2006
Ontologies For Bioinformatics written by Kenneth Baclawski and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2006 with Computers categories.
Ontologies as a critical framework for the vast amounts of data in the postgenomic era: an introduction to the basic concepts and applications of ontologies and ontology languages for the life sciences. Recent advances in biotechnology, spurred by the Human Genome Project, have resulted in the accumulation of vast amounts of new data. Ontologies--computer-readable, precise formulations of concepts (and the relationship among them) in a given field--are a critical framework for coping with the exponential growth of valuable biological data generated by high-output technologies. This book introduces the key concepts and applications of ontologies and ontology languages in bioinformatics and will be an essential guide for bioinformaticists, computer scientists, and life science researchers.The three parts of Ontologies for Bioinformatics ask, and answer, three pivotal questions: what ontologies are; how ontologies are used; and what ontologies could be (which focuses on how ontologies could be used for reasoning with uncertainty). The authors first introduce the notion of an ontology, from hierarchically organized ontologies to more general network organizations, and survey the best-known ontologies in biology and medicine. They show how to construct and use ontologies, classifying uses into three categories: querying, viewing, and transforming data to serve diverse purposes. Contrasting deductive, or Boolean, logic with inductive reasoning, they describe the goal of a synthesis that supports both styles of reasoning. They discuss Bayesian networks as a way of expressing uncertainty, describe data fusion, and propose that the World Wide Web can be extended to support reasoning with uncertainty. They call this inductive reasoning web the Bayesian web.
Semantic Web
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Author : Christopher J. O. Baker
language : en
Publisher: Springer Science & Business Media
Release Date : 2007-04-14
Semantic Web written by Christopher J. O. Baker and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2007-04-14 with Science categories.
This book introduces advanced semantic web technologies, illustrating their utility and highlighting their implementation in biological, medical, and clinical scenarios. It covers topics ranging from database, ontology, and visualization to semantic web services and workflows. The volume also details the factors impacting on the establishment of the semantic web in life science and the legal challenges that will impact on its proliferation.
Applied Ontology
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Author : Katherine Munn
language : en
Publisher: Walter de Gruyter
Release Date : 2013-05-02
Applied Ontology written by Katherine Munn and has been published by Walter de Gruyter this book supported file pdf, txt, epub, kindle and other format this book has been release on 2013-05-02 with Philosophy categories.
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 created them, and unable to serve as inputs for automated reasoning. This volume shows, in a non-technical way and using examples from medicine and biology, how the rigorous application of theories and insights from philosophical ontology can improve the ontologies upon which information management depends.
The Ontology Of Physics For Biology
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Author : Daniel L. Cook
language : en
Publisher: CRC Press
Release Date : 2023-12-15
The Ontology Of Physics For Biology written by Daniel L. Cook and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2023-12-15 with Science categories.
This book introduces semantic representations of multiscale, multidomain physiological systems that link to qualitative reasoning and to quantitative analysis of biophysical processes in health and disease. Two major public health problems, diabetes and hypertension, serve as use-cases to illustrate the depth and rigor of such representations for logical inference and quantitative analysis. Central to this approach is the Ontology of Physics for Biology (OPB) that formally represents the foundations of classical physics and engineering system dynamics that are the basis for our understanding of biomedical entities, processes, and functional relationships. Furthermore, we introduce OPB-based software for annotating and abstracting available biosimulation models for reuse, recombination, and for archiving of physics-based biomedical knowledge. We have formalized and leveraged physics-based biological knowledge as a working view of physiology and biophysics from three distinct perspectives: (1) biologists and biomedical investigators, (2) biophysicists and bioengineers, and (3) biomedical ontologists and informaticists. We present a logical and intuitive semantics of classical physics as a tool for mediating and translating biophysical knowledge among biomedical domains. Daniel L. Cook, MD, PhD John H. Gennari, PhD Maxwell L. Neal, PhD
Life And Process
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Author : Spyridon A. Koutroufinis
language : en
Publisher: Walter de Gruyter GmbH & Co KG
Release Date : 2014-05-21
Life And Process written by Spyridon A. Koutroufinis and has been published by Walter de Gruyter GmbH & Co KG this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014-05-21 with Philosophy categories.
Alfred North Whitehead is arguably the most original 20th-century philosopher of nature and metaphysics. In recent decades a number of physicists have produced ground-breaking new theories in fundamental physics influenced by his process philosophy. In contrast, few biologists are even aware that Whitehead’s radical rethinking of the Cartesian assumptions implicit in 19th-century sciences might be relevant to their enterprise. This book seeks to fill this gap by exploring how Whitehead’s process ontology might provide a new philosophical foundation for the biosciences of the 21st century. The central premise shared by all of the volume’s authors is the idea that all living processes are irreducible processes. Each chapter focuses on assumptions implicit in some of the core concepts of biology– such as organism, evolution, information, and teleology – that play crucial explanatory roles in the biosciences, but as metaphysical concepts fall outside its purview. The authors each identify important shortcomings implicit in contemporary biological paradigms and show how an approach grounded in a process-oriented metaphysics can avoid them.