Biological Ontologies And Semantic Biology

Author : John Hancock
Publisher : Frontiers Media SA
Page : 107 pages
File Size : 45,6 Mb
Release : 2014-10-03
Category : Biotechnology
ISBN : 9782889192779

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Biological Ontologies and Semantic Biology by John Hancock Pdf

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.

Author : Peter N. Robinson,Sebastian Bauer
Publisher : CRC Press
Page : 514 pages
File Size : 47,5 Mb
Release : 2011-06-22
Category : Computers
ISBN : 9781439836668

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Introduction to Bio-Ontologies by Peter N. Robinson,Sebastian Bauer Pdf

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 importan

Author : Christopher J. O. Baker,Kei-Hoi Cheung
Publisher : Springer Science & Business Media
Page : 449 pages
File Size : 40,8 Mb
Release : 2007-04-14
Category : Science
ISBN : 9780387484389

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Semantic Web by Christopher J. O. Baker,Kei-Hoi Cheung Pdf

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.

Author : Bijan Parsia,Michel Dumontier
Publisher : Wiley
Page : 400 pages
File Size : 54,8 Mb
Release : 2013-03-25
Category : Medical
ISBN : 047050496X

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Bio-Ontologies by Bijan Parsia,Michel Dumontier Pdf

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.

Author : Daniel L. Cook,John H. Gennari,Maxwell L. Neal
Publisher : CRC Press
Page : 241 pages
File Size : 41,9 Mb
Release : 2023-12-15
Category : Science
ISBN : 9780429892332

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The Ontology of Physics for Biology by Daniel L. Cook,John H. Gennari,Maxwell L. Neal Pdf

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

Author : Albert Burger,Duncan Davidson,Richard Baldock
Publisher : Springer Science & Business Media
Page : 356 pages
File Size : 54,8 Mb
Release : 2007-12-20
Category : Technology & Engineering
ISBN : 9781846288852

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Anatomy Ontologies for Bioinformatics by Albert Burger,Duncan Davidson,Richard Baldock Pdf

This book provides a timely and first-of-its-kind collection of papers on anatomy ontologies. It is interdisciplinary in its approach, bringing together the relevant expertise from computing and biomedical studies. The book aims to provide readers with a comprehensive understanding of the foundations of anatomical ontologies and the-state-of-the-art in terms of existing tools and applications. It also highlights challenges that remain today.

Author : Mihail Popescu,Dong Xu
Publisher : Artech House
Page : 279 pages
File Size : 47,5 Mb
Release : 2009
Category : Medical
ISBN : 9781596933712

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Data Mining in Biomedicine Using Ontologies by Mihail Popescu,Dong Xu Pdf

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.

Author : Katherine Munn,Barry Smith
Publisher : Walter de Gruyter
Page : 342 pages
File Size : 47,7 Mb
Release : 2013-05-02
Category : Philosophy
ISBN : 9783110324860

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Applied Ontology by Katherine Munn,Barry Smith Pdf

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.

Author : Kenneth Baclawski,Tianhua Niu
Publisher : Unknown
Page : 448 pages
File Size : 44,5 Mb
Release : 2006
Category : Computers
ISBN : UOM:39015063182078

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Ontologies for Bioinformatics by Kenneth Baclawski,Tianhua Niu Pdf

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.

Author : Wyatt Travis Clark
Publisher : Springer Science & Business Media
Page : 50 pages
File Size : 51,6 Mb
Release : 2014-01-09
Category : Computers
ISBN : 9783319041384

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Information-Theoretic Evaluation for Computational Biomedical Ontologies by Wyatt Travis Clark Pdf

The development of effective methods for the prediction of ontological annotations is an important goal in computational biology, yet evaluating their performance is difficult due to problems caused by the structure of biomedical ontologies and incomplete annotations of genes. This work proposes an information-theoretic framework to evaluate the performance of computational protein function prediction. A Bayesian network is used, structured according to the underlying ontology, to model the prior probability of a protein's function. The concepts of misinformation and remaining uncertainty are then defined, that can be seen as analogs of precision and recall. Finally, semantic distance is proposed as a single statistic for ranking classification models. The approach is evaluated by analyzing three protein function predictors of gene ontology terms. The work addresses several weaknesses of current metrics, and provides valuable insights into the performance of protein function prediction tools.

Author : Anonim
Publisher : Unknown
Page : 128 pages
File Size : 44,8 Mb
Release : 2024-07-02
Category : Electronic
ISBN : 9781614998549

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by Anonim Pdf

Author : Marcello Barbieri
Publisher : Cambridge University Press
Page : 320 pages
File Size : 53,5 Mb
Release : 2003
Category : Medical
ISBN : 0521531004

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The Organic Codes by Marcello Barbieri Pdf

The genetic code appeared on Earth with the first cells. The codes of cultural evolution arrived almost four billion years later. These are the only codes that are recognized by modern biology. In this book, however, Marcello Barbieri explains that there are many more organic codes in nature, and their appearance not only took place throughout the history of life but marked the major steps of that history. A code establishes a correspondence between two independent 'worlds', and the codemaker is a third party between those 'worlds'. Therefore the cell can be thought of as a trinity of genotype, phenotype and ribotype. The ancestral ribotypes were the agents which gave rise to the first cells. The book goes on to explain how organic codes and organic memories can be used to shed new light on the problems encountered in cell signalling, epigenesis, embryonic development, and the evolution of language.

Author : Robert Arp,Barry Smith,Andrew D. Spear
Publisher : MIT Press
Page : 245 pages
File Size : 53,8 Mb
Release : 2015-08-28
Category : Science
ISBN : 9780262329590

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Building Ontologies with Basic Formal Ontology by Robert Arp,Barry Smith,Andrew D. Spear Pdf

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 : Sabina Leonelli
Publisher : University of Chicago Press
Page : 282 pages
File Size : 42,7 Mb
Release : 2016-11-18
Category : Science
ISBN : 9780226416502

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Data-Centric Biology by Sabina Leonelli Pdf

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.

Author : Christophe Dessimoz,Nives Škunca
Publisher : Humana
Page : 305 pages
File Size : 47,6 Mb
Release : 2018-06-23
Category : Science
ISBN : 1493981269

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The Gene Ontology Handbook by Christophe Dessimoz,Nives Škunca Pdf

This book is open access under a CC BY 4.0 license. This book provides a practical and self-contained overview of the Gene Ontology (GO), the leading project to organize biological knowledge on genes and their products across genomic resources. Written for biologists and bioinformaticians, it covers the state-of-the-art of how GO annotations are made, how they are evaluated, and what sort of analyses can and cannot be done with the GO. In the spirit of the Methods in Molecular Biology book series, there is an emphasis throughout the chapters on providing practical guidance and troubleshooting advice. Authoritative and accessible, The Gene Ontology Handbook serves non-experts as well as seasoned GO users as a thorough guide to this powerful knowledge system.