Introduction To Bio Ontologies

Author : Peter N. Robinson
Publisher : CRC Press
ISBN 13 : 1439836663
Total Pages : 514 pages
Book Rating : 4.68/5 ( download)

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Download or read book Introduction to Bio-Ontologies written by Peter N. Robinson and published by CRC Press. This book was released on 2011-06-22 with total page 514 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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 : Bijan Parsia
Publisher : Wiley
ISBN 13 : 9780470504963
Total Pages : 400 pages
Book Rating : 4.6X/5 ( download)

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Download or read book Bio-Ontologies written by Bijan Parsia and published by Wiley. This book was released on 2013-03-25 with total page 400 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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 : John Hancock
Publisher : Frontiers Media SA
ISBN 13 : 2889192776
Total Pages : 107 pages
Book Rating : 4.79/5 ( download)

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Download or read book Biological Ontologies and Semantic Biology written by John Hancock and published by Frontiers Media SA. This book was released on 2014-10-03 with total page 107 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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 : Kenneth Baclawski
Publisher :
ISBN 13 :
Total Pages : 448 pages
Book Rating : 4.78/5 ( download)

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Download or read book Ontologies for Bioinformatics written by Kenneth Baclawski and published by . This book was released on 2006 with total page 448 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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 : Katherine Munn
Publisher : Walter de Gruyter
ISBN 13 : 3110324865
Total Pages : 342 pages
Book Rating : 4.60/5 ( download)

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Download or read book Applied Ontology written by Katherine Munn and published by Walter de Gruyter. This book was released on 2013-05-02 with total page 342 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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 : Christophe Dessimoz
Publisher :
ISBN 13 : 9781013267710
Total Pages : 298 pages
Book Rating : 4.10/5 ( download)

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Download or read book The Gene Ontology Handbook written by Christophe Dessimoz and published by . This book was released on 2020-10-08 with total page 298 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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. This work was published by Saint Philip Street Press pursuant to a Creative Commons license permitting commercial use. All rights not granted by the work's license are retained by the author or authors.

Author : Robert Arp
Publisher : MIT Press
ISBN 13 : 026232959X
Total Pages : 245 pages
Book Rating : 4.90/5 ( 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 2015-08-28 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 : Paul Buitelaar
Publisher : IOS Press
ISBN 13 : 9781586035235
Total Pages : 188 pages
Book Rating : 4.31/5 ( download)

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Download or read book Ontology Learning from Text written by Paul Buitelaar and published by IOS Press. This book was released on 2005 with total page 188 pages. Available in PDF, EPUB and Kindle. Book excerpt: The latest title in Black Library's premium line. Perturabo - master of siegecraft, and executioner of Olympia. Long has he lived in the shadow of his more favoured primarch brothers, frustrated by the mundane and ignominious duties which regularly fall to his Legion. When Fulgrim offers him the chance to lead an expedition in search of an ancient and destructive xenos weapon, the Iron Warriors and the Emperor's Children unite and venture deep into the heart of the great warp-rift known only as 'the Eye'. Pursued by a ragged band of survivors from Isstvan V and the revenants of a dead eldar world, they must work quickly if they are to unleash the devastating power of the Angel Exterminatus

Author : Christopher J. O. Baker
Publisher : Springer Science & Business Media
ISBN 13 : 0387484388
Total Pages : 449 pages
Book Rating : 4.89/5 ( download)

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Download or read book Semantic Web written by Christopher J. O. Baker and published by Springer Science & Business Media. This book was released on 2007-04-14 with total page 449 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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 : Francisco M. Couto
Publisher : Springer
ISBN 13 : 3030138453
Total Pages : 98 pages
Book Rating : 4.55/5 ( download)

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Download or read book Data and Text Processing for Health and Life Sciences written by Francisco M. Couto and published by Springer. This book was released on 2019-06-10 with total page 98 pages. Available in PDF, EPUB and Kindle. Book excerpt: This open access book is a step-by-step introduction on how shell scripting can help solve many of the data processing tasks that Health and Life specialists face everyday with minimal software dependencies. The examples presented in the book show how simple command line tools can be used and combined to retrieve data and text from web resources, to filter and mine literature, and to explore the semantics encoded in biomedical ontologies. To store data this book relies on open standard text file formats, such as TSV, CSV, XML, and OWL, that can be open by any text editor or spreadsheet application. The first two chapters, Introduction and Resources, provide a brief introduction to the shell scripting and describe popular data resources in Health and Life Sciences. The third chapter, Data Retrieval, starts by introducing a common data processing task that involves multiple data resources. Then, this chapter explains how to automate each step of that task by introducing the required commands line tools one by one. The fourth chapter, Text Processing, shows how to filter and analyze text by using simple string matching techniques and regular expressions. The last chapter, Semantic Processing, shows how XPath queries and shell scripting is able to process complex data, such as the graphs used to specify ontologies. Besides being almost immutable for more than four decades and being available in most of our personal computers, shell scripting is relatively easy to learn by Health and Life specialists as a sequence of independent commands. Comprehending them is like conducting a new laboratory protocol by testing and understanding its procedural steps and variables, and combining their intermediate results. Thus, this book is particularly relevant to Health and Life specialists or students that want to easily learn how to process data and text, and which in return may facilitate and inspire them to acquire deeper bioinformatics skills in the future.