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Author: Peter N. Robinson Publisher: CRC Press ISBN: 1439836663 Category : Computers Languages : en Pages : 514
Book Description
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: Peter N. Robinson Publisher: CRC Press ISBN: 1439836663 Category : Computers Languages : en Pages : 514
Book Description
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: 9780470504963 Category : Medical Languages : en Pages : 400
Book Description
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: 2889192776 Category : Biotechnology Languages : en Pages : 107
Book Description
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: Category : Computers Languages : en Pages : 448
Book Description
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: Christophe Dessimoz Publisher: ISBN: 9781013267710 Category : Science Languages : en Pages : 298
Book Description
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: Katherine Munn Publisher: Walter de Gruyter ISBN: 3110324865 Category : Philosophy Languages : en Pages : 342
Book Description
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: Mihail Popescu Publisher: Artech House ISBN: 1596933712 Category : Medical Languages : en Pages : 279
Book Description
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: Francisco M. Couto Publisher: Springer ISBN: 3030138453 Category : Medical Languages : en Pages : 98
Book Description
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.
Author: Kevin Bretonnel Cohen Publisher: John Benjamins Publishing Company ISBN: 9027271062 Category : Computers Languages : en Pages : 174
Book Description
Biomedical Natural Language Processing is a comprehensive tour through the classic and current work in the field. It discusses all subjects from both a rule-based and a machine learning approach, and also describes each subject from the perspective of both biological science and clinical medicine. The intended audience is readers who already have a background in natural language processing, but a clear introduction makes it accessible to readers from the fields of bioinformatics and computational biology, as well. The book is suitable as a reference, as well as a text for advanced courses in biomedical natural language processing and text mining.
Author: Peter N. Robinson
Author: Peter N. Robinson
Author: Bijan Parsia
Author: John Hancock
Author: Kenneth Baclawski
Author: Christophe Dessimoz
Author: Katherine Munn
Author: Mihail Popescu
Author: Peter Karp
Author: Francisco M. Couto
Author: Kevin Bretonnel Cohen