Biological Ontologies And Semantic Biology PDF Download
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| Author | : John Hancock |
| Publisher | : Frontiers Media SA |
| Total Pages | : 107 |
| Release | : 2014-10-03 |
| Genre | : Biotechnology |
| ISBN | : 2889192776 |
Download Biological Ontologies and Semantic Biology Book in PDF, ePub and Kindle
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 |
| Publisher | : CRC Press |
| Total Pages | : 514 |
| Release | : 2011-06-22 |
| Genre | : Computers |
| ISBN | : 1439836663 |
Download Introduction to Bio-Ontologies Book in PDF, ePub and Kindle
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 |
| Publisher | : Springer Science & Business Media |
| Total Pages | : 449 |
| Release | : 2007-04-14 |
| Genre | : Science |
| ISBN | : 0387484388 |
Download Semantic Web Book in PDF, ePub and Kindle
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 | : Albert Burger |
| Publisher | : Springer Science & Business Media |
| Total Pages | : 356 |
| Release | : 2007-12-20 |
| Genre | : Technology & Engineering |
| ISBN | : 1846288851 |
Download Anatomy Ontologies for Bioinformatics Book in PDF, ePub and Kindle
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 | : Bijan Parsia |
| Publisher | : Wiley |
| Total Pages | : 400 |
| Release | : 2013-03-25 |
| Genre | : Medical |
| ISBN | : 9780470504963 |
Download Bio-Ontologies Book in PDF, ePub and Kindle
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 | : Mihail Popescu |
| Publisher | : Artech House |
| Total Pages | : 279 |
| Release | : 2009 |
| Genre | : Medical |
| ISBN | : 1596933712 |
Download Data Mining in Biomedicine Using Ontologies Book in PDF, ePub and Kindle
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 | : Wyatt Travis Clark |
| Publisher | : Springer Science & Business Media |
| Total Pages | : 50 |
| Release | : 2014-01-09 |
| Genre | : Computers |
| ISBN | : 331904138X |
Download Information-Theoretic Evaluation for Computational Biomedical Ontologies Book in PDF, ePub and Kindle
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 | : Kenneth Baclawski |
| Publisher | : |
| Total Pages | : 448 |
| Release | : 2006 |
| Genre | : Computers |
| ISBN | : |
Download Ontologies for Bioinformatics Book in PDF, ePub and Kindle
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 | : |
| Total Pages | : 298 |
| Release | : 2020-10-08 |
| Genre | : Science |
| ISBN | : 9781013267710 |
Download The Gene Ontology Handbook Book in PDF, ePub and Kindle
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 | : Z. Sun |
| Publisher | : |
| Total Pages | : |
| Release | : 2009 |
| Genre | : |
| ISBN | : |
Download Using Ontology and Semantic Web Services to Support Modeling in Systems Biology Book in PDF, ePub and Kindle
This thesis addresses the problem of collaboration among experimental biologists and modelers in the study of systems biology by using ontology and Semantic Web Services techniques. Modeling in systems biology is concerned with using experimental information and mathematical methods to build quantitative models across different biological scales. This requires interoperation among various knowledge sources and services. Ontology and Semantic Web Services potentially provide an infrastructure to meet this requirement. In our study, we propose an ontology-centered framework within the Semantic Web infrastructure that aims at standardizing various areas of knowledge involved in the biological modeling processes. In this framework, first we specify an ontology-based meta-model for building biological models. This meta-model supports using shared biological ontologies to annotate biological entities in the models, allows semantic queries and automatic discoveries, enables easy model reuse and composition, and serves as a basis to embed external knowledge. We also develop means of transforming biological data sources and data analysis methods into Web Services. These Web Services can then be composed together to perform parameterization in biological modeling. The knowledge of decision-making and workflow of parameterization processes are then recorded by the semantic descriptions of these Web Services, and embedded in model instances built on our proposed meta-model. We use three cases of biological modeling to evaluate our framework. By examining our ontology-centered framework in practice, we conclude that by using ontology to represent biological models and using Semantic Web Services to standardize knowledge components in modeling processes, greater capabilities of knowledge sharing, reuse and collaboration can be achieved. We also conclude that ontology-based biological models with formal semantics are essential to standardize knowledge in compliance with the Semantic Web vision.
