Introduction To 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 importan
The Gene Ontology Handbook
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Author : Christophe Dessimoz
language : en
Publisher: Humana
Release Date : 2018-06-23
The Gene Ontology Handbook written by Christophe Dessimoz and has been published by Humana this book supported file pdf, txt, epub, kindle and other format this book has been release on 2018-06-23 with Science categories.
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.
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.
Handbook On Ontologies
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Author : Steffen Staab
language : en
Publisher: Springer Science & Business Media
Release Date : 2010-03-14
Handbook On Ontologies written by Steffen Staab 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 2010-03-14 with Computers categories.
An ontology is a formal description of concepts and relationships that can exist for a community of human and/or machine agents. The notion of ontologies is crucial for the purpose of enabling knowledge sharing and reuse. The Handbook on Ontologies provides a comprehensive overview of the current status and future prospectives of the field of ontologies considering ontology languages, ontology engineering methods, example ontologies, infrastructures and technologies for ontologies, and how to bring this all into ontology-based infrastructures and applications that are among the best of their kind. The field of ontologies has tremendously developed and grown in the five years since the first edition of the "Handbook on Ontologies". Therefore, its revision includes 21 completely new chapters as well as a major re-working of 15 chapters transferred to this second edition.
Building Ontologies With Basic Formal Ontology
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Author : Robert Arp
language : en
Publisher: MIT Press
Release Date : 2015-07-31
Building Ontologies With Basic Formal Ontology written by Robert Arp and has been published by MIT Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2015-07-31 with Science categories.
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.
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.
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.
Information Theoretic Evaluation For Computational Biomedical Ontologies
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Author : Wyatt Travis Clark
language : en
Publisher: Springer Science & Business Media
Release Date : 2014-01-09
Information Theoretic Evaluation For Computational Biomedical Ontologies written by Wyatt Travis Clark 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 2014-01-09 with Computers categories.
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.
Knowledge Engineering Practice And Patterns
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Author : Aldo Gangemi
language : en
Publisher: Springer
Release Date : 2008-09-22
Knowledge Engineering Practice And Patterns written by Aldo Gangemi and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2008-09-22 with Computers categories.
Knowledge is considered as the most important asset in our modern society. It has now penetrated all facets of computing practice: from the rise of knowledge management to the Semantic Web and from the blog culture to the knowledge economy. This penetration has made proper knowledge engineering a most - quired feature. This volume contains the papers presented at the 16th International C- ference on Knowledge Engineering and Knowledge Management (EKAW 2008) held in Acitrezza, Sicily, Italy, September 29 to October 3 2008. EKAW 2008 is concerned with all aspects of eliciting, acquiring, modelling and managing knowledge, and their role in the construction of knowledge-intensive systems and services for the Semantic Web, knowledge management, e-business, natural language processing, intelligent integration information, etc. This year we paid special attention to the topic of “knowledge patterns” that can be considered as good practice or models that are applied or reused throughout the knowledge engineering life cycle. Hence, beyond traditional t- icsofEKAW,wesolicitedpapersthatcoverresearchonhowtodescribe,classify, model, extract and apply knowledge patterns in the design of ontologies, app- cations and products. We have paid special attention to the description of ex- riences that involve the application and identi?cation of knowledge patterns in social network analysis, natural language processing, multimedia analysis, p- tern recognition, etc.
Rna Seq Data Analysis
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Author : Eija Korpelainen
language : en
Publisher: CRC Press
Release Date : 2014-09-19
Rna Seq Data Analysis written by Eija Korpelainen and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014-09-19 with Computers categories.
The State of the Art in Transcriptome AnalysisRNA sequencing (RNA-seq) data offers unprecedented information about the transcriptome, but harnessing this information with bioinformatics tools is typically a bottleneck. RNA-seq Data Analysis: A Practical Approach enables researchers to examine differential expression at gene, exon, and transcript le