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

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.

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.

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.

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.

Download or read book An Introduction to Ontology Engineering written by C. Maria Keet and published by . This book was released on 2018-11-07 with total page 344 pages. Available in PDF, EPUB and Kindle. Book excerpt: An Introduction to Ontology Engineering introduces the student to a comprehensive overview of ontology engineering, and offers hands-on experience that illustrate the theory. The topics covered include: logic foundations for ontologies with languages and automated reasoning, developing good ontologies with methods and methodologies, the top-down approach with foundational ontologies, and the bottomup approach to extract content from legacy material, and a selection of advanced topics that includes Ontology-Based Data Access, the interaction between ontologies and natural languages, and advanced modelling with fuzzy and temporal ontologies. Each chapter contains review questions and exercises, and descriptions of two group assignments are provided as well. The textbook is aimed at advanced undergraduate/postgraduate level in computer science and could fi t a semester course in ontology engineering or a 2-week intensive course. Domain experts and philosophers may fi nd a subset of the chapters of interest, or work through the chapters in a different order. Maria Keet is an Associate Professor with the Department of Computer Science, University of Cape Town, South Africa. She received her PhD in Computer Science in 2008 at the KRDB Research Centre, Free University of Bozen-Bolzano, Italy. Her research focus is on knowledge engineering with ontologies and Ontology, and their interaction with natural language and conceptual data modelling, which has resulted in over 100 peer-reviewed publications. She has developed and taught multiple courses on ontology engineering and related courses at various universities since 2009.

Download or read book Encyclopedia of Bioinformatics and Computational Biology written by and published by Elsevier. This book was released on 2018-08-21 with total page 3421 pages. Available in PDF, EPUB and Kindle. Book excerpt: Encyclopedia of Bioinformatics and Computational Biology: ABC of Bioinformatics, Three Volume Set combines elements of computer science, information technology, mathematics, statistics and biotechnology, providing the methodology and in silico solutions to mine biological data and processes. The book covers Theory, Topics and Applications, with a special focus on Integrative –omics and Systems Biology. The theoretical, methodological underpinnings of BCB, including phylogeny are covered, as are more current areas of focus, such as translational bioinformatics, cheminformatics, and environmental informatics. Finally, Applications provide guidance for commonly asked questions. This major reference work spans basic and cutting-edge methodologies authored by leaders in the field, providing an invaluable resource for students, scientists, professionals in research institutes, and a broad swath of researchers in biotechnology and the biomedical and pharmaceutical industries. Brings together information from computer science, information technology, mathematics, statistics and biotechnology Written and reviewed by leading experts in the field, providing a unique and authoritative resource Focuses on the main theoretical and methodological concepts before expanding on specific topics and applications Includes interactive images, multimedia tools and crosslinking to further resources and databases

Download or read book Biomedical Natural Language Processing written by Kevin Bretonnel Cohen and published by John Benjamins Publishing Company. This book was released on 2014-02-15 with total page 174 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Semantic Similarity from Natural Language and Ontology Analysis written by Sébastien Harispe and published by Morgan & Claypool Publishers. This book was released on 2015-05-01 with total page 256 pages. Available in PDF, EPUB and Kindle. Book excerpt: Artificial Intelligence federates numerous scientific fields in the aim of developing machines able to assist human operators performing complex treatments---most of which demand high cognitive skills (e.g. learning or decision processes). Central to this quest is to give machines the ability to estimate the likeness or similarity between things in the way human beings estimate the similarity between stimuli. In this context, this book focuses on semantic measures: approaches designed for comparing semantic entities such as units of language, e.g. words, sentences, or concepts and instances defined into knowledge bases. The aim of these measures is to assess the similarity or relatedness of such semantic entities by taking into account their semantics, i.e. their meaning---intuitively, the words tea and coffee, which both refer to stimulating beverage, will be estimated to be more semantically similar than the words toffee (confection) and coffee, despite that the last pair has a higher syntactic similarity. The two state-of-the-art approaches for estimating and quantifying semantic similarities/relatedness of semantic entities are presented in detail: the first one relies on corpora analysis and is based on Natural Language Processing techniques and semantic models while the second is based on more or less formal, computer-readable and workable forms of knowledge such as semantic networks, thesauri or ontologies. Semantic measures are widely used today to compare units of language, concepts, instances or even resources indexed by them (e.g., documents, genes). They are central elements of a large variety of Natural Language Processing applications and knowledge-based treatments, and have therefore naturally been subject to intensive and interdisciplinary research efforts during last decades. Beyond a simple inventory and categorization of existing measures, the aim of this monograph is to convey novices as well as researchers of these domains toward a better understanding of semantic similarity estimation and more generally semantic measures. To this end, we propose an in-depth characterization of existing proposals by discussing their features, the assumptions on which they are based and empirical results regarding their performance in particular applications. By answering these questions and by providing a detailed discussion on the foundations of semantic measures, our aim is to give the reader key knowledge required to: (i) select the more relevant methods according to a particular usage context, (ii) understand the challenges offered to this field of study, (iii) distinguish room of improvements for state-of-the-art approaches and (iv) stimulate creativity toward the development of new approaches. In this aim, several definitions, theoretical and practical details, as well as concrete applications are presented

Download or read book Semantic Web for Effective Healthcare Systems written by Vishal Jain and published by John Wiley & Sons. This book was released on 2021-11-12 with total page 352 pages. Available in PDF, EPUB and Kindle. Book excerpt: SEMANTIC WEB FOR EFFECTIVE HEALTHCARE SYSTEMS The book summarizes the trends and current research advances in web semantics, delineating the existing tools, techniques, methodologies, and research solutions Semantic Web technologies have the opportunity to transform the way healthcare providers utilize technology to gain insights and knowledge from their data and make treatment decisions. Both Big Data and Semantic Web technologies can complement each other to address the challenges and add intelligence to healthcare management systems. The aim of this book is to analyze the current status on how the semantic web is used to solve health data integration and interoperability problems, and how it provides advanced data linking capabilities that can improve search and retrieval of medical data. Chapters analyze the tools and approaches to semantic health data analysis and knowledge discovery. The book discusses the role of semantic technologies in extracting and transforming healthcare data before storing it in repositories. It also discusses different approaches for integrating heterogeneous healthcare data. This innovative book offers: The first of its kind and highlights only the ontology driven information retrieval mechanisms and techniques being applied to healthcare as well as clinical information systems; Presents a comprehensive examination of the emerging research in areas of the semantic web; Discusses studies on new research areas including ontological engineering, semantic annotation and semantic sentiment analysis; Helps readers understand key concepts in semantic web applications for the biomedical engineering and healthcare fields; Includes coverage of key application areas of the semantic web. Audience: Researchers and graduate students in computer science, biomedical engineering, electronic and software engineering, as well as industry scientific researchers, clinicians, and systems managers in biomedical fields.

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 107 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.

Download or read book Sustainable Bioeconomy written by V. Venkatramanan and published by Springer Nature. This book was released on 2020-11-06 with total page 337 pages. Available in PDF, EPUB and Kindle. Book excerpt: Sustainable development is the most important challenge facing humanity in the 21st century. The global economic growth in the recent past has indeed exhibited marked progress in many countries. Nevertheless, the issues of income disparity, poverty, gender gaps, and malnutrition are not uncommon in the global landscape, in spite of the upward growth of the economy and technological advances. This grim picture is further exacerbated by our growing human population, unmindful resource use, ever-increasing consumption trends, and changing climate. In order to protect humanity and preserve the planet, the United Nations issued the “2030 agenda for sustainable development,” which includes but is not limited to sustainable production and consumption practices, e.g. in a sustainable bioeconomy. The hallmark of the sustainable bioeconomy is a paradigm shift from a fossil-fuel-based economy to a biological-based one, which is driven by the virtues of sustainability, efficient utilization of resources, and “circular economy.” As the sustainable bioeconomy is based on the efficient utilization of biological resources and societal transformations, it holds the immense potential to achieve the UN’s Sustainable Development Goals. This book shares valuable insights into the linkages between the sustainable bioeconomy and Sustainable Development Goals, making it an essential read for policymakers, researchers and students of environmental studies.

Download or read book Idea and Ontology written by Marc A. Hight and published by Penn State Press. This book was released on 2010-11 with total page 294 pages. Available in PDF, EPUB and Kindle. Book excerpt: "A wide-ranging study of the 'way of ideas' and its metaphysics, culminating in a bold reinterpretation of Berkeley."

Download or read book Introduction to Description Logic written by Franz Baader and published by Cambridge University Press. This book was released on 2017-04-20 with total page 264 pages. Available in PDF, EPUB and Kindle. Book excerpt: The first introductory textbook on description logics, relevant to computer science, knowledge representation and the semantic web.

Download or read book Handbook Of Metadata Semantics And Ontologies written by Miguel-angel Sicilia and published by World Scientific. This book was released on 2013-12-17 with total page 579 pages. Available in PDF, EPUB and Kindle. Book excerpt: Metadata research has emerged as a discipline cross-cutting many domains, focused on the provision of distributed descriptions (often called annotations) to Web resources or applications. Such associated descriptions are supposed to serve as a foundation for advanced services in many application areas, including search and location, personalization, federation of repositories and automated delivery of information. Indeed, the Semantic Web is in itself a concrete technological framework for ontology-based metadata. For example, Web-based social networking requires metadata describing people and their interrelations, and large databases with biological information use complex and detailed metadata schemas for more precise and informed search strategies.There is a wide diversity in the languages and idioms used for providing meta-descriptions, from simple structured text in metadata schemas to formal annotations using ontologies, and the technologies for storing, sharing and exploiting meta-descriptions are also diverse and evolve rapidly. In addition, there is a proliferation of schemas and standards related to metadata, resulting in a complex and moving technological landscape — hence, the need for specialized knowledge and skills in this area.The Handbook of Metadata, Semantics and Ontologies is intended as an authoritative reference for students, practitioners and researchers, serving as a roadmap for the variety of metadata schemas and ontologies available in a number of key domain areas, including culture, biology, education, healthcare, engineering and library science.

Download or read book Ontologies in Medicine written by Domenico M. Pisanelli and published by IOS Press. This book was released on 2004 with total page 186 pages. Available in PDF, EPUB and Kindle. Book excerpt: Title Page -- Contents -- If Ontology is the Solution, What is the Problem? -- Biodynamic Ontology: Applying BFO in the Biomedical Domain -- Bodily Systems and the Spatial-Functional Structure of the Human Body -- Inflammation Ontology Design Pattern: An Exercise in Building a Core Biomedical Ontology With Descriptions and Situations -- Context-Based Task Ontologies for Clinical Guidelines -- An Ontological Framework for the Implementation of Clinical Guidelines in Health Care Organizations -- Gene Ontology Application to Genomic Functional Annotation, Statistical Analysis and Knowledge Mining -- Evolving from Standard Vocabularies to Formal Ontology for an Information System Dedicated to Organ Transplantation -- Mistakes in Medical Ontologies: Where Do They Come From and How Can They Be Detected? -- Author Index

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.