Bio Ontologies

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

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.

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.

This book introduces semantic representations of multiscale, multidomain physiological systems that link to qualitative reasoning and to quantitative analysis of biophysical processes in health and disease. Two major public health problems, diabetes and hypertension, serve as use-cases to illustrate the depth and rigor of such representations for logical inference and quantitative analysis. Central to this approach is the Ontology of Physics for Biology (OPB) that formally represents the foundations of classical physics and engineering system dynamics that are the basis for our understanding of biomedical entities, processes, and functional relationships. Furthermore, we introduce OPB-based software for annotating and abstracting available biosimulation models for reuse, recombination, and for archiving of physics-based biomedical knowledge. We have formalized and leveraged physics-based biological knowledge as a working view of physiology and biophysics from three distinct perspectives: (1) biologists and biomedical investigators, (2) biophysicists and bioengineers, and (3) biomedical ontologists and informaticists. We present a logical and intuitive semantics of classical physics as a tool for mediating and translating biophysical knowledge among biomedical domains. Daniel L. Cook, MD, PhD John H. Gennari, PhD Maxwell L. Neal, PhD

In recent decades, there has been a major shift in the way researchers process and understand scientific data. Digital access to data has revolutionized ways of doing science in the biological and biomedical fields, leading to a data-intensive approach to research that uses innovative methods to produce, store, distribute, and interpret huge amounts of data. In Data-Centric Biology, Sabina Leonelli probes the implications of these advancements and confronts the questions they pose. Are we witnessing the rise of an entirely new scientific epistemology? If so, how does that alter the way we study and understand life—including ourselves? Leonelli is the first scholar to use a study of contemporary data-intensive science to provide a philosophical analysis of the epistemology of data. In analyzing the rise, internal dynamics, and potential impact of data-centric biology, she draws on scholarship across diverse fields of science and the humanities—as well as her own original empirical material—to pinpoint the conditions under which digitally available data can further our understanding of life. Bridging the divide between historians, sociologists, and philosophers of science, Data-Centric Biology offers a nuanced account of an issue that is of fundamental importance to our understanding of contemporary scientific practices.

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

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.

Ontology was once understood to be the philosophical inquiry into the structure of reality: the analysis and categorization of ‘what there is’. Recently, however, a field called ‘ontology’ has become part of the rapidly growing research industry in information technology. The two fields have more in common than just their name. Theory and Applications of Ontology is a two-volume anthology that aims to further an informed discussion about the relationship between ontology in philosophy and ontology in information technology. It fills an important lacuna in cutting-edge research on ontology in both fields, supplying stage-setting overview articles on history and method, presenting directions of current research in either field, and highlighting areas of productive interdisciplinary contact. Theory and Applications of Ontology: Computer Applications presents ontology in ways that philosophers are not likely to find elsewhere. The volume offers an overview of current research in ontology, distinguishing basic conceptual issues, domain applications, general frameworks, and mathematical formalisms. It introduces the reader to current research on frameworks and applications in information technology in ways that are sure to invite reflection and constructive responses from ontologists in philosophy.