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Biological Ontologies and Semantic Biology
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 ...
Building Ontologies with Basic Formal Ontology
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 appli...
The Oxford Handbook of Computational Linguistics
Ruslan Mitkov's highly successful Oxford Handbook of Computational Linguistics has been substantially revised and expanded in this second edition. Alongside updated accounts of the topics covered in the first edition, it includes 17 new chapters on subjects such as semantic role-labelling, text-to-speech synthesis, translation technology, opinion mining and sentiment analysis, and the application of Natural Language Processing in educational and biomedical contexts, among many others. The volume is divided into four parts that examine, respectively: the linguistic fundamentals of computational linguistics; the methods and resources used, such as statistical modelling, machine learning, and corpus annotation; key language processing tasks including text segmentation, anaphora resolution, and speech recognition; and the major applications of Natural Language Processing, from machine translation to author profiling. The book will be an essential reference for researchers and students in computational linguistics and Natural Language Processing, as well as those working in related industries.
Protein Bioinformatics
This volume introduces bioinformatics research methods for proteins, with special focus on protein post-translational modifications (PTMs) and networks. This book is organized into four parts and covers the basic framework and major resources for analysis of protein sequence, structure, and function; approaches and resources for analysis of protein PTMs, protein-protein interactions (PPIs) and protein networks, including tools for PPI prediction and approaches for the construction of PPI and PTM networks; and bioinformatics approaches in proteomics, including computational methods for mass spectrometry-based proteomics and integrative analysis for alternative splice isoforms, for functional ...
The Journal of Cell Biology
No. 2, pt. 2 of November issue each year from v. 19 (1963)-47 (1970) and v. 55 (1972)- contain the Abstracts of papers presented at the Annual Meeting of the American Society for Cell Biology, 3d (1963)-10th (1970) and 12th (1972)-
Biomedical Natural Language Processing
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.
MongoDB: The Definitive Guide
Manage the huMONGOus amount of data collected through your web application with MongoDB. This authoritative introduction—written by a core contributor to the project—shows you the many advantages of using document-oriented databases, and demonstrates how this reliable, high-performance system allows for almost infinite horizontal scalability. This updated second edition provides guidance for database developers, advanced configuration for system administrators, and an overview of the concepts and use cases for other people on your project. Ideal for NoSQL newcomers and experienced MongoDB users alike, this guide provides numerous real-world schema design examples. Get started with MongoD...
Radical SAM Enzymes
Radical SAM Enzymes, Volume 606, the latest release in the Methods in Enzymology series, highlights new advances in the field, with this new volume presenting interesting chapters on the Characterization of the glycyl radical enzyme choline trimethylamine-lyase and its radical S-adenosylmethionine activating enzyme, Diphathimide biosynthesis, Radical SAM glycyl radical activating enzymes, Radical SAM enzyme BioB in the biosynthesis of biotin, Biogenesis of the PQQ cofactor, Role of MoaAC in the biogenesis of the molybdenum cofactor, Biosynthesis of the nitrogenase cofactor, Bioinformatics of the radical SAM superfamily, The involvement of SAM radical enzymes in the biosynthesis of methanogenic coenzymes, methanopterin and coenzyme F420, and more.
The Fragment Molecular Orbital Method
Answering the need to facilitate quantum-chemical calculations of systems with thousands of atoms, Kazuo Kitaura and his coworkers developed the Fragment Molecular Orbital (FMO) method in 1999. Today, the FMO method can be applied to the study of whole proteins and protein-ligand interactions, and is extremely effective in calculating the propertie
