Classification Made Relevant: How Scientists Build and Use Classifications and Ontologies explains how classifications and ontologies are designed and used to analyze scientific information. The book presents the fundamentals of classification, leading up to a description of how computer scientists use object-oriented programming languages to model classifications and ontologies. Numerous examples are chosen from the Classification of Life, the Periodic Table of the Elements, and the symmetry relationships contained within the Classification Theorem of Finite Simple Groups. When these three classifications are tied together, they provide a relational hierarchy connecting all of the natural sciences. The book's chapters introduce and describe general concepts that can be understood by any intelligent reader. With each new concept, they follow practical examples selected from various scientific disciplines. In these cases, technical points and specialized vocabulary are linked to glossary items where the item is clarified and expanded.

All too often, individuals engaged in the biomedical sciences assume that numeric data must be left to the proper authorities (e.g., statisticians and data analysts) who are trained to apply sophisticated mathematical algorithms to sets of data. This is a terrible mistake. Individuals with keen observational skills, regardless of their mathematical training, are in the best position to draw correct inferences from their own data and to guide the subsequent implementation of robust, mathematical analyses. Volume 2 of Logic and Critical Thinking in the Biomedical Sciences provides readers with a repertoire of deductive non-mathematical methods that will help them draw useful inferences from their own data. Volumes 1 and 2 of Logic and Critical Thinking in the Biomedical Sciences are written for biomedical scientists and college-level students engaged in any of the life sciences, including bioinformatics and related data sciences.

Taxonomic Guide to Infectious Diseases: Understanding the Biologic Classes of Pathogenic Organisms, Second Edition tackles the complexity of clinical microbiology by assigning every infectious organism to one of 40+ taxonomic classes and providing a description of the defining traits that apply to all the organisms within each class. This edition is an updated, revised and greatly expanded guide to the classes of organisms that infect humans. This book will provide students and clinicians alike with a simplified way to understand the complex fields of clinical microbiology and parasitology.

Data Simplification: Taming Information With Open Source Tools addresses the simple fact that modern data is too big and complex to analyze in its native form. Data simplification is the process whereby large and complex data is rendered usable. Complex data must be simplified before it can be analyzed, but the process of data simplification is anything but simple, requiring a specialized set of skills and tools. This book provides data scientists from every scientific discipline with the methods and tools to simplify their data for immediate analysis or long-term storage in a form that can be readily repurposed or integrated with other data. Drawing upon years of practical experience, and using numerous examples and use cases, Jules Berman discusses the principles, methods, and tools that must be studied and mastered to achieve data simplification, open source tools, free utilities and snippets of code that can be reused and repurposed to simplify data, natural language processing and machine translation as a tool to simplify data, and data summarization and visualization and the role they play in making data useful for the end user.

"Rare Diseases and Orphan Drugs" shows that much of what we now know about common diseases has been achieved by studying rare diseases. It proposes that future advances in the prevention, diagnosis, and treatment of common diseases will come as a consequence of our accelerating progress in the field of rare diseases.

Understanding the complex steps in the development of common diseases, such as cancer, cardiovascular disease, and metabolic diseases, has proven a difficult problem. Rare diseases, however, are often caused by aberrations of a single gene. In rare diseases, we may study how specific genetic defects can trigger a series of events that lead to the expression of a particular disease. Often, the disease process manifested in a certain rare disease is strikingly similar to the disease process observed in a common disease.

This work ties the lessons learned about rare diseases to our understanding of common ones. Chapters covering the number of common diseases are minimized, while rare diseases are introduced as single diseases or as members of diseases classes. After reading this book, readers will appreciate how further research into the rare diseases may lead to new methods for preventing, diagnosing, and treating all diseases, rare or common.
Makes rare diseases relevant to clinicians and researchers by tying lessons learned about the rare diseases to our understanding of the common diseasesStresses basic pathologic mechanisms that account for human disease (e.g., disorders of cell development, replication, maintenance, function and structure), that can be understood without prior training in pathologyDiscusses advanced concepts in molecular biology and genetics in a simple, functional context appropriate for medical trainees and new researchersOffers insights into how further research into rare diseases may lead to new methods for preventing, diagnosing, and treating all diseases.

Science is not a collection of facts. Science is the process by which we draw inferences from facts. Volume I of Logic and Critical Thinking in the Biomedical Sciences invites readers to linger over a collection of common observations to see what inferences can be drawn, when one applies a bit of deductive logic. If we just think about what we observe, it is often possible to discover profound biomedical insights. Volumes 1 and 2 of Logic and Critical Thinking in the Biomedical Sciences are written for biomedical scientists and college-level students engaged in any of the life sciences, including bioinformatics and related data sciences.

Despite what you may have read in the popular press and in social media, Precision Medicine is not devoted to finding unique treatments for individuals, based on analyzing their DNA. To the contrary, the goal of Precision Medicine is to find general treatments that are highly effective for large numbers of individuals who fall into precisely diagnosed groups. We now know that every disease develops over time, through a sequence of defined biological steps, and that these steps may differ among individuals, based on genetic and environmental conditions. We are currently developing rational therapies and preventive measures, based on our precise understanding of the steps leading to the clinical expression of diseases. Precision Medicine and the Reinvention of Human Disease explains the scientific breakthroughs that have changed the way that we understand diseases, and reveals how medical scientists are using this new knowledge to launch a medical revolution.

In the past few decades, there have been great advances in the phylogenetic classification of infectious diseases of man. "Taxonomic Guide to Infectious Diseases" organizes this information into a standard biological classification and provides a short, clinically-oriented description of every genus (class) of infectious organism. It covers an overview of modern taxonomy, including a description of the kingdoms of life and the evolutionary principles underlying the class hierarchy, and each following chapter will describe one phylum and the genera that contain infectious species. "Taxonomic Guide to Infectious Diseases" iswritten in an engaging, narrative style, providing the reader with an easy to digest yet clinically-oriented story of the pathogenic features of each genus. Designed for researchers, clinicians and students of infectious diseases, medical microbiology and pathology.
Offers genus-by-genus classification of infectious diseases along with short, clinically-oriented descriptions of each genusPresentscomprehensive lists of infectious species for each genera and identifies diseases caused by each speciesCompiled and written by a well-known pathologist with extensive experience in diagnosing human infectious diseases"

Evolution's Clinical Guidebook: Translating Ancient Genes into Precision Medicine demonstrates, through well-documented examples, how an understanding of the phylogenetic ancestry of humans allows us to make sense out of the flood of genetic data streaming from modern laboratories and how it can lead us to new ways to prevent, diagnose and treat diseases. Topics cover evolution and human genome, meiosis and other recombinants events, embryology, speciation, phylogeny, rare and common diseases, and the evolution of aging. This book is a valuable source for bioinformaticians and those in the biomedical field who need knowledge, down to gene level, to fully comprehend currently available data.

Repurposing Legacy Data: Innovative Case Studies takes a look at how data scientists have re-purposed legacy data, whether their own, or legacy data that has been donated to the public domain. Most of the data stored worldwide is legacy data-data created some time in the past, for a particular purpose, and left in obsolete formats. As with keepsakes in an attic, we retain this information thinking it may have value in the future, though we have no current use for it. The case studies in this book, from such diverse fields as cosmology, quantum physics, high-energy physics, microbiology, psychiatry, medicine, and hospital administration, all serve to demonstrate how innovative people draw value from legacy data. By following the case examples, readers will learn how legacy data is restored, merged, and analyzed for purposes that were never imagined by the original data creators.

Too often, healthcare workers are led to believe that medical informatics is a complex field that can only be mastered by teams of professional programmers. This is simply not the case. With just a few dozen simple algorithms, easily implemented with open source programming languages, you can fully utilize the medical information contained in clinical and research datasets. The common computational tasks of medical informatics are accessible to anyone willing to learn the basics. Methods in Medical Informatics: Fundamentals of Healthcare Programming in Perl, Python, and Ruby demonstrates that biomedical professionals with fundamental programming knowledge can master any kind of data collection. Providing you with access to data, nomenclatures, and programming scripts and languages that are all free and publicly available, this book - Describes the structure of data sources used, with instructions for downloading Includes a clearly written explanation of each algorithm Offers equivalent scripts in Perl, Python, and Ruby, for each algorithm Shows how to write short, quickly learned scripts, using a minimal selection of commands Teaches basic informatics methods for retrieving, organizing, merging, and analyzing data sources Provides case studies that detail the kinds of questions that biomedical scientists can ask and answer with public data and an open source programming language Requiring no more than a working knowledge of Perl, Python, or Ruby, Methods in Medical Informatics will have you writing powerful programs in just a few minutes. Within its chapters, you will find descriptions of the basic methods and implementations needed to complete many of the projects you will encounter in your biomedical career.

Principles and Practice of Big Data: Preparing, Sharing, and Analyzing Complex Information, Second Edition updates and expands on the first edition, bringing a set of techniques and algorithms that are tailored to Big Data projects. The book stresses the point that most data analyses conducted on large, complex data sets can be achieved without the use of specialized suites of software (e.g., Hadoop), and without expensive hardware (e.g., supercomputers). The core of every algorithm described in the book can be implemented in a few lines of code using just about any popular programming language (Python snippets are provided). Through the use of new multiple examples, this edition demonstrates that if we understand our data, and if we know how to ask the right questions, we can learn a great deal from large and complex data collections. The book will assist students and professionals from all scientific backgrounds who are interested in stepping outside the traditional boundaries of their chosen academic disciplines.

"Principles of Big Data" helps readers avoid the common mistakes that endanger all Big Data projects. By stressing simple, fundamental concepts, this book teaches readers how to organize large volumes of complex data, and how to achieve data permanence when the content of the data is constantly changing. General methods for data verification and validation, as specifically applied to Big Data resources, are stressed throughout the book. The book demonstrates how adept analysts can find relationships among data objects held in disparate Big Data resources, when the data objects are endowed with semantic support (i.e., organized in classes of uniquely identified data objects). Readers will learn how their data can be integrated with data from other resources, and how the data extracted from Big Data resources can be used for purposes beyond those imagined by the data creators.

Learn general methods for specifying Big Data in a way that is understandable to humans and to computers.

Avoid the pitfalls in Big Data design and analysis.

Understand how to create and use Big Data safely and responsibly with a set of laws, regulations and ethical standards that apply to the acquisition, distribution and integration of Big Data resources. "

Too often, healthcare workers are led to believe that medical informatics is a complex field that can only be mastered by teams of professional programmers. This is simply not the case. With just a few dozen simple algorithms, easily implemented with open source programming languages, you can fully utilize the medical information contained in clinical and research datasets. The common computational tasks of medical informatics are accessible to anyone willing to learn the basics. Methods in Medical Informatics: Fundamentals of Healthcare Programming in Perl, Python, and Ruby demonstrates that biomedical professionals with fundamental programming knowledge can master any kind of data collection. Providing you with access to data, nomenclatures, and programming scripts and languages that are all free and publicly available, this book - Describes the structure of data sources used, with instructions for downloading Includes a clearly written explanation of each algorithm Offers equivalent scripts in Perl, Python, and Ruby, for each algorithm Shows how to write short, quickly learned scripts, using a minimal selection of commands Teaches basic informatics methods for retrieving, organizing, merging, and analyzing data sources Provides case studies that detail the kinds of questions that biomedical scientists can ask and answer with public data and an open source programming language Requiring no more than a working knowledge of Perl, Python, or Ruby, Methods in Medical Informatics will have you writing powerful programs in just a few minutes. Within its chapters, you will find descriptions of the basic methods and implementations needed to complete many of the projects you will encounter in your biomedical career.