Oncology Informatics: Using Health Information Technology to Improve Processes and Outcomes in Cancer Care encapsulates National Cancer Institute-collected evidence into a format that is optimally useful for hospital planners, physicians, researcher, and informaticians alike as they collectively strive to accelerate progress against cancer using informatics tools. This book is a formational guide for turning clinical systems into engines of discovery as well as a translational guide for moving evidence into practice. It meets recommendations from the National Academies of Science to "reorient the research portfolio" toward providing greater "cognitive support for physicians, patients, and their caregivers" to "improve patient outcomes." Data from systems studies have suggested that oncology and primary care systems are prone to errors of omission, which can lead to fatal consequences downstream. By infusing the best science across disciplines, this book creates new environments of "Smart and Connected Health." Oncology Informatics is also a policy guide in an era of extensive reform in healthcare settings, including new incentives for healthcare providers to demonstrate "meaningful use" of these technologies to improve system safety, engage patients, ensure continuity of care, enable population health, and protect privacy. Oncology Informatics acknowledges this extraordinary turn of events and offers practical guidance for meeting meaningful use requirements in the service of improved cancer care. Anyone who wishes to take full advantage of the health information revolution in oncology to accelerate successes against cancer will find the information in this book valuable. Presents a pragmatic perspective for practitioners and allied health care professionals on how to implement Health I.T. solutions in a way that will minimize disruption while optimizing practice goals Proposes evidence-based guidelines for designers on how to create system interfaces that are easy to use, efficacious, and timesaving Offers insight for researchers into the ways in which informatics tools in oncology can be utilized to shorten the distance between discovery and practice

Cancer Informatics chronicles the development of the National Cancer Institute's new Cancer Informatics Infrastructure (CII) - an information management system infrastructure designed to faciliate clinical trials, provide for reliable, secure information exchange, and improve patient care. The book details the challenges involved in creating and managing such a knowledge base, including technologies, standards, and current, state-of-the-art applications. The ultimate goal of CII is to function as an enabler of clinical trials, expediting the clinical trials lifecycle, faciliating faster and safer drug development and more appropriate treatment choices for cancer patients. Contributors address the role the CII must play in converting the growing knowledge of genes, proteins, and pathways into appropriate preventative, diagnostic, and therapeutic measures. Presented in four sections, the first provides an overview of the processes involved in moving the infrastructure for cancer from theory into practice. Sections two through four offer the latest work done in the areas of technology, cancer-specific and national standards, and applications to faciliate clinical trials.

This second edition of a pioneering technical work in biomedical informatics provides a very readable treatment of the deep computational ideas at the foundation of the field. Principles of Biomedical Informatics, 2nd Edition is radically reorganized to make it especially useable as a textbook for courses that move beyond the standard introductory material. It includes exercises at the end of each chapter, ideas for student projects, and a number of new topics, such as:• tree structured data, interval trees, and time-oriented medical data and their use• On Line Application Processing (OLAP), an old database idea that is only recently coming of age and finding surprising importance in biomedical informatics• a discussion of nursing knowledge and an example of encoding nursing advice in a rule-based system• X-ray physics and algorithms for cross-sectional medical image reconstruction, recognizing that this area was one of the most central to the origin of biomedical computing• an introduction to Markov processes, and• an outline of the elements of a hospital IT security program, focusing on fundamental ideas rather than specifics of system vulnerabilities or specific technologies. It is simultaneously a unified description of the core research concept areas of biomedical data and knowledge representation, biomedical information access, biomedical decision-making, and information and technology use in biomedical contexts, and a pre-eminent teaching reference for the growing number of healthcare and computing professionals embracing computation in health-related fields. As in the first edition, it includes many worked example programs in Common LISP, the most powerful and accessible modern language for advanced biomedical concept representation and manipulation. The text also includes humor, history, and anecdotal material to balance the mathematically and computationally intensive development in many of the topic areas. The emphasis, as in the first edition, is on ideas and methods that are likely to be of lasting value, not just the popular topics of the day. Ira Kalet is Professor Emeritus of Radiation Oncology, and of Biomedical Informatics and Medical Education, at the University of Washington. Until retiring in 2011 he was also an Adjunct Professor in Computer Science and Engineering, and Biological Structure. From 2005 to 2010 he served as IT Security Director for the University of Washington School of Medicine and its major teaching hospitals. He has been a member of the American Medical Informatics Association since 1990, and an elected Fellow of the American College of Medical Informatics since 2011. His research interests include simulation systems for design of radiation treatment for cancer, software development methodology, and artificial intelligence applications to medicine, particularly expert systems, ontologies and modeling. - Develops principles and methods for representing biomedical data, using information in context and in decision making, and accessing information to assist the medical community in using data to its full potential - Provides a series of principles for expressing biomedical data and ideas in a computable form to integrate biological, clinical, and public health applications - Includes a discussion of user interfaces, interactive graphics, and knowledge resources and reference material on programming languages to provide medical informatics programmers with the technical tools to develop systems

view, showing that multiple molecular pathways must be affected for cancer to develop, but with different specific proteins in each pathway mutated or differentially expressed in a given tumor (The Cancer Genome Atlas Research Network 2008; Parsons et al. 2008). Different studies demonstrated that while widespread mutations exist in cancer, not all mutations drive cancer development (Lin et al. 2007). This suggests a need to target only a deleterious subset of aberrant proteins, since any tre- ment must aim to improve health to justify its potential side effects. Treatment for cancer must become highly individualized, focusing on the specific aberrant driver proteins in an individual. This drives a need for informatics in cancer far beyond the need in other diseases. For instance, routine treatment with statins has become widespread for minimizing heart disease, with most patients responding to standard doses (Wilt et al. 2004). In contrast, standard treatment for cancer must become tailored to the molecular phenotype of an individual tumor, with each patient receiving a different combination of therapeutics aimed at the specific aberrant proteins driving the cancer. Tracking the aberrations that drive cancers, identifying biomarkers unique to each individual for molecular-level di- nosis and treatment response, monitoring adverse events and complex dosing schedules, and providing annotated molecular data for ongoing research to improve treatments comprise a major biomedical informatics need.

Ideal for healthcare workers, students and biomedical researchers who wish to use informatics technologies in their own clinics and laboratories, Biomedical Informatics describes the fundamental issues and questions in the field and reviews the different types of biomedical data resources and open source tools needed to fully utilize biomedical data. You are shown how to navigate through the legal, ethical, and technical hazards of biomedical informatics to become self-sufficient and productive. You will finish with an understanding of how to acquire, organize, annotate, and share biomedical data, how to render confidential data harmless through de-identification, and how to use a variety of free and open source utilities to solve common computational tasks. Berman also discusses how the Perl Language is used in biomedical informatics and provides short Perl scripts that can be applied in the biological research and healthcare settings.

BIOMEDICAL DATA MINING FOR INFORMATION RETRIEVAL This book not only emphasizes traditional computational techniques, but discusses data mining, biomedical image processing, information retrieval with broad coverage of basic scientific applications. Biomedical Data Mining for Information Retrieval comprehensively covers the topic of mining biomedical text, images and visual features towards information retrieval. Biomedical and health informatics is an emerging field of research at the intersection of information science, computer science, and healthcare and brings tremendous opportunities and challenges due to easily available and abundant biomedical data for further analysis. The aim of healthcare informatics is to ensure the high-quality, efficient healthcare, better treatment and quality of life by analyzing biomedical and healthcare data including patient’s data, electronic health records (EHRs) and lifestyle. Previously, it was a common requirement to have a domain expert to develop a model for biomedical or healthcare; however, recent advancements in representation learning algorithms allows us to automatically to develop the model. Biomedical image mining, a novel research area, due to the vast amount of available biomedical images, increasingly generates and stores digitally. These images are mainly in the form of computed tomography (CT), X-ray, nuclear medicine imaging (PET, SPECT), magnetic resonance imaging (MRI) and ultrasound. Patients’ biomedical images can be digitized using data mining techniques and may help in answering several important and critical questions relating to healthcare. Image mining in medicine can help to uncover new relationships between data and reveal new useful information that can be helpful for doctors in treating their patients. Audience Researchers in various fields including computer science, medical informatics, healthcare IOT, artificial intelligence, machine learning, image processing, clinical big data analytics.

This collection of 25 research papers comprised of 22 original articles and 3 reviews is brought together from international leaders in bioinformatics and biostatistics. The collection highlights recent computational advances that improve the ability to analyze highly complex data sets to identify factors critical to cancer biology. Novel deep learning algorithms represent an emerging and highly valuable approach for collecting, characterizing and predicting clinical outcomes data. The collection highlights several of these approaches that are likely to become the foundation of research and clinical practice in the future. In fact, many of these technologies reveal new insights about basic cancer mechanisms by integrating data sets and structures that were previously immiscible. Accordingly, the series presented here bring forward a wide range of artificial intelligence approaches and statistical methods that can be applied to imaging and genomics data sets to identify previously unrecognized features that are critical for cancer. Our hope is that these articles will serve as a foundation for future research as the field of cancer biology transitions to integrating electronic health record, imaging, genomics and other complex datasets in order to develop new strategies that improve the overall health of individual patients.