XⅣ Preface to the Fourth Edition informatics is needed, then the requirement for trained faculty to teach the courses will be obvious. Some people might argue, however, that a course on this subject could be taught by a computer scientist who had an interest in biomedical computing, or by a physician or biologist who had taken a few computing courses. Indeed, in the past, most teaching-and research--has been undertaken by faculty trained primarily in one of the fields and later drawn to the other. Today, however, schools have come to realize the need for professionals trained specifically at the interfaces among biomedicine, bio- medical informatics, and related disciplines such as computer science, statis- tics, cognitive science, health economics, and medical ethics. This book outlines a first course for students training for careers in the biomedical infor- matics field. We specifically address the need for an educational experience in d information-science concepts are synthesized with bio- medical issues regarding research, training, and clinical practice. It is the inte gration of the related disciplines that traditionally has been lacking in the educational opportunities available to students with career interests in bio- medical informatics. If schools are to establish such courses and training pro- grams(and there are growing numbers of examples of each), they clearly need educators who have a broad familiarity with the field and who can develop curricula for students of the health professions as well as of informatics itself. The increasing introduction of computing techniques into biomedical envi ronments will require that well-trained individuals be available not only to teach students, but also to design, develop, select, and manage the biomedical- computing systems of tomorrow. There is a wide range of context-dependent omputing issues that people can appreciate only by working on problems defined by the healthcare setting and its constraints. The field's development has been hampered because there are relatively few trained personnel to design research programs, to carry out the experimental and developmental activities, nd to provide academic leadership in biomedical informatics. A frequently cited problem is the difficulty a health professional (or a biologist) and a techni ally trained computer scientist experience when they try to communicate with one another. The vocabularies of the two fields are complex and have little over- lap, and there is a process of acculturation to biomedicine that is difficult for computer scientists to appreciate through distant observation. Thus, interdisci- plinary research and development projects are more likely to be successful when they are led by people who can effectively bridge the biomedical and computing fields. Such professionals often can facilitate sensitive communication among program personnel whose backgrounds and training differ substantially It is exciting to be working in a field that is maturing and that is having a beneficial effect on society. There is ample opportunity remaining for innova- tion as new technologies evolve and fundamental computing problems succumb to the creativity and hard work of our colleagues. In light of the
xiv informatics is needed, then the requirement for trained faculty to teach the courses will be obvious. Some people might argue, however, that a course on this subject could be taught by a computer scientist who had an interest in biomedical computing, or by a physician or biologist who had taken a few computing courses. Indeed, in the past, most teaching—and research—has been undertaken by faculty trained primarily in one of the fi elds and later drawn to the other. Today, however, schools have come to realize the need for professionals trained specifi cally at the interfaces among biomedicine, biomedical informatics, and related disciplines such as computer science, statistics, cognitive science, health economics, and medical ethics. This book outlines a fi rst course for students training for careers in the biomedical informatics fi eld. We specifi cally address the need for an educational experience in which computing and information-science concepts are synthesized with biomedical issues regarding research, training, and clinical practice. It is the integration of the related disciplines that traditionally has been lacking in the educational opportunities available to students with career interests in biomedical informatics. If schools are to establish such courses and training programs (and there are growing numbers of examples of each), they clearly need educators who have a broad familiarity with the fi eld and who can develop curricula for students of the health professions as well as of informatics itself. The increasing introduction of computing techniques into biomedical environments will require that well-trained individuals be available not only to teach students, but also to design, develop, select, and manage the biomedicalcomputing systems of tomorrow. There is a wide range of context- dependent computing issues that people can appreciate only by working on problems defi ned by the healthcare setting and its constraints. The fi eld’s development has been hampered because there are relatively few trained personnel to design research programs, to carry out the experimental and developmental activities, and to provide academic leadership in biomedical informatics. A frequently cited problem is the diffi culty a health professional (or a biologist) and a technically trained computer scientist experience when they try to communicate with one another. The vocabularies of the two fi elds are complex and have little overlap, and there is a process of acculturation to biomedicine that is diffi cult for computer scientists to appreciate through distant observation. Thus, interdisciplinary research and development projects are more likely to be successful when they are led by people who can effectively bridge the biomedical and computing fi elds. Such professionals often can facilitate sensitive communication among program personnel whose backgrounds and training differ substantially. It is exciting to be working in a fi eld that is maturing and that is having a benefi cial effect on society. There is ample opportunity remaining for innovation as new technologies evolve and fundamental computing problems succumb to the creativity and hard work of our colleagues. In light of the Preface to the Fourth Edition
Preface to the fourth edition increasing sophistication and specialization required in computer science in general, it is hardly surprising that a new discipline should arise at that field interface with biomedicine. This book is dedicated to clarifying the definition and to nurturing the effectiveness of that discipline: biomedical informatics New York. NY Edward H. Shortliffe Bethesda. mD James j. cimino October 2013
xv increasing sophistication and specialization required in computer science in general, it is hardly surprising that a new discipline should arise at that fi eld’s interface with biomedicine. This book is dedicated to clarifying the defi nition and to nurturing the effectiveness of that discipline: biomedical informatics. New York, NY Edward H. Shortliffe Bethesda, MD James J. Cimino October 2013 Preface to the Fourth Edition
Acknowledgments In the 1980s, when I was based at Stanford University, I conferred with colleagues Larry Fagan and Gio Wiederhold and we decided to compile the first comprehen sive textbook on what was then called medical informatics. as it turned out none of us predicted the enormity of the task we were about to undertake Our challenge was to create a multi-authored textbook that captured the collective expertise of leaders in the field yet was cohesive in content and style. The concept for the book first developed in 1982. We had begun to teach a course on computer applications in health care at Stanford's School of Medicine and had quickly determined that there was no comprehensive introductory text on the subject. Despite several pub- lished collections of research descriptions and subject reviews, none had been developed with the needs of a rigorous introductory course in mind. The thought of writing a textbook was daunting due to the diversity of top- ics. None of us felt that he was sufficiently expert in the full range of impor- tant subjects for us to write the book ourselves. Yet we wanted to avoid putting together a collection of disconnected chapters containing assorted subject reviews. Thus, we decided to solicit contributions from leaders in the respective fields to be represented but to provide organizational guidelines advance for each chapter. We also urged contributors to avoid writing subject reviews but, instead, to focus on the key conceptual topics in their field and to pick a handful of examples to illustrate their didactic point As the draft chapters began to come in, we realized that major editing would be required if we were to achieve our goals of cohesiveness and a uniform orien tation across all the chapters. We were thus delighted when, in 1987, Leslie Perreault, a graduate of our training program, assumed responsibility for rework ing the individual chapters to make an integral whole and for bringing the project to completion. The final product, published in 1990, was the result of many compromises, heavy editing, detailed rewriting, and numerous iterations. We were gratified by the positive response to the book when it finally appeared, and especially by the students of biomedical informatics who have often come to at scientific meetings and told us about their appreciation of the book. As the 1990s progressed, however, we began to realize that, despite our aphasis on basic concepts in the field(rather than a survey of existing sys tems), the volume was beginning to show its age. A great deal had changed since the initial chapters were written, and it became clear that a new edition would be required. The original editors discussed the project and decided that we should redesign the book, solicit updated chapters, and publish a new edition. Leslie Perreault by this time was a busy Director at First Consulting
xvii In the 1980s, when I was based at Stanford University, I conferred with colleagues Larry Fagan and Gio Wiederhold and we decided to compile the fi rst comprehensive textbook on what was then called medical informatics. As it turned out, none of us predicted the enormity of the task we were about to undertake. Our challenge was to create a multi-authored textbook that captured the collective expertise of leaders in the fi eld yet was cohesive in content and style. The concept for the book fi rst developed in 1982. We had begun to teach a course on computer applications in health care at Stanford’s School of Medicine and had quickly determined that there was no comprehensive introductory text on the subject. Despite several published collections of research descriptions and subject reviews, none had been developed with the needs of a rigorous introductory course in mind. The thought of writing a textbook was daunting due to the diversity of topics. None of us felt that he was suffi ciently expert in the full range of important subjects for us to write the book ourselves. Yet we wanted to avoid putting together a collection of disconnected chapters containing assorted subject reviews. Thus, we decided to solicit contributions from leaders in the respective fi elds to be represented but to provide organizational guidelines in advance for each chapter. We also urged contributors to avoid writing subject reviews but, instead, to focus on the key conceptual topics in their fi eld and to pick a handful of examples to illustrate their didactic points. As the draft chapters began to come in, we realized that major editing would be required if we were to achieve our goals of cohesiveness and a uniform orientation across all the chapters. We were thus delighted when, in 1987, Leslie Perreault, a graduate of our training program, assumed responsibility for reworking the individual chapters to make an integral whole and for bringing the project to completion. The fi nal product, published in 1990, was the result of many compromises, heavy editing, detailed rewriting, and numerous iterations. We were gratifi ed by the positive response to the book when it fi nally appeared, and especially by the students of biomedical informatics who have often come to us at scientifi c meetings and told us about their appreciation of the book. As the 1990s progressed, however, we began to realize that, despite our emphasis on basic concepts in the fi eld (rather than a survey of existing systems), the volume was beginning to show its age. A great deal had changed since the initial chapters were written, and it became clear that a new edition would be required. The original editors discussed the project and decided that we should redesign the book, solicit updated chapters, and publish a new edition. Leslie Perreault by this time was a busy Director at First Consulting Acknowledgments
Acknowledgments Group in New York City and would not have as much time to devote to the project as she had when we did the first edition. With trepidation, in light of our knowledge of the work that would be involved, we embarked on the new As before, the chapter authors did a marvelous job, trying to meet our deadlines, putting up with editing changes that were designed to bring a uni- form style to the book, and contributing excellent chapters that nicely reflected the changes in the field in the preceding decade. No sooner had the second edition appeared in print than we started to get inquiries about when the next update would appear. We began to realize that the maintenance of a textbook in a field such as biomedical informatics was nearly a constant, ongoing process. By this time I had moved to Columbia University nd the initial group of editors had largely disbanded to take on other responsi- bilities, with Leslie Perreault no longer available. Accordingly, as plans for a third edition began to take shape, my Columbia colleague Jim Cimino joined me as the new associate editor, whereas Drs. Fagan, wiederhold, and Perreault ontinued to be involved as chapter authors. Once again the authors did their best to try to meet our deadlines as the third edition took shape. This time we lded several chapters, attempting to cover additional key topics that readers and authors had identified as being necessary enhancements to the earlier edi tions. We were once again extremely appreciative of all the authors'commit- ment and for the excellence of their work on behalf of the book and the field Predictably, it was only a short time after the publication of the third edi- tion that we began to get queries about a fourth edition. We resisted for a year or two but it became clear that the third edition was becoming rapidly stale in some key areas and that there were new topics that were not in the book and needed to be added. with that in mind we in consultation with grant weston from Springers offices in London, agreed to embark on a fourth edition. Progress was slowed by my professional moves(to Phoenix, Arizona, then Houston, Texas, and then back to New York) with a very busy three-year stint as President and ceo of the american medical Informatics association Similarly, Jim Cimino left Columbia to assume new responsibilities at the NIH Clinical Center in Bethesda, MD. With several new chapters in mind, and the need to change authors of some of the existing chapters due to retire- ments(this too will happen, even in a young field like informatics! ) we began working on the fourth edition, finally completing the effort in early 2013 The completed fourth edition reflects the work and support of many peo- ple in addition to the editors and chapter authors. Particular gratitude is owed to Maureen Alexander, our developmental editor whose rigorous attention to detail was crucial given the size and the complexity of the undertaking. At Springer we have been delighted to work on this edition with Grant Weston, who has been extremely supportive despite our missed deadlines. And I want to offer my sincere personal thanks to Jim Cimino, who has been a superb and talented collaborator in this effort for the last two editions without his hard work and expertise, we would still be struggling to complete the massive editing job associated with this now very long manuscript. New York. ny Edward h. shortliffe
xviii Group in New York City and would not have as much time to devote to the project as she had when we did the fi rst edition. With trepidation, in light of our knowledge of the work that would be involved, we embarked on the new project. As before, the chapter authors did a marvelous job, trying to meet our deadlines, putting up with editing changes that were designed to bring a uniform style to the book, and contributing excellent chapters that nicely refl ected the changes in the fi eld in the preceding decade. No sooner had the second edition appeared in print than we started to get inquiries about when the next update would appear. We began to realize that the maintenance of a textbook in a fi eld such as biomedical informatics was nearly a constant, ongoing process. By this time I had moved to Columbia University and the initial group of editors had largely disbanded to take on other responsibilities, with Leslie Perreault no longer available. Accordingly, as plans for a third edition began to take shape, my Columbia colleague Jim Cimino joined me as the new associate editor, whereas Drs. Fagan, Wiederhold, and Perreault continued to be involved as chapter authors. Once again the authors did their best to try to meet our deadlines as the third edition took shape. This time we added several chapters, attempting to cover additional key topics that readers and authors had identifi ed as being necessary enhancements to the earlier editions. We were once again extremely appreciative of all the authors’ commitment and for the excellence of their work on behalf of the book and the fi eld. Predictably, it was only a short time after the publication of the third edition that we began to get queries about a fourth edition. We resisted for a year or two but it became clear that the third edition was becoming rapidly stale in some key areas and that there were new topics that were not in the book and needed to be added. With that in mind we, in consultation with Grant Weston from Springer’s offi ces in London, agreed to embark on a fourth edition. Progress was slowed by my professional moves (to Phoenix, Arizona, then Houston, Texas, and then back to New York) with a very busy three-year stint as President and CEO of the American Medical Informatics Association. Similarly, Jim Cimino left Columbia to assume new responsibilities at the NIH Clinical Center in Bethesda, MD. With several new chapters in mind, and the need to change authors of some of the existing chapters due to retirements (this too will happen, even in a young fi eld like informatics!), we began working on the fourth edition, fi nally completing the effort in early 2013. The completed fourth edition refl ects the work and support of many people in addition to the editors and chapter authors. Particular gratitude is owed to Maureen Alexander, our developmental editor whose rigorous attention to detail was crucial given the size and the complexity of the undertaking. At Springer we have been delighted to work on this edition with Grant Weston, who has been extremely supportive despite our missed deadlines. And I want to offer my sincere personal thanks to Jim Cimino, who has been a superb and talented collaborator in this effort for the last two editions. Without his hard work and expertise, we would still be struggling to complete the massive editing job associated with this now very long manuscript. New York, NY Edward H. Shortliffe Acknowledgments
Contents Parti Recurrent Themes in Biomedical Informatics 1 Biomedical Informatics: The Science and the pragmatics Edward h. shortliffe and marsden s. blois 2 Biomedical Data: Their Acquisition, Storage, and Use Edward h. shortliffe and g. Octo barnett 3 Biomedical Decision Making: Probabilistic Clinical Reasoning Douglas K. Owens and Harold C. Sox 4 Cognitive Science and Biomedical Informatics Vimla l. patel and david. Kaufman 5 Computer Architectures for Health Care and Biomedicine.. 149 Jonathan C. silverstein and lan T. Foster 6 Software Engineering for Health Care and Biomedicine 185 Adam B. Wilcox, Scott P. Narus, and David K. Vawdrey 7 Standards in Biomedical Informatics W. Edward Hammond. Charles Jaffe James J. Cimino, and Stanley M. Huff 8 Natural Language Processing in Health Care and Biomedicine Carol friedman and Noemie elhadad 9 Biomedical Imaging Informatics Daniel L. Rubin, Hayit Greenspan and James F. Brinkley 10 Ethics in Biomedical and Health Informatics: Users, Standards, and Outcomes Kenneth w. Goodman, Reid Cushman, and Randolph A Miller 11 Evaluation of Biomedical and health Information Resources 355 Charles P. Friedman and Jeremy C. Wyatt
xix Contents Part I Recurrent Themes in Biomedical Informatics 1 Biomedical Informatics: The Science and the Pragmatics . . . . 3 Edward H. Shortliffe and Marsden S. Blois 2 Biomedical Data: Their Acquisition, Storage, and Use . . . . . . . 39 Edward H. Shortliffe and G. Octo Barnett 3 Biomedical Decision Making: Probabilistic Clinical Reasoning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67 Douglas K. Owens and Harold C. Sox 4 Cognitive Science and Biomedical Informatics . . . . . . . . . . . . . 109 Vimla L. Patel and David R. Kaufman 5 Computer Architectures for Health Care and Biomedicine . . . 149 Jonathan C. Silverstein and Ian T. Foster 6 Software Engineering for Health Care and Biomedicine . . . . . 185 Adam B. Wilcox, Scott P. Narus, and David K. Vawdrey 7 Standards in Biomedical Informatics . . . . . . . . . . . . . . . . . . . . . 211 W. Edward Hammond, Charles Jaffe, James J. Cimino, and Stanley M. Huff 8 Natural Language Processing in Health Care and Biomedicine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 255 Carol Friedman and Noémie Elhadad 9 Biomedical Imaging Informatics . . . . . . . . . . . . . . . . . . . . . . . . . 285 Daniel L. Rubin, Hayit Greenspan, and James F. Brinkley 10 Ethics in Biomedical and Health Informatics: Users, Standards, and Outcomes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 329 Kenneth W. Goodman, Reid Cushman, and Randolph A. Miller 11 Evaluation of Biomedical and Health Information Resources . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 355 Charles P. Friedman and Jeremy C. Wyatt