Intensive Course in Biomedical Informatics

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Intensive Course in Biomedical Informatics
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Biomedical Informatics Overview Part 1An
Introduction to the Discipline
Edward H. Shortliffe, MD, PhD College of
Physicians and Surgeons Columbia University

• Intensive Course in Biomedical Informatics
• New York, New York
• May 23, 2005

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Some Questions for Discussion

• What is the field of biomedical informatics and
  how has it evolved from its early roots?
• What are its methods and research emphases?
• What are the opportunities for synergy between
  the biomedical informatics and the computational
  biology communities?

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Historical Perspective

• Computers in medicine emerged as a young
  discipline in the 1960s
• First NIH study section
• Most applications dealt with clinical issues
• No consistency in naming the field for many years
• Computer applications in medicine
• Medical information sciences
• Medical computer science
• Emergence in the 1980s of a single, consistent
  name, derived from the European (French) term for
  computer science informatique
• Medical Informatics

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The Last 20 Years

• NLM-supported medical informatics training
  programs at several universities (now 18
  programs)
• Application areas broadened in recent years to
  include biological sciences, imaging, and other
  biomedical domains
• Creation of professional societies, degree
  programs, quality scientific meetings, journals,
  and other indicators of a maturing scientific
  discipline
• Broadening of applications base, but with a
  growing tension between the fields service role
  and its fundamental research goals

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Whats in a Name?

• Medical informatics is the scientific field that
  deals with the storage, retrieval, sharing, and
  optimal use of biomedical information, data, and
  knowledge for problem solving and decision making.

Medical informatics touches on all basic and
applied fields in biomedical science and is
closely tied to modern information technologies,
notably in the areas of computing and
communication.
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Relationship of Medical Informatics and
Bioinformatics
Biological and Clinical Applications of
Interrelated Techniques and Methods Anticipation
of their Future Clinical Interdependencies
Medical Informatics
Bioinformatics
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The Biomedical Information Science and Technology
Initiative (BISTI)

• Identified the key role of computers and
  quantitative methods in the future of biology and
  biomedical research
• Called for training of a new kind of biologist
  (and a new kind of computer scientist)
• Called for the creation of centers of excellence
  in biocomputation
• Led to broad interest in biological applications
  of computing across NIH and in the biomedical
  research community
• Led to a tendency to refer to the entire field as
  bioinformatics, with resulting confusion in
  environments where informatics units had predated
  this trend

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Terminology Issues Abound(after NCRR Advisory
Council - 2000)

• Biomedical Computing 1. The application and
  development of computer methods for biomedical
  research.
• Computational Biology2. A subfield of biology
  involving the computer analysis of biological
  data.3. The application and development of
  computer methods for biological research.4. The
  application and development of mathematical and
  algorithmic computer methods for biological
  research.
• Bioinformatics5. The application and
  development of computer methods for biological
  research.6. The application and development of
  computer methods for genomics and molecular
  biology.7. The application and development of
  database-related computer methods for biological
  research.

Medical Informatics?
Biomedical Informatics?
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Biomedical Informatics

• The scientific field that deals with the storage,
  retrieval, sharing, and optimal use of biomedical
  information, data, and knowledge for problem
  solving and decision making.

Biomedical informatics touches on all basic and
applied fields in biomedical science and is
closely tied to modern information technologies,
notably in the areas of computing and
communication.
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Recent Announcement
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Biomedical Informatics in Perspective
Biomedical Informatics Methods, Techniques, and
Theories
Basic Research
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Biomedical Informatics in Perspective
Biomedical Informatics Methods, Techniques, and
Theories
Basic Research
Imaging Informatics
Clinical Informatics
Public Health Informatics
Bioinformatics
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Journal of Biomedical Informatics

• Formerly Computers and Biomedical Research
• Volume 38 in 2005
• Emphasizes methodologic innovation rather than
  applications, although all innovations are
  motivated by applied biomedical goals

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Biomedical Informatics in Perspective
Biomedical Informatics Methods, Techniques, and
Theories
Basic Research
Natural Language Processing
Database Theory
Cognitive Science
Math Modeling
Statistics
Data Mining
Imaging Informatics
Clinical Informatics
Public Health Informatics
Bioinformatics
Molecular and Cellular Processes
Tissues and Organs
Individuals (Patients)
Populations And Society
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Biomedical Informatics in Perspective
Biomedical Informatics Methods, Techniques,
and Theories
Other Component Sciences
Management Sciences
Information Sciences
Decision Science
Cognitive Science
Applied Informatics
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Core of Biomedical Informatics As A Scientificic
Discipline
Images Microarray Data Physiological Signals (for
example)
Biomedical Knowledge
Biomedical Data
Combined Genotypic and Phenotypic Datasets
Data Base
Inferencing System
Knowledge Base
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Biomedical Informatics Research Areas
Biomedical Knowledge
Biomedical Data
Real-time acquisition Imaging Speech/language/text
Specialized input devices
Machine learning Text interpretation Knowledge
engineering
Knowledge Base
Data Base
Inferencing System
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Biomedical Informatics Disciplines
Biomedical Informatics
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Medical Informatics Textbook (2nd edition)
Springer Verlag - 2000
2006
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Fundamental Research in Informatics

• Although projects are inspired by biomedical
  application goals, basic research in biomedical
  informatics typically
• offers methodological innovation, not simply
  interesting programming artifacts
• generalizes to other domains, within or outside
  biomedicine
• Inherently interdisciplinary, biomedical
  informatics provides bridging expertise and
  opportunities for collaboration between computer
  scientists and biomedical researchers and
  practitioners

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Department of Biomedical Informatics

• Department (since 1995) in the College of
  Physicians and Surgeons (medical school) of
  Columbia University
• Grants Masters and Doctoral degrees through
  Columbias Graduate School of Arts and Sciences
• Close relationships with other health science
  schools (nursing, dentistry, public health) as
  well as with the Computer Science Department in
  the School of Engineering
• Major service and collaborative roles with the
  clinical services of the Columbia University
  Medical Center (Columbia campus of the New York
  Presbyterian Healthcare System)

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Training Program Characteristics

• Steady-state program size 50-60 students
• Applications per year 120 candidates
• Admissions per year (PhD/postdocs) 8-10 students
• Trainees generally supported on a training grant,
  as graduate research assistants on sponsored
  projects, or as teaching assistants

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Trends

• Creation of several new biomedical informatics
  departments or independent academic units
• Strong job market for graduates of informatics
  degree programs
• Government investment in training and research is
  reasonably strong, especially for applications
  and demonstrations
• Increasing acceptance of biomedical informatics
  as a subspecialty area by biomedical professional
  societies
• Increasing recognition that biomedical problems
  can drive the development of basic theory and
  capabilities in information technology research

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Some Implications

• Need to stop thinking of the pertinent fields as
  distinct from one another
• Interdisciplinary science abhors artificial
  boundaries
• Need to describe the field and activities in
  terms that are as inclusive as possible
• Sensitivities exist and need to be considered
• Need to recognize the substantial synergies
  between the methods developed in one biomedical
  domain and their potential applicability in
  another

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Intensive Course in Biomedical Informatics