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Intensive Course in Biomedical Informatics

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Title: Intensive Course in Biomedical Informatics


1
Intensive Course in Biomedical Informatics
2
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

3
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?

4
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

5
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

6
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.
7
Relationship of Medical Informatics and
Bioinformatics
Biological and Clinical Applications of
Interrelated Techniques and Methods Anticipation
of their Future Clinical Interdependencies
Medical Informatics
Bioinformatics
8
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

9
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?
10
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.
11
Recent Announcement
12
Biomedical Informatics in Perspective
Biomedical Informatics Methods, Techniques, and
Theories
Basic Research
13
Biomedical Informatics in Perspective
Biomedical Informatics Methods, Techniques, and
Theories
Basic Research
Imaging Informatics
Clinical Informatics
Public Health Informatics
Bioinformatics
14
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

15
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
16
Biomedical Informatics in Perspective
Biomedical Informatics Methods, Techniques,
and Theories
Other Component Sciences
Management Sciences
Information Sciences
Decision Science
Cognitive Science
Applied Informatics
17
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
18
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
19
Biomedical Informatics Disciplines
Biomedical Informatics
20
Medical Informatics Textbook (2nd edition)
Springer Verlag - 2000
2006
21
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

22
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23
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)

24
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

25
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

26
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

27
Intensive Course in Biomedical Informatics
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