Biomedical Informatics
in Engineering:
A New Frontier for Engineering Librarians
Sheila J. Young, Engineering Librarian
Olivia B. Sparks, Engineering and Chemistry Librarian
ASEE 2008
Pittsburgh, PA
June 24, 2008
Biomedical Informatics
http://www.dbmi.columbia.edu/about/definition/definition.html
Shortliffe & Cimino, 2006.
Biomedical Informatics
Definition
“…an umbrella term that names the core discipline while also
denoting the union of the information and computer sciences
with domains including clinical practice, biomedical research,
imaging, public health, and health professions education. We
believe that use of ‘‘biomedical informatics’’ as the overarching
term and ‘‘bioinformatics’’ in a more focused sense will lead over
time to the clearest portrayal of the field and, as such, will
promote effective communication among the varied
constituencies that work in the field.”
Friedman, C.P. et.al (2004)
Biomedical Informatics Programs
http://www.amia.org/informatics/acad&training/index.asp
Examples of Departments/Programs with
Biomedical Informatics in title
• Arizona State University, Tempe, Arizona
• Columbia University, New York, NY
• Stanford University, Stanford, CA
• University of Utah, Salt Lake City, UT
• University of Washington, Seattle, WA
• Vanderbilt University, Nashville, TN
Biomedical Informatics at ASU
http://bmi.asu.edu/downloads/IMIAYearbook08_preprint.pdf
Biomedical Informatics at ASU
Ira A. Fulton School of Engineering
•New Department in the School of Computing
and Informatics
http://www.asu.edu/tour/tempe/byeng.html
•Physical Location – Phoenix Biomedical
Campus
http://www.asu.edu/tour/downtown/abc1.html
http://bmi.asu.edu/downloads/IMIAYearbook08_preprint.pdf
Biomedical Informatics at
Arizona State University
Phoenix Biomedical Campus
• ASU Department of Biomedical Informatics
• COM-PHX – “University of Arizona College of
Medicine – Phoenix, in partnership with Arizona
State University”
• ASU College of Nursing and Health Innovation
• TGen
• UA CPharm
• NAU Allied Health
Areas of Concentration at ASU
• Bioinformatics – “develop computational tools for
the analysis of biomedical data and systems”
• Clinical informatics – “develop novel information
technology, computer science and knowledge
management methodologies for disease
prevention, treatment, more efficient and safer
patient care delivery, and knowledge access.”
http://bmi.asu.edu/graduate/bmi_phd.php
Areas of Concentration at ASU
• Cognitive science – “…study of medical decisionmaking, cognitive foundations of health behaviors,
and the effective use of computer-based information
technologies.”
Areas include: analysis of medical error, models of
naturalistic problem solving and decision-making,
development and use of clinical guidelines, and
evaluation of human-computer interactions
http://bmi.asu.edu/graduate/bmi_phd.php
Areas of Concentration at ASU
• Imaging Informatics – develop “information
technology and computational tools to manage and
analyze biomedical images (such as radiological films,
CAT scans, pathology/microscopy or surgical
simulation environments)…”
• Public Health Informatics – “…systematic application
of information and computer sciences to public health
practice, research, and learning…”
http://bmi.asu.edu/graduate/bmi_phd.php
From the Literature: Systems Biology
“Engineering sciences provides a bundles of
computational tools and theoretical methods that
are frequently applied in systems biology research.”
– Modeling
– Model analysis
Kremling (2007) p. 348
From the Literature: Systems Biology
“Systems biology is the merger of systems theory
(engineering approaches) and molecular/cell
biology…is particularly attractive for researchers
from the engineering and physical sciences. What
this indicates is that an “engineering or “systemstheoretic” approach is different to the way cellbiological systems have been studied.”
Wolkenhauer (2007)
From the Literature: Systems Biology
• “…the engineering approach is a necessity,
not a choice, if we are to understand the
functioning of the cell.”
• Mathematical models and rich data sets
Wolkenhauer (2007)
From the literature: Systems Biology
“…1) a biological system can be viewed as an
engineering system, 2) biological information
integration can be approached by reverse
engineering, and 3) biological systems can be
represented in the form of modern
engineering system architectures.”
Zheng (2006)
Literature Sources
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PubMed
Inspec
Compendex
ACM Digital Library
IEEE Xplore
MeSH Headings
• Information Science 1993
– Informatics 2005
• Dental Informatics 2005
• Medical Informatics 1987
– Decision Making, Computer-Assisted+ 1987
– Information Storage and Retrieval+ 1991
– Information Systems+ 1982
– Medical Informatics Computing 1987
• Nursing Informatics 2005
• Public Health Informatics 2003
• Biology
– Computational Biology (Bioinformatics) 1997
“Biomedical Informatics” Not a MeSH term
Beyond PubMed
• Sheetal Agarwal, et al. “A pervasive computing system for the operating
room of the future.” (2007) Mobile Networks and Applications. 12 (2-3)
– “…a prototype context aware perioperative information
system to capture and interpret data in an operating room
of the future.”
• Pratt, Wanda et al. “Personal health information management.” (2006)
Communications of the ACM.49 (1)
• Guiducci, C. and Nardini, C. (2008). “High parallelism, portability, and
broad accessibility: Technologies for genomics.” ACM Journal of
Emerging Technologies in Computing Systems. 4, 1 (Mar. 2008), 1-39.
Beyond PubMed
• Zhang et al. 2008. “BioPortal Infectious Disease Informatics
research: disease surveillance and situational awareness.”
Proceedings of the 2008 international conference on Digital
government research
– “…disease monitoring and situational awareness infrastructure
developed in BioPortal, our NSF-funded Infectious Disease
Informatics project.”
• Zhou, Z. 2007. The role of a data grid in worldwide imagingbased clinical trials. Journal of High Speed Networks, v 16, n
1, 2007, p 21-33
INSPEC Terms
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•
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•
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Biology computing 1977
Medical computing 1977
Medical diagnostic computing 1977
Medical information systems 1995
Biomedical imaging 1995
“Biomedical Informatics” is Not an INSPEC
Controlled Vocabulary term
Compendex Terms
• Bioinformatics 2006
• Medical Imaging 1993
• Medical computing 1993
“Biomedical Informatics” is Not an Compendex
Controlled Vocabulary term
ACM Terms
Computing Classification System (1998)
• E. Data
• H. Information Systems
• I. Computing Methodologies
• J.3 Life and Medical Sciences
– Biology and genetics
– Health
– Medical information systems
INSPEC “Biology and Medical Computing”
Records per Year 1997-2007
12000
Number of Records
10000
8000
6000
4000
2000
0
1997
1998
1999
2000
2001
2002
Year
2003
2004
2005
2006
2007
INSPEC CV terms in
C7330- “Biology and Medical Computing”
82498 records (1997-2007)
• Medical Image Processing – 32233
• Biology Computing – 12672
• Medical Computing – 10923
• Medical Signal Processing – 10480
• Biomedical MRI – 8243
• Image Reconstruction – 7781
• Image Segmentation – 7659
• Computerised Tomography – 6597
• Medical Information Systems – 5705
• Diseases – 5394
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Number of Records
INSPEC CV terms in
C7330- “Biology and Medical Computing”
35000
30000
25000
20000
15000
10000
5000
0
INSPEC CV “Medical Image Processing”
Records per Year 1997-2007
4500
4000
Number of Records
3500
3000
2500
2000
1500
1000
500
0
1997
1998
1999
2000
2001
2002
Year
2003
2004
2005
2006
2007
Compendex “Medical Imaging”
Records per Year 1997-2007
4000
Number of Records
3500
3000
2500
2000
1500
1000
500
0
1997
1998
1999
2000
2001
2002
Year
2003
2004
2005
2006
2007
Journals:
Computer Science/Engineering Literature
ACM Journal on Emerging Technologies in Computing
Systems (2005)
IEEE Engineering in Biology and Medicine (1988)
IEEE Transactions on Information Technology in
Biomedicine (1997)
IEEE - ACM Transactions on Computational Biology and
Bioinformatics (2004)
IET Systems Biology (2004)
Journals: Engineering Literature
SPIE Journals
• Optical Engineering (1990)
• Journal of Electronic Imaging (1992)
• Journal of Biomedical Optics (1996)
Conferences - Examples
IEEE
• Bioinformatics and
Bioengineering
• Biomedical Imaging
• Computer Based
Medical Systems
SPIE
• Biomedical Electronic
Imaging & Processing
• Medical Imaging
Systems
• Molecular Biology &
Genetics
References
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Friedman C.P. et al. (2004). “Training the Next Gererations of Informaticians: The
Impact of “BISTI” and Bioinformatics – A Report from the American College of Medical
Informatics.” JAMIA 11 (3): 167-72.
Greenes, R.A. et al. (2008). “Biomedical Informatics in the Desert – A New and Unique
Program at Arizona State University.” IMIA Yearbook of Medical Informatics. Preprint.
http://bmi.asu.edu/downloads/IMIAYearbook08_preprint.pdf
Kremling, A, & Saez-Rodriguez, J. (2007). Systems biology – an engineering
perspective. Journal of Biotechnology, 129 (2), 329-351.
Shortliffe, E.H. & Cimino, J.J. (2006) Biomedical Informatics: Computer Applications in
Healthcare and Biomedicine, 3rd edition. Springer: New York. Pp. 34.
Shortliffe, E.H. “Biomedical Informatics : The nature of the discipline.”
http://www.dbmi.columbia.edu/about/definition/definition.html (accessed April 17,
2008).
Zheng, W.J.,(2006). “Engineering Approached Toward Biological Information
Intergration at the Systems Level.” Current Bioinformatics 1 (1), 85-93.
Questions?