Overview of Biomedical Informatics
Rakesh Nagarajan
Clinical Research
Needs
Data Integration
Analysis
Visualization
Participant Recruitment/
Biospecimen Selection
Population
-
based
Research Needs
Data Integration
Analysis
Visualization
Study
Health
Records
Disseminate
Clinical Practice
Modifications
Identify clinical/pharmacologic factors
adversely affecting patient health care
What is Biomedical
Informatics?
Bench Science
Computer Science
Medicine
Mathematics/Biostatistics
Biomedical
Informatics
What is Biomedical
Informatics?
Public Health Informatics
What is Biomedical
Informatics?
Public Health Informatics
Aspects of public health informatics
Vital statistics
Communicable disease cases
Immunization records
Emergency room data
Insurance data sets
Geographical information systems
Adapted from
http://en.wikipedia.org/wiki/Public_health_informatics
What is Biomedical
Informatics?
Public Health Informatics
Medical Informatics
What is Biomedical
Informatics?
Public Health Informatics
Medical Informatics
Aspects of medical informatics
Collection of electronic health record information
Natural language processing
Medical decision making
Decision support systems
Adapted from
http://en.wikipedia.org/wiki/Clinical_informatics
What is Biomedical
Informatics?
Public Health Informatics
Medical Informatics
Imaging/Pathology Informatics
1
Image source:
http://www.aperio.com/imageanalysis/image
-
analysis.asp
2
Image source:
http://www.spectroscopynow.com/FCKeditor/UserFiles/Image/$pectroscopyNOW_ezines_2009/SN45a/SN45a_M_alz(1).jpg
1
2
What is Biomedical
Informatics?
Public Health Informatics
Medical Informatics
Imaging/Pathology Informatics
1
Image source:
http://www.aperio.com/imageanalysis/image
-
analysis.asp
2
Image source:
http://www.spectroscopynow.com/FCKeditor/UserFiles/Image/$pectroscopyNOW_ezines_2009/SN45a/SN45a_M_alz(1).jpg
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2
Aspects of imaging/pathology informatics
Image/report de
-
identification algorithms
Automation of image processing engines
Discrete quantification of image components (e.g.
brain regions or nuclear size)
What is Biomedical
Informatics?
Public Health Informatics
Medical Informatics
Imaging/Pathology Informatics
Bioinformatics
1
Image source:
http://www.aperio.com/imageanalysis/image
-
analysis.asp
2
Image source:
http://www.spectroscopynow.com/FCKeditor/UserFiles/Image/$pectroscopyNOW_ezines_2009/SN45a/SN45a_M_alz(1).jpg
1
2
What is Biomedical
Informatics?
Public Health Informatics
Medical Informatics
Imaging/Pathology Informatics
Bioinformatics
1
Image source:
http://www.aperio.com/imageanalysis/image
-
analysis.asp
2
Image source:
http://www.spectroscopynow.com/FCKeditor/UserFiles/Image/$pectroscopyNOW_ezines_2009/SN45a/SN45a_M_alz(1).jpg
1
2
Aspects of bioinformatics
Development of computational algorithms
In
silico
analysis of high dimensional, molecular
profiling data sets
Integration of genome annotation information
Prediction of gene relational networks
Relationships of
Basic Data Types
Patient
Participant
Integration of Clinical
and Research Systems
Inpatient Data
Patient
Participant
Outpatient
Data
Imaging Data
Clinical Research
Data
Clinical
Studies Data
Biospecimen
Data
Research
Imaging Data
Molecular and
Genomic Data
Integrated Data Analysis and
Visualization
Integration of Clinical
and Research Systems
Inpatient Data
Patient
Participant
Outpatient
Data
Imaging Data
Clinical Research
Data
Clinical
Studies Data
Biospecimen
Data
Research
Imaging Data
Molecular and
Genomic Data
Integrated Data Analysis and
Visualization
Data integration requires that software systems
are
interoperable
with each other
What is
Interoperability?
Semantic
interoperability
Syntactic
interoperability
in∙ter∙op∙er∙a∙bil∙i∙ty
ability of a system...to use the parts or equipment of
another system
Source: Merriam
-
Webster web site
interoperability
ability of two or more systems or components to
exchange information and to use the information that
has been exchanged.
Source: IEEE Standard Computer Dictionary:
A Compilation of IEEE Standard Computer Glossaries, IEEE, 1990
Syntactic interoperability
-
Use of standardized
programming interfaces
Semantic
interoperability
Use of controlled vocabularies and
ontologies
Unique concept codes for each term
One or more textual representations
Examples
LOINC
-
Laboratory tests
SNOMED
-
Clinical terms (e.g. diagnoses)
CPT
-
Medical procedures
RxNORM
-
Medications
Facilitating
Interoperability
ca
ncer
B
iomedical
I
nformatics
G
rid (caBIG®)
Domain Workspaces
Clinical Trials
Tissue Banking and Technology Tools
Integrative Cancer Research
In Vivo Imaging
Population Science
Cross
-
cutting Workspaces
Vocabularies and Common Data Elements
Architecture
National and Global
Data Integration
C
linical and
T
ranslational
S
cience
A
ward (CTSA)
Clinical Research Repositories
Education
Collaboration Facilitation (Research Networking)
National and Global
Data Integration
Course Lectures
Public Health Informatics
Medical Informatics
Imaging/Pathology Informatics
Bioinformatics
1
Image source:
http://www.aperio.com/imageanalysis/image
-
analysis.asp
2
Image source:
http://www.spectroscopynow.com/FCKeditor/UserFiles/Image/$pectroscopyNOW_ezines_2009/SN45a/SN45a_M_alz(1).jpg
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2
Lectures 2
-
8
Course Lectures
Public Health Informatics
Medical Informatics
Imaging/Pathology Informatics
Bioinformatics
1
Image source:
http://www.aperio.com/imageanalysis/image
-
analysis.asp
2
Image source:
http://www.spectroscopynow.com/FCKeditor/UserFiles/Image/$pectroscopyNOW_ezines_2009/SN45a/SN45a_M_alz(1).jpg
1
2
Lecture 9
Course Lectures
Public Health Informatics
Medical Informatics
Imaging/Pathology Informatics
Bioinformatics
1
Image source:
http://www.aperio.com/imageanalysis/image
-
analysis.asp
2
Image source:
http://www.spectroscopynow.com/FCKeditor/UserFiles/Image/$pectroscopyNOW_ezines_2009/SN45a/SN45a_M_alz(1).jpg
1
2
Lectures 10
-
11
Course Lectures
Public Health Informatics
Medical Informatics
Imaging/Pathology Informatics
Bioinformatics
1
Image source:
http://www.aperio.com/imageanalysis/image
-
analysis.asp
2
Image source:
http://www.spectroscopynow.com/FCKeditor/UserFiles/Image/$pectroscopyNOW_ezines_2009/SN45a/SN45a_M_alz(1).jpg
1
2
Lectures 12
-
14
Course Labs
Inpatient Data
Patient
Participant
Outpatient
Data
Imaging Data
Clinical Research
Data
Clinical
Studies Data
Biospecimen
Data
Research
Imaging Data
Molecular and
Genomic Data
Integrated Data Analysis and
Visualization
CIDER
ClinPortal
Tissue Suite
Course Labs
CIDER
-
Learn how to use the electronic health
record for research purposes
ClinPortal and Tissue Suite
-
Learn best practices
and the process of clinical studies and biospecimen
data management
Complete a research project that employs the
above tools
Ongoing project or assigned
Course Grading
25% laboratory quizzes
25% laboratory short assignments
50% project presentation
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