CBMI Course- Lecture 1- Overview of Biomedical Informatics

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

1

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