CBMI Course- Lecture 1- Overview of Biomedical Informatics

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4 Οκτ 2013 (πριν από 4 χρόνια και 9 μέρες)

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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

1

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