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DiagnosisPrognosisM anagem ent
Clinica l Tria l
ExpressionProfiling
Proteom icProfiling
CGHAnalysis
Mutation/SNPProfiling
ExpressionProfiling
ClinicalData
BiospecimenData
GeneAnnotation
Genom eAnnotationDatabases
Analysis Results
Query Tools and Statistical Tools
NEWCLINICAL
TRIAL
Review Preparatoryto Research
ParticipantRecruitm ent
Identification of im portant pathways
Propose new targets for rationally designed therapies
Integrated DB
Biom arkers for:
Clinical Research Needs
Data Integration
Analysis
Visualization
Participant Recruitment/Biospecimen Selection
DiagnosisPrognosisM anagem ent
Clinica l Tria l
ExpressionProfiling
Proteom icProfiling
CGHAnalysis
Mutation/SNPProfiling
ExpressionProfiling
ClinicalData
BiospecimenData
GeneAnnotation
Genom eAnnotationDatabases
Analysis Results
Query Tools and Statistical Tools
NEWCLINICAL
TRIAL
Review Preparatoryto Research
ParticipantRecruitm ent
Identification of im portant pathways
Propose new targets for rationally designed therapies
Integrated DB
Biom arkers for:
Population-based Research Needs
Data Integration
Analysis
Visualization
Study
HealthRecords
DisseminateClinical Practice
Modifications
Identify clinical/pharmacologic factorsadversely affecting patient health care
What is Biomedical Informatics?
Bench Science
Computer Science
Medicine
Mathematics/
Biostatistics
Biomedical Informatics
What is Biomedical Informatics?
Public Health InformaticsAspects 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
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
1Image source: http://www.aperio.com/imageanalysis/image-analysis.asp2Image source: http://www.spectroscopynow.com/FCKeditor/UserFiles/Image/$pectroscopyNOW_ezines_2009/SN45a/SN45a_M_alz(1).jpg
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What is Biomedical Informatics?
Public Health Informatics
Medical Informatics
Imaging/Pathology Informatics
1Image source: http://www.aperio.com/imageanalysis/image-analysis.asp2Image source: http://www.spectroscopynow.com/FCKeditor/UserFiles/Image/$pectroscopyNOW_ezines_2009/SN45a/SN45a_M_alz(1).jpg
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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
1Image source: http://www.aperio.com/imageanalysis/image-analysis.asp2Image source: http://www.spectroscopynow.com/FCKeditor/UserFiles/Image/$pectroscopyNOW_ezines_2009/SN45a/SN45a_M_alz(1).jpg
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What is Biomedical Informatics?
Public Health Informatics
Medical Informatics
Imaging/Pathology Informatics
Bioinformatics
1Image source: http://www.aperio.com/imageanalysis/image-analysis.asp2Image source: http://www.spectroscopynow.com/FCKeditor/UserFiles/Image/$pectroscopyNOW_ezines_2009/SN45a/SN45a_M_alz(1).jpg
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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
C/T
C/T
Sense
Antisense
C/T
C/T
Sense
Antisense
Integration of Clinical and Research Systems
Inpatient DataPatient
Participant
Outpatient Data
Imaging Data
Clinical Research Data
Clinical Studies Data
Biospecimen Data
Research Imaging Data
Molecular and Genomic Data In
teg
rate
d D
ata
An
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V
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Integration of Clinical and Research Systems
Inpatient DataPatient
Participant
Outpatient Data
Imaging Data
Clinical Research Data
Clinical Studies Data
Biospecimen Data
Research Imaging Data
Molecular and Genomic Data In
teg
rate
d D
ata
An
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nd
V
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Data integration requires that software systems are interoperable with each other
What is Interoperability?
Semanticinteroperability
Syntacticinteroperability
in·ter·op·er·a·bil·i·ty ability of a system...to use the parts or equipment of
another systemSource: 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
cancer Biomedical Informatics Grid (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
Clinical and Translational Science Award (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
1Image source: http://www.aperio.com/imageanalysis/image-analysis.asp2Image source: http://www.spectroscopynow.com/FCKeditor/UserFiles/Image/$pectroscopyNOW_ezines_2009/SN45a/SN45a_M_alz(1).jpg
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Lectures 2-8
Course Lectures
Public Health Informatics
Medical Informatics
Imaging/Pathology Informatics
Bioinformatics
1Image source: http://www.aperio.com/imageanalysis/image-analysis.asp2Image source: http://www.spectroscopynow.com/FCKeditor/UserFiles/Image/$pectroscopyNOW_ezines_2009/SN45a/SN45a_M_alz(1).jpg
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Lecture 9
Course Lectures
Public Health Informatics
Medical Informatics
Imaging/Pathology Informatics
Bioinformatics
1Image source: http://www.aperio.com/imageanalysis/image-analysis.asp2Image source: http://www.spectroscopynow.com/FCKeditor/UserFiles/Image/$pectroscopyNOW_ezines_2009/SN45a/SN45a_M_alz(1).jpg
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Lectures 10-11
Course Lectures
Public Health Informatics
Medical Informatics
Imaging/Pathology Informatics
Bioinformatics
1Image source: http://www.aperio.com/imageanalysis/image-analysis.asp2Image source: http://www.spectroscopynow.com/FCKeditor/UserFiles/Image/$pectroscopyNOW_ezines_2009/SN45a/SN45a_M_alz(1).jpg
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Lectures 12-14
Course Labs
Inpatient DataPatient
Participant
Outpatient Data
Imaging Data
Clinical Research Data
Clinical Studies Data
Biospecimen Data
Research Imaging Data
Molecular and Genomic Data In
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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