Overview of Biomedical Informatics Rakesh Nagarajan.

Overview of Biomedical Informatics

Rakesh Nagarajan

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 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

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

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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

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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

Course Grading

25% laboratory quizzes

25% laboratory short assignments

50% project presentation