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Topics in BMI: Course ObjectivesTopics in BMI: Course Objectives

Prof. Steven A. Demurjian, Sr. Computer Science & Engineering Department

The University of Connecticut371 Fairfield Road, Box U-255

Storrs, CT 06269-2155

steve@engr.uconn.eduhttp://www.engr.uconn.edu/~steve

(860) 486 - 4818

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What is Informatics?What is Informatics? Informatics is:Informatics is:

Management and Processing of Data From Multiple Sources/Contexts Involves Classification (Ontologies), Collection,

Storage, Analysis, Dissemination Informatics is Multi-DisciplinaryInformatics is Multi-Disciplinary

Computing (Model, Store, Process Information) Social Science (User Interactions, HCI) Statistics (Analysis)

Informatics Can Apply to Multiple Domains:Informatics Can Apply to Multiple Domains: Business, Biology, Fine Arts, Humanities Pharmacology, Nursing, Medicine, etc.

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What is Informatics?What is Informatics? Heterogeneous Field – Heterogeneous Field –

Interaction between Interaction between People, Information and People, Information and TechnologyTechnology Computer Science

and Engineering Social Science

(Human Computer Interface)

Information Science (Data Storage, Retrieval and Mining)

People

Information Technology

Informatics

Adapted from Shortcliff textbook

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What is Biomedical Informatics (BMI)?What is Biomedical Informatics (BMI)? BMI is Information and its Usage Associated with the BMI is Information and its Usage Associated with the

Research and Practice of Medicine Including:Research and Practice of Medicine Including: Clinical Informatics for Patient Care

Medical Record + Personal Health Record Bioinformatics for Research/Biology to Bedside

From Genomics To Proteomics Public Health Informatics (State and Federal)

Tracking Trends in Public Sector Clinical Research Informatics

Deidentified Repositories and Databases Facilitate Epidemiological Research and Ongong

Clinical Studies (Drug Trails, Data Analysis, etc.)

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What are Key BMI Focal Areas?What are Key BMI Focal Areas? T1 Research T1 Research

Transition Bench Results into Clinical Research Clinical ResearchClinical Research

Applying Clinical Research Results via Trials with Patients on Medication, Devices, Treatment Plans

T2 Research T2 Research Translating “Successful” Clinical Trials into

Practice and the Community Clinical Practice Clinical Practice

Tracking all of the Information Associated with a Patient and his/her Care

Integrated and Inter-Disciplinary Information Integrated and Inter-Disciplinary Information Spectrum Spectrum

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Where/How is BMI Utilized?Where/How is BMI Utilized?

T1 Research (Bench T1 Research (Bench Clinical) Clinical) Transfer of Knowledge from Laboratory or Bench to Transfer of Knowledge from Laboratory or Bench to

Clinical TrialsClinical Trials Move Genomic Research from Bench (Lab) to Move Genomic Research from Bench (Lab) to

Clinical Trial (or Genetic/Test Intervention)Clinical Trial (or Genetic/Test Intervention) Transfer in Lab/Bench Research to Pre-Clinical and Transfer in Lab/Bench Research to Pre-Clinical and

Early Clinical Human Subject ResearchEarly Clinical Human Subject Research Exs: Exs:

New Genetic Test for Autism Tested on Samples from DNA Repository Transition to Actual Patient Population

Growing new Jaw Bone in Mice for Dental Implants – Transition to Human Tissue

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Where/How is BMI Utilized?Where/How is BMI Utilized?

Clinical Research (Trials) Clinical Research (Trials) Wide Range of Implications from Medical Treatment to Wide Range of Implications from Medical Treatment to

Medication RegimeMedication Regime Multi-Phased Process for Clinical Trials:Multi-Phased Process for Clinical Trials:

Phase I: First Stage – 20-80 Healthy Patients Phase II: Second Stage – 20-300 Patients

IIA – Dosing – How Much of Drug Should be Used IIB – Efficacy – How Well Does Drug Work Randomized Clinical Trials (Not all Get Drug)

Phase III: Multi-Center Trials – 300-3000 Longer Term, Data Collected, Multiple Locations Preparation of Data for Regulatory Approval (FDA)

Phase IV: Ongoing Monitoring of Drug After Approval

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Where/How is BMI Utilized?Where/How is BMI Utilized?

Clinical Research (Trials) Clinical Research (Trials) Differing Perspectives for Carrying out Research:Differing Perspectives for Carrying out Research:

Patients: Drug, Treatment Regime, or Device Increased Dose of Existing Drug (Safety/Effective) Applying Drug to New Disease Compare Two or more Treatments

Epidemiological Study Existing Data for Trend Against Existing Data Repositories Patients with CHF and Diabetes Taking Statins Tracking Communicable Disease/Outbreaks

Phases I, II, III, and IV ApplyPhases I, II, III, and IV Apply Bad Results in IV – Pull Drug (Vioxx)Bad Results in IV – Pull Drug (Vioxx)

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Where/How is BMI Utilized?Where/How is BMI Utilized?

T2 Research (Clinical ResearchT2 Research (Clinical Research Practice/Community) Practice/Community) Practice-Oriented Translation ResearchPractice-Oriented Translation Research Results: Clinical Trails Results: Clinical Trails Clinical Practice Clinical Practice

Strategies for Establishing/Implementing New Technologies

Improvements in Practice New Evidence-Based Guidelines New Care Models

Phase III Success Translated to Health ProvidersPhase III Success Translated to Health Providers ExamplesExamples

Statin Drugs (Lipitor) and Exercise New Treatment Regime for Chronic Disease

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Where/How is BMI Utilized?Where/How is BMI Utilized?

Clinical Practice Clinical Practice Dealing with Patients – Direct Medical CareDealing with Patients – Direct Medical Care

Hospital or Clinic Physician’s Office Testing Facility Insurance/Reimbursement

Tracking All Data Associated with PatientsTracking All Data Associated with Patients Medical Record Medical Tests (Lab, Diagnostic, Scans, etc.) Prescriptions

Stringent Data Protection (HIPAA)Stringent Data Protection (HIPAA) Distributed Repositories, Inability to Access Data in Distributed Repositories, Inability to Access Data in

Emergent Situations, Competition, etc.Emergent Situations, Competition, etc.

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What is Medical Informatics?What is Medical Informatics? Clinical Informatics, Pharmacy InformaticsClinical Informatics, Pharmacy Informatics Public Health InformaticsPublic Health Informatics Consumer Health InformaticsConsumer Health Informatics Nursing InformaticsNursing Informatics Systems and People Issues Systems and People Issues

Intended to Improve Clinical outcomes, Satisfaction and Efficiency

Workflow Changes, Business Implications, Implementation, etc…

Patient Centered – Personal Health Record and Medical Home

Care Centered – Pay for Performance, Improving Treatment Compliance

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What is Bionformatics? What is Bionformatics? Focused on Research Tools for T1:Focused on Research Tools for T1:

Genomic and Proteomic Tools, Evaluation Methods, Computing And Database Needs

Information Retrieval and Manipulation of Large Distributed (caBIG) Data Sets (cabig.cancer.gov/index.asp)

Often Requires Grid Computing Includes Cancer and Immunology Research

Increasing Need to Tie These Separate Types of Increasing Need to Tie These Separate Types of Systems Together = Personalized MedicineSystems Together = Personalized Medicine

Biology and the Bedside (Biology and the Bedside (www.i2b2.orgwww.i2b2.org))

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Where is Data/How is it Used?Where is Data/How is it Used? Medical And Administrative Data Found in Clinical Medical And Administrative Data Found in Clinical

Information Systems (CIS) Such As:Information Systems (CIS) Such As: Hospital Info. Systems Electronic Medical Records Personal Health Records such as Google Health

and Microsoft Healthvault Pharmacy, Nursing, Picture Archiving Systems Complex Data Storage and Retrieval – Many

Different Systems T1 Research Increasingly Reliant on CIST1 Research Increasingly Reliant on CIS T2 Research is Reliant on:T2 Research is Reliant on:

End Systems for Embedding EBM (Evidence-Based Medicine) Guidelines

Measuring Outcomes, Looking at Policy

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What are Major Informatics Challenges?What are Major Informatics Challenges? Shortage of Trained People NationallyShortage of Trained People Nationally Slows adoption of Health Information TechnologySlows adoption of Health Information Technology Results in Poor Planning and Coordination, Results in Poor Planning and Coordination,

Duplication of Efforts and Incomplete EvaluationDuplication of Efforts and Incomplete Evaluation What are Critical Needs?What are Critical Needs?

Dually Trained Clinicians or Researchers in Leadership of some Initiatives

Connect all folks with Informatics Roles across Institutions to Improve Efficiency

Multi-Disciplinary: CSE, Statistics, Biology, Medicine, Nursing, Pharmacy, etc.

Emerging Standards for Information Modeling and Emerging Standards for Information Modeling and Exchange (Exchange (www.hl7.orgwww.hl7.org) based on XML) based on XML

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What is UConn Doing in this Area?What is UConn Doing in this Area? NIH’s CTSA Program: Transform the Way Clinical NIH’s CTSA Program: Transform the Way Clinical

and Translational Science Research is Conductedand Translational Science Research is Conducted From Bench to Clinical Research to Translational

Research to the Bedside and Back Again 45+ Academic Medical Centers Awarded to Date

see: http://www.ctsaweb.org/ Under President Mike Hogan’s LeadershipUnder President Mike Hogan’s Leadership

UConn Submitted a CTSA Proposal in Oct 2008 Formed CICaTS: Connecticut Institute for Clinical

and Translational Science (Sept. 29th 09) University Initiative with Partners

John Dempsey, St. Francis, Hartford Hospital, CCMC, Hospital for Central CT, Institute for Living, etc.

http://cicats.uconn.edu/

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CICATS CICATS Official Launching:Official Launching:

Tuesday September 29, 10:30am-1:30pmTuesday September 29, 10:30am-1:30pm UConn Global Business Learning Center, HartfordUConn Global Business Learning Center, Hartford Speakers Include: Pres. M. Hogan, Provost P. Speakers Include: Pres. M. Hogan, Provost P.

Nichols, and Dean Cato Laurencin (Med School)Nichols, and Dean Cato Laurencin (Med School) Mission:Mission:

to educate and nurture new scientiststo educate and nurture new scientists toto  increaseincrease  clinical and translational clinical and translational

research being conducted at UCHC, regional research being conducted at UCHC, regional hospitals, UConn Storrs, and healthcare hospitals, UConn Storrs, and healthcare organizations throughout greater Hartford organizations throughout greater Hartford 

to work collaboratively with regional stakeholders to work collaboratively with regional stakeholders to combat the leading causes of morbidity, to combat the leading causes of morbidity, mortality, disability, and health disparitiesmortality, disability, and health disparities

CICATS will have Biomedical Informatics CenterCICATS will have Biomedical Informatics Center

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Biomedical Informatics in CICATSBiomedical Informatics in CICATS

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Summary of Web Sites of Note:Summary of Web Sites of Note: AMIA (www.amia.org)AMIA (www.amia.org) IHE (http://www.ihe.net/)IHE (http://www.ihe.net/) Smartplatform (http://www.smartplatforms.org/)Smartplatform (http://www.smartplatforms.org/) Mysis MOSS (Mysis MOSS (http://www.misys.com/OpenSourcehttp://www.misys.com/OpenSource)) NSF Clinical and Translational Science ProgramNSF Clinical and Translational Science Program

http://www.ctsaweb.org/ Emerging Patient Data StandardEmerging Patient Data Standard

http://www.hl7.org/ Informatics for Integrating Biology & the Bedside.Informatics for Integrating Biology & the Bedside.

https://www.i2b2.org/ Cancer Biomedical Informatics GridCancer Biomedical Informatics Grid

http://cabig.cancer.gov/index.asp

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Semester Topics (weeks)Semester Topics (weeks) Four Core Topics:Four Core Topics:

Semester and Course Overview (0.5) Informatics/Information Engineering (1.5) Software Architectures (2) Security and Dynamic Coalition Problem (2) Service Based Computing (2)

CORBA, JINI, .NET, Interoperability, Web Security

Discussion of Semester Project (0.5)Discussion of Semester Project (0.5) Presentations by Outside Speakers (2.5) Presentations by Outside Speakers (2.5) Student Presentations on Biomedical Informatics Student Presentations on Biomedical Informatics

Materials (3)Materials (3)

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Planned SpeakersPlanned Speakers Dr. L. Fagan, Co-Director, Stanford Biomedical Dr. L. Fagan, Co-Director, Stanford Biomedical

Informatics Training Program, March 31Informatics Training Program, March 31 Dr. M. Smith, Pharmacy Practice, UConn, April 5Dr. M. Smith, Pharmacy Practice, UConn, April 5 Dr. T. Shortliffe, President, AMIA, April 28Dr. T. Shortliffe, President, AMIA, April 28 Others to be Scheduled:Others to be Scheduled:

Dr. Thomas Agresta Dr. Michael Blechner Dr. Xiaoyan Wang

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Class Materials, Textbook, Projects, etc.Class Materials, Textbook, Projects, etc. Course Web Site: Course Web Site:

http://www.engr.uconn.edu/~steve/Cse300/cse300.htmlhttp://www.engr.uconn.edu/~steve/Cse300/cse300.html Reading List Constant Updates and Changes

TextbookTextbook Biomedical Informatics: Computer Applications in

Health Care and Biomedicine (Health Informatics), Edward H. Shortliffe (Editor), James J. Cimino (Editor), ISBN-10: 0387289860

Project 1 – Due in 2 weeksProject 1 – Due in 2 weeks Project 2 – Out in 2 weeksProject 2 – Out in 2 weeks Team Project – Out in 2 weeks as wellTeam Project – Out in 2 weeks as well Questions? Comments? Suggestions?Questions? Comments? Suggestions?

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Course Projects and Exam (???) …Course Projects and Exam (???) … Individual/Team Course Project(s) Throughout the Individual/Team Course Project(s) Throughout the

SemesterSemester Individual Projects have two Goals

Increase Student Knowledge on BMI Assist in Creating Courseware

Project will be the Entire Class Explore and Learn about BMI Technologies Span Subset of: T1 Research - Clinical Research - T2

Research - Clinical Practice Explore Open Source and Other Solutions Develop Extensible Plug and Play Framework

Exam – At MOST Final Exam (Still open to debate!)Exam – At MOST Final Exam (Still open to debate!)

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Individual Semester ProjectsIndividual Semester Projects Readings, Readings, and More ReadingsReadings, Readings, and More Readings Project 1: Annotated BibliographyProject 1: Annotated Bibliography

Accumulate Web/Hard Links on T1 Research - Clinical Research - T2 Research - Clinical Practice

Read 7 Papers on Clinical & Translational Science Project 2: Courseware MaterialsProject 2: Courseware Materials

Choose two Different Areas for Indepth Examination

Topics include (but not Limited to): HIE I2b2 Standards (HL7, Common Data Architecture CDA) caBIG BIRN (Biomedical Informatics Research Network) Another NIH Computing Initiative

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Semester ProjectSemester Project Still Evolving – Possible Projects Include:Still Evolving – Possible Projects Include:

Usage of SmartPlatform Utilization of Personal Health Records (PHR) Such

as Google Health and/or MS Healthvault in New or Extended Context Interoperability with EMR Google Health Hibernate API Available

XML (HL7/CDA) to i2b2 DB Translation Supervised by M. Blechner (UCHC BMI Faculty)

Extending Cell Phone Applications (iphone, blackberry, and android) for Maintaining Prescriptions Observations of Daily Living Prior Work by Undergraduate Teams (with Source)

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Semester Project ObjectivesSemester Project Objectives Objective – Wide Scale Open Source FrameworkObjective – Wide Scale Open Source Framework Envision Plug and Play ArchitectureEnvision Plug and Play Architecture High Reliance on Open Source Solutions for PHR and High Reliance on Open Source Solutions for PHR and

EMREMR Support Interoperability to Components via XML and Support Interoperability to Components via XML and

StandardsStandards Develop Complete, Integrated, and Extensible Develop Complete, Integrated, and Extensible

FrameworkFramework

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SmartPlatformSmartPlatform Substitutable Medical Apps, reusable technologySubstitutable Medical Apps, reusable technology

(http://www.smartplatforms.org/) NSF/NIH Funded SHARP Proposal at HarvardNSF/NIH Funded SHARP Proposal at Harvard Intended to:Intended to:

“A platform with substitutable apps constructed “A platform with substitutable apps constructed around core services is a promising approach to around core services is a promising approach to driving down healthcare costs, supporting standards driving down healthcare costs, supporting standards evolution, accommodating differences in care evolution, accommodating differences in care workflow, fostering competition in the market, and workflow, fostering competition in the market, and accelerating innovation”accelerating innovation”

Likely Led by Timo ZiminskiLikely Led by Timo Ziminski

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Personal Health RecordsPersonal Health Records Google HealthGoogle Health

Detailed Hibernate API to Allow Programmatic Transfer of Information to/From Google Health

Utilized in Web-Based Application Utilized by Cell Phone Projects (see later slides) Existing Platform Available for Future Design,

Development, and Usage Explore EMR/PHR InteroperabilityExplore EMR/PHR Interoperability

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TMR ArchitectureTMR Architecture

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XML (HL7/CDA) to i2b2 DB TranslationXML (HL7/CDA) to i2b2 DB Translation Work with Dr. Michael Blechner (UCHC BMI Faculty Work with Dr. Michael Blechner (UCHC BMI Faculty

Member)Member) Explore a Prototype that can take:Explore a Prototype that can take:

HL7/CDA Data (Simulated from an EMR) Store in a i2b2 Compatible Database

Utilization of Standards, New Technologies, etc.Utilization of Standards, New Technologies, etc.

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Cell Phone ApplicationsCell Phone Applications RWJ Project Health DesignRWJ Project Health Design Observations of Daily Living and PHRsObservations of Daily Living and PHRs

Passive – Once Initiated, Collects Data Accelerometer Pedometer Pill Bottle that Sends a Time Stamp Message (over

Bluetooth?) to SmartPhone Active – Patient Initiated

Providing Information via Smartphone on:– Diabetes (Glucose, Weight, Insulin)

– Asthma (Peak Flow, use of Inhaler)

– Heart Disease (Pulse, BP, Diet)

– Pain, Functional status, Fatigue, etc. http://www.engr.uconn.edu/~steve/Cse4904/cse4904.htmlhttp://www.engr.uconn.edu/~steve/Cse4904/cse4904.html

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Focus of GrantFocus of Grant Management of Two Diseases in Women of ColorManagement of Two Diseases in Women of Color

Obesity and Osteoarthritis TeamTeam

TRIPP (Crowell, Fifield) and AHFP (Agresta) SisterTalk (Headley) and CHCAT (Granger) UConn Storrs (Demurjian) and Netsoft (Collins)

MicrosoftHealthVault

Patient Demographicsand ODLs

Figure 1: Architecture Diagram of the Proposed System.

Patients

Providers

Researchers

LifelinesRepository

Web/ApplicationServer

SQL ServerDatabase

Client Side Technologieshttps, html, Ajax, XML

Server Side TechnologiesJava, JSP, Hibernate, Relational Database, XML

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CSE4904 – Spring 2010CSE4904 – Spring 2010 Smartphone Projects on ODLs and Other Medical Smartphone Projects on ODLs and Other Medical

Data Tracking and AlertsData Tracking and Alerts Three Platforms:Three Platforms:

Google’s Android (Java) Blackberry (Java) iPhone (Objective C)

Three Teams of Three Students EachThree Teams of Three Students Each

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Blackberry TeamBlackberry Team Ability to Track Information on ODLs and Ability to Track Information on ODLs and

PrescriptionsPrescriptions Login Screen Connection to Google Health Health Screen to Track ODLs Charting of ODLs over Time Loading Scripts from Google Health Prescription Alarms

Adam Siena, Kristopher Collins, William FidrychAdam Siena, Kristopher Collins, William Fidrych

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Android TeamAndroid Team Similar Capabilities to Blackberry ProjectSimilar Capabilities to Blackberry Project

Wellness Diary and Medication Alarm Integration with Google Health Much Improved ODL Screens

Male and Female Faces Change “Face” Based on Value

Tracking Prescriptions and Alarms Reports via. Google Charts

Ishmael Smyrnow, Kevin Morillo, James RedwayIshmael Smyrnow, Kevin Morillo, James Redway

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iPhone TeamiPhone Team Similar Capabilities to Blackberry ProjectSimilar Capabilities to Blackberry Project

Tracking of Conditions, Medications, and Allergies

ODLs for: Blood-Glucose, Peak-Flow, and Hypertension

Generation of Reports Synchronization with Google Health

Brendan Heckman, Ryan McGivern, Matthew FusaroBrendan Heckman, Ryan McGivern, Matthew Fusaro

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Questions?Questions?