topics in bmi: course objectives - university of...

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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

[email protected]://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 DataFrom Multiple Sources/ContextsInvolves Classification (Ontologies), Collection, Storage, Analysis, Dissemination

Informatics is MultiInformatics is Multi--DisciplinaryDisciplinaryComputing (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, HumanitiesPharmacology, 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 EngineeringSocial 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 CareMedical Record + Personal Health Record

Bioinformatics for Research/Biology to BedsideFrom 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 OngongClinical 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 InterIntegrated and Inter--Disciplinary Information 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 TrialsMove 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 PreTransfer in Lab/Bench Research to Pre--Clinical and Clinical and Early Clinical Human Subject ResearchEarly Clinical Human Subject ResearchExsExs: :

New Genetic Test for AutismTested on Samples from DNA RepositoryTransition 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 Wide Range of Implications from Medical Treatment to Medication Regimeto Medication RegimeMultiMulti--Phased Process for Clinical Trials:Phased Process for Clinical Trials:

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

IIA – Dosing – How Much of Drug Should be UsedIIB – Efficacy – How Well Does Drug WorkRandomized Clinical Trials (Not all Get Drug)

Phase III: Multi-Center Trials – 300-3000Longer Term, Data Collected, Multiple LocationsPreparation 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 DiseaseCompare Two or more Treatments

EpidemiologicalStudy Existing Data for Trend Against Existing Data RepositoriesPatients with CHF and Diabetes Taking StatinsTracking Communicable Disease/Outbreaks

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

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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)

PracticePractice--Oriented Translation ResearchOriented Translation ResearchResults: Clinical Trails Results: Clinical Trails →→ Clinical PracticeClinical Practice

Strategies for Establishing/Implementing New TechnologiesImprovements in PracticeNew Evidence-Based GuidelinesNew Care Models

Phase III Success Translated to Health ProvidersPhase III Success Translated to Health ProvidersExamplesExamples

Statin Drugs (Lipitor) and ExerciseNew 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 Dealing with Patients –– Direct Medical CareDirect Medical CareHospital or ClinicPhysician’s OfficeTesting FacilityInsurance/Reimbursement

Tracking All Data Associated with PatientsTracking All Data Associated with PatientsMedical RecordMedical 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 InformaticsPublic Health InformaticsPublic Health InformaticsConsumer Health InformaticsConsumer Health InformaticsNursing InformaticsNursing InformaticsSystems and People Issues Systems and People Issues

Intended to Improve Clinical outcomes, Satisfaction and EfficiencyWorkflow Changes, Business Implications, Implementation, etc…Patient Centered – Personal Health Record and Medical HomeCare Centered – Pay for Performance, Improving Treatment Compliance

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

Genomic and Proteomic Tools, Evaluation Methods, Computing And Database NeedsInformation Retrieval and Manipulation of Large Distributed (caBIG) Data Sets (cabig.cancer.gov/index.asp) Often Requires Grid ComputingIncludes 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 MedicineBiology 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 RecordsPersonal Health Records such as Google Health and Microsoft HealthvaultPharmacy, Nursing, Picture Archiving SystemsComplex Data Storage and Retrieval – Many Different Systems

T1 Research Increasingly Reliant on CIST1 Research Increasingly Reliant on CIST2 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 NationallySlows adoption of Health Information TechnologySlows adoption of Health Information TechnologyResults in Poor Planning and Coordination, Results in Poor Planning and Coordination, Duplication of Efforts and Incomplete EvaluationDuplication of Efforts and Incomplete EvaluationWhat 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 EfficiencyMulti-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 What is UConnUConn Doing in this Area?Doing in this Area?NIHNIH’’ss CTSA Program: Transform the Way Clinical 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 Again45+ Academic Medical Centers Awarded to Datesee: http://www.ctsaweb.org/

Under President Mike HoganUnder President Mike Hogan’’s Leaderships LeadershipUConn Submitted a CTSA Proposal in Oct 2008Formed 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, 10:30amTuesday September 29, 10:30am--1:30pm1:30pmUConnUConn Global Business Learning Center, HartfordGlobal Business Learning Center, HartfordSpeakers 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 scientiststoto increaseincrease clinical and translational clinical and translational researchresearch being conducted at UCHC, regional being conducted at UCHC, regional hospitals, hospitals, UConnUConn Storrs, and healthcare Storrs, and healthcare organizations throughout greater Hartfordorganizations throughout greater Hartfordto work collaboratively with regional stakeholders to work collaboratively with regional stakeholders toto combat the leading causes of morbidity, 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 (AMIA (www.amia.orgwww.amia.org))IHE (http://IHE (http://www.ihe.netwww.ihe.net/)/)SmartplatformSmartplatform (http://(http://www.smartplatforms.orgwww.smartplatforms.org/)/)MysisMysis MOSS (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, WebSecurity

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 SpeakersDr. L. Fagan, CoDr. L. Fagan, Co--Director, Stanford Biomedical Director, Stanford Biomedical Informatics Training Program, March 31Informatics Training Program, March 31Dr. M. Smith, Pharmacy Practice, UConn, April 5Dr. M. Smith, Pharmacy Practice, UConn, April 5Dr. T. Dr. T. ShortliffeShortliffe, President, AMIA, April 28, President, AMIA, April 28Others to be Scheduled:Others to be Scheduled:

Dr. Thomas AgrestaDr. Michael BlechnerDr. 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 ListConstant Updates and Changes

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

Project 1 Project 1 –– Due in 2 weeksDue in 2 weeksProject 2 Project 2 –– Out in 2 weeksOut in 2 weeksTeam Project Team Project –– Out in 2 weeks as wellOut in 2 weeks as wellQuestions? 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 GoalsIncrease Student Knowledge on BMIAssist in Creating Courseware

Project will be the Entire ClassExplore and Learn about BMI Technologies Span Subset of: T1 Research - Clinical Research - T2 Research - Clinical Practice Explore Open Source and Other SolutionsDevelop Extensible Plug and Play Framework

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

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Individual Semester ProjectsIndividual Semester ProjectsReadings, Readings, and More ReadingsReadings, Readings, and More ReadingsProject 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 MaterialsChoose two Different Areas for IndepthExaminationTopics include (but not Limited to):

HIE I2b2Standards (HL7, Common Data Architecture CDA)caBIGBIRN (Biomedical Informatics Research Network)Another NIH Computing Initiative

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

Usage of SmartPlatformUtilization of Personal Health Records (PHR) Such as Google Health and/or MS Healthvault in New or Extended Context

Interoperability with EMRGoogle Health Hibernate API Available

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

Extending Cell Phone Applications (iphone, blackberry, and android) for

Maintaining PrescriptionsObservations of Daily LivingPrior Work by Undergraduate Teams (with Source)

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Semester Project ObjectivesSemester Project ObjectivesObjective Objective –– Wide Scale Open Source FrameworkWide Scale Open Source FrameworkEnvision Plug and Play ArchitectureEnvision Plug and Play ArchitectureHigh Reliance on Open Source Solutions for PHR and High Reliance on Open Source Solutions for PHR and EMREMRSupport Interoperability to Components via XML and Support Interoperability to Components via XML and StandardsStandardsDevelop Complete, Integrated, and Extensible Develop Complete, Integrated, and Extensible FrameworkFramework

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SmartPlatformSmartPlatformSubstitutable Medical Apps, reusable technologySubstitutable Medical Apps, reusable technology

(http://www.smartplatforms.org/)NSF/NIH Funded SHARP Proposal at HarvardNSF/NIH Funded SHARP Proposal at HarvardIntended 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 innovationaccelerating innovation””Likely Led by Likely Led by TimoTimo ZiminskiZiminski

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Personal Health RecordsPersonal Health RecordsGoogle HealthGoogle Health

Detailed Hibernate API to Allow Programmatic Transfer of Information to/From Google HealthUtilized in Web-Based ApplicationUtilized 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 TranslationWork with Dr. Michael Work with Dr. Michael BlechnerBlechner (UCHC BMI Faculty (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 ApplicationsRWJ Project Health DesignRWJ Project Health DesignObservations of Daily Living and Observations of Daily Living and PHRsPHRs

Passive – Once Initiated, Collects DataAccelerometer PedometerPill Bottle that Sends a Time Stamp Message (over Bluetooth?) to SmartPhone

Active – Patient InitiatedProviding 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 GrantManagement of Two Diseases in Women of ColorManagement of Two Diseases in Women of Color

Obesity and OsteoarthritisTeamTeam

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 CSE4904 –– Spring 2010Spring 2010Smartphone Projects on Smartphone Projects on ODLsODLs and Other Medical and Other Medical Data Tracking and AlertsData Tracking and AlertsThree 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 TeamAbility to Track Information on Ability to Track Information on ODLsODLs and and PrescriptionsPrescriptions

Login ScreenConnection to Google HealthHealth Screen to Track ODLsCharting of ODLs over TimeLoading Scripts from Google HealthPrescription Alarms

Adam Siena, Kristopher Collins, William Adam Siena, Kristopher Collins, William FidrychFidrych

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Screen Shots Screen Shots

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Screen ShotsScreen Shots

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Android TeamAndroid TeamSimilar Capabilities to Blackberry ProjectSimilar Capabilities to Blackberry Project

Wellness Diary and Medication AlarmIntegration with Google HealthMuch Improved ODL Screens

Male and Female FacesChange “Face” Based on Value

Tracking Prescriptions and Alarms Reports via. Google Charts

Ishmael Ishmael SmyrnowSmyrnow, Kevin , Kevin MorilloMorillo, James , James RedwayRedway

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iPhoneiPhone TeamTeamSimilar Capabilities to Blackberry ProjectSimilar Capabilities to Blackberry Project

Tracking of Conditions, Medications, and AllergiesODLs for:

Blood-Glucose, Peak-Flow, and HypertensionGeneration of ReportsSynchronization with Google Health

Brendan Heckman, Ryan Brendan Heckman, Ryan McGivernMcGivern, Matthew , Matthew FusaroFusaro

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Questions?Questions?

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