topics in bmi: course objectives
DESCRIPTION
Topics in BMI: Course Objectives. Prof. Steven A. Demurjian, Sr. Computer Science & Engineering Department The University of Connecticut 371 Fairfield Road, Box U-255 Storrs, CT 06269-2155. [email protected] http://www.engr.uconn.edu/~steve (860) 486 - 4818. What is Informatics?. - PowerPoint PPT PresentationTRANSCRIPT
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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 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?