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Topics in BMI: Course Objectives CSE 300

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] (860) 486 - 4818


What is Informatics?  CSE 300

Informatics is:  Management and Processing of Data  From Multiple Sources/Contexts  Involves Classification (Ontologies), Collection, Storage, Analysis, Dissemination Informatics is Multi-Disciplinary  Computing (Model, Store, Process Information)  Social Science (User Interactions, HCI)  Statistics (Analysis) Informatics Can Apply to Multiple Domains:  Business, Biology, Fine Arts, Humanities  Pharmacology, Nursing, Medicine, etc.


What is Informatics?  CSE 300

Heterogeneous Field – Interaction between People, Information and Technology  Computer Science and Engineering  Social Science (Human Computer Interface)  Information Science (Data Storage, Retrieval and Mining)

Informatics People



Adapted from Shortcliff textbook


What is Biomedical Informatics (BMI)?  CSE 300

BMI is Information and its Usage Associated with the 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.)


What are Key BMI Focal Areas?  CSE 300

T1 Research  Transition Bench Results into  Clinical Research Clinical Research  Applying Clinical Research Results via Trials with Patients on Medication, Devices, Treatment Plans T2 Research  Translating “Successful” Clinical Trials into Practice and the Community Clinical Practice  Tracking all of the Information Associated with a Patient and his/her Care Integrated and Inter-Disciplinary Information Spectrum IntroOH-5

Where/How is BMI Utilized? CSE 300

T1 Research (Bench  Clinical)  Transfer of Knowledge from Laboratory or Bench to Clinical Trials  Move Genomic Research from Bench (Lab) to Clinical Trial (or Genetic/Test Intervention)  Transfer in Lab/Bench Research to Pre-Clinical and Early Clinical Human Subject Research  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 IntroOH-6

Where/How is BMI Utilized? CSE 300

Clinical Research (Trials)  Wide Range of Implications from Medical Treatment to Medication Regime  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 IntroOH-7

Where/How is BMI Utilized? CSE 300

Clinical Research (Trials)  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    

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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 Apply Bad Results in IV – Pull Drug (Vioxx) IntroOH-8

Where/How is BMI Utilized? CSE 300

T2 Research (Clinical Research Practice/Community)  Practice-Oriented Translation Research  Results: Clinical Trails  Clinical Practice  Strategies for Establishing/Implementing New Technologies  Improvements in Practice  New Evidence-Based Guidelines  New Care Models  Phase III Success Translated to Health Providers  Examples  Statin Drugs (Lipitor) and Exercise  New Treatment Regime for Chronic Disease


Where/How is BMI Utilized? CSE 300

Clinical Practice  Dealing with Patients – Direct Medical Care  Hospital or Clinic  Physician’s Office  Testing Facility  Insurance/Reimbursement  Tracking All Data Associated with Patients  Medical Record  Medical Tests (Lab, Diagnostic, Scans, etc.)  Prescriptions  Stringent Data Protection (HIPAA)  Distributed Repositories, Inability to Access Data in Emergent Situations, Competition, etc. IntroOH-10

What is Medical Informatics?  CSE 300

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Clinical Informatics, Pharmacy Informatics Public Health Informatics Consumer Health Informatics Nursing Informatics 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 IntroOH-11

What is Bionformatics?  CSE 300

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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 (  Often Requires Grid Computing  Includes Cancer and Immunology Research Increasing Need to Tie These Separate Types of Systems Together = Personalized Medicine Biology and the Bedside (


Where is Data/How is it Used?  CSE 300

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Medical And Administrative Data Found in Clinical 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 CIS T2 Research is Reliant on:  End Systems for Embedding EBM (EvidenceBased Medicine) Guidelines  Measuring Outcomes, Looking at Policy IntroOH-13

What are Major Informatics Challenges?  CSE 300

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Shortage of Trained People Nationally Slows adoption of Health Information Technology Results in Poor Planning and Coordination, Duplication of Efforts and Incomplete Evaluation 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 Exchange ( based on XML IntroOH-14

What is UConn Doing in this Area?  CSE 300

NIH’s CTSA Program: Transform the Way Clinical and 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: Under 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.  IntroOH-15


Official Launching:  Tuesday September 29, 10:30am-1:30pm  UConn Global Business Learning Center, Hartford  Speakers Include: Pres. M. Hogan, Provost P. Nichols, and Dean Cato Laurencin (Med School) Mission:  to educate and nurture new scientists  to increase clinical and translational research being conducted at UCHC, regional hospitals, UConn Storrs, and healthcare organizations throughout greater Hartford  to work collaboratively with regional stakeholders to combat the leading causes of morbidity, mortality, disability, and health disparities CICATS will have Biomedical Informatics Center IntroOH-16

Biomedical Informatics in CICATS CSE 300


Summary of Web Sites of Note:  CSE 300

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AMIA ( IHE ( Smartplatform ( Mysis MOSS ( NSF Clinical and Translational Science Program  Emerging Patient Data Standard  Informatics for Integrating Biology & the Bedside.  Cancer Biomedical Informatics Grid  IntroOH-18

Semester Topics (weeks)  CSE 300

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

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Discussion of Semester Project (0.5) Presentations by Outside Speakers (2.5) Student Presentations on Biomedical Informatics Materials (3) IntroOH-19

Planned Speakers  CSE 300

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Dr. L. Fagan, Co-Director, Stanford Biomedical Informatics Training Program, March 31 Dr. M. Smith, Pharmacy Practice, UConn, April 5 Dr. T. Shortliffe, President, AMIA, April 28 Others to be Scheduled:  Dr. Thomas Agresta  Dr. Michael Blechner  Dr. Xiaoyan Wang


Class Materials, Textbook, Projects, etc.  CSE 300

Course Web Site:  Reading List  Constant Updates and Changes Textbook

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 weeks Project 2 – Out in 2 weeks Team Project – Out in 2 weeks as well Questions? Comments? Suggestions? 

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Course Projects and Exam (???) …  CSE 300

Individual/Team Course Project(s) Throughout the Semester  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!) IntroOH-22

Individual Semester Projects  CSE 300

Readings, Readings, and More Readings Project 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 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 IntroOH-23

Semester Project  CSE 300

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) IntroOH-24

Semester Project Objectives  CSE 300

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Objective – Wide Scale Open Source Framework Envision Plug and Play Architecture High Reliance on Open Source Solutions for PHR and EMR Support Interoperability to Components via XML and Standards Develop Complete, Integrated, and Extensible Framework


SmartPlatform  CSE 300

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Substitutable Medical Apps, reusable technology  ( NSF/NIH Funded SHARP Proposal at Harvard Intended to: “A platform with substitutable apps constructed around core services is a promising approach to driving down healthcare costs, supporting standards evolution, accommodating differences in care workflow, fostering competition in the market, and accelerating innovation” Likely Led by Timo Ziminski


Personal Health Records  CSE 300

Google 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 Interoperability


TMR Architecture CSE 300


CSE 300


XML (HL7/CDA) to i2b2 DB Translation  CSE 300

Work with Dr. Michael Blechner (UCHC BMI Faculty Member) 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.


Cell Phone Applications  CSE 300

RWJ Project Health Design Observations 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. IntroOH-31

Focus of Grant  CSE 300

Management of Two Diseases in Women of Color  Obesity and Osteoarthritis Team  TRIPP (Crowell, Fifield) and AHFP (Agresta)  SisterTalk (Headley) and CHCAT (Granger)  UConn Storrs (Demurjian) and Netsoft (Collins) Providers

Web/Application Server

SQL Server Database

Microsoft HealthVault Patient Demographics and ODLs

Patients Researchers Client Side Technologies https, html, Ajax, XML Server Side Technologies Java, JSP, Hibernate, Relational Database, XML

Lifelines Repository

Figure 1: Architecture Diagram of the Proposed System.


CSE4904 – Spring 2010  CSE 300

Smartphone Projects on ODLs and Other Medical Data Tracking and Alerts Three Platforms:  Google’s Android (Java)  Blackberry (Java)  iPhone (Objective C) Three Teams of Three Students Each


Blackberry Team  CSE 300

Ability to Track Information on ODLs and Prescriptions  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 Fidrych


Screen Shots CSE 300


Screen Shots CSE 300


Screen Shots CSE 300


Screen Shots CSE 300


Screen Shots CSE 300


Android Team  CSE 300

Similar 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 Redway 


Screen Shots CSE 300


Screen Shots CSE 300


Screen Shots CSE 300


Screen Shots CSE 300


iPhone Team  CSE 300

Similar 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 Fusaro 


Screen Shots CSE 300


Screen Shots CSE 300


Screen Shots CSE 300


Screen Shots CSE 300


Questions? CSE 300


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