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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]
http://www.engr.uconn.edu/~steve
(860) 486 - 4818
IntroOH-1
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.
IntroOH-2
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
Information
Technology
Adapted from Shortcliff textbook
IntroOH-3
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.)
IntroOH-4
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
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
IntroOH-9
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
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
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
Systems Together = Personalized Medicine
Biology and the Bedside (www.i2b2.org)
IntroOH-12
Where is Data/How is it Used?
CSE
300
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
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 (www.hl7.org) 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: http://www.ctsaweb.org/
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.
http://cicats.uconn.edu/
IntroOH-15
CICATS
CSE
300
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
IntroOH-17
Summary of Web Sites of Note:
CSE
300
AMIA (www.amia.org)
IHE (http://www.ihe.net/)
Smartplatform (http://www.smartplatforms.org/)
Mysis MOSS (http://www.misys.com/OpenSource)
NSF Clinical and Translational Science Program
http://www.ctsaweb.org/
Emerging Patient Data Standard
http://www.hl7.org/
Informatics for Integrating Biology & the Bedside.
https://www.i2b2.org/
Cancer Biomedical Informatics Grid
http://cabig.cancer.gov/index.asp
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
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
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
IntroOH-20
Class Materials, Textbook, Projects, etc.
CSE
300
Course Web Site:
http://www.engr.uconn.edu/~steve/Cse300/cse300.html
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?
IntroOH-21
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
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
IntroOH-25
SmartPlatform
CSE
300
Substitutable Medical Apps, reusable technology
(http://www.smartplatforms.org/)
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
IntroOH-26
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
IntroOH-27
TMR Architecture
CSE
300
IntroOH-28
CSE
300
IntroOH-29
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.
IntroOH-30
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.
http://www.engr.uconn.edu/~steve/Cse4904/cse4904.html
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.
IntroOH-32
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
IntroOH-33
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
IntroOH-34
Screen Shots
CSE
300
IntroOH-35
Screen Shots
CSE
300
IntroOH-36
Screen Shots
CSE
300
IntroOH-37
Screen Shots
CSE
300
IntroOH-38
Screen Shots
CSE
300
IntroOH-39
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
IntroOH-40
Screen Shots
CSE
300
IntroOH-41
Screen Shots
CSE
300
IntroOH-42
Screen Shots
CSE
300
IntroOH-43
Screen Shots
CSE
300
IntroOH-44
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
IntroOH-45
Screen Shots
CSE
300
IntroOH-46
Screen Shots
CSE
300
IntroOH-47
Screen Shots
CSE
300
IntroOH-48
Screen Shots
CSE
300
IntroOH-49
Questions?
CSE
300
IntroOH-50