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
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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.
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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
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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.)
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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
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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)
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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
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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
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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?
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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
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
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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
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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
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TMR Architecture CSE 300
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CSE 300
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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.
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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.
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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
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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
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Screen Shots CSE 300
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Screen Shots CSE 300
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Screen Shots CSE 300
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Screen Shots CSE 300
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Screen Shots CSE 300
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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
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Screen Shots CSE 300
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Screen Shots CSE 300
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Screen Shots CSE 300
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Screen Shots CSE 300
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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
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Screen Shots CSE 300
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Screen Shots CSE 300
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Screen Shots CSE 300
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Screen Shots CSE 300
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Questions? CSE 300
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