1. IntroOH-1 CSE 5810 CSE5810: Intro to Biomedical Informatics Prof. Steven A. Demurjian, Sr. Computer Science & Engineering Department The University of Connecticut 371 Fairfield Road, Box U-255 Storrs, CT 06269-2155 steve@engr.uconn.edu http://www.engr.uconn.edu/~steve (860) 486 - 4818

2. IntroOH-2 CSE 5810 What is Informatics?  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.

3. IntroOH-3 CSE 5810 What is Informatics?  Heterogeneous Field – Interaction between People, Information and Technology  Computer Science and Engineering  Social Science (Human Computer Interface)  Information Science (Data Storage, Retrieval and Mining) People Information Technology Informatics Adapted from Shortcliff textbook

4. IntroOH-4 CSE 5810 What is Biomedical Informatics (BMI)?  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.)  Clinical Informatics, Pharmacy Informatics, Consumer Health Informatics, Nursing Informatics

5. IntroOH-5 CSE 5810 What is Biomedical Informatics (BMI)?  A Exciting Emerging Discipline  Biomedical Informatics/Health Information Technology Rapidly Emerging Discipline  Cutting Edge, Incredible Career and Research Opportunities  Wide Range of Data  Clinical Data on Patients  Diagnostic Data (Scans, Labs, EKG, etc.)  Population Data (Public Health Surveillance)  Research on Genomic and Biological Data  Any Data Involved in  Care of Patients  Medical and Clinical Research

6. IntroOH-6 CSE 5810 Why is BMI/Clinical Practice Important?  Tracking all Information for Patient and his/her Care  Medical Record, Medical Tests (Lab, Diagnostic, Scans, etc.), Prescriptions  Dealing with Patients – Direct Medical Care  Hospital or Clinic, Physician’s Office  Testing Facility, Insurance/Reimbursement  Bringing Together Information for Different Sources  Health Information Exchange  Gather Data from MD Offices, Clinics, Hospitals  Informatics Support via:  Personal Health Records  Electronic Medical Record  Linking/Accessing Data Repositories  Collaborative and Secure (HIPPA) Web Portals

7. IntroOH-7 CSE 5810 © T. Shortliffe 2006 Columbia University

8. IntroOH-8 CSE 5810 BMI and Computer Science & Engineering  Significant Impact Across CS&E Fields Including:  Security and Data Protection/Privacy  Sensor Networks to Monitor Elderly  Artificial Intelligence &Clinical Decision Support  Software Architectures for Integrating Health Information  Bioinformatics (BI) to Process Biological Data  Supercomputing for Genomic and Clinical Data Analysis  Visualization to Conceptualize BMI/BI Data  Algorithms for BMI/Clinical Data Analysis  Mobile Computing to Impact Patient Health and Data Availability  Etc…

9. IntroOH-9 CSE 5810 Semester Topics (14.5 weeks)  Four Core Topics:  Introduction to BMI (1)  Informatics/Information and Standards (2)  Ontologies (0.5 weeks)  EHRs and PHRs and MockEMR (0.5)  Software Architectures and Interoperability (2)  Security and Dynamic Coalition Problem (4)  Service Based Computing (1)  CORBA, JINI,.NET, Interoperability, Web  Security  Discussion of Semester Project (1)  Outside Presentations (UCHC Faculty) and Student Presentations on Biomedical Informatics (2.5)

10. IntroOH-10 CSE 5810 Class Materials, Textbook, Projects, etc.  Course Web Site: http://www.engr.uconn.edu/~steve/Cse5810/cse5810.html  Reading List  Constant Updates and Changes  Textbook – out by end of January in Print  Biomedical Informatics: Computer Applications in Health Care and Biomedicine (Health Informatics), 4 th edition, Edward H. Shortliffe (Editor), James J. Cimino (Editor), ISBN-10: 0387289860  http://www.springer.com/978-1-4471-4473-1  http://www.amazon.com/Biomedical-Informatics- Computer-Applications-Biomedicine/dp/1447144732/  4 th edition on itunes and amazon kindle.  Questions? Comments? Suggestions?

11. IntroOH-11 CSE 5810 Biomedical Informatics Textbook (4 th edition) Springer - 2013

12. IntroOH-12 CSE 5810 Course Projects  Research Project (due end of semester)  Choose a Computer Science Topic  Explore the Topic related to BMI  Individual Project (due mid-semester)  Mobile Tools for Patients and Providers  Medication/Chronic Disease Management  Interactions and Exchange  Android and iOS Platforms  Team Project (due end of semester)  Explore Health Information Technology Systems  Explore Open Source and Other Solutions  Focus on Information Exchange and Interactions  No Exam

13. IntroOH-13 CSE 5810 Research Project  Deliverables  15 page paper  40-45 slide powerpoint  Three Samples on Web page  Potential Topics:  Security and Data Protection/Privacy  Sensor Networks to Monitor Elderly  Artificial Intelligence & Clinical Decision Support  Software Architectures for Integrating Health Information  Bioinformatics (BI) to Process Biological Data  Super /Grid computing for Genomic/Clinical Data Analysis  Visualization to Conceptualize BMI/BI Data  Algorithms for BMI/Clinical Data Analysis  Any other CSE topic Area  http://www.engr.uconn.edu/~steve/Cse5810/ResProj.pdf

14. IntroOH-14 CSE 5810 Individual Project – Current Software  Review Powerpoint Background Presentation  Extending the PHA Application Three Versions  Android PHA-Patient  iOS PHA-Patient  iOS PHA-Provider using Titanium/Javascript  Security Backend for PHA  Integration with External HIT Sytems  Microsoft HealthVault  OpenEMR  RxNorm, RxTerms, and NDF-RT Web Services

15. IntroOH-15 CSE 5810 Individual Project Possibilities   Primary Projects P1 Extending Android PHA-Patient with Improved Med Reconciliation, Data storage in MSHV, and Security P2 Extending Titanium/iOS PHA-Patient with missing Capabilities from Android PHA-Patient P3 Extending iOS PHA-Provider: Complete Functions P4 Creating Android PHA-Provider: Using iOS PHA-Provider as Guide  In addition, for P1 and P2, Institute Data Consistency Checks on all Values Entered  http://www.engr.uconn.edu/~steve/Cse5810/individualproject.docx

16. IntroOH-16 CSE 5810 Individual Project Possibilities   Secondary Projects S1 Advanced Medication/OTC/NS Data Entry using UPC and NDC Codes S2 Patient/Provider Communication across PHAs Real-Time Chat Secure Email or Text Messaging S3 Adding Tailored Education Materials to PHA S4 Adding On-Line Support Groups to PHA   Chose one Primary Project  Complete by End of 1 st Week   Choose one Secondary Project  Complete by Tuesday after Spring Break

17. IntroOH-17 CSE 5810 Comparing PHA Versions

18. IntroOH-18 CSE 5810 Team Project  Objectives  Explore larger scale Health Information Technology Systems and their Interaction  Support Interoperability via XML and Other Standards  Team Structure  Work in Teams of 4 to 6 students  18 students in Class – so Four Teams  http://www.engr.uconn.edu/~steve/Cse5810/teamproject.docx

19. IntroOH-19 CSE 5810 Proposed Projects  Health Information Exchange (HIE) Team of 4 - 5  Among OpenEMR, WorldVista, SMART EMR  Multiple Instance of First Two  Varied Granularity Level for Data Exchange  Records, Patients, Entire Data Set  Programmatically, Databases, or APIs  Promote Framework for HIE  HIT Infra-structure for UConn/UCHC Team of 4 - 5  Expand Utility of MSHV and OpenEMR  Include Additional Modules  Include Capabilities for Triggers, etc.  Expand APIs to Facilitate Easy Usage of Both for Web-Based and Mobile Apps

20. IntroOH-20 CSE 5810 Proposed Projects  Evolving SpoonfedMD Team of 4  Transition SpoonfedMD as to BMI Domain  Intelligent Tutoring System  Web-based Infrastructure Backend  Mobile Computing Front End  Clinical Decision Support (CDS) Team of 5-6  Incorporate CDS into Open EMR  Set up Infrastructure in MSHV to Support Data Collection  Develop Various Analysis of Disease and ODL data for PHA  Server-Side CDS and Client Side PHAs  Upgrade P1 to P4 with CDS

21. IntroOH-21 CSE 5810 Chosen Team Projects  Health Information Exchange (HIE) Team of 9  Among OpenEMR, WorldVista, SMART EMR  Multiple Instance of First Two  Varied Granularity Level for Data Exchange  Records, Patients, Entire Data Set  Programmatically, Databases, or APIs  Promote Framework for HIE  HIT Infra-structure for UConn/UCHC Team of 6  Expand Utility of MSHV and OpenEMR  Include Additional Modules  Include Capabilities for Triggers, etc.  Expand APIs to Facilitate Easy Usage of Both for Web-Based and Mobile Apps

22. IntroOH-22 CSE 5810 T1 TeamT2 Team  Albayram, Yusuf  Baihan, Mohammed  Devoe, Gordon  Diffenderfer, Joshua  Etim, David  Martin, Robert  Moledina,Saahil  Papavasileiou, Ioannis  Rivera Sanchez, Yaira  Sanzi, Eugene  Algwaiz,Aljoharah  Billava, Ashish  Lopez, Kevin  Mathur, Anubhav  Mathur, Nitish  Shao, Xian

23. IntroOH-23 CSE 5810 Team T1 Advice  Survey and Identify Other Open Source and Freely Available EMRs  For each EMR Assess regarding  Database Platform and Accessibility  APIs  Patient vs. Provider Access  Availability of Patient Portal, PHR, ePrescribing  Support for CDS  Explore Capabilities of Each re. Exporting/Importing via Standards and File Formats  Review HIE and other Interop PPlatforms such as: (http://www.nchica.org/HIT_HIE/NHIN.htm ), Connect (http://www.connectopensource.org/), and http://wiki.directproject.org/home and http://wiki.directproject.org/Best+Practices+for+HISPs http://wiki.directproject.org/Best+Practices+for+HISPs  http://www.cms.gov/Regulations-and- Guidance/Legislation/EHRIncentivePrograms/Certification.html

24. IntroOH-24 CSE 5810 Team T1 Division of Work Suggestions  Identify Two Individuals to co-Lead the Team  Search and Identify EMR Open Source Platforms  Try to Identify 9 Platforms (1 per team member)  OpenEMR, World Vista, OpenMRS, gaiaehr  If less than 9 …Two Options  Look for Commercial Products with well-Defined APIs/Web Services/Import/Export Capabilities OR  Look for Open Source Platforms such as Harvard SMART, open mhealth, etc.  Explore Capabilities of Each (Comparison Metric) in terms of import/export/CCR/CDA/etc. See Matrix  Objective – Propose Blueprint for Their Integration

25. IntroOH-25 CSE 5810 OEMR Export/Exchange Patient Data Set Filter Option Patient Set Size ScenarioExport Format Path after Sign In. Role Req. Tech Skill Req. Nativ e Setup Backup All Data (no subset)N/AAll PatientsBackup or migration SQL Create Statement Admin> Create Backup AdminNoYes Batch Personal Financial HIPAA Provider Age range App Date HIPAA All PatientsList of data with non clinical info for exchange CSV, Email, Phone Call List Misc> Batch> Process AdminNoYes SQL All DataSQL Filter Any Patient Set Size Granular data search and export CSVMisc> Batch> Process AdminSQLNo CCR Patient Demographics, Immunizations, Vital Signs, Problems & Diagnoses, Insurance Information, Health Care Providers, Encounter Information, Allergies/Alerting Data, Appropriate Results, Medication, Procedures, Results, Necessary Medical Equipment, Social History, Statistics, Family History, Care Plan Date Range Single PatientPrint and handoutWebPatient> Demo.> Reports> Button Admin; Physician; Clinician; FrontOffice Accounting NoYes CCD Header, Purpose, Problems, Procedures, Family history, Social history, Payers, Advance directives, Alerts, Medications, Immunizations, Medical equipment, Vital signs, Functional stats, Results, Encounters, Plan of care N/ASingle PatientPrint and handoutWebPatient> Demo.> Reports> Button Admin; Physician; Clinician; FrontOffice Accounting NoYes EMR Direct Header, Purpose, Problems, Procedures, Family history, Social history, Payers, Advance directives, Alerts, Medications, Immunizations, Medical equipment, Vital signs, Functional stats, Results, Encounters,Plan of care N/ASingle PatientMessages are processed and a new Patient Note is delivered to a specified user and appears in that user's Message and Reminder Center. WebPatient > Demo > Reports > Transmit Admin; Physician; Clinician; FrontOffice Accounting No Export All Data (no subset)N/AAll PatientsFast and easy export of entire data set. CSV, CSV, LaTeX, PDF, SQL, YAML Admin > Database > Export Button AdminDatabase - PHPMyAd min No

26. IntroOH-26 CSE 5810 Team T2 Advice  Explore the Open Community and Wiki for OpenEMR  Search for Universities Using OpenEMR in a Classsetting  Search for Free Addons/Plug-ins for  Patient Portal and PHR  ePrescribing, and others  Expand existing APIs with ability to retrieve, store, exchange and display information in MSHV and OpenEMR – Assess Backend impact of to PHA  Design a set of Generalized APIs towards an ability to allow Interactions with an PHR/EMR Combination  Demonstrate Generalized APIs by Adding API for another EMR and another PHR.  Each Team Member Must Decide  Focus on Addons/Usability (1/2 team?)  Focus on API Development (1/2 team?)  http://www.cms.gov/Regulations-and- Guidance/Legislation/EHRIncentivePrograms/Certification.html

27. IntroOH-27 CSE 5810 Team T2 Division of Work Suggestions  Identify One Individual to Lead the Team  Each Team Member should  Immerse Him/Herself into the OpenEMR Community (wiki)  Conduct Web Searches for AddOns  Divide Responsibilities by:  Entire Team Should  Provide Detailed Survey of Adds on Including an Assessment/Evaluation of Each  Propose Recommendations of AddOns  Expand Current APIs for MHSV/OpenEMR  Using REST to “Hide” both Behind the Scene  REST Implement call Product APIs  Develop New APIS for AddOns If Relevant

28. IntroOH-28 CSE 5810 OEMR Export/Exchange Patient Data Set Filter Option Patient Set Size ScenarioExport Format Path after Sign In. Role Req. Tech Skill Req. Nativ e Setup Backup All Data (no subset)N/AAll PatientsBackup or migration SQL Create Statement Admin> Create Backup AdminNoYes Batch Personal Financial HIPAA Provider Age range App Date HIPAA All PatientsList of data with non clinical info for exchange CSV, Email, Phone Call List Misc> Batch> Process AdminNoYes SQL All DataSQL Filter Any Patient Set Size Granular data search and export CSVMisc> Batch> Process AdminSQLNo CCR Patient Demographics, Immunizations, Vital Signs, Problems & Diagnoses, Insurance Information, Health Care Providers, Encounter Information, Allergies/Alerting Data, Appropriate Results, Medication, Procedures, Results, Necessary Medical Equipment, Social History, Statistics, Family History, Care Plan Date Range Single PatientPrint and handoutWebPatient> Demo.> Reports> Button Admin; Physician; Clinician; FrontOffice Accounting NoYes CCD Header, Purpose, Problems, Procedures, Family history, Social history, Payers, Advance directives, Alerts, Medications, Immunizations, Medical equipment, Vital signs, Functional stats, Results, Encounters, Plan of care N/ASingle PatientPrint and handoutWebPatient> Demo.> Reports> Button Admin; Physician; Clinician; FrontOffice Accounting NoYes EMR Direct Header, Purpose, Problems, Procedures, Family history, Social history, Payers, Advance directives, Alerts, Medications, Immunizations, Medical equipment, Vital signs, Functional stats, Results, Encounters,Plan of care N/ASingle PatientMessages are processed and a new Patient Note is delivered to a specified user and appears in that user's Message and Reminder Center. WebPatient > Demo > Reports > Transmit Admin; Physician; Clinician; FrontOffice Accounting No Export All Data (no subset)N/AAll PatientsFast and easy export of entire data set. CSV, CSV, LaTeX, PDF, SQL, YAML Admin > Database > Export Button AdminDatabase - PHPMyAd min No