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CSE5810

CSE5810: Intro to Biomedical InformaticsCSE5810: Intro to Biomedical Informatics

Prof. Steven A. Demurjian, Sr. Computer Science & Engineering Department

The University of Connecticut371 Fairfield Road, Box U-255

Storrs, CT 06269-2155

steve@engr.uconn.eduhttp://www.engr.uconn.edu/~steve

(860) 486 - 4818

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CSE5810

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.) Clinical Informatics, Pharmacy Informatics,

Consumer Health Informatics, Nursing Informatics

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What is Biomedical Informatics (BMI)?What is Biomedical Informatics (BMI)? A Exciting Emerging DisciplineA Exciting Emerging Discipline Biomedical Informatics/Health Information Biomedical Informatics/Health Information

Technology Rapidly Emerging DisciplineTechnology Rapidly Emerging Discipline Cutting Edge, Incredible Career and Research Cutting Edge, Incredible Career and Research

OpportunitiesOpportunities Wide Range of DataWide 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 Any Data Involved in Care of Patients Medical and Clinical Research

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Why is BMI/Clinical Practice Important?Why is BMI/Clinical Practice Important? Tracking all Information for Patient and his/her CareTracking all Information for Patient and his/her Care

Medical Record, Medical Tests (Lab, Diagnostic, Scans, etc.), Prescriptions

Dealing with Patients – Direct Medical CareDealing with Patients – Direct Medical Care Hospital or Clinic, Physician’s Office Testing Facility, Insurance/Reimbursement

Bringing Together Information for Different SourcesBringing Together Information for Different Sources Health Information Exchange Gather Data from MD Offices, Clinics, Hospitals

Informatics Support via:Informatics Support via: Personal Health Records Electronic Medical Record Linking/Accessing Data Repositories Collaborative and Secure (HIPPA) Web Portals

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© T. Shortliffe 2006 Columbia University© T. Shortliffe 2006 Columbia University

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CSE5810

BMI and Computer Science & EngineeringBMI and Computer Science & Engineering Significant Impact Across CS&E Fields Including: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…

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Semester Topics (14.5 weeks)Semester Topics (14.5 weeks) Four Core Topics: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)Discussion of Semester Project (1) Outside Presentations (UCHC Faculty) and Student Outside Presentations (UCHC Faculty) and Student

Presentations on Biomedical Informatics (2.5) Presentations on Biomedical Informatics (2.5)

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CSE5810

Class Materials, Textbook, Projects, etc.Class Materials, Textbook, Projects, etc. Course Web Site: Course Web Site:

http://www.engr.uconn.edu/~steve/Cse5810/cse5810.htmlhttp://www.engr.uconn.edu/~steve/Cse5810/cse5810.html Reading ListReading List

Constant Updates and Changes Textbook – out by end of January in PrintTextbook – out by end of January in Print

Biomedical Informatics: Computer Applications in Health Care and Biomedicine (Health Informatics), 4th 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/ 4th edition on itunes and amazon kindle.

Questions? Comments? Suggestions?Questions? Comments? Suggestions?

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Biomedical Biomedical Informatics Informatics TextbookTextbook

(4(4thth edition) edition)

Springer - 2013

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Course Projects Course Projects Research Project (due end of semester)Research Project (due end of semester)

Choose a Computer Science Topic Explore the Topic related to BMI

Individual Project (due mid-semester)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)Team Project (due end of semester) Explore Health Information Technology Systems Explore Open Source and Other Solutions Focus on Information Exchange and Interactions

No ExamNo Exam

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Research ProjectResearch Project DeliverablesDeliverables

15 page paper 40-45 slide powerpoint Three Samples on Web page

Potential Topics: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.pdfhttp://www.engr.uconn.edu/~steve/Cse5810/ResProj.pdf

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Individual Project – Current SoftwareIndividual Project – Current Software Review Powerpoint Background PresentationReview Powerpoint Background Presentation Extending the PHA Application Three VersionsExtending 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 SytemsIntegration with External HIT Sytems Microsoft HealthVault OpenEMR RxNorm, RxTerms, and NDF-RT Web Services

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CSE5810

Individual Project PossibilitiesIndividual Project Possibilities Primary Projects

P1 Extending Android PHA-Patient with Improved Med Reconciliation, Data storage in MSHV, and SecurityP2 Extending Titanium/iOS PHA-Patient with missing Capabilities from Android PHA-Patient P3 Extending iOS PHA-Provider: Complete FunctionsP4 Creating Android PHA-Provider: Using iOS PHA-Provider as Guide

In addition, for P1 and P2, Institute Data Consistency In addition, for P1 and P2, Institute Data Consistency Checks on all Values EnteredChecks on all Values Entered

http://www.engr.uconn.edu/~steve/Cse5810/individualproject.docxhttp://www.engr.uconn.edu/~steve/Cse5810/individualproject.docx

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Individual Project PossibilitiesIndividual Project Possibilities Secondary Projects

S1 Advanced Medication/OTC/NS Data Entry using UPC and NDC CodesS2 Patient/Provider Communication across PHAs

Real-Time Chat

Secure Email or Text MessagingS3 Adding Tailored Education Materials to PHAS4 Adding On-Line Support Groups to PHA

Chose one Primary ProjectComplete by End of 1st Week

Choose one Secondary ProjectComplete by Tuesday after Spring Break

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Comparing PHA VersionsComparing PHA Versions

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Team ProjectTeam Project ObjectivesObjectives

Explore larger scale Health Information Technology Systems and their Interaction

Support Interoperability via XML and Other Standards

Team StructureTeam Structure Work in Teams of 4 to 6 students 18 students in Class – so Four Teams

http://www.engr.uconn.edu/~steve/Cse5810/teamproject.docxhttp://www.engr.uconn.edu/~steve/Cse5810/teamproject.docx

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CSE5810

Proposed ProjectsProposed Projects Health Information Exchange (HIE) Health Information Exchange (HIE) Team of 4 - 5Team 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 HIT Infra-structure for UConn/UCHC Team of 4 - 5Team 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

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Proposed ProjectsProposed Projects Evolving SpoonfedMD Evolving SpoonfedMD Team of 4 Team of 4

Transition SpoonfedMD as to BMI Domain Intelligent Tutoring System Web-based Infrastructure Backend Mobile Computing Front End

Clinical Decision Support (CDS) Clinical Decision Support (CDS) Team of 5-6Team 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

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Chosen Team ProjectsChosen Team Projects Health Information Exchange (HIE) Health Information Exchange (HIE) Team of 9Team 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 HIT Infra-structure for UConn/UCHC Team of 6Team 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

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T1 TeamT1 Team T2 TeamT2 Team Albayram, YusufAlbayram, Yusuf Baihan, MohammedBaihan, Mohammed Devoe, Gordon Devoe, Gordon Diffenderfer, Joshua Diffenderfer, Joshua Etim, DavidEtim, David Martin, RobertMartin, Robert Moledina,SaahilMoledina,Saahil Papavasileiou, IoannisPapavasileiou, Ioannis Rivera Sanchez, YairaRivera Sanchez, Yaira Sanzi, Eugene Sanzi, Eugene

Algwaiz ,AljoharahAlgwaiz ,Aljoharah Billava, Ashish Billava, Ashish Lopez, KevinLopez, Kevin Mathur, AnubhavMathur, Anubhav Mathur, NitishMathur, Nitish Shao, XianShao, Xian

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Team T1 AdviceTeam T1 Advice Survey and Identify Other Open Source and Freely Available Survey and Identify Other Open Source and Freely Available

EMRsEMRs For each EMR Assess regardingFor 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 Explore Capabilities of Each re. Exporting/Importing via Standards and File FormatsStandards and File Formats

Review HIE and other Interop PPlatforms such as: Review HIE and other Interop PPlatforms such as: (http://www.nchica.org/HIT_HIE/NHIN.htm ), Connect (http://www.nchica.org/HIT_HIE/NHIN.htm ), Connect (http://www.connectopensource.org/), and (http://www.connectopensource.org/), and http://wiki.directproject.org/home and http://wiki.directproject.org/home and http://wiki.directproject.org/Best+Practices+for+HISPs http://www.cms.gov/Regulations-and-Guidance/Legislation/

EHRIncentivePrograms/Certification.html

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Team T1 Division of Work SuggestionsTeam T1 Division of Work Suggestions Identify Two Individuals to co-Lead the TeamIdentify Two Individuals to co-Lead the Team Search and Identify EMR Open Source PlatformsSearch 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 Explore Capabilities of Each (Comparison Metric) in

terms of import/export/CCR/CDA/etc. See Matrixterms of import/export/CCR/CDA/etc. See Matrix Objective – Propose Blueprint for Their Integration Objective – Propose Blueprint for Their Integration

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CSE5810

OEMRExport/Exchange

PatientData Set

FilterOption

PatientSet Size

Scenario ExportFormat

Path afterSign In.

RoleReq.

Tech Skill Req.

NativeSetup

BackupAll Data (no subset) N/A All Patients Backup or

migrationSQL CreateStatement

Admin>CreateBackup

Admin No Yes

BatchPersonalFinancialHIPAAProvider

Age range App DateHIPAA

All Patients List of data with non clinical info for exchange

CSV, Email, Phone Call List

Misc>Batch>Process

Admin No Yes

SQLAll Data SQL

FilterAny PatientSet Size

Granular data search and export

CSV Misc>Batch>Process

Admin SQL No

CCRPatient 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 Patient Print and handout Web Patient> Demo.> Reports> Button

Admin; Physician;Clinician;FrontOfficeAccounting

No Yes

CCDHeader, 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/A Single Patient Print and handout Web Patient> Demo.> Reports> Button

Admin; Physician;Clinician;FrontOfficeAccounting

No Yes

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/A Single Patient Messages are processed and a new Patient Note is delivered to a specified user and appears in that user's Message and Reminder Center.

Web Patient > Demo > Reports > Transmit

Admin; Physician;Clinician;FrontOfficeAccounting

No No

ExportAll Data (no subset) N/A All Patients Fast and easy export

of entire data set.CSV, CSV, LaTeX, PDF, SQL, YAML

Admin > Database > Export Button

Admin Database -PHPMyAdmin

No

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Team T2 AdviceTeam T2 Advice Explore the Open Community and Wiki for OpenEMRExplore the Open Community and Wiki for OpenEMR Search for Universities Using OpenEMR in a ClasssettingSearch for Universities Using OpenEMR in a Classsetting Search for Free Addons/Plug-ins forSearch 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 Demonstrate Generalized APIs by Adding API for another EMR and another PHR.and another PHR.

Each Team Member Must DecideEach 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

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Team T2 Division of Work SuggestionsTeam T2 Division of Work Suggestions Identify One Individual to Lead the TeamIdentify One Individual to Lead the Team Each Team Member shouldEach Team Member should

Immerse Him/Herself into the OpenEMR Community (wiki)

Conduct Web Searches for AddOns Divide Responsibilities by:

Entire Team ShouldEntire 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

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CSE5810

OEMRExport/Exchange

PatientData Set

FilterOption

PatientSet Size

Scenario ExportFormat

Path afterSign In.

RoleReq.

Tech Skill Req.

NativeSetup

BackupAll Data (no subset) N/A All Patients Backup or

migrationSQL CreateStatement

Admin>CreateBackup

Admin No Yes

BatchPersonalFinancialHIPAAProvider

Age range App DateHIPAA

All Patients List of data with non clinical info for exchange

CSV, Email, Phone Call List

Misc>Batch>Process

Admin No Yes

SQLAll Data SQL

FilterAny PatientSet Size

Granular data search and export

CSV Misc>Batch>Process

Admin SQL No

CCRPatient 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 Patient Print and handout Web Patient> Demo.> Reports> Button

Admin; Physician;Clinician;FrontOfficeAccounting

No Yes

CCDHeader, 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/A Single Patient Print and handout Web Patient> Demo.> Reports> Button

Admin; Physician;Clinician;FrontOfficeAccounting

No Yes

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/A Single Patient Messages are processed and a new Patient Note is delivered to a specified user and appears in that user's Message and Reminder Center.

Web Patient > Demo > Reports > Transmit

Admin; Physician;Clinician;FrontOfficeAccounting

No No

ExportAll Data (no subset) N/A All Patients Fast and easy export

of entire data set.CSV, CSV, LaTeX, PDF, SQL, YAML

Admin > Database > Export Button

Admin Database -PHPMyAdmin

No