bmiandcse-1 an overview of biomedical informatics and computing prof. steven a. demurjian, sr....

BMIandCSE-1

An Overview of An Overview of Biomedical Informatics and Computing Biomedical Informatics and Computing

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

The University of Connecticut371 Fairfield Road, Box U-255

Storrs, CT 06269-2155

[email protected]://www.engr.uconn.edu/~steve

(860) 486 - 4818

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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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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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What is BMI Used to Support?What is BMI Used to Support?

Clinical Practice Clinical Practice Dealing with Patients – Direct Medical CareDealing with Patients – Direct Medical Care

Hospital or Clinic Physician’s Office Testing Facility Insurance/Reimbursement

Tracking All Data Associated with PatientsTracking All Data Associated with Patients Medical Record Medical Tests (Lab, Diagnostic, Scans, etc.) Prescriptions

Stringent Data Protection (HIPAA)Stringent Data Protection (HIPAA) Distributed Repositories, Inability to Access Data in Distributed Repositories, Inability to Access Data in

Emergent Situations, Competition, etc.Emergent Situations, Competition, etc.

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What is Medical Informatics?What is Medical Informatics? Clinical Informatics, Pharmacy InformaticsClinical Informatics, Pharmacy Informatics Public Health InformaticsPublic Health Informatics Consumer Health InformaticsConsumer Health Informatics Nursing InformaticsNursing Informatics Systems and People Issues 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

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What is Bionformatics? What is Bionformatics? Focused on Research :Focused on Research :

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 Increasing Need to Tie These Separate Types of Systems Together = Personalized MedicineSystems Together = Personalized Medicine

Biology and the Bedside (Biology and the Bedside (www.i2b2.org)) Significant Expertise in BI in CS&E, MCB, Statistics, Significant Expertise in BI in CS&E, MCB, Statistics,

and UCHCand UCHC

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Where is Data/How is it Used?Where is Data/How is it Used? Medical and Administrative Data Found in Clinical Medical and Administrative Data Found in Clinical

Information Systems (CIS) Such As:Information Systems (CIS) Such As: Personal Health Records - Microsoft Healthvault Electronic Medical Records – OpenEMR Patient Portals E Prescribing (electronic Rx) Hospital Info. Systems Laboratory, Imaging and Other Systems Pharmacy, Nursing, Picture Archiving Systems Complex Data Storage and Retrieval – Many

Different Systems Research Increasingly Reliant on CISResearch Increasingly Reliant on CIS Jump to PDF Presentation with ScreenshotsJump to PDF Presentation with Screenshots

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What are Major Informatics Challenges?What are Major Informatics Challenges? Shortage of Trained People NationallyShortage of Trained People Nationally Slows adoption of Health Information TechnologySlows adoption of Health Information Technology Results in Poor Planning and Coordination, Results in Poor Planning and Coordination,

Duplication of Efforts and Incomplete EvaluationDuplication of Efforts and Incomplete Evaluation What are Critical Needs?What are Critical Needs?

CS/CSE/CompE with Health/Medical Domain Knowledge

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 Emerging Standards for Information Modeling and Exchange (Exchange (www.hl7.org) based on XML) based on XML

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Summary of Web Sites of Note:Summary of Web Sites of Note: AMIA (www.amia.org)AMIA (www.amia.org) IHE (http://www.ihe.net/)IHE (http://www.ihe.net/) Smartplatform (http://www.smartplatforms.org/)Smartplatform (http://www.smartplatforms.org/) Mysis MOSS (Mysis MOSS (http://www.misys.com/OpenSource)) NSF Clinical and Translational Science ProgramNSF Clinical and Translational Science Program

http://www.ctsaweb.org/ Emerging Patient Data StandardEmerging Patient Data Standard

http://www.hl7.org/ Informatics for Integrating Biology & the Bedside.Informatics for Integrating Biology & the Bedside.

https://www.i2b2.org/ Cancer Biomedical Informatics GridCancer Biomedical Informatics Grid

http://cabig.cancer.gov/index.asp

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BMI in Computing: InteroperabilityBMI in Computing: Interoperability Need to Integrate Across Health Care EnterpriseNeed to Integrate Across Health Care Enterprise

Practice management systems (PMS) for management of non-medical patient information

Electronic medical records (EMR) Decision Support Systems (both within and

external to EMRs) Medical laboratory information systems (MLIS) Personal health records (PHR) Electronic Prescribing Patient Portal (Tests, Appointments, Refills) Billing Systems

Employ Computing w.r.t. Standards, Interoperability, Software Architectures, Security, Privacy, Decision Support, etc.

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Stakeholders for HIE and Virtual ChartStakeholders for HIE and Virtual Chart

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Who are the Major Stakeholders?Who are the Major Stakeholders? PatientsPatients that require short-term treatments, long-term that require short-term treatments, long-term

treatments, emergency help, inpatient care, ambulatory treatments, emergency help, inpatient care, ambulatory care, home care, etc.care, home care, etc.

ProvidersProviders that administer care (MDs, medical that administer care (MDs, medical specialists, ER MDs, nurses, hospitals, long term care specialists, ER MDs, nurses, hospitals, long term care facilities, home health care, nurse practitioners, etc.)facilities, home health care, nurse practitioners, etc.)

Public health organizationsPublic health organizations that monitor health trends that monitor health trends and include disease control and prevention and include disease control and prevention organizations, medical associations, etc.organizations, medical associations, etc.

ResearchersResearchers that explore new health treatments, that explore new health treatments, medications, and medical devicesmedications, and medical devices

LaboratoriesLaboratories that conduct tests and include chemistry, that conduct tests and include chemistry, microbiology, radiology, blood, genome, etc.microbiology, radiology, blood, genome, etc.

PayersPayers that are responsible for cost management that are responsible for cost management

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What are Interoperability Issues?What are Interoperability Issues? In Computing: For heterogeneous software systems, In Computing: For heterogeneous software systems,

interoperability means exchanging information interoperability means exchanging information efficiently and without any additional effort of the userefficiently and without any additional effort of the user

For Medical Software Systems:For Medical Software Systems:

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Syntactic InteroperabilitySyntactic Interoperability Defined as the Ability to read and Write the Same File Defined as the Ability to read and Write the Same File

Formats and Communicate over Same ProtocolsFormats and Communicate over Same Protocols Available Solutions Include:Available Solutions Include:

Custom Adapter Interfaces XML Web Services Cloud Computing Standards and their Usage

CDA and HL7 (both in XML) OpenEHR (http://www.open-emr.org/) Continuity of Care Record (CCR

http://www.ccrstandard.com/)

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Semantic Interoperability Semantic Interoperability Defined as Defined as ability of systems to exchange data and

interpret information while automatically allowing said information to be used across the systems without user intervention and without additional agreements between the communicating parties

Must Understand the Data to be Integrated In a PHR – Patient may refer to “Stroke” In an EMR – Provider may indicate

“cerebrovascular incident” These need to be Reconciled Semantically

Available Technologies Include: SNOMED LOINC NDC

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BMI in Computing: SW ArchitecturesBMI in Computing: SW Architectures Can we Leverage Software Architectural Alternatives Can we Leverage Software Architectural Alternatives

from Computing:from Computing: Data Warehouse Service-Oriented Architectures Grid Computing Cloud Computing Publisher-Subscriber Paradigm Web-Architectures and Services

Objectives:Objectives: Understand their Capabilities in Support of Health

Information Exchange A Solution may Require a Combination of

Approaches

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Hybrid Architecture: Applied to Real SettingHybrid Architecture: Applied to Real Setting

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Patients

Providers

Clinical Researchers

BMI in Computing: SecurityBMI in Computing: Security

Web Server

Appl Server

DB Server

Firewall

https Encryptionhttps

Encryption

Encryption

Secure Communication

XML

html

Web Content

GUI Look and Feel

Patient GUI for RN vs. MD

Web - Control Services

Appl. – Control Methods

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Security Issues for PatientsSecurity Issues for Patients

HIPPA Overriding ConcernHIPPA Overriding Concern All Patient Interfaces Web-BasedAll Patient Interfaces Web-Based Secure CommunicationSecure Communication

To/From Web Server (https) Among Discussion Group Members

Is this https or Peer-to-Peer? Role-Based Access Control to AuthorizeRole-Based Access Control to Authorize

Providers to Interact PHR Data to Individual Providers

Patients Providers


Web-BasedPortal(XML + HL7)Open Source XML DB

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Security Issues for ProvidersSecurity Issues for Providers

Patients Providers


EMR

HIPPA Concerns for any EMR Data HIPPA Concerns for any EMR Data Transmitted into PortalTransmitted into Portal

Need to Consider DelegationNeed to Consider Delegation Provider P Access to Portal for

Patient X Provider Q on Call Can P Delegate his Permission to

Access Portal to Q? Will Q’s Role (e.g., EMT) Limit

Access Even with Delegation?

Web-BasedPortal(XML + HL7)Open Source XML DB

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Motivation: General ConceptsMotivation: General Concepts AuthenticationAuthentication

Proving you are who you are Signing a Message Is Client who s/he Says they are?

AuthorizationAuthorization Granting/Denying Access Revoking Access Does Client have Permission to do what s/he

Wants? EncryptionEncryption

Establishing Communications Such that No One but Receiver will Get the Content of the Message

Symmetric Encryption and Public Key Encryption

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Motivation: Type of Security IssuesMotivation: Type of Security Issues Legal and Ethical Issues Legal and Ethical Issues

Information that Must be Protected Information that Must be Accessible HIPPA vs. Emergent Health Situations

Policy Issues Policy Issues Who Can See What Information When? Applications Limits w.r.t. Data vs. Users?

System Level EnforcementSystem Level Enforcement What is Provided by the DBMS? Programming

Language? OS? Application? Web Server? Client? How Do All of the Pieces Interact?

Multiple Security Levels/Organizational EnforcementMultiple Security Levels/Organizational Enforcement Mapping Security to Organizational Hierarchy Protecting Information in Organization

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BMI: SecurityBMI: Security Security is Multi-Step, Multi-Discipline ProcessSecurity is Multi-Step, Multi-Discipline Process

Definition of Security Requirements Realization of Security at Web, Application, and

Database Levels Integration of Security from Client to Web to

Application to DB Rigorous Definition of Security Policy Dynamic Nature of Security Privileges Enforcement of Defined Privileges Across and within

Multiple Tiers Overall, Security in Today’s World Integral Part of Overall, Security in Today’s World Integral Part of

Everyday Life - Some Key ConcernsEveryday Life - Some Key Concerns Confidentiality of an Individuals Data – PHR/EMR Identity Theft Protecting National Infrastructure

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BMI Cell Phone ApplicationsBMI Cell Phone Applications Observations of Daily Living and PHRsObservations 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.

Medication/OTC/Supplement Tracking http://www.engr.uconn.edu/~steve/Cse4904/cse4904.htmlhttp://www.engr.uconn.edu/~steve/Cse4904/cse4904.html

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History of Mobile Computing 2009History of Mobile Computing 2009

Platform Symbian BlackBerry iPhoneWindows Mobile

Android

World market share 47.10% 19.50% 10.70% 12.40% > 1%

# US users 888,535 9,668,977 5,258,254 6,807,554 427,914

US market share 3.9% 41.9% 22.8% 29.5% 1.9%

Development C++ Java Objective C Windows Linux

Dev Environment Visual Studio Blackerry/Java Mac OSX Visual Studio Linux

Resolution various various 480x320 various various

Table 1: SmartPhone Varieties and Market Share in 2009.

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History of Mobile Computing – Aug 2013History of Mobile Computing – Aug 2013

Table 2: SmartPhone Varieties and Market Share in August 2013.

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History of Mobile Computing - TabletsHistory of Mobile Computing - TabletsTable 3: Tablet Market Share in Q2 2013.

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Semester Project in CSE2102 – Fall 2013Semester Project in CSE2102 – Fall 2013 Personal Health Assistant (PHA)Personal Health Assistant (PHA)

Patient Version for Medication and Chronic Disease Management and Authorizing Providers Identify Overmedication , adverse interactions, and

adverse reactions Provider Version for Viewing Patient Data that has

been Authorized Personal Health Record Microsoft HealthVaultPersonal Health Record Microsoft HealthVault

A Person Can Track Medical Information Used as Backend Repository to PHA

OpenEMR Standalone version for ProvidersOpenEMR Standalone version for Providers Seek to Integrate into PHA Support Medication Reconciliation

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Software Architecture DiagramSoftware Architecture Diagram

Personal HealthRecord (PHR)

Microsoft Healtvault

Figure 1: Architecture Diagram of the CSE2102 Project this Semester.

PHA Provider

OpenEMR

Medication & Observations of Chronic Disease Daily Living (ODL)Management

Apache/TomcatWeb/Application

Server

MySQL Database

Server

Medication/Supplement

Interaction Checker

ODL and ChronicDisease Analyzer

PHA Patient

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Architecture for CSE2102 in Fall 2013Architecture for CSE2102 in Fall 2013

Middle-Layer ServerWith REST API

Patient App

Security Policies

• Medications• Allergies• Procedures• Demographic

Provider List

Personal Health Assistant (PHA)

New External Sources

RxTerms

NDF-RT

RxNorm

XMLJSON

JSON

MS Health Vault

XM

L

ASP.Net API

Proivder App

Authorization by Role

• Medications• Allergies• Procedures• Demographic

Patient List

JAVA APIs

XM

LOpenEMR

NewInteractionChecker Screen

FDA DailyMeds

XML

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Four Part Semester Project in CSE2102Four Part Semester Project in CSE2102 Part 1: Installing TechnologiesPart 1: Installing Technologies

Android SDK, EclipseUML, openEMR Part 2a: Design and Implementation of Class LibraryPart 2a: Design and Implementation of Class Library

Meds, ODLs, Diseases, Exercise, Nutrition Part 2b: Expansion of PHA Android Source toPart 2b: Expansion of PHA Android Source to

Chronic Diseases, Exercise, Nutrition

Part 3: Integrating PHA with MS HealthVaultPart 3: Integrating PHA with MS HealthVault Use of REST API – Linkage to Common Server Read/Store Data from HealthVault

Part 4: Extending PHA and Integrating with openEMRPart 4: Extending PHA and Integrating with openEMR Medication Interactions – Use RxNorm, RxTerms,

NDF-RT and other Federal REST APIs Pull Medications from openEMR

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Android SDKAndroid SDK

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Android SDK ManagerAndroid SDK Manager

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Android Virtual Device ManagerAndroid Virtual Device Manager

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Android Virtual Device ManagerAndroid Virtual Device Manager

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PHA in Andriod EmulatorPHA in Andriod Emulator

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openEMRopenEMR

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iOS PHA – Patient VersioniOS PHA – Patient Version

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iOS PHA – Provider VersioniOS PHA – Provider Version

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Android PHA ScreenshotsAndroid PHA Screenshots

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ConclusionsConclusions Please Contact me with Questions on these TopicsPlease Contact me with Questions on these Topics Look for CSE Offerings in Coming YearsLook for CSE Offerings in Coming Years

Undergrad Bioinformatics Course CSE3800 – Usually each Fall Semseter

Undergrad Introduction to Biomedical Informatics In Spring – Cross Listed with CSE5810!

Lab Based Courses Software and Hardware Foci

Industry Sponsored Student Projects Undergraduate Info and Data Security Course

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CSE4904 – Spring 2010CSE4904 – Spring 2010 Smartphone Projects on ODLs and Other Medical Smartphone Projects on ODLs and Other Medical

Data Tracking and AlertsData Tracking and Alerts Three Platforms:Three Platforms:

Google’s Android (Java) Blackberry (Java) iPhone (Objective C)

Three Teams of Three Students EachThree Teams of Three Students Each Work ongoing this Semester Work ongoing this Semester

Joint CSE (4 students) and PharmD (4 students) CSE Fac (Demurjian) and PharmD Fac (Smith)

CSE4939W in Spring 2012CSE4939W in Spring 2012 Industry Sponsored Projects Cell/Mobile Platform Based

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Blackberry TeamBlackberry Team Ability to Track Information on ODLs and Ability to Track Information on ODLs and

PrescriptionsPrescriptions 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 FidrychAdam Siena, Kristopher Collins, William Fidrych

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Screen Shots Screen Shots

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Screen ShotsScreen Shots

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Android TeamAndroid Team Similar Capabilities to Blackberry ProjectSimilar 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 RedwayIshmael Smyrnow, Kevin Morillo, James Redway

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iPhone TeamiPhone Team Similar Capabilities to Blackberry ProjectSimilar 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 FusaroBrendan Heckman, Ryan McGivern, Matthew Fusaro

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PHA iOS ApplicationPHA iOS Application

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Main Menu & Settings MenuMain Menu & Settings Menu

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ProfileProfile

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MedicationsMedications

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Wellness DiaryWellness Diary

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Observations of Daily LivingObservations of Daily Living

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Dietary ManagementDietary Management

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bmiandcse-1 an overview of biomedical informatics and computing prof. steven a. demurjian, sr....

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