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 (860)

IntroOH-2 CSE 5810 Biomedical Informatics  Biomedical informatics (BMI) is the interdisciplinary field that studies and pursues the effective uses of biomedical data, information, and knowledge for scientific inquiry, problem solving, and decision making, motivated by efforts to improve human health. © 2014, W. Yasnoff, Uconn Health Center

IntroOH-3 CSE 5810 BMI: Corollaries to the Definition 1. BMI develops, studies and applies theories, methods and processes for the generation, storage, retrieval, use, and sharing of biomedical data, information, and knowledge. 2. BMI builds on computing, communication and information sciences and technologies and their application in biomedicine. © 2014, W. Yasnoff, Uconn Health Center

IntroOH-4 CSE 5810 BMI: Corollaries to the Definition 3. BMI investigates and supports reasoning, modeling, simulation, experimentation and translation across the spectrum from molecules to populations, dealing with a variety of biological systems, bridging basic and clinical research and practice, and the healthcare enterprise. 4. BMI, recognizing that people are the ultimate users of biomedical information, draws upon the social and behavioral sciences to inform the design and evaluation of technical solutions and the evolution of complex economic, ethical, social, educational, and organizational systems. © 2014, W. Yasnoff, Uconn Health Center

IntroOH-5 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.

IntroOH-6 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

IntroOH-7 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

IntroOH-8 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

IntroOH-9 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

IntroOH-10 CSE 5810 What is Bionformatics?  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 (

IntroOH-11 CSE 5810 © T. Shortliffe 2006 Columbia University Biomedical Informatics ≠ Bioinformatics

IntroOH-12 CSE 5810 © T. Shortliffe 2006 Columbia University

IntroOH-13 CSE 5810 © T. Shortliffe 2006 Columbia University

IntroOH-14 CSE 5810 © 2014, W. Yasnoff, Uconn Health Center

IntroOH-15 CSE 5810 © 2014, W. Yasnoff, Uconn Health Center

IntroOH-16 CSE 5810 © 2014, W. Yasnoff, Uconn Health Center

IntroOH-17 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…

IntroOH-18 CSE 5810 What is BMI Used to Support? 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-19 CSE 5810 What is Medical Informatics?  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-20 CSE 5810 Where is Data/How is it Used?  Medical and Administrative Data Found in Clinical 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 CIS  Jump to PDF Presentation with Screenshots

IntroOH-21 CSE 5810 What are Major Informatics Challenges?  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?  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 Exchange ( based on XML

IntroOH-22 CSE 5810 Summary of Web Sites of Note:  AMIA (  IHE (  Smartplatform (  Mysis MOSS (  NSF Clinical and Translational Science Program   Emerging Patient Data Standard   Informatics for Integrating Biology & the Bedside.   Cancer Biomedical Informatics Grid 

IntroOH-23 CSE 5810 BMI in Computing: Interoperability  Need 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.

IntroOH-24 CSE 5810 Stakeholders for HIE and Virtual Chart

IntroOH-25 CSE 5810 Who are the Major Stakeholders?  Patients that require short-term treatments, long-term treatments, emergency help, inpatient care, ambulatory care, home care, etc.  Providers that administer care (MDs, medical specialists, ER MDs, nurses, hospitals, long term care facilities, home health care, nurse practitioners, etc.)  Public health organizations that monitor health trends and include disease control and prevention organizations, medical associations, etc.  Researchers that explore new health treatments, medications, and medical devices  Laboratories that conduct tests and include chemistry, microbiology, radiology, blood, genome, etc.  Payers that are responsible for cost management

IntroOH-26 CSE 5810 What are Interoperability Issues?  In Computing: For heterogeneous software systems, interoperability means exchanging information efficiently and without any additional effort of the user  For Medical Software Systems:

IntroOH-27 CSE 5810 Syntactic Interoperability  Defined as the Ability to read and Write the Same File Formats and Communicate over Same Protocols  Available Solutions Include:  Custom Adapter Interfaces  XML  Web Services  Cloud Computing  Standards and their Usage  CDA and HL7 (both in XML)  OpenEHR (  Continuity of Care Record (CCR

IntroOH-28 CSE 5810 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

IntroOH-29 CSE 5810 BMI in Computing: SW Architectures  Can we Leverage Software Architectural Alternatives from Computing:  Data Warehouse  Service-Oriented Architectures  Grid Computing  Cloud Computing  Publisher-Subscriber Paradigm  Web-Architectures and Services  Objectives:  Understand their Capabilities in Support of Health Information Exchange  A Solution may Require a Combination of Approaches

IntroOH-30 CSE 5810 Hybrid Architecture: Applied to Real Setting

IntroOH-31 CSE 5810 Hybrid Architecture: Applied to Real Setting

IntroOH-32 CSE 5810 Hybrid Architecture: Applied to Real Setting

IntroOH-33 CSE 5810 Hybrid Architecture: Applied to Real Setting

IntroOH-34 CSE 5810 Hybrid Architecture: Applied to Real Setting

IntroOH-35 CSE 5810 Patients Providers Clinical Researchers BMI in Computing: Security Web Server Appl Server DB Server Firewall https Encryption https Encryption Secure Communication XML html Web Content GUI Look and Feel Patient GUI for RN vs. MD Web - Control Services Appl. – Control Methods

IntroOH-36 CSE 5810 Security Issues for Patients  HIPPA Overriding Concern  All Patient Interfaces Web-Based  Secure Communication  To/From Web Server (https)  Among Discussion Group Members Is this https or Peer-to-Peer?  Role-Based Access Control to Authorize  Providers to Interact  PHR Data to Individual Providers Patients Providers Clinical Researchers Web-Based Portal(XML + HL7) Open Source XML DB

IntroOH-37 CSE 5810 Security Issues for Providers Patients Providers Clinical Researchers EMR  HIPPA Concerns for any EMR Data Transmitted into Portal  Need 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-Based Portal(XML + HL7) Open Source XML DB

IntroOH-38 CSE 5810 Motivation: General Concepts  Authentication  Proving you are who you are  Signing a Message  Is Client who s/he Says they are?  Authorization  Granting/Denying Access  Revoking Access  Does Client have Permission to do what s/he Wants?  Encryption  Establishing Communications Such that No One but Receiver will Get the Content of the Message  Symmetric Encryption and Public Key Encryption

IntroOH-39 CSE 5810 Motivation: Type of Security Issues  Legal and Ethical Issues  Information that Must be Protected  Information that Must be Accessible  HIPPA vs. Emergent Health Situations  Policy Issues  Who Can See What Information When?  Applications Limits w.r.t. Data vs. Users?  System 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 Enforcement  Mapping Security to Organizational Hierarchy  Protecting Information in Organization

IntroOH-40 CSE 5810 BMI: Security  Security 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 Everyday Life - Some Key Concerns  Confidentiality of an Individuals Data – PHR/EMR  Identity Theft  Protecting National Infrastructure