1. 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)

2. 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

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

4. BMI: Corollaries to the Definition
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.
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

5. 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.

6. 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

7. 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

8. 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

9. 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

10. 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 (

11. Biomedical Informatics ≠ Bioinformatics
© T. Shortliffe 2006 Columbia University

12. © T. Shortliffe 2006 Columbia University

13. © T. Shortliffe 2006 Columbia University

14. © 2014, W. Yasnoff, Uconn Health Center

15. © 2014, W. Yasnoff, Uconn Health Center

16. © 2014, W. Yasnoff, Uconn Health Center

17. 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…

18. 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.

19. 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

20. 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

21. 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

22. 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

23. 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.

24. Stakeholders for HIE and Virtual Chart

25. 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

26. 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:

27. 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

28. Semantic Interoperability
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

29. 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

30. Hybrid Architecture: Applied to Real Setting

31. Hybrid Architecture: Applied to Real Setting

32. Hybrid Architecture: Applied to Real Setting

33. Hybrid Architecture: Applied to Real Setting

34. Hybrid Architecture: Applied to Real Setting

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

36. Security Issues for Patients
Providers
Web-Based
Portal(XML + HL7)
Open Source XML DB
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
Clinical Researchers

37. Security Issues for Providers
Patients
EMR
Web-Based
Portal(XML + HL7)
Open Source XML DB
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?
Clinical Researchers

38. 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

39. 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
Legal and ethical issues regarding to the right to access certain information
Policy issues at governmental, institutional or corporate level
System related issues such as the system levels at which various security functions should be enforced
The need in some organizations to identify multiple security levels and to characterize the data and users based on the classifications

40. 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

41. What are HIT Systems? What is HIT? Health Information Technology
Wide Variety of Systems Available for Use
Sample Systems:
Personal Health Records - Microsoft Healthvault
Electronic Medical Records – OpenEMR
Patient Portals
E Prescribing (electronic Rx)

42. What is a Personal Health Record?

43. What is a Personal Health Record?

44. What is a Personal Health Record?

45. What is an Electronic Medication Record?

46. What is an Electronic Medication Record?

47. What is an Electronic Medication Record?

48. What is a Patient Portal?

49. What is a Patient Portal?

50. What is a Patient Portal?

51. What is E-prescribing?

52. What is E-prescribing?

53. What is E-prescribing?