CSE5810: Intro to Biomedical Informatics
CSE
5810
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
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What is Informatics?
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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.
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What is Informatics?
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Heterogeneous Field –
Interaction between
People, Information and
Technology
 Computer Science
and Engineering
 Social Science
(Human Computer
Interface)
 Information Science
(Data Storage,
Retrieval and
Mining)
Informatics
People
Information
Technology
Adapted from Shortcliff textbook
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What is Biomedical Informatics (BMI)?
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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
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What is Biomedical Informatics (BMI)?
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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
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Why is BMI/Clinical Practice Important?
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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
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© T. Shortliffe 2006 Columbia University
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BMI and Computer Science & Engineering
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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)
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Core Topics:
 Introduction to BMI (1)
 Informatics/Information and Standards (2)
 Ontologies (1 week)
 EHRs and PHRs and MockEMR (1)
 Software Architectures and Interoperability (2)
 Security and Dynamic Coalition Problem (4)
 Service Based Computing (1)
 FHIR (1)
Discussion of Individual/Team Project (1-2)
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Class Materials, Textbook, Projects, etc.
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Course Web Site:
http://www.engr.uconn.edu/~steve/Cse5810/cse5810.html
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Reading List
 Constant Updates and Changes
Textbook –
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-InformaticsComputer-Applications-Biomedicine/dp/1447144732/
 4th edition on itunes and amazon kindle.
Questions? Comments? Suggestions?
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Biomedical
Informatics
Textbook
(4th edition)
Springer - 2013
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Course Projects
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Research Project (due end of semester)
 Choose a Computer Science Topic
 Explore the Topic related to BMI
Individual/Team Project (due thru semester)
 Explore Health Information Technology Systems
 Explore Open Source and Other Solutions
 Focus on Information Exchange and Interactions
No Exam
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Research Project
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Deliverables
 15 page paper
 40-45 slide powerpoint
 Three Samples on Web page
Potential Topics:
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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
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Individual/Team Design/Development Project
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Objectives
 Desire of Patients to Control Access to Own
Health Data
 Pervasiveness & Ubiquity of Mobile Devices
 Explosion of Fitness/Health Devices, Apps, Data
Collection
 Explore larger scale Health Information
Technology Systems and their Interaction
 Standards, Frameworks, & Systems
Support Interoperability via XML and Other
Standards
Individual/Team Structure
 To be Developed over Course of the Semester
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http://www.engr.uconn.edu/~steve/Cse5810/project.docx
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Motivation
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Control Access to Protected health information PHI
Fine-Grained Access
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‘‘Anyone whom I designate as a family member may view
my medication list, except for one of my medications that
I’d rather not share. . .”;
‘‘Anyone whom I designate as a health care provider may
view my medication list and my history of office visits and
hospitalizations, but not modify these data. . .;
‘‘My primary physician, Dr. Albright, may view and
modify my medication list and may view and annotate my
log of meals and physical activities. . .”
‘‘Dr. Albright’s (Electronic Health Record) EHR system
may automatically add new items to my medication list, but
it may not change or retrieve any items unless Dr. Albright
is logged in.”
Sujansky WV1, Faus SA, Stone E, Brennan PF. A method to implement fine-grained
access control for personal health records through standard relational database queries. J
Biomed Inform. 2010 Oct;43(5 Suppl):S46-50. doi: 10.1016/j.jbi.2010.08.001. Epub
2010 Aug 7.
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Motivation
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Survey of Patients on type and granularity of health
and other information that they wanted control of their
data in electronic medical records (EMRs)
 a family member may view my medication list (but
not all of them)
 a medical provider may view my medication list
and history of hospital visits (but not modify)
 my personal physician may both view and modify
my health care and fitness data, etc.
Define Recipients and Data Item
Caine K1, Hanania R., Patients want granular privacy control
over health information in electronic medical records. J Am
Med Inform Assoc. 2013 Jan 1;20(1):7-15. doi:
10.1136/amiajnl-2012-001023. Epub 2012 Nov 26.
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Recipents
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Data Items
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Motivation
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2015 of 1.9 billion mobile phones and 230 million
tablets, “Gartner Says Global Devices Shipments to
Grow 2.8 Percent in 2015”
October 2014, 64% of American adults own a
Smartphone while as of January 2014, 42% own a
Tablet, and 32% own an e-reader.
In 2014 that 497 million mobile devices were added
that year, and 88% of that growth is accounted to
smartphones and, predicted that by 2019
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Motivation
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Accessing data and executing apps on a mobile
platform is substantially more dynamic than traditional
computing on laptops and desktops
Simultaneously open:
 email accounts (corporate, Gmail, yahoo, etc.)
 browsers
 social network apps (Facebook, Twitter, LinkedIn)
 communication apps (Skype, Snapchat, SMS)
shopping apps (Amazon, JCPenney, Walgreens)
 health and fitness apps (CVS Health, Microsoft
HealthVault, MyQuest, etc.)
Need for users to be authenticated on each individual
application and often re-authenticated during sessions
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Motivation
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Proliferation of health and fitness applications
 medications (myCVS, MEDWatcher, Drugs.com
Medication guide and Pill Identifier Applications,
etc.)
 personal health record (PHR) applications
(CAPZULE PHR, MTBC PHR, suite of WebMD
Applications, etc.)
 a wide array of fitness devices and applications
that work with phones and wearables
Frameworks and Smartwatches
 Apple’s HealthKit app
 Google Fit fitness tracker
 Apple’s ResearchKit, which is an open source
framework for mobile applications to support
medical research
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Motivation
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Patients also seek to have access via their mobile
devices to
 electronic medical records (EMRs) utilized by their
medical providers,
 health information technology (HIT) systems that
contain medical testing results or results from
imaging testing
Managing Chronic Diseases
 Diabetes, Asthma, Obesity, CHF
 Social media and mobile applications in chronic
disease prevention and management
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4423338/

Evaluating Diabetes Mobile Applications for
Health Literate Designs and Functionality, 2014
http://www.cdc.gov/pcd/issues/2015/14_0433.htm
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Motivation
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Integration of Blue-Tooth Enabled Devices
 glucometers (for diabetes)
 weight scales
 blood pressure monitors
 peak-flow monitors
 ECG (heart)
Microsoft HealthVault Can Accept Data from all of
these Devices
Physicians order Devices
 Holter Monitor
 24hr or Longer Heart Trace
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Issues
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Fitness/Health/Medical/Disease Data from a myriad of
different and non-integrated sources
 collected and made available to patients
 easily provided to medical providers in either
detailed or summary form.
A patient may be utilizing multiple mobile apps to
manage the different fitness and medical devices,
 Dedicated data repository (perhaps SQL lite on a
phone or SQL DB on a server) with limited ability
 Inability to collect the data in a consistent format
from multiple for integration
Medical providers (hospitals, clinics, MD offices,
pharmacies, imaging centers, etc.) all have their own
health information technology (HIT) systems to
manage healthcare and medical data on patients
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Challenges
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Patients need the ability to be able to manage
health/medical/fitness/chronic disease data
 across a wide range of applications (may be both
mobile and web-based)
 involve separate and independent repositories
Patients need the ability to share with stakeholders
 patient him/herself
 family members (child care, elder care, spousal
care)
 nutritionists, personal trainers, therapists (physical,
occupational, pulmonary), home health care aides
 internist, family medicine MD, nurse practitioner,
physician assistants, pediatricians
 cardiologists, ENTs, orthopedic surgeons,
physiatrist, phycologist, therapist, etc
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Challenges
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Medical providers which need to have access to
 Granular/aggregated health/medical/fitness/chronic
disease data
 Within an Electronic Medical Record (EMR)
 Each Provider has Separate EMR
 Sharing Across EMRs Difficult
 Want Information in EMR to Mesh with Medical
Treatment/Workflow for Patients
Medical providers give medical devices to patients
 collect data over a specific time period
 delivered back to the medical provider by phone,
internet, or by returning the device itself
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Purpose of Project
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Explore all of these different issues utilizing a variety
of health information technology standards,
frameworks, and systems
Develop a working group of the entire class that will
leverage the varied skill sets
 mobile app design/development
 interacting with devices
 databases, APIs)
Exploring, evaluating, and utilizing a wide range of
HIT standards, frameworks, and actual systems
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Standards include:
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JSON: http://www.json.org/
RDF: https://www.w3.org/RDF/
XML: http://www.w3schools.com/xml/
HL7: http://www.hl7.org/implement/standards
HL7 CDA:
http://www.hl7.org/implement/standards/product_brief
.cfm?product_id=7
HL7 CCD :
http://www.hl7.org/implement/standards/product_brief
.cfm?product_id=6
ICD-10: https://www.medicaid.gov/medicaid-chipprogram-information/by-topics/data-and-systems/icdcoding/icd.html
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Framworks include:
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FHIR: Fast Healthcare Interoperability Resources
 https://www.hl7.org/fhir/overview.html
 https://www.hl7.org/fhir/index.html
SMART: An App Platform for Healthcare
 http://smarthealthit.org with multiple apps
 https://gallery.smarthealthit.org/
 Usage of FHIR http://smarthealthit.org/smart-onfhir/
Open mHealth: Open Source Code to Integrate digital
health data http://www.openmhealth.org
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Systems include:
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Open MRS: open source enterprise electronic medical
record system
 http://openmrs.org with standalone version
http://openmrs.org/download/
Open EMR: A Stage II meaningful use certified EHR
 http://www.open-emr.org with standalone version
http://www.openemr.org/wiki/index.php/OpenEMR_Downloads
Top 7 Free/Open Source:
 http://blog.capterra.com/top-7-free-open-sourceemr-software-products/
Open Clinical Organization:
 http://www.openclinical.org/opensource.html
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Spring 2014 Chosen Team Projects
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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
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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
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Team T1 Advice
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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://www.cms.gov/Regulations-andGuidance/Legislation/EHRIncentivePrograms/Certification.html
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Team T1 Division of Work Suggestions
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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
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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.
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Explore Capabilities of Each (Comparison Metric) in
terms of import/export/CCR/CDA/etc. See Matrix
Objective – Propose Blueprint for Their Integration
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OEMR
Export/Exchange
Patient
Data Set
Filter
Option
Patient
Set Size
Scenario
Export
Format
Path after
Sign In.
Role
Req.
Tech
Skill
Req.
Nativ
e
Setup
Backup
All Data (no subset)
N/A
All Patients
Backup or
migration
SQL Create
Statement
Admin>
Create
Backup
Admin
No
Yes
CSE
Batch
5810
Personal
Financial
HIPAA
Provider
Age range App
Date
HIPAA
All Patients
List of data with non
clinical info for
exchange
CSV, Email,
Phone Call
List
Misc>
Batch>
Process
Admin
No
Yes
SQL
All Data
SQL
Filter
Any Patient
Set Size
Granular data search
and export
CSV
Misc>
Batch>
Process
Admin
SQL
No
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 Patient
Print and handout
Web
Patient>
Demo.>
Reports>
Button
Admin;
Physician;
Clinician;
FrontOffice
Accounting
No
Yes
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/A
Single Patient
Print and handout
Web
Patient>
Demo.>
Reports>
Button
Admin;
Physician;
Clinician;
FrontOffice
Accounting
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;
FrontOffice
Accounting
No
No
Export
All 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 PHPMyAd
min
No
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Team T2 Advice
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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-andGuidance/Legislation/EHRIncentivePrograms/Certification.html
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Team T2 Division of Work Suggestions
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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
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OEMR
Export/Exchange
Patient
Data Set
Filter
Option
Patient
Set Size
Scenario
Export
Format
Path after
Sign In.
Role
Req.
Tech
Skill
Req.
Nativ
e
Setup
Backup
All Data (no subset)
N/A
All Patients
Backup or
migration
SQL Create
Statement
Admin>
Create
Backup
Admin
No
Yes
CSE
Batch
5810
Personal
Financial
HIPAA
Provider
Age range App
Date
HIPAA
All Patients
List of data with non
clinical info for
exchange
CSV, Email,
Phone Call
List
Misc>
Batch>
Process
Admin
No
Yes
SQL
All Data
SQL
Filter
Any Patient
Set Size
Granular data search
and export
CSV
Misc>
Batch>
Process
Admin
SQL
No
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 Patient
Print and handout
Web
Patient>
Demo.>
Reports>
Button
Admin;
Physician;
Clinician;
FrontOffice
Accounting
No
Yes
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/A
Single Patient
Print and handout
Web
Patient>
Demo.>
Reports>
Button
Admin;
Physician;
Clinician;
FrontOffice
Accounting
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;
FrontOffice
Accounting
No
No
Export
All 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 PHPMyAd
min
No
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