intrto-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)

intrto-2 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.

intrto-3 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

intrto-4 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

intrto-5 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

intrto-6 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

intrto-7 CSE 5810 © T. Shortliffe 2006 Columbia University

intrto-8 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…

intrto-9 CSE 5810 Semester Topics (14.5 weeks)  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)

intrto-10 CSE 5810 Class Materials, Textbook, Projects, etc.  Course Web Site:  Reading List  Constant Updates and Changes  Textbook – Biomedical Informatics: Computer Applications in Health Care and Biomedicine (Health Informatics), 4 th edition, Edward H. Shortliffe (Editor), James J. Cimino (Editor), ISBN-10:   Computer-Applications-Biomedicine/dp/ /  4 th edition on itunes and amazon kindle.  Questions? Comments? Suggestions?

intrto-11 CSE 5810 Biomedical Informatics Textbook (4 th edition) Springer

intrto-12 CSE 5810 Course Projects  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

intrto-13 CSE 5810 Research Project  Deliverables  15 page paper  slide powerpoint  Three Samples on Web page  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 

intrto-14 CSE 5810 Projects Posted on Web Page  Prior Projects (Spring 2012)  Clinical Decision Support: PPT and ReportPPT Report  Data Mining and BMI: PPT and ReportPPT Report  Cloud Computing and BMI: PPT and ReportPPT Report  Sample Final Presentations (Spring 2014):  Albayram: PPT and Algwaiz: PPTPPT  Baihan: PPT and Martin: PPTPPT  Papavasileiou: PPT and Sanzi: PPTPPT

intrto-15 CSE 5810 Individual/Team Design/Development Project  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 

intrto-16 CSE 5810Motivation  Control Access to PHI  Control Access to Protected health information PHI  Fine-Grained Access  ‘‘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 WV Sujansky WV 1, 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 Oct;43(5 Suppl):S doi: /j.jbi Epub 2010 Aug 7.Faus SAStone EBrennan PFJ Biomed Inform.

intrto-17 CSE 5810Motivation   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 K 1, Hanania R., Patients want granular privacy control over health information in electronic medical records. J Am Med Inform Assoc Jan 1;20(1):7-15. doi: /amiajnl Epub 2012 Nov 26. Caine KHanania RJ Am Med Inform Assoc.

intrto-18 CSE 5810Recipients

intrto-19 CSE 5810 Data Items

intrto-20 CSE 5810Motivation   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

intrto-21 CSE 5810Motivation   Accessing data and executing apps on a mobile platform is substantially more dynamic than traditional computing on laptops and desktops   Simultaneously open:  accounts (corporate, Gmail, yahoo, etc.)  browsers  Social network apps (Facebook, Twitter, LinkedIn)  Communication apps (Skype, Snapchat, SMS) shopping apps (Amazon, JCPenney, Walgreens)  Health apps (CVS Health, Microsoft HealthVault, MyQuest, etc.)   Need for users to be authenticated on each individual application and often re-authenticated during sessions

intrto-22 CSE 5810Motivation   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.)  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

intrto-23 CSE 5810Motivation   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  Evaluating Diabetes Mobile Applications for Health Literate Designs and Functionality,

intrto-24 CSE 5810 Chronic Disease Tracking - Diabetes   Time stamp for the entire entry entered by patient   Type of test: Fasting (no eating for at least 8 hours), 2 hours after eating, casual (any time during day)   Glucose Level measured in mg/dL taken from meter   Insulin taken (value comes up from the meter after testing)   Carbohydrates

intrto-25 CSE 5810 Chronic Disease Tracking – CHF/High BP   Time stamp for the entire entry entered by patient   Pulse   Blood Pressure (systolic mm Hg – upper number, Diastolic mm Hg –lower number)   Respirations per minute   Pulse Ox – out of 100%   Peak Flow Meter PERF L/min (adults and children

intrto-26 CSE 5810 Chronic Disease Tracking - Asthma   Time stamp for the entire entry entered by patient   Pulse   Respiration   Pulse Ox – out of 100% (now available on mobile phone – see )   Peak Flow Meter PERF L/min (adults and children

intrto-27 CSE 5810 Chronic Disease Tracking - Obesity   Time stamp for the entire entry entered by patient   Weight (entered daily? Weekly? Set differently for different patients?)   Blood pressure   Calories/Diet (How do we gather this information? What is available out there already?)   Pulse and Blood Pressure after exercise

intrto-28 CSE 5810Motivation  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

intrto-29 CSE 5810Issues   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

intrto-30 CSE 5810Challenges   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 (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

intrto-31 CSE 5810Challenges   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

intrto-32 CSE 5810 What is Big Picture?

intrto-33 CSE 5810 Purpose of Project   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 Bluetooth devices  Databases  APIs   Exploring, evaluating, and utilizing a wide range of HIT standards, frameworks, and actual systems

intrto-34 CSE 5810 Standards include:  JSON:  RDF:  XML:  HL7:  HL7 CDA:  HL7 CCD :  ICD-10: program-information/by-topics/data-and-systems/icd- coding/icd.html program-information/by-topics/data-and-systems/icd- coding/icd.htmlhttps:// program-information/by-topics/data-and-systems/icd- coding/icd.html

intrto-35 CSE 5810 Framworks include:  FHIR: Fast Healthcare Interoperability Resources    SMART: An App Platform for Healthcare  with multiple apps  /  Usage of FHIR fhir/ fhir/  Open mHealth: Open Source Code to Integrate digital health data

intrto-36 CSE 5810 Systems include:   Open MRS: open source enterprise electronic medical record system  with standalone version   Open EMR: A Stage II meaningful use certified EHR  with standalone version emr.org/wiki/index.php/OpenEMR_Downloads emr.org/wiki/index.php/OpenEMR_Downloads   Top 7 Free/Open Source:  emr-software-products/ emr-software-products/   Open Clinical Organization: 

intrto-37 CSE 5810 The OpenMRS Sample Database Schema  99 Tables, Sample Database with 5000 patients and 500,000 observations

intrto-38 CSE 5810 Project Scope   Define and track fitness, medical, health, and chronic disease data   Develop an ER DB Design to support  Info from Multiple Sources/Repositories  Stage to/from Mobile App   Explore Frameworks (SMART, FHIR, etc.) and Ability to Model Info   Role of JSON/XML?   What Does Google Fit and Apple Healthkit Store for Such Data?   Storage in Mobile App (SQLite) vs. Server Side   Storing information for Medical Providers into EMRs

intrto-39 CSE 5810 Project Possibilities   Explore standards available for Health/Fitness/Medical/Chronic Disease data.   Investigate what Fitness/Wearable Devices support in terms of Storing/Analyzing Data collected by users and the way that information can be collected from different platforms.   Investigating FHIR to support Health/Fitness/Medical/Chronic Disease data including a proof of concept prototype.   Investigating SMART to support Health/Fitness/Medical/Chronic Disease data including a proof of concept prototype.   chnology_solutions_vendors_markets_and_forecast_2 014__2019.php chnology_solutions_vendors_markets_and_forecast_2 014__2019.php

intrto-40 CSE 5810 Project Possibilities   Design an ER Diagram for Health/Fitness/Medical/Chronic Disease data collected by patients.   Applications in Android (using Google Fit) or iOS (using Apple Healthkit).   Linking up Bluetooth devices (Fitness, Scales, Glucometers, BP, etc.) to a mobile app, the database on health/fitness/medical/chronic data being defined   Ability to feed from Bluetooth devices into an EMR via REST APIs, FHIR, SMART, etc.   Server/REST Infrastructure to allow data from multiple sources (different data repositories) to be staged back and forth to a mobile app and interaction with EMRs.

intrto-41 CSE 5810 Important Web Page Links  Research Project: DOCX or PDF DOCX  Individual/Team Project: DOCX DOCX  Spring 2014 Project Open Source EMRs: PDF PDF  OpenEMR Install, Schema and Documentation InstallSchema DocumentationInstallSchema Documentation  OpenMRS Install, Website, and  OpenMRS Install, Website, openmrs.mwb and demo InstallWebsiteInstallWebsiteopenmrs.mwbdemo  MySQL:, and  MySQL: Install, PPTX and SampleCodeInstallPPTXSampleCode  Other Technologies: DOCX DOCX  MSHV and OpenEMR APIs: PDF PDF

intrto-42 CSE 5810 Spring 2014 Open Source EMRs

intrto-43 CSE 5810 Spring 2014 Chosen Team Projects  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  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

intrto-44 CSE 5810 Team T1 Advice  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: ( ), Connect ( and and  Guidance/Legislation/EHRIncentivePrograms/Certification.html

intrto-45 CSE 5810 Team T1 Division of Work Suggestions  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  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 terms of import/export/CCR/CDA/etc. See Matrix  Objective – Propose Blueprint for Their Integration

intrto-46 CSE 5810 OEMR Export/Exchange Patient Data Set Filter Option Patient Set Size ScenarioExport Format Path after Sign In. Role Req. Tech Skill Req. Nativ e Setup Backup All Data (no subset)N/AAll PatientsBackup or migration SQL Create Statement Admin> Create Backup AdminNoYes Batch Personal Financial HIPAA Provider Age range App Date HIPAA All PatientsList of data with non clinical info for exchange CSV, , Phone Call List Misc> Batch> Process AdminNoYes SQL All DataSQL Filter Any Patient Set Size Granular data search and export CSVMisc> Batch> Process AdminSQLNo 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 PatientPrint and handoutWebPatient> Demo.> Reports> Button Admin; Physician; Clinician; FrontOffice Accounting NoYes 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/ASingle PatientPrint and handoutWebPatient> Demo.> Reports> Button Admin; Physician; Clinician; FrontOffice Accounting NoYes 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/ASingle PatientMessages are processed and a new Patient Note is delivered to a specified user and appears in that user's Message and Reminder Center. WebPatient > Demo > Reports > Transmit Admin; Physician; Clinician; FrontOffice Accounting No Export All Data (no subset)N/AAll PatientsFast and easy export of entire data set. CSV, CSV, LaTeX, PDF, SQL, YAML Admin > Database > Export Button AdminDatabase - PHPMyAd min No

intrto-47 CSE 5810 Team T2 Advice  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?)  Guidance/Legislation/EHRIncentivePrograms/Certification.html

intrto-48 CSE 5810 Team T2 Division of Work Suggestions  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

intrto-49 CSE 5810 OEMR Export/Exchange Patient Data Set Filter Option Patient Set Size ScenarioExport Format Path after Sign In. Role Req. Tech Skill Req. Nativ e Setup Backup All Data (no subset)N/AAll PatientsBackup or migration SQL Create Statement Admin> Create Backup AdminNoYes Batch Personal Financial HIPAA Provider Age range App Date HIPAA All PatientsList of data with non clinical info for exchange CSV, , Phone Call List Misc> Batch> Process AdminNoYes SQL All DataSQL Filter Any Patient Set Size Granular data search and export CSVMisc> Batch> Process AdminSQLNo 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 PatientPrint and handoutWebPatient> Demo.> Reports> Button Admin; Physician; Clinician; FrontOffice Accounting NoYes 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/ASingle PatientPrint and handoutWebPatient> Demo.> Reports> Button Admin; Physician; Clinician; FrontOffice Accounting NoYes 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/ASingle PatientMessages are processed and a new Patient Note is delivered to a specified user and appears in that user's Message and Reminder Center. WebPatient > Demo > Reports > Transmit Admin; Physician; Clinician; FrontOffice Accounting No Export All Data (no subset)N/AAll PatientsFast and easy export of entire data set. CSV, CSV, LaTeX, PDF, SQL, YAML Admin > Database > Export Button AdminDatabase - PHPMyAd min No