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 06269-2155 steve@engr.uconn.edu http://www.engr.uconn.edu/~steve (860) 486 - 4818

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.

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

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

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

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

© T. Shortliffe 2006 Columbia University

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…

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)

Class Materials, Textbook, Projects, etc. Course Web Site: http://www.engr.uconn.edu/~steve/Cse5810/cse5810.html 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-Informatics-Computer-Applications-Biomedicine/dp/1447144732/ 4th edition on itunes and amazon kindle. Questions? Comments? Suggestions?

Biomedical Informatics Textbook (4th edition) Springer - 2013

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

Research Project Deliverables 15 page paper 40-45 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 http://www.engr.uconn.edu/~steve/Cse5810/ResProj.pdf

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 http://www.engr.uconn.edu/~steve/Cse5810/project.docx

Motivation 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 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.

Motivation 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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Data Items

Motivation 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

Motivation 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

Motivation 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

Motivation 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

Motivation 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

Issues 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

Challenges 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

Challenges 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

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 devices databases, APIs) Exploring, evaluating, and utilizing a wide range of HIT standards, frameworks, and actual systems

Standards include: 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-chip-program-information/by-topics/data-and-systems/icd-coding/icd.html

Framworks include: 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-on-fhir/ Open mHealth: Open Source Code to Integrate digital health data http://www.openmhealth.org

Systems include: 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.open-emr.org/wiki/index.php/OpenEMR_Downloads Top 7 Free/Open Source: http://blog.capterra.com/top-7-free-open-source-emr-software-products/ Open Clinical Organization: http://www.openclinical.org/opensource.html

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

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: (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-and-Guidance/Legislation/EHRIncentivePrograms/Certification.html

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

Backup Batch SQL CCR CCD EMR Direct OEMR Export/Exchange Patient Data Set Filter Option Set Size Scenario Export Format Path after Sign In. Role Req. Tech Skill Req. Native Setup Backup All Data (no subset) N/A All Patients Backup or migration SQL Create Statement Admin> Create Admin No Yes Batch Personal Financial HIPAA Provider Age range App Date List of data with non clinical info for exchange CSV, Email, Phone Call List Misc> Batch> Process SQL All Data Any Patient Granular data search and export CSV 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 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 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 Messages are processed and a new Patient Note is delivered to a specified user and appears in that user's Message and Reminder Center. Patient > Demo > Reports > Transmit Fast and easy export of entire data set. CSV, CSV, LaTeX, PDF, SQL, YAML Admin > Database > Export Button Database - PHPMyAdmin

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?) http://www.cms.gov/Regulations-and-Guidance/Legislation/EHRIncentivePrograms/Certification.html

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

Backup Batch SQL CCR CCD EMR Direct OEMR Export/Exchange Patient Data Set Filter Option Set Size Scenario Export Format Path after Sign In. Role Req. Tech Skill Req. Native Setup Backup All Data (no subset) N/A All Patients Backup or migration SQL Create Statement Admin> Create Admin No Yes Batch Personal Financial HIPAA Provider Age range App Date List of data with non clinical info for exchange CSV, Email, Phone Call List Misc> Batch> Process SQL All Data Any Patient Granular data search and export CSV 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 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 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 Messages are processed and a new Patient Note is delivered to a specified user and appears in that user's Message and Reminder Center. Patient > Demo > Reports > Transmit Fast and easy export of entire data set. CSV, CSV, LaTeX, PDF, SQL, YAML Admin > Database > Export Button Database - PHPMyAdmin