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CSE5810

CSE5810: Intro to Biomedical Informatics

Prof. Steven A. Demurjian, Sr. Computer Science & Engineering Department

The University of Connecticut371 Fairfield Road, Box U-255

Storrs, CT 06269-2155

steve@engr.uconn.eduhttp://www.engr.uconn.edu/~steve

(860) 486 - 4818

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CSE5810

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.

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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

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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

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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

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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

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© T. Shortliffe 2006 Columbia University

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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…

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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)

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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?

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Biomedical Informatics Textbook

(4th edition)

Springer - 2013

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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

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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

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Projects Posted on Web Page Prior Projects (Spring 2012)

Clinical Decision Support: PPT and Report Data Mining and BMI: PPT and Report Cloud Computing and BMI: PPT and Report

Sample Final Presentations (Spring 2014): Albayram: PPT and  Algwaiz: PPT Baihan: PPT  and  Martin:  PPT Papavasileiou:  PPT and Sanzi:  PPT

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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

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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.

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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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Recipients

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Data Items

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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

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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 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 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

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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

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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

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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

http://www.peakflow.com/pefr_normal_values.pdf and children http://www.peakflow.com/paediatric_normal_values.pdf)

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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 http://www.ncbi.nlm.nih.gov/pubmed/22954855 )

Peak Flow Meter PERF L/min (adults http://www.peakflow.com/pefr_normal_values.pdf and children http://www.peakflow.com/paediatric_normal_values.pdf)

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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

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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

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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

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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 (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 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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What is Big Picture?

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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

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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

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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

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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-e

mr-software-products/

Open Clinical Organization: http://www.openclinical.org/opensource.html

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The OpenMRS Sample Database Schema 99 Tables, Sample Database with 5000 patients and

500,000 observations

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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

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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.

http://www.mindcommerce.com/wearable_wireless_technology_solutions_vendors_markets_and_forecast_2014__2019.php

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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.

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Important Web Page Links Research Project:  DOCX or PDF Individual/Team Project:  DOCX Spring 2014 Project  Open Source EMRs: PDF OpenEMR Install, Schema and Documentation OpenMRS Install,  Website, openmrs.mwb and

demo-1.11.0 MySQL: Install, PPTX and SampleCode Other Technologies: DOCX MSHV and OpenEMR APIs: PDF

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Spring 2014 Open Source EMRs

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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

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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

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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 CapabilitiesOR 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

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CSE5810

OEMRExport/Exchange

PatientData Set

FilterOption

PatientSet Size

Scenario ExportFormat

Path afterSign In.

RoleReq.

Tech Skill Req.

NativeSetup

Backup All Data (no subset) N/A All Patients Backup ormigration

SQL CreateStatement

Admin>CreateBackup

Admin No Yes

Batch PersonalFinancialHIPAAProvider

Age range App DateHIPAA

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 SQLFilter

Any PatientSet 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;FrontOfficeAccounting

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;FrontOfficeAccounting

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;FrontOfficeAccounting

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 -PHPMyAdmin

No

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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

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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

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OEMRExport/Exchange

PatientData Set

FilterOption

PatientSet Size

Scenario ExportFormat

Path afterSign In.

RoleReq.

Tech Skill Req.

NativeSetup

Backup All Data (no subset) N/A All Patients Backup ormigration

SQL CreateStatement

Admin>CreateBackup

Admin No Yes

Batch PersonalFinancialHIPAAProvider

Age range App DateHIPAA

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 SQLFilter

Any PatientSet 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;FrontOfficeAccounting

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;FrontOfficeAccounting

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;FrontOfficeAccounting

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 -PHPMyAdmin

No