Health IT and OpenMRS

Health IT and OpenMRSAn introduction

Tutorial at the OpenMRS Worldwide SummitDec 8th, 2015 - Singapore

What will we do in this tutorial?• In this full-day tutorial, you will learn basic overview of electronic

medical records systems, health data management and how you can use the OpenMRS system for data and information management.

• Terms in health information systems, electronic health records and how the OpenMRS platform can meet (or not meet) you information needs

• We will cover– Requirements gathering before selecting OpenMRS– OpenMRS Installation– User management– Location management– Patient dashboards– Showcasing some modules and customization (a preview of sorts for the

Extending and customizing OpenMRS tutorial)

What you need to complete this tutorial• An internet connected computer/device• At least 4GB RAM and 1Ghz to install OpenMRS, with Linux, OSX

or Windows• Elementary English language skills• Elementary-level computer proficiency

Learning objectivesAt the end of the tutorial, you should be able to:1. Identify the non-technical factors that influence the adoption of

electronic medical record (EMR) system by clinicians and describe strategies for promoting effective use of EMR systems.

2. Describe the processes of developing or selecting an EMR system, preparing and supporting clinicians for system implementation, and evaluating system effectiveness.

3. Describe the role of EMR systems and how they are used in different health care settings.

4. Identify key features of OpenMRS platform and reference application, such that they correlate with the health care setting

5. Install OpenMRS reference application for testing purposes6. Understand privileges, roles, locations and learn how to manage them.

Learning objectives (cont’d)7. Understand the difference between metadata and data in OpenMRS8. Describe the OpenMRS data model and how information is modelled

in OpenMRS9. Register a patient, create visits, capture vitals, capture visit notes,

diagnosis and other types of clinical information10.Describe some health care settings in which the OpenMRS platform

has been customized and used

How will you learn these objectives?• Are majority of these objectives in sync with your objectives to

be in this room?• Pay attention to the speaker. Ask doubts while we are still on the

topic• Participate in discussion, when you see this icon next to a bullet point

• Do reflection internally,when you see this icon next to a bullet point

• Do work on your laptop individuallywhen you see this icon next to a bullet point

Health data/information management

Information management• A method of using technology to collect, process and condense

information with a goal of efficient management (Gartner).• A cycle of organisational activity concerned with the acquisition

of information from one or more sources, the custodianship and the distribution of that information to those who need it, and its ultimate disposition through archiving or deletion (Wikipedia).

• In health care settings, the goal is providing care to the patient in a way that is appropriate, safe and effective.– Efficient and effective might have different meanings based on your

health care environment. Discuss some differences between the terms in your health setting

Source: Association for Information and Image Managementhttp://www.aiim.org/What-is-Information-Management

Health data/information management• Health information management (HIM) is the practice of

acquiring, analyzing and protecting digital and traditional medical information vital to providing quality patient care (Wikipedia).– Advocacy to use digital/electronic means for information management

• Referred to by different names:– Health information systems– Health informatics tools– Health information technology– …

• An inter-disciplinary field of– Medicine and related health care services– Computer science– Management and library science

Why is health information management important?• The World Health Organization (WHO) stated that the proper

collection, management and use of information within healthcare systems “will determine the system’s effectiveness in detecting health problems, defining priorities, identifying innovative solutions and allocating resources to improve health outcomes. (Stansfield, 2005)

Institute of Healthcare Improvement

1) Improving the patient experience of care (including quality and satisfaction);

2) Improving the health of populations; and3) Reducing the per capita cost of health care.Not just for resource-rich environments, but more important for low-resource environments because the limited resources need to be distributed appropriately with most effectivenessAll of these goals have information availability and information use at the core.

More than patient records• To meet those goals, Health information systems need to manage than

health records. They range from process-related systems like:– Logistics systems (like OpenBoxes)– Billing systems– Ordering/acquisition systems (beyond patient) (like OpenERP/Odoo)

• To strategic and management related systems like:– Health management information systems (HMIS like DHIS2)– Strategic information systems– Simulation systems

• Our focus in this community is health data systems. OpenMRS is designed with a patient-centric approach. This is different from a process-centric approach, which is adopted by many health information systems.

Needs for health information are different at different levels

Source: Braa et al. (2007), Hierarchy of standards

Electronic health records (EHR)

Take a break of 10mins

Electronic health record• Electronic health record (EHR) refers to the systematized collection of

patient and population electronically-stored health information in a digital format (Wikipedia).

• Electronic medical record (EMR) systems, defined as "an electronic record of health-related information on an individual that can be created, gathered, managed, and consulted by authorized clinicians and staff within one health care organization“ (Agency of Healthcare Research and Quality).

• These systems can facilitate workflow and improve the quality of patient care and patient safety (AHRQ).

• The process to computerize patient medical records has been going on for the last 30 years

• These range from single-practice records to large hospitals to entire state or country encompassing shared patient records

Electronic health record (cont’d)• These have been referred to with multiple names:

– electronic medical records (EMR)– computerized medical records– longitudinal patient records– electronic charts

• Different from Health information exchanges (HIE), but HIEs exchange electronic health records between EHR systems

• An early contributor to EHR - computer based patient record institute (CPRI) suggested the following characteristics of EHRs:– Capture data at point of care– Integrate data from multiple sources– Provide decision support

Do clinicians really want EHRs?• At least in the USA, large-scale EHR adoption is fairly recent. The factors for

adoption are shown below:• According to a Bloomberg News report

from 2015, the top 10 countries with the highest EHR adoption rates are:– Norway (98%)– Netherlands (98%)– United Kingdom (97%)– New Zealand (97%)– Australia (92%)– Germany (82%)– United States (69%)– France (67%)– Canada (56%)– Switzerland (41%)

Source: Office of National Coordinator (ONC). 2013

What are the benefits for EHR use?• Providers who have adopted EHRs, report the

following benefits:– Accurate and complete information

about a patient's health. This enables providers to give the best possible care, whether during a routine office visit or in a medical emergency

– The ability to quickly provide care. In a crisis, EHRs provide instant access to information about a patient's medical history, allergies, and medications.

– The ability to better coordinate the care they give. This is especially important if a patient has a serious or chronic medical condition, such as diabetes.

– A way to share information with patients and their family caregivers. This means patients and their families can more fully take part in decisions about their health care.

Source: Jamoom et al. (2011)

Barriers to EHR adoption• While the benefits of EHRs are both care-related and efficiency-

related, the following are barriers to EHR adoption:

Source: Ajami & Bagheri-Tadi, 2013

• Time – limited physician time• Cost – in owning/maintaining• Absence of computer skill• Workflow disruption• Concern about security and

privacy• Communication among users• Interfaces with doctor-

patient relationship

• Lack of incentives• Complexity and UI

challenges• Technical support• Interoperability• Vendor trust• Concern about data entry

Selecting EHRs

Core functions of an EHR• IOM (Institute of medicine) puts forth 8 core functions:

1. Health information and data2. Result management3. Order management4. Decision support5. Electronic communication and connectivity6. Patient support7. Administrative processes and reporting8. Reporting and population health

Where OpenMRS fits best?• OpenMRS is a patient-centric application, meaning data is captured about

interactions between a health care provider and a patient. • Your main information needs should also focus on direct patient care. If you

primarily intend to capture data about something other than the patient (for example, about lab specimens), you should consider other alternatives.

• OpenMRS is designed to manage patient data longitudinally, linking multiple interactions over time into a single patient chart.

• If you only care about individual patient visits, and not about linking those together into a longitudinal chart, then OpenMRS may not be the right tool for you.

• There are EHR components like PACS (Picture archiving systems) or Lab Information Systems, or Pharmacy management systems. Depending on the scale of your needs, you can choose a module or a full-fledged system.

OpenMRS platform (also referred to as Core)• The OpenMRS Platform is the shared platform upon which all distributions of

OpenMRS are based. • Its goal is to be a minimal Java (a programming language) and RESTful (the

design pattern of HTTP and the internet) services that developers can use to build their own clinical data applications. It does not aim to provide a user interface (UI) or application itself

• Developers can use the OpenMRS Platform to a build a separate application that uses OpenMRS as a RESTful clinical data store. Developers can use the OpenMRS Platform to build a Java server-side web application.

• Implementers can use the OpenMRS Platform and the legacy UI (with the addition of common community-supported add-on modules like the HTML Form Entry module or the XForms Module) to build an EMR for retrospective data entry.

• Upto v1.12, the legacy UI was provided in the platform. From v2.0 of the platform, no UI is provided. The legacyui module can be installed to get the 1.x UI

OpenMRS documentation (OpenMRS Wiki)

OpenMRS platform architecture

OpenMRS distributions• OpenMRS is a flexible, modular, multi-layered system, and one of its

strengths is that its platform can be used in many different configurations

• To implement an OpenMRS system, you typically start from an existing OpenMRS Distribution, and configure that distribution for your implementation use case..

• Depending on which distribution you choose, and what your use case is, this may range from:– configuring metadata through a UI– to writing custom add-on modules,– or your own custom UI backed by OpenMRS REST web services.

• Implementations with strong development teams may choose to build their own custom application(s) on top of the Platform

OpenMRS reference application• The OpenMRS reference application is a sample EMR application

running atop the OpenMRS API.  • OpenMRS has always had a web application component; however, the

web application focused primarily on basic administrative features and lacked most content, leaving it up to modules and administrators to provide EMR functionality and content.  

• The Reference Application, on the other hand, strives to provide more of a starter set of content along with basic EMR functionality (e.g., registration, basic reports, etc.).

• The Reference Application comprises a handful of modules that run within the Java web application and provides a Groovy (a scripting language)-based framework for web development.

• In community lingo, you’ll hear this distribution referred to as “RefApp”

OpenMRS reference application (cont’d)• The RefApp distribution demonstrates how the OpenMRS platform

can be used to build a facility EMR, and it is where the community develops starter sets of metadata and terminology.

• The RefApp is a good starting point for implementing OpenMRS in a facility, and it intends to eventually be a full-featured EMR system, but it is dependent on distributed volunteer efforts, and hasn't yet achieved that goal.

• This distribution does not intend to cover the entire Hospital Information System use case, e.g. we won't cover billing or pharmacy stock management.

• In this tutorial, we use the Reference application as a starter EMR on which you will be able to explore the different features provided by OpenMRS.

Readiness assessment• The assessment should look at the current state of your health

system:– Are administrative processes organized, efficient, and well documented?– Are clinical workflows efficient, clearly mapped out, and understood by all staff?– Are data collection and reporting processes well established and documented?– Are staff members computer literate and comfortable with information

technology?– Does the health system have access to technology resources like internet

connectivity, hardware/software upgrade plan?– Does the health system have access to the financial capital required to purchase

new or additional hardware?– Are there clinical priorities or needs that should be addressed?– Does the practice have specialty specific requirements?

Source: healthit.gov

Setting “SMART” Goals• You should set “SMART” goals during your readiness assessment.

Goals should be:• Specific – Achieving the goal would make a difference for our

patients and our organization.• Measureable – We can quantify the current level and the target

goal.• Attainable – Although the goal may be a stretch, we can achieve it.• Relevant – The goal is worth the effort.• Time bound – There are deadlines and opportunities to celebrate

success!

Source: healthit.gov

Your organizational goals and practice• For now, forget about technology and instead think about your

organizational goals and processes. Here's a list of questions to start:• What are the high level goals of your organization?• What are the teams and staff in the clinic? What roles exists? What

functions does each role perform?• What tasks are staff involved with on a day to day basis?• What services does the clinic provide to your patients? What activities

are involved?• What other 3rd-party or government organizations do you report to?

What information is included in each of these reports?• Answering these questions will probably help you think of more related

questions. Make sure you consider them thoroughly.

Outcome of readiness assessment• Critical outcomes of the assessment process include:• A designated leadership team for the EHR implementation

process (clinical and practice management staff, or for small practices, the entire team). Having strong and positive advocate(s) for change can be one of the strongest tools to guide the transition.

• A unified vision, where each member of the practice team understands how they will be affected by the change and understands the roadmap to success.

• Measureable, quantifiable, realistic goals, which are the key to the assessment phase

Source: healthit.gov

Planning phase for EHR implementation

Map your needs to OpenMRS• OpenMRS has been designed to be flexible and adaptable, based on

input from many different partners, but it may not be an exact fit for the ways that your organization currently works.

• Doing things the "OpenMRS way" could mean adapting your workflow and adopting best practices in medical informatics.

• Be pragmatic and flexible, and think about whether your current working practices might need to change.

• Remember that OpenMRS offers many opportunities to capture and analyze information in new ways not previously possible.

• Taking advantage of these new possibilities might possibly lead to positive changes and improvements for your organization.

Do not "reinvent the wheel"• The open source ethos of OpenMRS extends beyond just the

application, to a much larger open community where ideas and experiences are shared. There are many existing resources available in the form of pre-built OpenMRS features (modules)

• Reuse an existing concept dictionary • A well-constructed, mature concept dictionary (we’ll learn about this

later) is a strong foundation for any OpenMRS Implementation.• The CIEL dictionary and Maternal Concept Lab (MCL) maintains a well

curated concept dictionary. If this dictionary is applicable to your domain of care, we strongly recommend that you consider using it.

• Other OpenMRS implementers can also help advise you about other concept references for your domain.

Do not "reinvent the wheel“ (cont’d)• Adapt existing forms• Implementers should evaluate data collection forms built by other

OpenMRS users before creating new custom forms for their specific needs.

• Implementers across the OpenMRS community have invested a lot of resources in ensuring that their forms reflect clinical best practices, international standards, and current research. These forms have already been optimized for electronic data entry.

• Many OpenMRS partners develop forms using medical informatics experts that may not be available to all projects

• Creating forms is time consuming - those resources could be redirected to other efforts.

• The OpenMRS Form Bank is a new community-driven project which is beginning to collect existing forms from other users

Steps of the planning phase1. Analyze and map out the practice’s current workflow and processes of how the

practice currently gets work done (the current state).2. Map out how EHRs will enable desired workflows and processes, creating new

workflow patterns to improve inefficiency or duplicative processes (the future state).

3. Create a contingency plan – or back-up plan – to combat issues that may arise throughout the implementation process.

4. Create a project plan for transitioning from paper to EHRs, and appoint someone to manage the project plan.

5. Establish a chart abstraction plan, a means to convert or transform, information from paper charts to electronic charts. Identify specific data elements that will need to be entered into the new EHR and if there are items that will be scanned.

6. Understand what data elements may be migrated from your old system to your new one, such as patient demographics or provider schedule information. Sometimes, being selective with which data or how much data you want to migrate can influence the ease of transition. Source: healthit.gov

Steps of the planning phase (cont’d)7. Identify concerns and obstacles regarding privacy and security and create a plan

to address them. It is essential to emphasize the importance of privacy and security when transitioning to EHRs.

Source: healthit.gov

Common errors in EHR implementation closely related to planning

Source: healthit.gov

ONC’s EHR evaluation

matrixhttps://www.healthit.gov/sites/default/files/vendor_evaluation_matrix_tool_v1.0_0.xlsx

Project team planningYour EHR implementation team should include clinic staff:• Management are aware of funding obligations and 3rd party reporting

requirements.• Health care providers are focused on improving patient care.• Administrative staff are specialists of workflow issues and clinic processes.

The team could also include the following people that may or may not be from the clinic:• A system administrator is in charge of installing and maintaining OpenMRS inside

of the clinic's ICT infrastructure.• Medical informatics expert(s) create clinical documentation and ensure that data

is managed properly in the system. Develop reports.• (Optional) A project manager or coordinator. For larger implementations, this

person works to hold people accountable to finishing their work in a timely manner, and ensures the project is on track.

• (Optional) Software developers may be needed for locations that decide to customize the system.

OpenMRS key features

Take a break of 10mins

OpenMRS implementations around the world

1. Central Concept Dictionary: Definitions of all data (both questions and answers) are defined in a centralized dictionary, allowing for robust, coded data which can be mapped to multiple reference terminologies like ICD-10, SNOMED, LOINC, RxNorm etc.

2. Security: User authentication with complex password support. Support for roles, privileges to separate what user can and cannot do. Users can also login through a single-sign on system like CAS for centralized enterprise authentication.

3. Patient Repository: Creation and maintenance of patient data, including demographics, clinical observations, encounter data, orders, etc.

4. Multiple identifiers per patient: A single patient may have single or multiple identifier numbers like passport number, national id, medical record number etc.

5. Flexible Data entry: With the FormEntry module, clients with InfoPath (included in Microsoft Office 2003 and later) can design and enter data using flexible, electronic forms. With the HTML FormEntry module, forms can be created with customized HTML and run directly within the web application. With XForms module, users have a drag-drop interface to design forms that can then be filled online in a web page.

OpenMRS top-ten features

6. Data export: Data can be exported into a spreadsheet format for use in other tools (Excel, Access, etc.), including aggregation HMIS systems like DHIS2.

7. Modular architecture: An OpenMRS Module can extend and add any type of functionality to the existing API and web application. 200+ available modules.

8. Support for complex data: Radiology images, sound files, etc. can be stored as “complex” observations

9. Cohort management: The cohort builder allows you to create groups of patients that match a “criteria” for data exports, reporting, analysis etc.

10. Localization / internationalization: Multiple language support and the possibility to extend to other languages with full UTF-8 support.

OpenMRS top-ten features (cont’d)

https://www.youtube.com/watch?v=Fvc__rmS7lkOpenMRS: history of 10 years

People are using the OpenMRS platform for

all sorts of things.

OpenMRS forms for WHO HIV Treatment

Chart of a patient’s lab

results

Disease-specific EMR (MDR-TB)Credit: WHO-TB and PIH

Inpatient Care

Credit: Andrey Kozhushkov, Ghislain Kouematchoua (Göttingen)

Registration Module with fingerprint and patient image

Credit: HISP India

Research Data Coordination

Credit:Dave Thomas

Adaptive Turnaround Documents

Credit: Vibha Anand,Paul Biondich (Regenstrief)

Eligibility Across InstitutionsCredit: Monica Waggoner

Google Maps IntegrationCredit: IRDOwais Ahmed, Aamir Khan

ID Cards and Barcodes Credit: Brian Mckown (AMPATH)

“Mateme” Touchscreen Registration

Credit: Jeff Rafter (Baobab), Evan Waters (PIH)

iPhone App

Credit: Rowan Seymour& Parker Erway

Notifiable Condition Detector

Credit: Shaun Grannis,Regenstrief Institute

Health Data ExchangeCredit:Odysseas Pentakalos

OpenMRS installation

1. OpenMRS Standalone - OpenMRS Standalone provides a simplified, all-inclusive installation option with both an embedded database and web server. You can have a local copy of OpenMRS running within minutes: simply download and expand the archive, and then run the extracted openmrs-standalone.jar file. Your browser will open a new instance of the OpenMRS system. The default username is "admin" and the default password is "Admin123".

2. OpenMRS Platform - Recommended for advanced users using OpenMRS 2.x or Platform in production. Requires an existing Java servlet container such as Apache Tomcat, and an existing database such as MySQL.

3. OpenMRS Reference application – The reference application download is a zip archive which includes the platform war (webapplication archive) and OpenMRS addon (omod files).

Choosing which OpenMRS to install

1. Web browser – Since the OpenMRS reference application is a web application, you will need a web browser to install and use OpenMRS. Mozilla Firefox or Chrome are the recommended the browsers.

2. Java is the platform on which OpenMRS has been programmed. OpenMRS platform since v2.0 requires Java 8. The reference application till v2.3 can run on Java 7 since they use the Platform 1.x line. Later releases that use platform v2.0 will require Java 8. Due to backwards compatibility, Java 8 can run previous versions of OpenMRS too.

3. MySQL 5.6 is recommended as the database management system (DBMS). Due to the use of Hibernate (a database abstraction library), OpenMRS is also supposed to work with MariaDB (a MySQL fork), PostgreSQL and MS SQL server. But these other DBMS have not been tested to work with the reference application.

4. Apache Tomcat – a Java servlet container to run web applications. OpenMRS has been deployed on Jboss and Glassfish previously, but the reference application has not been tested to work on these other Java application servers.

Install dependencies

• OpenMRS works on Sun/Oracle Java or OpenJDK. It has not been tested with other Java virtual machines such as JRockit or IBM J9

• Java installation instructions can be found here:http://www.oracle.com/technetwork/java/javase/downloads/jdk7-downloads-1880260.html

• The webupd8 has a popular ppa that is used in Ubuntu. See here:http://www.webupd8.org/2012/01/install-oracle-java-jdk-7-in-ubuntu-via.html

• Once Java 7 is installed, configure the JAVA_OPTS environment variable to allocate adequate heap memory as well as PermSize variable.

JAVA_OPTS="-Xms512m –Xmx1024m –XX:MaxPermSize=256m" (Sets the heap min size and max size)

• In linux, set this in /etc/environment or .bashrc file• In Windows, control panel System Advanced system settings Environment

variables New (under user variables) variable name: JAVA_OPTS and value provided above

Java Download and installation

• The OpenMRS reference application downloads can be found here:http://openmrs.org/download/

• Choose the OpenMRS Standalone download for now. https://sourceforge.net/projects/openmrs/files/releases/OpenMRS_2.3.1/openmrs-standalone-2.3.1.zip/download

• In this tutorial we will also show you provide you information for more advanced installation. You can use this for extending OpenMRS tutorial.

• After the above download completes, please extract all files. Here you will see openmrs-standalone.jar. If you double-click on this, it should start Java and start deploying OpenMRS. The browser will open once OpenMRS is ready to be used

OpenMRS download

Starting OpenMRS standalone

You will see a screen once you start the standalone

Choose the Demonstration mode, because we want demo data and the starter dictionary that is part of the reference application.

Allow ports to communicate with MySQL

The 2.x standalone uses Tomcat on port 8081 and MySQL on port 3316. These are not the default ports of Tomcat and MySQL deliberately, so that there is no conflict with existing installations

You can run the standalone side-by-side with the platform or more advanced installation by using the individual components, as shown in the slides later.

OpenMRS Standalone configuration options

Tomcat Port This is the port at which to run TomcatMySQL Port This is the port at which to run MySQLFile → Quit This stops Tomcat and MySQL and then closes the

applicationFile → Launch Browser

This opens the OpenMRS login page for the current web application context

File → Clear Output This clears the output log in the user interface text area, but does not clear the log file written on the file system

StartThis button runs Tomcat, which will automatically start the MySQL database engine if it was not already running. For the embedded MySQL, the first connection automatically starts the MySQL engine

Stop This button stops Tomcat and then also stops the MySQL database engine, without closing the application

OpenMRS Starts with Login• Browser should start with OpenMRS 2.x login page.• If there is any error, you will see a different screen along with the error

message. The error message is also known as Exception. Remember to report error messages with the error log (the box which showed OpenMRS starting).

• Username: admin• Password: Admin123

• Remember that aLocation must beSelected or else the Login button will not be activated

Administering OpenMRS

Lunch break here

OpenMRS Apps page• After successful login, you will see the navBar the top black bar,

showing username, Location for the session and Logout• The list of apps are the ones that are available. Depending on the user

privileges and roles, the available list of apps can be changed. Since everyone now logged in as admin, you’ll see all apps.

• When you click on any app, you will see the path to that app in breadcrumb, like shown on the right screen. You can click the home icon

to come back.

OpenMRS Administration page• The Administration page can be

reached from:Administration System administration

• The Administration page still uses the Legacy UI and thus, has a different look-and-feel. This is in the process of being moved to the new 2.x UI

• Understand the difference between legacyUI and 2.x UI by recalling the architecture diagram from earlier.

OpenMRS Roles and Privileges• Roles and Privileges are controlled through the Administration page, under

the Manage Users section.• OpenMRS uses privileges and roles to control access to data within the system.

Privileges define what can or cannot be done in the system (e.g., Edit Patients or Add Users) while roles are used to group privileges into more manageable groupings.

• We will use this example: you are working with several privileges related to patient data - e.g., View Patients, Edit Patients, and Add Patients. The View Patients privilege lets users look at patients in the system, the Edit Patients privilege lets users edit information about existing patients, and the Add Patients privilege allows users to create a completely new patient record within the system.

• Now imagine that you need to assign the proper rules to three people: Mary the Medical Student, Bob the Data Assistant, and Erica the Data Manager. You want medical students to be able to view patients, but not edit or add them. Data assistants should be able to not only view, but also edit patient data. And you want your data managers to be able to create new patients within your system

OpenMRS Roles and Privileges (2)• Very often, certain roles can be defined as a combination of other roles. In our

example, a Data Manager oversees the Data Assistants and therefore should have all of their privileges plus some additional privileges. So, let's redesign our roles slightly to show how this might work.

• You can see that the Data Manager role can be more clearly defined as a Data Assistant with the extra ability to add patients to the system. 

 RoleInherit Privileges from Role(s)

Additional Privilege(s) 

 Medical Student   View Patient 

 Data Assistant   View PatientEdit Patient 

 Data Manager Data Assistant  Add Patient 

• In addition, if you should change or enhance the privileges of the Data Assistant role at any time in the future, the Data Manager will automatically adapt to those changes.

• E.g. if you decided a month later to allow any Data Assistant to Edit Encounters (by adding the Edit Encounters privilege to the Data Assistant role), the Data Manager role would automatically gain the ability to edit encounters as well.

OpenMRS Built-in roles• There are some special roles that are predefined within OpenMRS and cannot be

deleted: Anonymous, Authenticated, and System Developer. • Any privileges granted to the Anonymous role will be available to people without

logging into the system. Generally, Anonymous privileges should be kept very restricted, since patient information might otherwise be compromised.

• Privileges granted to the Authenticated role are granted to anyone that logs into your system, no matter what other role(s) they might be assigned. Granting privileges to Authenticated role is an easy way to grant privileges to all users of the system.

• The System Developer role is automatically granted full access to the system and should only be granted to system administrators.

• The roles with Application: (prefix) and Organizational: (prefix) are UI 2.x roles

Adding new roles• If you then follow the Add Role link, you will see a form for adding a new role.

– Enter Role Name– Choose Roles Privileges of which you want to inherit– Choose Privileges which you want this Role to have

• The privileges are made available by pages in add-on modules

• This is specified as part of the config.xml in the OpenMRS module source code. You will learn more detail about this in the Extending OpenMRS… tutorial

• Go ahead and create the Medical Student role, which will have inherited Application: Registers Patients, App: coreapps.findPatient.

• Then, save the Role.

Manage users• To create these users, we'll go through Administration > Manage Users. This

page also lets you find and edit existing users.– Create a new User– Search Users by Name or Roles– Edit a single Use

• Users in OpenMRS need to be associated with Persons. You either need to create a new Person, or attach the user account to an existing one

• Go ahead and create new Person, give your first, last name and gender, you date of birth and create the person. This person will then be given the Medical Student role that you created in the earlier slides. See next screen

Add user• Provide the username with which the user

will login and type password twice.• The following global properties (we’ll show

you later) will let you configure the complexity of your password (default values below):– security.passwordCannotMatchUsername = true– security.passwordMinimumLength = 8– security.passwordRequiresDigit = true– security.passwordRequiresNonDigit = true– security.passwordRequiresUpperAndLowerCase =

true

• You can also checkbox for the user to set their own password after first login

• Checkbox the Medical student role that you had created earlier

Doing System settings using global properties

• Go to Administration Settings to work with global properties. The UI is divided into global properties based on each module

• Each add-on module exposes a set of settings that can be configured to show the system setting. Remember that these settings are system-wide and not per-user. Thus, it affects all the users that have access to the module• Be very careful to change these

settings because there is no way to undo the changes.

• Global properties are not voided or backed up when they are changed.

Logging in as Medical student• Press logout from the top right link.• Login as the medical student username and password that you just created. You will

see that there are only 3 apps available to this user now.

• We next move to clinical management functions. We first need to understand how OpenMRS stores patient information. So lets get back to the conceptual level from the hands on work that we have been doing.

OpenMRS Data Model

• While OpenMRS has a nearly 1:1 relationship between Entities and database tables, this is not necessarily the most efficient way to design APIs.

• Yet, it is something that makes it easier for newcomers to understand and comprehend (and then contribute code) to OpenMRS.

• This means that for nearly every OpenMRS object, there is a linked table that has similar properties that represent the column names of the tables.

• So for the Person entity, there is a Person table. For the User entity, there is a User table. Similarly, there is for Patient, Encounter, Obs etc.

• Please open the below link and zoom into the diagram. It is large in size and you can look at the complex relationship between the tables, shown using the interconnected lines.

• https://wiki.openmrs.org/display/docs/Data+Model?preview=/589829/34374263/openmrs_data_model_1.9.0.png

Database tables

• When you zoom into the image, you’ll see sectional blocks in them. These are different domains within the data model.– Concept: Concepts are defined and used to support coded data throughout the

system– Encounter: Contains the meta-data regarding providers interventions with a

patient.– Form: Essentially, the user interface description for the various components of a

form.– Observation: This is where the actual health care information is stored. There are

many observations per Encounter.– Order: Things/actions that have been requested to occur.– Patient: Basic information about patients in this system.– User: Basic information about the people that use this system.– Person: Basic information about person in the system.– Business: Non medical data used to administrate openmrs– Groups/Workflow: Workflows and Cohort data

Domains in the data model

• Look here in more details at the OpenMRS data modelhttp://burkeware.com/openmrs-data-model/

Exploring the OpenMRS data model

OpenMRS Information Model

• The actual information you want to record in OpenMRS is called Data. Examples of Data in OpenMRS are Patients, Encounters, and Observations. To support this data, and describe its meaning, you need additional Metadata.

Data• When a user deletes a piece of data in OpenMRS, the information actually remains

in the database. It is marked as voided, so that it will not show up in the interface, but it is not immediately deleted from the database.

• If a user deletes a piece of data by accident, an administrator can unvoid it to return it to the system. To permanently delete data from the database, an administrator must purge that data. Typically, this should never be done in a production system.

Metadata• Generally speaking, the things that you need to configure in order to describe the

real patient information you will be capturing are referred to as Metadata. An example of a piece of metadata is a Location that represents a hospital.

Data and Metadata

• An administrator may also retire metadata in OpenMRS. This does not mean that the metadata is deleted, but rather that it is not intended to be used going forwards. Old information that refers to the retired metadata remains valid.

• An administrator may unretire metadata if it becomes relevant to active use again. If no actual data refers to a piece of metadata, an administrator may purge the metadata to permanently remove it from the database.

• For example, the hospital you refer patients to closes. Therefore, you can no longer refer patients there. This Location can now be retired in OpenMRS. This would not invalidate the fact that many patients were referred there in the past.

• Thus, whenever you see retired or retired_by columns in the tables, it means that it is metadata related table, where as when you see voided or voided_by in the tables, it means that it is data table.

Data and Metadata (cont’d)

• The OpenMRS concept dictionary is the central knowledge base of medical as well as non-medical/program-related terms that need to be captured.

• E.g. suppose we want to capture the patient vitals after a patient has been registered at a clinic. We want to define all the terms that should be captured in Vitals. i.e. Height, weight, systolic blood pressure, diastolic blood pressure etc.

• Each of these need to be defined as a CONCEPT in OpenMRS and concepts are managed through the concept dictionary.

• If you want to ask a question that has a fixed set of coded answers, those answers are also Concepts. (For example, the question concept Blood Type may have 4 different answer concepts: A, B, AB, and O)

• To understand what medical terms (Concepts) are available in your dictionary, let us look at the reference application’s pre-installed concept dictionary now

•More details about this is covered in the Manage concept dictionary tutorial

Concept dictionary

•Once you’ve successfully logged in you will see a number of apps like Find patient record, Active Visits etc.•Press the System administration and then go to Advanced Administration•Here you will be able to see the legacy UI of OpenMRS. What you were using till now was the new OpenMRS 2.x reference UI

Viewing the Concept dictionary

•Click on the Dictionary link in the header bar. This shows the UI for concept management.•DO NOT download the concept dictionary.•You can search for the same concept ‘systolic’ in the OpenMRS concept dictionary. You will see two results. Click on systolic blood pressure.

Viewing the Concept dictionary (2)

•A good thing to do for interoperability and linking with other providers that may use OpenMRS or other EMR systems, is to be able to use standardized terminology like ICD, SNOMED or RxNorm.•As we saw earlier, the MCL allows you to look at shared concepts. Please open MCL and search for the terms and compare “Systolic blood pressure”.•Edit you local concept if you’d like to make your Implementation interoperablewith others.

Correlating this concept with MCL

• Every individual who is referred to in any patient's record in OpenMRS must be stored in the system as a Person. Most persons will also be Patients or Users.

Names• A person can have one or more names, one of which must be marked as the

preferred name. The preferred name will be displayed in search results and patient screens.

Addresses• A person may have zero or more contact addresses. You may configure the format

of these addresses for your particular locale.Person Attributes• To support your local needs, you can define additional pieces of information about

the people in your system, on top of those that are natively supported by OpenMRS. You can define the datatype of a Person Attribute, as well as any constraints on the possible values, using metadata. This metadata is called a Person Attribute Type.

• Person Attributes are suitable for storing other information. But historical values of person attributes are not retained. For example, you should use a person attribute to record a patient's contact telephone number.

Person

• Anyone who receives care in OpenMRS must be a Patient (for example, anyone who has an Encounter or who is enrolled in a Program). Every Patient must have at least one Identifier, which is explained below.

• A Patient is also a Person, meaning they must have at least one name and they may have addresses.

Patient Identifier• The Patient Identifier is a medical record number assigned by your facility, used to

identify and re-identify the patient on subsequent visits.• A Patient Identifier Type defines the format of a particular kind of patient

identifier. For example, you might define that your facility patient ID is an identifier type that is required for every patient; the format is 2 letters followed by 6 digits and uses a particular check digit1 algorithm.

Patient

•A Visit in OpenMRS represents exactly what it sounds like: a time period when a patient is actively interacting with the healthcare system, typically at a location

• The metadata differentiating different types of visits is a Visit Type. Visit Types are displayed in the user interface, and can be searched against.

•A visit contains Encounters, which store more granular data about treatments or services.

•A patient may receive several kinds of care and services while at a health clinic. For example, they may see a clinician, have an X-ray taken, and be given a lab test. Each of these services is an Encounter, recorded in a form. OpenMRS uses Visits to collect these related encounters into one group

•Visits are managed in Administration > Visits. Here you can define the kinds of visits and their attributes, and set the default behaviour for how visits are created.

Visits and Encounters

•Manage Visit Types:A Visit Type is a name and description of a kind of visit. Every visit has a type. You should create visit types that match how your health site classifies visits, such as "Outpatient", "Hospitalization", "Dental", "Patient Education", or "TB Clinic".

•Manage Visit Attribute Types:If you wish to record extra information about visits, you can create Visit Attributes and assign them to Visit Types. For example, you might create attributes for "Followup Visit,"or "Distance Patient Traveled".

Visits Types

•Visit is enabled by default, but is an optional feature. While Visit is enabled, the patient dashboard will show a tab called Visits and group all encounters by visit. If disabled, the patient dashboard will show the Encounters tab and list encounters chronologically with no grouping.

•A visit has a start time and an end time. The start date and time is automatically set when a visit is created. The end date and time is left blank by default. It is set manually by a data clerk

• The Start auto close visits task option changes this. If enabled, auto-close will automatically set the end date to the

start date, and the end time to 23:59. 

Visits Configuration

What is an encounter?•A patient visits a health center or hospital.  For each electronic form completed for a patient, a new encounter is created. • Each encounter has a unique encounter_id and encounter_type.  Forms could be completed by different departments/location (ie.  drug pickup, visit to HIV clinic), and will have an associated encounter_type (ie. ART Drug Regimen Pickup, Adult intake, food assistance, lab test, etc).  Each encounter has an encounter type, date/time, location and provider.

What is an observation (obs)?Within an encounter, different observations (aka obs) are recorded.  Obs_ids are unique (like snowflakes).  A new and unique obs_id is generated for every obs. These are possible scenarios:•One visit with one encounter without observations•One visit with one encounter with one observation•One visit with one encounter and many observations•One visit with multiple encounters and many observations

Encounters and Obs

Reference app – clinical workflows

Take a break of 10mins

• Data is recorded in an EMR for a patient, so creating a patient is the first task to record data. Press the Home button and you’ll go back to 2.x UI

• Press the Register a patient button. Create a patient with your details.• After filling the details, press the Confirm button to save the patient.• You can configure the fields based on Person attributes

Register a patient

• Press the Find Patient Record button at the home page• You can search a patient based on their name, or patient identifier. There have been

deployments on OpenMRS that use barcodes of patient identifiers. These can be read directly into these fields just like keyboard typing. Type John in the field

• Click on Betty Johnson from the list of existing patients to go to their patient dashboard.

Find a patient and go to patient dashboard

• The top most section of the dashboard shows Patient name, date of birth and identifiers. This can be customized through modules or global properties

• The patient dashboard lists all the forms that are available, under the General actions section. You will also see DIAGNOSES, RECENT VISITS, ALLERGIES, VITALS, APPOINTMENTS

• You can add data by either selecting General Actions or selecting a visit or the edit icon on the sections. Click on the start visit to create a new visit for the patient. Press confirm and

select the Capture Vitals from the actions that can done in the Current visit

Using the Patient dashboard

• The vitals is an example form. You could create many such forms that are important to your clinical setting. This can be learnt in detail in the extending and customizing OpenMRS tutorial.

• Recall from the data model, that the Form is nothing but a view or bundling of the fields (that have underlying Concepts) into a user interface.

• There are multiple formtechnologies that are availablein OpenMRS. These types of formsare generally developed using theHTMLFormEntry module.

• Once you’ve captured all the Vitals, save the form. An encounteris created with the obs for thispatient.

Capture patient vitals

• Charts are important decision making tools for clinicians. These are used to look at observations over a period of time and monitor changes in the obs values.

• You can return to the patient dashboard, by click on the name of the patient from the breadcrumb. Under General Actions click on the Chart Search link.

• Once you see the chart search interface, click on the QuickSearch link. This will display all the observations for the patient. Scroll down from the left list and click on Weight. You will see a chart for the weight across different visits for the patient

Charting the vitals

• One of the primary tasks that clinician perform during a patient visit is to capture visit notes.

• Click on a visit from the list of visits shown on the patient dashboard or the Current visit actions, if this is for the current visit Visit note.

• Here you can select the Primary and secondary diagnosis, which are coded values into the note. This is configured using the global property - emr.concept.diagnosisSetOfSets

Capturing visit notes

• The clinical note section is free-text that can be written to capture unstructed notes about the patient visit.

• There are certain modules that can be used to analyze the information stored in unstructured clinical notes.

• Implementers need to make a balanced choice between using structured or unstructured data fields in the patient records

• There are other workflows. Demonstrate these:– Capture allergies– Schedule appointments– Create programs– Create program states– Create orders (through the LegacyUI interface)– Look at existing patient orders– Difference between drug orders (drug concept) and other kinds of orders

• There are other types of clinical workflows that are not in the reference application. We will discuss this in the use-case section of the tutorials

Going through other workflows

OpenMRS use-cases and Q&A

OpenMRS advancedinstallation

If time permits at the end

• Instructions to install MySQL 5.5 for different platforms can be found here: http://dev.mysql.com/doc/refman/5.5/en/installing.html

• Most real-world installations for large scale MySQL happen on Linux/Ubuntu servers using the command.

$ sudo apt-get install mysql-server

• You can either install on your local Windows or Mac OSX using the binary installer (sorry, Chrome OS users)

http://dev.mysql.com/downloads/mysql/

MySQL server installation

MySQL is an open-source database system, which means the source code is available for people to modify, change, rebuild and sell… all free of costHere you see the GNU GPL v2 license that is a popular open-source license.

• The developer default installs a system that’s appropriate for developers and testing. It installs the server, workbench and connectors to different programming languages

• In production i.e. real server, you want to install to Server only option

Selecting installation type

Summary of what is to be installed

MySQL server configuration

• While the installation happens, you can get to the configuration step. Configuration can also be done once the installation is complete and people have started using the database server.

• The port number is the location through which the database will be connected by external users or programs. By default this port is 3306

MySQL server configuration (2)

• The main database user is called root. This user is installed by default and this password is crucial to remember. The root user has privileges to all the database tables, so this user should never be used other than DBA tasks

• The password for root user is set in this installation screen. You can also create other non-privileged users by pressing the “Add User” button

MySQL server configuration (3)

• Installing MySQL as a service, means that the database system will start along with the system startup. Here you can configure the name of the service and whether the database service should start on system startup

MySQL server configuration (4)

• Logs are important information that is maintained by MySQL during the time it is running. The Advanced Options during installation can be used to specify the location where the logs are saved on the system.

MySQL server configuration (5)

• In the last step MySQL shows its progress in installation and configuration, where you have to press the “Execute” button and the installation should run and finish all the steps.

MySQL upgrade

• The installer can also be used to upgrade the server installation.

• Download the zip archive for Apache tomcat from here:http://download.nextag.com/apache/tomcat/tomcat-7/v7.0.65/bin/apache-tomcat-7.0.65.zip

Installation for Windows is just unpacking this archive into a location that you will remember. Right click Extract all.

• Platform specific versions come with Tomcat native bundled. You can use Ubuntu’s repo to install apache tomcat 7

$ sudo apt-get install tomcat7

• Detailed installation for Ubuntu can be found here:https://help.ubuntu.com/lts/serverguide/tomcat.html

• The tomcat documentation is an excellent resource that should be read for better understanding its functioning and configuration options:

http://tomcat.apache.org/tomcat-7.0-doc/index.html

Apache tomcat download

• Move the downloaded openmrs.war to TOMCAT_HOME/webapps folder.

• Start tomcat• Go to localhost:8080/openmrs – here you will be redirected to the

initialsetup page.• Follow the instructions on the screen and install OpenMRS.• It is recommended that you do not use the root account to connect to

OpenMRS. Instead, use the user interface to select the option where the installer will create a new user account for you, based on you providing the root MySQL username and password.

Deploy OpenMRS on Apache tomcat

Please attend the certification discussion to understand how you can use the skills you’ve gained today.

We are working on OpenMRS Fundamentals Exam – this tutorial will help you in giving that exam