Smart Container Technical Documentation for OpenMRS Developers

Primary objective of this module is to convert OpenMRS into a SMART container. After installing this module, OpenMRS users will be able to install and launch SMART Apps easily. Before going deep into the detail of the module architecture we have to understand some terminologies related to SMART Apps and SMART Containers.

What is a SMART App?

A SMART app is a substitutable medical app built using reusable techniques. It can be a web app built using reusable technologies such as HTML and JavaScript. It uses the SMART API to retrieve data from data sources. The data source may be a EMR like OpenMRS, a PHR like Indivo, or a data analytic platform such as i2b2. There are two types of SMART apps: SMART Connect app and SMART REST apps.

SMART Connect app
These are embedded in to the SMART container using HTML iframes and uses interframe communication (using javaScript callbacks) to get the data from the container. The API that SMART connect apps use is called the SMART Connect API.

SMART REST apps
These are standalone applications(clients) that are running separately as a back-end server to a SMART connect app and uses a set of REST calls to get its data from the container. The API used by SMART REST apps is called as SMART REST API.

More information is available on the following page http://wiki.chip.org/smart-project/index.php/Main_Page#What_is_SMART.3F.

What is SMART Container?

A SMART container is a data source that exposes its data through the SMART API and provides a UI for SMART connect apps. Every EMR can be a SMART container when it is providing the SMART API, UI and secure way of accessing the API. Additionally, it can provide its own way of installing and managing of the SMART apps.

For more information refer to this page: http://wiki.chip.org/smartproject/index.php/Developers_Documentation:_Terminology#SMART_Container.

How to convert OpenMRS into SMART Container

In order to convert OpenMRS into a SMART container the module should provide at least the following to the SMART Apps:

UI: where the SMART App is launched
Expose data: which are going to consumed by SMART Apps
Authentication: Enables secure way of transferring data.

Providing UI for SMART Apps

Almost all SMART Apps are centered around patient data. Therefore the apps are displayed as a tab on the patient dashboard.

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SMART Apps are displayed at patient dashboard under the SMART tab. The SMART Apps which are selected by the user on the Manage User Apps admin page will be displayed at the side pane. When its icon is clicked the app will be launched within the HTML iframe. Using the available extension point (PatientDashboardTabExt) at the patient dashboard the SMART app tab was created.

Exposing Data

The idea the smartcontainer module adopts is initially expose SMART REST API and convert SMART connect javaScript callback into a ajax call to SMART REST API. So the smartcontainer module is proxying SMART connect API with SMART REST API. This proxying mechanism is done at smartAppForm.jsp as following:

$j.ajax({
	beforeSend : function(xhr) {
		xhr.setRequestHeader("Authorization", " ");
	},
	dataType : "text",
	url : "${pageContext.request.contextPath}" + "/ws/smartcontainer/api" + api_call.func,
	contentType : activity.contentType,
	data : activity.params,
	type : activity.method,
	success : callback,
	error : function(data) {
		alert("error");
	}
});

SMART REST API

We created our own controllers which process the REST because of some technical difficulties in generating RDF payloads. Each SMART data types smartcontainer has a controller. For example there is a ProblemController to serve the requests which are asking problems. Those requests are in following form:

GET http://localhost:8080/openmrs/ws/smartcontainer/api/records/{patientId}/problems

In a nutshell
ProblemController asks the SmartProblemHandler to convert Problems (openmrs objects) to SmartProblem objects.

The SmartProblems are then passed to the ProblemRDFSource to be converted to RDF XML form.

In a bigger nutshell
Smartcontainer uses OpenRDF library to generate RDF payloads. The SmartDataService is responsible for generating appropriate SMART domain objects such as SmartProblem from a selected patient. Appropriate handlers are supplied to the SmartDataService class through the moduleApplicationContext.xml which are used to convert the OpenMRS domain object into SMART domain object.Currently the module has handlers and RDFSources for following SMART data types.

Patient demographics

SMART field	Description	Data format	OpenMRS terminology
Given name	A person's given, or first, name	Free text	patient.getFamilyName()
Family name	A person's family, or last, name	Free text	patient.getGivenName()
Gender	A person's gender	'male' or 'female'	patient.getGender().equals("M") ? "male" : "female"
Zip code	A person's zip code	Free text	patient.getPersonAddress().getPostalCode()
Birth day	A person's birth date	ISO-8601 string	patient.getBirthdate()

Medication (mapped to RxNorm)

SMART field	Description	Data format	OpenMRS terminology
Drug name	RxNorm Concept ID for this medication	RDF CodedValue node with code drawn from http://rxnav.nlm.nih.gov/REST/rxcui/{rxcui}	DrugOder.getDrug().getConcept() is used to retrieve the mapped RxNorm concept code, if the code available it is used to set the code of the drug name concept and the title of the coded value is still filled with OpenMRS concept name.
Instruction	Clinician-supplied instructions from the prescription signature	Free text	DrugOder.getFrequency()
Quantity	For a medication with a simple dosing schedule, record the amount to take with each administration.	RDF ValueAndUnit node	value:DrugOder.getQuantity() unit:DrugOrder.getunits()
Frequency	For a medication with a simple dosing schedule, record how often to take the medication	RDF ValueAndUnit node	DrugOder.getFrequency() is first split-ed for '/' and then first part is converted into number,it gives the value .The second part is mapped from Openmrs format("daily") to SMART format("/d") or if the OpenMRS format is different it gives unstructured unit as "\'{my units}".
Start date	when the patient started taking a medication	ISO-8601 string	DrugOrder.getStartDate()
End date	when the patient stopped taking a medication	ISO-8601 string	First DrugOder.getDiscontinued() is checked if it so the end date is set to that otherwise DruOrder.getAutoExpireDate() is set .
Fulfilment		RDF Fulfillment node	NOT IMPLEMENTED YET

Problems (Mapped to SNOMED CT)

OpenMRS data model represents problem in two way. First is using problem table for which the mapping to SMART problem is done directly as follows.

SMART field	Description	Data format	OpenMRS terminology
Notes	Additional notes about the problem	Free text	Problem.getComments();
Problem name	SNOMED-CT Concept for the problem	CodedValue node referencinghttp://www.ihtsdo.org/snomed-ct/concepts/{concept_id}	Problem.getProblem() is used to retrieve related mapped SNOMED-CT concept code and this value is used to set the code of the coded value node and the OpenMRS concept name is used to fill the title of the coded value node.
Resolution	Date of problem resolution	ISO-8601 string	Problem.getEndDate()
Title	Human-readable problem name	Free text	It is already included within the problem name
Onset	Date of problem onset	ISO-8601 string	Problem.getStartDate()

Second way is using problem added/problem removed obs to represent the problems.

SMART field	Description	Data format	OpenMRS terminology
Notes	Additional notes about the problem	Free text	Obs.getComments()
Problem name	SNOMED-CT Concept for the problem	CodedValue node referencing[[http://www.ihtsdo.org/snomed-ct/concepts/]{concept_id}	Obs.getValueCoded().getName()
Resolution	Date of problem resolution	ISO-8601 string	The obs table is searched for another obs with the same obs.valued_coded but with obs.concept_id == user-chosen-PROBLEM_RESOLVED-concept-id. If found, the obs.obsdatetime is used, otherwise null.
Title	Human-readable problem name	Free text
Onset	Date of problem onset	ISO-8601 string	Obs.getObsDatetime()

From both method user have to select one method at Administration->Set up problem object page

Lab result

The Obs related to lab result are separated by only taking the obs whose concept.conceptClass is "Test".

SMART field	Description	Data format	OpenMRS terminology
Lab name	LOINC Coded Value for result	RDF CodedValue node *drawn from LOINC	Obs.getConcept() is used to retrieve related mapped LOINC concept code and this value is used to set the code of the coded value node and the OpenMRS concept name is used to fill the title of the coded value node.
Quantitative result	Qualitative result, if any	RDF QuantitativeResult node	If the obs.concept is numeric then quantity.valueAndUnit=(Obs.ValueNumeric,ConceptNumeric.units) quantity.normalRange=(ConceptNumeric.hiNormal,ConceptNumeric.lowNormal,ConceptNum) quantity.nonCriticalRange=NOT IMPLEMENTED else if Obs.concept is coded value then quantity.valueAndUnit=(Obs.ValueCoded.Name,null)
Nominal result	Nominal result, if any	RDF NominalResult node	NOT IMPLEMENTED
Narrative result	Narrative result, if any	RDF NarrativeResult node	NOT IMPLEMENTED
Ordinal result	Ordinal result, if any	RDF OrdinalResult node	NOT IMPLEMENTED
Accession number	External accession number for a lab result	Free Text	Obs.accessionNumber
Status	Status of this lab	RDF CodedValue node, drawn fromhttp://smartplatforms.org/terms/code/LabResultStatus#	NOT IMPLEMENTED
Abnormal interpretation	Abnormal interpretation status for this lab	RDF CodedValue node, drawn fromhttp://smartplatforms.org/terms/code/LabResultInterpretation#	NOT IMPLEMENTED
Specimen collected	Attribution for who collected the specimen for this result, and when	RDF Attribution node	Start date:Obs.ObsDateTime End Date:NOT IMPLEMENTED Participant:NOT IMPLEMENTED
Specimen received	Attribution for who received the specimen for this result, and when	RDF Attribution node	NOT IMPLEMENTED
Resulted	Attribution for who determined this result from the specimen, and when	RDF Attribution node	NOT IMPLEMENTED
Comments	Narrative comments for this result	Free Text	NOT IMPLEMENTED

Vital Signs

Obs whose concepts match a fixed list of LOINC codes

SMART field	Description	Data format	OpenMRS terminology
Encounter	Encounter during which vital signs were taken	RDF Encounter node	Currently typical OpenMRS installation has following encounter types ADULTINITIAL,ADULTRETURN,PEDSINITIAL and PEDSRETURN which are actually ambulatory encounter type. encouner.type="ambulatory" encounter.startDate=Encounter.visit.startDateTime encounter.endDate=Encounter.visit.endDateTime
Date	Date + time when vital signs were recorded	ISO-8601 string	Encounter.encounterDateTime
height	Patient's height in meters	RDF ValueAndUnit node where unit is: "m"	if Obs.concept's mapped conceptCode.equals("8302-2") vitalSign.valueAndUnit=(Obs.valueNumeric,ConceptNumeric.units)
weight	Patient's weight in kg	RDF ValueAndUnit node where unit is: "kg"	if Obs.concept's mapped conceptCode.equals("3141-9") vitalSign.valueAndUnit=(Obs.valueNumeric,ConceptNumeric.units)
Body Mass Index	Patient's Body Mass Index	RDF ValueAndUnit node where unit is: "{BMI}"	if Obs.concept's mapped conceptCode.equals("39156-5") vitalSign.valueAndUnit=(Obs.valueNumeric,ConceptNumeric.units)
Respiratory Rate	Patient's Respiratory Rate per minute	RDF ValueAndUnit node where unit is: "{breaths}/min"	if Obs.concept's mapped conceptCode.equals("9279-1") vitalSign.valueAndUnit=(Obs.valueNumeric,ConceptNumeric.units)
Heart Rate	Patient's Heart Rate per minute	RDF ValueAndUnit node where unit is: "{beats}/min"	if Obs.concept's mapped conceptCode.equals("8867-4") vitalSign.valueAndUnit=(Obs.valueNumeric,ConceptNumeric.units)
Temperature	Patient's Temperature in Celcius	RDF ValueAndUnit node where unit is: "Cel"	if Obs.concept's mapped conceptCode.equals("8310-5") vitalSign.valueAndUnit=(Obs.valueNumeric,ConceptNumeric.units)
Oxygen Saturation	Patient's Oxygen Saturation in percent hemoglobin	RDF ValueAndUnit node where unit is: "%{HemoglobinSaturation}"	if Obs.concept's mapped conceptCode.equals("2710-2") vitalSign.valueAndUnit=(Obs.valueNumeric,ConceptNumeric.units)
Blood Pressure	Patient's systolic + diastolic Blood Pressure in mmHg, with optinal position coding	RDF BloodPressure Node	if Obs.concept's mapped conceptCode.equals("8462-4") vitalSign(diastolic).valueAndUnit=(Obs.valueNumeric,ConceptNumeric.units) else if Obs.concept's mapped conceptCode.equals("8480-6") vitalSign(systolic).valueAndUnit=(Obs.valueNumeric,ConceptNumeric.units)

Authentication

Because the apps are running inside of openmrs, the standard openmrs authentication and privilege checking is used.

Managing Apps

OpenMRS administrators can add or remove SMART Apps. The actual hosting of the SMART apps is outside of this module. The container gets all information necessary to launch the remotely hosted SMART app from the uploaded manifest file of the SMART app. The ManifestParser is responsible for parsing the manifest file and the AppFactory generates the App object which can be saved in database.

The added Apps are only available on the patient dashboard after user adds SMART apps at Administration->Manage User Apps.

Detailed presentation: http://vimeo.com/23265477