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Using InterSystems OMOP to Transform FHIR Data

The 2026.1 release of InterSystems IRIS® data platform, InterSystems IRIS^® for Health, and InterSystems Health Connect™ is now Generally Available (GA). This is an Extended Maintenance (EM) release.

I need a %SYS.Python object that will be accessible from different processes. The goal is to avoid reinitializing the Python object whenever it is called. Ways that I checked and decided that it is NOT what I want:

• %-variables (process variables). Reusing only in the same process
• Save-and-restore via globals. Restoring means heavy initialization, which I want to avoid

Next, my ideas (none of them look like a silver bullet):

• Using Interoperability Production.

What is a Microservice?

A microservice is an architectural style that structures an application as a collection of small, autonomous services. Each component is developed around a specific business capability, can be deployed independently, and is typically managed by a miniature, specialized, self-governing team. (Source: https://microservices.io/)

The 2025.1.4 and 2024.1.6 maintenance releases of InterSystems IRIS^® data platform, InterSystems IRIS^® for Health, and InterSystemsHealth Connect™ are now Generally Available (GA). These releases include the fixes for a number of recently issued alerts and advisories, including the following: 

• April 15, 2026 – Alert: Removal of InterSystems IRIS for Health and Health Connect 2024.1.4 and 2024.1.5 Due to Health Interoperability Issues | IDC

Summary

Issue

• The impacted versions of InterSystems IRIS for Health and Health Connect are being removed from WRC distribution sites due to issues identified in several FHIR and healthcare interoperability features.

Introduction

FHIR (Fast Healthcare Interoperability Resources) is the modern standard for storing and exchanging clinical data. But once your data is in a FHIR server, how do you actually explore it? FHIR data is stored as JSON — powerful, but not practical to read directly. I wanted a tool where you could click on a patient, see their conditions, medications, lab results, and more — in a clean, readable format. So I built the FHIR Patient Viewer.

How It Works

The app runs entirely in Docker and connects directly to an InterSystems IRIS for Health FHIR server.

Working with files often starts off simple. open the file, read, and process. That approach works perfectly well, until the file happens to be an Excel file.

A Common Assumption

At first, an Excel file (.xlsx) looks like just another data file, rows, columns and values. nothing unusual. So it's natural to assume it can be read the same way as a .txt ot .csv file. But that's where things start to break.

Why Excel files behave differently

The key difference is how the data is stored:

-> .txt / .csv - plain text, line-by-line.

-> .

If you have long-running messages here's a simple code to catch them. You can also use Queue Wait Alert to get the same results, although this code will catch even a single active message with an empty queue. It also scans all namespaces with no production modification, so it can be used for debugging.

Include Ensemble

Class User.LongMessagesTask Extends %SYS.Task.Definition
{

Parameter TaskName = "Long running messages";

Property LongRunningMessageThreshold As %Integer(MINVAL = 1) [ InitialExpression = 60 ];

Method OnTask() As %Status
{
	set ts = $zdatetime($NOW(0),3,1)
	set ns = ""
	while 1 {
		// Iterate namespaces
		set ns = $o($$$EnsJobMonitorRoot(ns))
		quit:ns=""
		
		set job =""
		while 1 {
			// Iterate jobs
			set job = $o($$$EnsJobMonitorRoot(ns, job))
			quit:job=""
			
			// Get business host name
			set bh = $o($$$EnsJobMonitorRoot(ns,job,""))
			
			// Get the time of the last state change
			set lastActivity = $$$EnsJobMonitorRoot(ns,job,bh,"%LastActivity")
			
			// Get active message, if any - bh can be just idling
			set active = $d(^[ns]Ens.ActiveMessage(job),messageid) // From $$$EnsActiveMessage
			if active {
				set time = $system.SQL.Functions.DATEDIFF("s", lastActivity,  ts)
				if time > ..LongRunningMessageThreshold {
					set text = $$$FormatText("Long running message %1, in ns: %2, BH: %3, processing since %4, for %5 seconds", messageid, ns, bh, lastActivity, time)
					// For debug
					// write text, !
					do ##class(%SYS.System).WriteToConsoleLog(text)
				}
			}
		}
	}
	quit $$$OK
}

}

v2026.1 was just released as GA, and one of the features I'm looking forward to using is the DTL Explainer feature.

This allows you to take a Data Transformation, and with a click of a button get a human-readable description of the transformation (which you can also use as the basis for the DTL Description).

For complex DTLs, especially ones you didn't write yourself, or you did but a long time ago, this will allow you to get a clear quick understanding of what it's doing.

The Interoperability user interface project has continued from 2025.1 and has incorporated many of the items that you – our customers and partners – have suggested and observed.  We are continuing to invest in feedback and updating this important user experience.  In the latest release, 2026.1 for IRIS, IRIS for Health, Health Connect and Health Connect Cloud, the BPL Editor and Message Viewer/Visual Trace applications are now available for opt-in!
NOTE:

• Existing users can switch between the modernized and standard experiences.

As part of the new Interoperability UI wave (see what was new in 2025.1, and 2025.3 by @Aya Heshmat), v2026.1 which is available already as a Developer Preview, and this could be a reason for you to give it a ride - will be shipping the new UI for the Message viewing and searching, including Visual Trace (and other UI goodies).

He's a quick teaser:

As part of the new Interoperability UI wave (see what was new in 2025.1, and 2025.3 by @Aya Heshmat), v2026.1 which is available already as a Developer Preview, and this could be a reason for you to give it a ride - will be shipping the new UI for the BPL editor (and other UI goodies).

He's a quick teaser:

I may have mentioned this before: I believe the Visual Traces, these sequence diagrams with full content of each step, are a fantastic feature of the IRIS Data platform! Detailed information about how the API works internally, as a visual trace, can be very useful for projects on the IRIS platform. Of course, this applies when we are not developing a high-load solution, in which case we simply don't have time for saving/reading messages. For all other cases, welcome to this tutorial!

Hello everyone, thanks for reading this question.

I am currently working with Ens.Alerting.ManagedAlert in an interoperability production and I am using the alert suppression mechanism to avoid generating duplicate alerts within a defined time window (for example, 30 minutes).

The configuration works correctly in terms of preventing duplicate alerts from being generated, but I have a question regarding observability.

When an alert is suppressed during the configured time window, I can see log messages such as:

        "Managed alert not created for AlertRequest with ID 'XXXX' due to rule 'Rules.

Background

Emergency Medical Services (EMS) teams often arrive at the emergency department with patients whose demographics are incomplete or unknown—no medical record number (MRN), no confirmed name, and sometimes no date of birth. Yet EMS transportation notes still need to land in the correct chart.

To support safe and reliable documentation, EMS agencies, third-party integration services, and hospital integration teams build secure interfaces that exchange identifiers and clinical messages.

Hello everyone,

I am André from MedVertical. We are exploring InterSystems-native ways to operationalize continuous FHIR conformance: repeatable regression runs, baseline/delta comparisons, and evidence-style reporting to detect drift after releases and IG changes.

In many FHIR implementations, validation is done “point-in-time” in pre-prod, but conformance degrades in production due to IG/profile updates, terminology changes, mapping evolution, upstream releases, and configuration drift.

How to execute a stored procedure in a remote DB2 database?

Hi Everyone,

I want to access a stored procedure in a remote DB2 database. The stored procedure in question is linked and receives a numeric value, returning a cursor with N number of rows. Sometimes the number of rows reaches hundreds of thousands, so I need to apply pagination.

I've been reading about the %ScrollableResultSet library, but it doesn't allow me to call a stored procedure.

Here's part of the code:
Set pValor=12345678
Set callSql="CALL Paquete.ClaseSpRemoto(?)"
Set rs=##class(%ScrollableResultSet).

Hello, how are you?

Using Healthshare for Interoperability, we often see a wide variety of encoding issues. Some happen when transforming XML to HL7. Some happen the other ay around transforming HL7 to XML.

Is there a valid way to understand which encoding needs to be used?

I ask, because we use SOAP or REST or TCP HL7 services.

And we deliver messages with TCP HL7, SOAP, HTTP Operations.

And we often face this issue where special characters like ñ or á, are not encoded correctly.

Thanks for your replies.