Processing FHIR resources with FHIR SQL BUILDER to predict the probability of developing hepatitis C disease

With the development of technology, the medical industry is also constantly advancing, and humans often pay more attention to their own health,
By learning and processing datasets through computers, diseases can be predicted.

Pre condition: Ability to use FHIR and ML
Firstly, our dataset is obtained from kaggle and transformed into FHIR resources based on patient gender, age, ALP or ALT, and imported into the FHIR resource repository

InterSystems FAQ rubric

If the system does not stop for 24 hours, old journal files will be deleted at 0:30 according to the "Journal file deletion settings".

A possible cause of journal files remaining that are older than the "Journal file deletion settings" is that there are transactions that remain open.

In that case, you will be able to delete the journal file by searching for processes executing transactions and finalizing the transactions.

IRIS can use a KMS (Key Managment Service) as of release 2023.3. Intersystems documentation is a good resource on KMS implementation but does not go into details of the KMS set up on the system, nor provide an easily followable example of how one might set this up for basic testing.

The purpose of this article is to supplement the docs with a brief explanation of KMS, an example of its use in IRIS, and notes for setup of a testing system on AWS EC2 RedHat Linux system using the AWS KMS. It is assumed in this document that the reader/implementor already has access/knowledge to set up an AWS EC2 Linux system running IRIS (2023.3 or later), and that they have proper authority to access the AWS KMS and AWS IAM (for creating roles and polices), or that they will be able to get this access either on their own or via their organizations Security contact in charge of their AWS access.

I have been struggling with a docker run command that kept crashing, the error message was too generic to point me to the right direction.

Since the container is shut down after the failure, I was unable to login to it in order to figure out the problem.

I had to run the container in a way that I'll be able to log into it before it crashed, so I found the adding -u false prevents the docker run command to run the iris session IRIS and the container stayed up and running. then I was able to log into it using:

InterSystems FAQ rubric

If you need to migrate your server for some reason, you can reduce the setup work by copying configuration information from the pre-migration environment to the post-migration environment.

The following setting information can be migrated.

In the context of HL7 FHIR (Fast Healthcare Interoperability Resources), the terms "id" and "identifier" refer to specific elements used for identifying resources within the FHIR data model. For a newbie, these terms can be confusingly similar, but they serve distinct purposes.

Look at the below Patient resource for August T. Faulkner:

The resource has an id of “1” — generated by the FHIR server when the resource was created.
Patient August T. Faulkner also has a identifier (Medical Record Number) — possibly provided by the hospital — of 78510398960

InterSystems FAQ rubric

This error occurs when an instance of the class is already open at compile time.

There are two ways to deal with this issue:

1. Terminate the process or application that has the instance open
2. Compile options in the studio build menu: Check the compile flag “Compile classes in use” and compile.

If you want to determine which process is using the class, try the sample routine below.

InterSystems FAQ rubric

If a relationship is set and there is a large number of n in a 1:n ratio, a large amount of memory may be consumed due to sequential processing of the relationship.

After referencing a many-sided object in a program and internally swizzling it, simply releasing the variable containing the OREF (deleting it, setting another value, etc.) will not free the many-sided object and the relationship object. This is the cause.

InterSystems FAQ rubric

There is no need to recompile the routines after the version upgrade, but since the version update overwrites %SYS, user-created INT and OBJ format routines (*.INT,*.OBJ) in %SYS will be deleted. Therefore, you need to be careful.

MAC, INT and OBJ routines with the following names are not deleted.

%Z*.INT, %z*.INT, Z*.INT,z*.INT
%Z*.OBJ, %z*.OBJ, Z*.OBJ,z*.OBJ

Please note that classes/CSPs need to be compiled after upgrading.

Hi folks!

Recently I was in need to setup a local FHIR server using IRIS For Health and I think I found the easiest and simplest way ever.

Just run in terminal these two lines below :

docker run --rm --name my-iris -d --publish 9091:1972 --publish 9092:52773 intersystemsdc/irishealth-community

and

docker exec -it my-iris iris session iris -U "USER" '##class(%ZPM.PackageManager).Shell("install fhir-server")'

And you'll have FHIR server running locally at http://localhost:9092/fhir/r4.

That's it!

The FHIR server will use the latest build of InterSystems IRIS for Health Community Edition and will deploy FHIR server from this app via IPM package in FHIRSERVER namespace.

This is for Mac, so please add in comments how it works in Windows.

This is a very short article as it is really easy to setup a local FHIR server with InterSystems IRIS for Health and IPM Package Manager.

In part I of this article, we have already learned more about HL7, its messages, structure, segments, and fields. In this part II, we will show you how to transform proprietary/custom data into HL7 using IRIS for Health. For our sample, we used the data generated by the SYNTHEA bulk data generation project (https://synthea.mitre.org/downloads). So, we will show you how to convert 1000 patients from a CSV file to HL7 v2, using the Interoperability features of IRIS for Health.

In the world of Big Data, selecting the right file format is crucial for efficient data storage, processing, and analysis. With the massive amount of data generated every day, choosing the appropriate format can greatly impact the speed, cost, and accuracy of data processing tasks. There are several file formats available, each with its own set of advantages and disadvantages, making the decision of which one to use complex. Some of the popular Big Data file formats include CSV, JSON, Avro, ORC, and Parquet.

InterSystems FAQ rubric

To resolve the error <PROTECT>, remove the read-only attribute of the system-wide library database (IRISLIB for InterSystems IRIS, CACHELIB for Caché/Ensemble/HealthShare (Caché-based))

Once you have finished importing the routine, remember to change it back to read-only.

[Version 2013.1 and above]
[Management Portal] > [System Administration] > [Configuration] > [System Configuration] > [Local Database] Uncheck "Mount read-only" from the database name link.

I am often asked by customers, vendors or internal teams to explain CPU capacity planning for large production databases running on VMware vSphere.

In summary there are a few simple best practices to follow for sizing CPU for large production databases:

• Plan for one vCPU per physical CPU core.
• Consider NUMA and ideally size VMs to keep CPU and memory local to a NUMA node.
• Right-size virtual machines. Add vCPUs only when needed.

Generally this leads to a couple of common questions: