Month: July 2019

Categories
OpenSource Resources

Hephestus: Health data warehousing tool for public health and clinical research

Originally published by Bell Eapen at nuchange.ca on November 3, 2018. If you have some feedback, reach out to the author on Twitter, LinkedIn or Github.

Health data warehousing is becoming an important requirement for deriving knowledge from the vast amount of health data that healthcare organizations collect. A data warehouse is vital for collaborative and predictive analytics. The first step in designing a data warehouse is to decide on a suitable data model. This is followed by the extract-transform-load (ETL) process that converts source data to the new data model amenable for analytics.

The OHDSI – OMOP Common Data Model is one such data model that allows for the systematic analysis of disparate observational databases and EMRs. The data from diverse systems needs to be extracted, transformed and loaded on to a CDM database. Once a database has been converted to the OMOP CDM, evidence can be generated using standardized analytics tools that are already available.

Each data source requires customized ETL tools for this conversion from the source data to CDM. The OHDSI ecosystem has made some tools available for helping the ETL process such as the White Rabbit and the Rabbit In a Hat. However, health data warehousing process is still challenging because of the variability of source databases in terms of structure and implementations.

Hephestus is an open-source python tool for this ETL process organized into modules to allow code reuse between various ETL tools for open-source EMR systems and data sources. Hephestus uses SqlAlchemy for database connection and automapping tables to classes and bonobo for managing ETL. The ultimate aim is to develop a tool that can translate the report from the OHDSI tools into an ETL script with minimal intervention. This is a good python starter project for eHealth geeks.

Anyone anywhere in the world can build their own environment that can store patient-level observational health data, convert their data to OHDSI’s open community data standards (including the OMOP Common Data Model), run open-source analytics using the OHDSI toolkit, and collaborate in OHDSI research studies that advance our shared mission toward reliable evidence generation. Join the journey! here

Disclaimer: Hephestus is just my experiment and is not a part of the official OHDSI toolset.

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Categories
HIS

Serverless on FHIR: Management guidelines for the semi-technical clinician!

Originally published at nuchange.ca on February 12, 2018. If you have some feedback, reach out to the author on Twitter, LinkedIn or Github.

Serverless is the new kid on the block with services such as AWS Lambda, Google Cloud Functions or Microsoft Azure Functions. Essentially it lets users deploy a function (Function As A Service or FaaS) on the cloud with very little effort. Requirements such as security, privacy, scaling, and availability are taken care of by the framework itself. As healthcare slowly yet steadily progress towards machine learning and AI, serverless is sure to make a significant impact on Health IT. Here I will explain serverless (and some related technologies) for the semi-technical clinicians and put forward some architectural best practices for using serverless in healthcare with FHIR as the data interchange format.

artificial intelligence
Serverless on FHIR

Let us say, your analyst creates a neural network model based on a few million patient records that can predict the risk for MI from BP, blood sugar, and exercise. Let us call this model r = f(bp, bs, e). The model is so good that you want to use it on a regular basis on your patients and better still, you want to share it with your colleagues. So you contact your IT team to make this happen.

This is what your IT guys currently do: First, they create a web application that can take bp, bs and e as inputs using a standard interface such as REST and return r. Next, they rent a virtual machine (VM) from a cloud provider (such as DigitalOcean). Then they convert this application into a container (docker) and deploy it in the VM. You now can use this as an application from your browser (chrome) or your EMR (such as OpenMRS or OSCAR) can directly access this function. You can share it with your colleagues and they can access it in their browsers and you are happy. The VM can support up to 3 users at a time.

In a couple of months, your algorithm becomes so popular that at any one time hundreds of users try to access it and your poor VM crashes most of the time or your users have to wait forever. So you call your IT guys again for a solution. They make 100 copies of your container, but your hospital is reluctant to give you the additional funding required.

Your smart resident notices that your application is being used only in the morning hours and in the night all the 100 containers are virtually sleeping. This is not a good use of the funding dollars. You contact your IT guys again, and they set up Kubernetes for orchestrating the containers according to usage. So, what is Serverless? Serverless is a framework that makes all these so easy that you may not even need your IT guys to do this. (Well, maybe that is an exaggeration)

My personal favourite serverless toolset (if you care) is Kubernetes + Knative + riff. I don’t try to explain what the last two are or how to use them. They are so new that they keep changing every day. In essence, your IT team can complete all the above tasks with few commands typed on the command line on the cloud provider of your choice. The application (function rather) can even scale to zero! (You don’t pay anything when nobody uses it and add more containers as users increase, scaling down in the night as in your case).

Best Practices

What are the best practices when you design such useful cloud-based ‘functions’ for healthcare that can be shared by multiple users and organizations? Well, here are my two cents!

First, you need a standard for data exchange. As JSON is the data format for most APIs, FHIR wins hands down here.

Next, APIs need a mechanism to expose their capabilities and properties to the world. For example, r = f(bp, bs, e) needs to tell everyone what it accepts (bp, bs, e) and what it returns (at the bare minimum). FHIR has a resource specifically for this that has been (not so creatively) named as an Endpoint. So, a function endpoint should return a FHIR Endpoint resource with information about itself if there is no payload.

What should the payload be? Payload should be a FHIR Bundle that has all the FHIR Resources that the function needs (bp, bs and e as FHIR Observations in your case). The bundle should also include a FHIR Subscription resource that points to the receiving system (maybe your EMR) for the response ( r ).

So, what next?

Take the phone and call your IT team. Tell them to take
Kubernetes + Knative + riff for a spin! I might do the same and if I do, I will share it here.

Categories
Research

eHealth against antimicrobial resistance

This article was first published on Brighter World. Read the original article.

A forward-looking McMaster donor is investing $7 million in a new research centre dedicated specifically to tackle the growing global threat of antimicrobial resistance.

David Braley, whose gifts to the university include a $50-million investment in McMaster teaching, learning and health-care research and delivery, has allocated $7 million from that 2007 gift towards the new David Braley Centre for Antibiotic Discovery.

The centre will operate from the Michael G. DeGroote Institute for Infectious Disease Research, whose labs and offices are located on campus in the Michael G. DeGroote Centre for Learning and Discovery.

Researchers associated with the new David Braley Centre for Antibiotic Discovery. Photo by Georgia Kirkos.

“This is a very timely investment,” says Paul O’Byrne, dean and vice- president, Faculty of Health Sciences. “This provides fresh resources to a team of researchers who are among the world’s leaders in their field. Creating this centre gives them the chance to do their best work at a time in history when it’s needed most.”

The funding comes from a portion of Braley’s 2007 gift that had been designated for emerging health-care research priorities.

The David Braley Centre for Antibiotic Discovery will be home to McMaster’s leading researchers in the field of antimicrobial resistance, or AMR. The new resources will allow the team to concentrate more specific effort on that problem.

“Antimicrobial resistance is a slow-moving catastrophe, but make no mistake: within the next 30 years, it will kill millions, strangle our health-care systems and significantly alter life as we know it unless we develop new ways to attack the problem,” says Gerry Wright, who heads both the David Braley Centre for Antibiotic Discovery and the Institute for Infectious Disease Research.  “The opportunity to open this centre is a hopeful sign, and we are grateful for Mr. Braley’s vision and his vote of confidence. This problem must be solved, and it can be solved.”

Dr. Gerry Wright standing at a podium in a hallway in front of a black curtain at the opening of the David Braley Centre for Antibiotic Discovery
Gerry Wright, director of the Institute for Infectious Disease Research and the new David Braley Centre for Antibiotic Discovery, addresses the crowd at the opening of the new research centre. Photo by Georgia Kirkos.

The waning effectiveness of traditional antibiotics gives urgency to the search for new forms of antibiotics and other ways to boost the effectiveness of existing drugs.

Widespread use of antibiotics in agriculture and medicine has accelerated resistance to penicillin and its related medicines, as bacteria evolve to meet the threat.

Infection control and treatment without antibiotics could cast the world back to the early 1900s, when infectious diseases routinely killed people, Wright says.

Today, at least 700,000 people around the world – including 2,000 in Canada ­­– die each year as a result of drug-resistant diseases. The global total is expected to rise to 10 million deaths per year by 2050 if no new solutions are found.

The medical costs associated with AMR are predicted to reach $100 trillion within that same time frame.

Close-up of a lab coat that reads "David Braley Centre for Antibiotic Discovery."
Photo by Georgia Kirkos.

This year, the United Nations published a report projecting that without immediate global action, AMR could force up to 24 million people into extreme poverty by the year 2030.