Building eLab Environments with the University of Manchester

FHIR-based online research and teaching environments 

The University of Manchester is not just any university: it is ranked 35th in the world in the 2021 Academic Ranking of World Universities and has been the home to 25 Nobel Prize winners.  

The university’s Centre for Health Informatics is the cradle for the eLab software that is used to create virtual research and teaching environments. Under the academic leadership of Professor John Ainsworth and Dr Philip Couch, the software is now available for use by researchers across a number of studies in the UK and internationally. 

One example of an eLab-supported study is CREW, the Children’s Respiratory and Environmental Workgroup, led by the University of Madison, Wisconsin, USA. The CREW study combines data to address questions about early-life risk factors for asthma. What is the foundational data standard underpinning the CREW eLab? FHIR, of course. The eLab team uses the Firely .NET SDK, Firely Server and Forge to FHIR-enable the eLab environment. 

The challenge of multicenter research studies

Setting up a research study is often a challenge from an IT perspective, especially in the case of a multicenter longitudinal study like CREW. Different research institutions with different IT systems and different data formats have to achieve a shared infrastructure, taking into account high levels of security. This is expensive and difficult to achieve, often requiring specialist skills that are often hard to recruit, furthermore they need to be addressed again with each new research project.

This is where eLabs come in. Through standardization and containerization, an eLab uses tried-and-tested processes and tools to build a secure, rich and accessible digital research environment. An eLab can be configured to provide researchers with access to datasets, familiar off-the-shelf data science or programming tools or one could even be customized to house homegrown, bespoke tools and features. In its standard from it comes with fully featured modules to support data science, data modeling, data transformation, data storage and data and asset sharing. The aim is to ensure research data are simpler to manage, access and combine, and can be sufficiently well described to re-use in future studies. 

Blown away by the FHIR Data Standard 

The original eLab environments are older than FHIR, so the university team designed their own proprietary data model. When they later encountered FHIR, they were “blown away” by the fact that FHIR is supported by a global community, is continuously growing and maturing, and has a wealth of resources like tools, documentation and tutorials. All these made it an easy decision for the team to switch to FHIR. Back then, this was still DSTU2; most projects using eLab currently run on STU3, but R4 is supported and under consideration as the new standard set up. 

“In order to meet our objectives around data harmonization and tools, we needed to develop a common data model for eLabs. The FHIR REST API provides the standard for accessing and querying data. The FHIR XML and JSON formats describe the way that data are represented.”

Benjamin Green, Software Developer (eLab team) at The University of Manchester

Switching from build to buy 

Initially, the eLab team built their own FHIR capabilities. In 2015 when production level tools began to appear, the team decided to access this market to limit the necessity for fresh development. While buying software can seem expensive, it is often more complicated and expensive to build things from scratch. The use of existing tools allows the staff to benefit from the substantial time investment that is evident within most FHIR software products. This is when the collaboration with Firely started.  

“We found good documentation and paid support plans to be attractive, especially when we were starting out with FHIR.”  

Ruth Norris, Head of Strategy & Partnerships (Digital Health) at The University of Manchester

Firely products for eLab software

The University of Manchester’s eLab offers Firely Server with MongoDB to users. The server runs in a custom Docker container. The team makes extensive use of the open-source Firely .NET SDK in a command-line application that manages bulk import and upload of research data into FHIR and uploads data to the FHIR server. Data can then be accessed via an eLab analysis environment in the form of Jupyter notebooks.  

They also use Forge to create FHIR Profiles. A FHIR profile allows you to author and publish a customized resource definition by specifying a set of constraints and extensions. Forge is the only easy-to-use editor for building FHIR profiles, extensions and data models. 

Firely Server has been used to contain very large datasets, the largest to date spanning studies across 5 different organisations. This equates to about 3.5 million Observation resources, over 1 million QuestionnaireResponse resources, 36K Patient resources and over 18K RelatedPerson resources. 

Educating students about FHIR 

eLabs are not only used for research, they are also used for learning environments. Upon discovering FHIR, the University of Manchester has put quite some effort into making FHIR part of the curriculum of the Health Data Science and Health Informatics Masters Programmes as well as other courses for students at the university.

“The teaching piece is very important to us. Exposing currently active data managers, architects and owners, as well as full time students, to the tools and features of a FHIR pipeline allows us to introduce talent to the tools, processes and products that we and the FHIR community find valuable.”  

Georgina Moulton, Director of the Centre for Health Informatics at The University of Manchester

That’s how The University of Manchester created a FHIR-based eLab portal for online research and learning. For more information about eLabs, see https://assets.bmh.manchester.ac.uk/diids/elab/homepage/index.html or contact elabadmin@manchester.ac.uk.

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To learn more about Firely Server for powering apps, online portals or databases, check out our website. You can also download and try out Forge for free, so you can build your FHIR data model and tailor-fit it to your use case.  

Firely also maintains the official, open-source .NET SDK of HL7 FHIR. You can access the Firely .NET SDK on GitHub and read about it on our site.