NIHR Oxford

A Wayfarer’s Guide to the Galaxy of LabKey Inside the NIHR Oxford Biomedical Research Center

Oliver Freeman, Oxford Biomedical Research Centre Clinical Informatics Group, University of Oxford


Presentation Abstract: We will discuss a few of the use cases and key challenges of using LabKey inside the NIHR Oxford BRC starting with one of our first LabKey projects as a data collection tool for our Hepatology Research Project. This is a LabKey study with a custom-built UI on top of the LabKey UI and utilises LabKey ETLs for extracting information to be fed to the CDW for circular population. We will then look at the NIHR HIC Hepatitis Project and the way LabKey is used to allow submission of files into the collation system, followed by the viewing and querying of the collated data through LabKey’s external schemas. From here we will look at the deployment of LabKey inside the NIHR Oxford BRC and how we maintain multiple live copies with relatively little effort. Finally, we will explore the future (grand scheme) of our use of LabKey as a portal for clinical research data products; designed using the Metadata Catalogue, produced from the Clinical Data Warehouse and then rendered into LabKey’s datasets using project and folder level security combined with LDAP authentication to control who has access to the data product, in theory involving little, to no, development time from the Clinical Informatics Group.

Speaker Bio: Oliver Freeman has an MSc w/ Distinction in Computer Science from the University of Birmingham and has worked as a Software Engineer within the Clinical Informatics Group for five years. When Oliver started with the group, he redesigned and built the Genomics England Ltd Data Acquisition and Management System (DAMS), during which time he worked closely with LabKey, to engineer and optimise the interaction of DAMS with the LabKey Clinical Review Portals. Whilst doing this he repurposed the same data collection system to help collate data for the NIHR Health Informatics Collaborative (NIHR HIC) Hepatitis theme. Since then he has rebuilt the CIG’s Metadata Catalogue backend in Grails and augmented it to make future development faster and easier. He recently took over as the Technical Lead and Architect on the OUH NHS Foundation Trust’s Clinical Data Warehouse. This is aimed at collating all the clinical data from across the Trust’s systems into one standardised and modularised location for clinical and research use. The CIG uses LabKey to provide IG approved, research data products in a secure way to each team who needs them.

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