OMOP CDM for breast cancer research: transforming the Breast Cancer Now Biobank data
Institution: Barts Cancer
Corresponding Researcher: Claude Chelala
Data Link(s): NA
Keyword(s): common data models, OMOP, biobanking
Summary
Common data models (CDMs) are essential for health data standardisation, which
facilitates the governance and management of data, improves data quality and
enhances the findability, accessibility, interoperability and reusability of data. They allow
researchers to efficiently integrate health datasets and perform joint analysis on them,
promoting collaboration and maximising translation of research outputs for patients’
benefit. We describe the process of transforming the biobank data for over 2,850 donors
recruited at the Barts Cancer Institute (BCI) site of the Breast Cancer Now Biobank
(BCNB) - the UK’s first national breast cancer biobank hosting longitudinal biospecimens
and associated clinical, genomic and imaging data - into the Observational Medical
Outcomes Partnership (OMOP) CDM. Our transformation pipeline achieved high
coverage, with 83% of source concepts mapped, and our OMOP CDM achieved a total
pass rate of 100% in quality assessments. We present the breast cancer characteristics
of the resultant patient cohort. We report several challenges faced during the
transformation process and explain how we addressed them, and discuss the strengths
and limitations of adopting the OMOP CDM for breast cancer research. The OMOPmapped BCNB-BCI dataset is a valuable resource that can now be explored and
analysed alongside other health datasets.
