UKBCC: a cohort curation package for UK Biobank

Abstract

SummaryThe UK Biobank (UKB) has quickly become a critical resource for researchers conducting a wide-range of biomedical studies (Bycroft et al., 2018). The database is constructed from heterogeneous data sources, employs several different encoding schemes, and is disparately distributed throughout UKB servers. Consequently, querying these data remains complicated, making it difficult to quickly identify participants who meet a given set of criteria. We have developed UK Biobank Cohort Curator (UKBCC), a Python tool that allows researchers to rapidly construct cohorts based on a set of search terms. Here, we describe the UKBCC implementation, critical sub-modules and functions, and outline its usage through an example use case for replicable cohort creation. AvailabilityUKBCC is available through PyPi (https://pypi.org/project/ukbcc) and as open source code on GitHub (https://github.com/tool-bin/ukbcc). Contactisa.kiral@gmail.com