UK Biobank

UK Biobank

Overview

UK Biobank is a large-scale biomedical database and research resource, containing in-depth genetic and health information from half a million UK participants.

  • Population:
  • Data collected:
    • Population: M/F ages 9-65
  • Online questionnaire data (n=330,000)
    • Diet, cognitive function, occupational history, mental health, digestive health, chronic pain, food preferences, neurodevelopmental issues, sleep, pain
  • Genetic data
    • Whole genome sequencing data (n=200,000), whole exome sequencing data (n=450,000)
  • Health-related outcomes data (n=230,000)
    • Primary care data containing coded clinical events (consultations, diagnoses, procedures, laboratory tests), prescribed medication (referrals) - info on Covid-19 now.
    • Hospital inpatient data - diagnosis, date of admission, underlying conditions, discharge information.
    • First occurrences of medical conditions
    • Death data
    • Cancer data
  • Imaging data (n=50,000)
    • MRI (DTI maybe?) also scans of other body parts: liver, muscle, heart, abdomen
    • Post-covid scans on n=2000 participants
  • Baseline data (n=500,000)
    • Measurements, hand grip, spirometry, bone density
    • Blood, urine, saliva,
    • Diet preferences
  • COVID-19 data
    • MRI scans on n=2000 participants, what else has been collected?
  • Blood + Urine (n=500,000)
    • Saliva for 100,000
  • Activity Monitor (n=100,000)
    • Physical activity data over a 7-day period collected via a wrist-worn activity monitor
  • Biomarker data (n=500,000)
    • Also n=20,000 who completed a 4-5 year follow-up assessment.
    • 34 biomarkers chosen (e.g., HbA1c for diabetes).
    • Blood count (hematological assays)
    • Infectious disease markers
    • Metabolomic biomarkers
    • Telomere length

Data Storage - Questions

  • Which data are on openmind?
    • Imaging (rest, task, naturalistic)
    • Demographic info
    • Cognitive/Behavioral results
    • Clinical disorders
  • What is the format?
    • raw, derivatives
  • Have imaging (MRI/fMRI) data been preprocessed?
    • fmriprep
    • freesurfer
    • first-level glms
  • Where are the data stored on openmind?
    • are these data being transitioned to datalad?
  • How does a new user get access to the dataset?

Data on OpenMind

  • Phenotypic data are stored here: /om2/user/maedbh/ukbiobank_data
    • All data are saved in ukb670488.csv
    • Data dictionary are saved in ukb670488.html