UK Biobank Resources

A curated list for preprocessing, cleaning, mapping and analyzing UK Biobank data.

Data schema

• Tofu - Tofu is a Python tool for generating synthetic UK Biobank data.
• ukbschemas - Use R to generate a database containing the UK Biobank data schemas.
• Biobank Read - Python-based tools for the extraction, cleaning and pre-processing.
• FUNPACK - Python library for pre-processing of UK BioBank data.
• phemap - Python functions to map between ICD-10 terms and PheCodes.
• ukb_download_and_prep_template - Template for common processing operations.
• ukbiobank-loaders - a collection of Python tools to load data into Apache Parquet files developed by BenevolentAI.

Analytical tools

• PHEASANT - Run a phenome scan pheWAS, Mendelian randomisation (MR)-pheWAS.

  • 📝 Millard L. et al. Int J Epidem. 2019

• ukbrest - Efficient and streamlined data access for reproducible research of large biobanks

  • 📝 Pividori M and Kyung H, Bioinf. 2019

• ukbb_parser - Python tool to extract datasets

  • :octocat: https://github.com/nadavbra/ukbb_parser

• NETMAGE - NETMAGE: a humaN-disEase phenoType MAp GEnerator for the Visualization of PheWAS

  • :octocat: https://github.com/dokyoonkimlab/netmage

Information resources

• NealeLab GWAS statistics -- GWAS on latest UK Biobank data release using 4,203 phenotypes.
  • :octocat: https://github.com/Nealelab/UK_Biobank_GWAS
  • :floppy_disk: Results

Phenotypes

• Primary care EHR biomarkers -- machine-readable versions (CSV files) of electronic health record phenotyping algorithms for 31 commonly-measured biomakers.

Ops

• Docker utils - Docker image for UK Biobank utilities: ukbunpack, ukbfetch, ukblink, ukbgene, ukbmd5, ukbconv

Other resources

• WikiMedMap mapping of phenotype strings from questionnaires in the UK Biobank and from Mendelian diseases in Online Mendelian Inheritance in Man (OMIM) database to eight vocabularies: International Classification of Diseases, Ninth Revision (ICD-9), ICD-10, ICD-O, Medical Subject Headings (MeSH), OMIM, Disease Database, and MedlinePlus.

  • 📝 Sulieman L. et al. bioRxiv. 2019

• ukbb-srmed mapping of self-reported medication entries to the Anatomical Therapeutic Chemical (ATC) classification system and in the British National Formulary (BNF) coding systems.

Contributing

Your contributions are always welcome!

Please submit a pull request or create an issue to add a new package, library or software to the list.

License

To the extent possible under law, Spiros Denaxas has waived all copyright and related or neighboring rights to this work.