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 💾 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.

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