Curating metadata in OpenGWAS

There have been a few attempts to map ontologies to each dataset in OpenGWAS. Try to collect them here, though some might have been lost when UoB migrated from Google to Microsoft.

Ontologies

Manual mapping done here: https://docs.google.com/spreadsheets/d/1SskkWvx4t5TsPF288aNFXNKqMPLZocb52sVZfQd8gKo/edit?usp=sharing

Useful links

• Ontology lookup service (OLS): https://www.ebi.ac.uk/ols/index
• API for OLS: https://www.ebi.ac.uk/ols/docs/api
• UK Biobank dictionary: https://biobank.ctsu.ox.ac.uk/crystal/index.cgi
• Zooma automated ontology mapping tool: https://www.ebi.ac.uk/spot/zooma/

To obtain the meta data for an ontological term:

curl -L 'http://www.ebi.ac.uk/ols/api/terms?id=MONDO_0002009' -i -H 'Accept: application/json'

Mapping ieu-a to EFO terms

Common EFO terms

EFO:0009374 energy intake measurement
EFO:0005241 employment status
EFO:0009520 contraception
EFO:0004784 self reported educational attainment
EFO:0003931 bone fracture
EFO:0004731 eye measurement

Getting SD for ukb-b

library(parallel)
library(data.table)
library(dplyr)
setwd("/mnt/storage/private/mrcieu/research/mr-eve/UKBB_replication/replication/results")
d <- list.dirs()[-1]
o <- mclapply(d, function(x)
{
    a <- fread(file.path(x, "phen.txt"), header=TRUE)

    tibble(id=x, sd=c(a$discovery, a$replication) %>% sd(., na.rm=TRUE))
}) %>% bind_rows()
save(o, file="ukb-b_units.rdata")

Vectology

A first pass attempt using BioSentVec and EFO was done as part of the EpiGraphDB build. The scripts for this need tidying up, but i've put the file in the data folder - gwas-vec-efo-ids-0.7.tsv

We do plan to make significant improvements to this mapping as there are many errors.