Resnik [29] and Lin [30] similarities between MeSH headings were computed in R in the ontologySimilarity package [31], standardized to have a maximum value of 1 for each trait, and averaged to compute a similarity between each pair of MeSH headings (S4 Text). Two traits are considered similar if the similarity is greater than or equal to a critical value. Our assigned similarities are not identical to those of Nelson et al. because of using different versions of MeSH (2009 versus 2017), but were correlated with those originally reported (R2 = 0.86, S17 Fig). We determined a critical value of 0.73 in our analysis corresponded to the critical value 0.7 used in the original analysis, and used this to determine similar traits in our replication study. Manually assigned similarities were taken from the supplement of [3]. Manual assignment was performed because the MeSH ontology makes few connections between diseases and closely related quantitative phenotypes, for example osteoporosis and bone density.
