Human Phenotype Ontology (HPO) provides a standardized vocabulary of phenotypic abnormalities encountered in human disease. Each term in the HPO describes a phenotypic abnormality. HPO currently contains over 13,000 terms and over 156,000 annotations to hereditary diseases. See more at https://hpo.jax.org/app/.
Examples
hpo_data <- hpo_download()
hpo_data
#> # A tibble: 298,347 × 6
#> entrez_gene_id entrez_gene_symbol hpo_term_id hpo_term_name frequency_raw
#> <dbl> <chr> <chr> <chr> <chr>
#> 1 10 NAT2 HP:0000007 Autosomal recess… NA
#> 2 10 NAT2 HP:0001939 Abnormality of m… NA
#> 3 16 AARS1 HP:0002460 Distal muscle we… 15/15
#> 4 16 AARS1 HP:0002451 Limb dystonia 3/3
#> 5 16 AARS1 HP:0008619 Bilateral sensor… HP:0040283
#> 6 16 AARS1 HP:0001197 Abnormality of p… HP:0040283
#> 7 16 AARS1 HP:0410219 Hypoplasia of ma… HP:0040283
#> 8 16 AARS1 HP:0007266 Cerebral dysmyel… HP:0040283
#> 9 16 AARS1 HP:0007256 Abnormal pyramid… HP:0040283
#> 10 16 AARS1 HP:0010871 Sensory ataxia 1/2
#> # ℹ 298,337 more rows
#> # ℹ 1 more variable: frequency_hpo <chr>
# # A tibble: 231,738 x 9
# entrez_gene_id entrez_gene_symb. hpo_term_id hpo_term_name
# <dbl> <chr> <chr> <chr>
# 1 8192 CLPP HP:0000013 Hypoplasia of the ute.
# 2 8192 CLPP HP:0004322 Short stature
# 3 8192 CLPP HP:0000786 Primary amenorrhea
# 4 8192 CLPP HP:0000007 Autosomal recessive i.
# 5 8192 CLPP HP:0000815 Hypergonadotropic hyp.
# # . with 231,733 more rows, and 5 more variables:
# # frequency_raw <chr>, frequency_hpo <chr>, info_gd_source <chr>,
# # gd_source <chr>, disease_id <chr>