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: 268,983 × 9
#> entrez_gene…¹ entre…² hpo_t…³ hpo_t…⁴ frequ…⁵ frequ…⁶ info_…⁷ gd_so…⁸ disea…⁹
#> <dbl> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 8192 CLPP HP:000… Hypopl… NA NA NA mim2ge… OMIM:6…
#> 2 8192 CLPP HP:000… Hyperg… NA NA NA mim2ge… OMIM:6…
#> 3 8192 CLPP HP:000… Primar… NA NA NA mim2ge… OMIM:6…
#> 4 8192 CLPP HP:000… Autoso… NA NA NA mim2ge… OMIM:6…
#> 5 8192 CLPP HP:000… Microc… NA HP:004… NA mim2ge… OMIM:6…
#> 6 8192 CLPP HP:000… Seizure NA HP:004… NA mim2ge… OMIM:6…
#> 7 8192 CLPP HP:000… Short … NA HP:004… NA mim2ge… OMIM:6…
#> 8 8192 CLPP HP:000… Congen… NA NA NA mim2ge… OMIM:6…
#> 9 8195 MKKS HP:000… High p… NA HP:004… NA orphad… ORPHA:…
#> 10 8195 MKKS HP:000… Brachy… NA HP:004… NA orphad… ORPHA:…
#> # … with 268,973 more rows, and abbreviated variable names ¹entrez_gene_id,
#> # ²entrez_gene_symbol, ³hpo_term_id, ⁴hpo_term_name, ⁵frequency_raw,
#> # ⁶frequency_hpo, ⁷info_gd_source, ⁸gd_source, ⁹disease_id
# # 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>