Parse OMIM Entry Names

Parses OMIM entry names into case- and order-normalized names, preserving abbreviations, if present.

Usage

parse_omim_name(
  x,
  eponyms = disease_eponyms,
  patterns = disease_cap_patterns,
  qualifiers = omim_qualifiers
)

Arguments

x

A character vector of OMIM entry name strings.

eponyms

A named character vector for proper noun (eponym) capitalization, where names are lowercase words and values are their capitalized replacements, e.g. c("waardenburg" = "Waardenburg"), or NULL to disable (default: disease_eponyms).

patterns

A named character vector of phrase-level regex substitutions applied to the full lowercased name after eponyms, longest-first. Useful for context-sensitive capitalization, e.g. c("short syndrome" = "SHORT syndrome"), or NULL to disable (default: disease_cap_patterns).

qualifiers

A character vector of uppercase OMIM qualifier tokens that force name rearrangement, in addition to the hardcoded structural patterns (numbers, TYPE, and definitive inheritance terms). Use NULL to disable adjective qualifier matching (default: omim_qualifiers).

Value

A character vector of normalized OMIM entry names with abbreviations preserved.

Details

Reverses OMIM\'s inverted filing convention by reclassifying comma-separated qualifier tokens (inheritance terms, type codes, onset adjectives, etc.) and reassembling them in natural-language order. Rearrangement is only applied when at least one qualifier matches a recognized forcing pattern; otherwise tokens are kept in original order and lowercased. See the algorithm article for full details on qualifier classification, capitalization rules, and known limitations.

See also

disease_eponyms for the curated eponym replacement vector; disease_cap_patterns for the curated phrase pattern replacement vector; omim_qualifiers for the curated adjective qualifier vector; the algorithm article for full details on how parsing and rearrangement work.

Examples

omim_names <- c(
    "SCHIZOPHRENIA 12",
    "DYSTONIA 12; DYT12",
    "SPASTIC PARAPLEGIA 14, AUTOSOMAL RECESSIVE; SPG14",
    "OSTEOGENESIS IMPERFECTA, TYPE XI; OI11",
    "SCOLIOSIS, ISOLATED, SUSCEPTIBILITY TO, 1; IS1",
    "EPILEPSY, PROGRESSIVE MYOCLONIC, 4, WITH OR WITHOUT RENAL FAILURE; EPM4"
)

parse_omim_name(omim_names)
#> [1] "schizophrenia 12"                                                    
#> [2] "dystonia 12; DYT12"                                                  
#> [3] "autosomal recessive spastic paraplegia 14; SPG14"                    
#> [4] "osteogenesis imperfecta type XI; OI11"                               
#> [5] "susceptibility to isolated scoliosis 1; IS1"                         
#> [6] "progressive myoclonic epilepsy 4 with or without renal failure; EPM4"

# Proper noun correction via custom eponyms (overrides disease_eponyms)
parse_omim_name(
    "PERIPHERAL DEMYELINATING NEUROPATHY, CENTRAL DYSMYELINATION, WAARDENBURG SYNDROME, AND HIRSCHSPRUNG DISEASE; PCWH",
    eponyms = c("waardenburg" = "Waardenburg", "hirschsprung" = "Hirschsprung")
)
#> [1] "peripheral demyelinating neuropathy, central dysmyelination, Waardenburg syndrome, and Hirschsprung disease; PCWH"

# Context-sensitive capitalization via phrase patterns (overrides eponyms)
parse_omim_name(
    "SHORT SYNDROME; SHORTSYN",
    patterns = c("short syndrome" = "SHORT syndrome")
)
#> [1] "SHORT syndrome; SHORTSYN"