How parse_omim_name() Works • DO.utils

parse_omim_name() converts OMIM entry names from their raw all-uppercase, inverted-filing format into normalized lowercase names with proper noun capitalization. This article explains how the algorithm works, when rearrangement is and isn’t applied, what capitalization fixes are automatic, and what the current limitations are.

OMIM’s inverted filing convention

OMIM lists entry names with the primary disease term first, followed by comma-separated qualifier terms that in natural language would precede it:

SPASTIC PARAPLEGIA 14, AUTOSOMAL RECESSIVE

The natural form is: autosomal recessive spastic paraplegia 14. parse_omim_name() reverses this inversion when recognized qualifiers are present.

Qualifier classification

Comma-separated tokens after the primary term are classified as follows:

Pre-qualifiers — moved before the primary term

Adjective tokens such as AUTOSOMAL RECESSIVE, CONGENITAL, or FAMILIAL are placed before the primary term. When multiple pre-qualifiers are present they are reversed in order, so the last listed appears first — matching OMIM’s preferred-name conventions. Definitive inheritance terms (AUTOSOMAL DOMINANT, X-LINKED, Y-LINKED, MITOCHONDRIAL) always take priority and appear first, even when listed after other qualifiers.

parse_omim_name("SPASTIC PARAPLEGIA 14, AUTOSOMAL RECESSIVE; SPG14")
#> [1] "autosomal recessive spastic paraplegia 14; SPG14"
parse_omim_name("DEAFNESS, AUTOSOMAL DOMINANT, CONGENITAL; DFNA")
#> [1] "autosomal dominant congenital deafness; DFNA"

Post-qualifiers — attached after the primary term

Numeric & alphanumeric type codes (1, 23, 7A) are appended with a space.
TYPE ... tokens are appended with a space.

parse_omim_name("OSTEOGENESIS IMPERFECTA, TYPE XI; OI11")
#> [1] "osteogenesis imperfecta type XI; OI11"
parse_omim_name("SCOLIOSIS, ISOLATED, SUSCEPTIBILITY TO, 1; IS1")
#> [1] "susceptibility to isolated scoliosis 1; IS1"

Trailing phrases — appended last

Tokens beginning with WITH, DUE TO, AND, or OR are treated as descriptive trailing phrases and appended after the primary term (and any post-qualifiers).

parse_omim_name("EPILEPSY, PROGRESSIVE MYOCLONIC, 4, WITH OR WITHOUT RENAL FAILURE; EPM4")
#> [1] "progressive myoclonic epilepsy 4 with or without renal failure; EPM4"

`SUSCEPTIBILITY TO`

The token SUSCEPTIBILITY TO is always prepended before the entire assembled name.

parse_omim_name("DIABETES MELLITUS, SUSCEPTIBILITY TO")
#> [1] "susceptibility to diabetes mellitus"

When rearrangement is applied

Rearrangement is only triggered when at least one qualifier matches a forcing pattern:

A pure number or alphanumeric subtype code (e.g. 1, 7A)
A TYPE or MULTIPLE TYPES qualifier
A definitive inheritance term (AUTOSOMAL DOMINANT, X-LINKED, etc.)
A core set of strong adjective/onset qualifiers: BILATERAL, CHILDHOOD-ONSET, CONGENITAL, EARLY-ONSET, FAMILIAL, FOCAL, GENERALIZED, HEREDITARY, HYPOMYELINATING, ISOLATED, JUVENILE, LATE-ONSET, NEONATAL, POSTSYNAPTIC, PRESYNAPTIC, PROGRESSIVE, SUSCEPTIBILITY TO, UNILATERAL, VESTIBULAR

When no forcing pattern is present (e.g. multi-feature descriptor lists), the tokens are kept in original comma order and only lowercased:

# No forcing pattern → no rearrangement
parse_omim_name("SPASTIC TETRAPLEGIA, THIN CORPUS CALLOSUM, AND PROGRESSIVE MICROCEPHALY")
#> [1] "spastic tetraplegia, thin corpus callosum, and progressive microcephaly"

To extend the forcing list for edge cases, open an issue or submit a PR editing omim_has_forcing() in R/parse.R.

Capitalization fixes applied automatically

After rearrangement and lowercasing, fix_disease_caps() applies these rules:

Roman numerals following type are uppercased (e.g. type xi → type XI).
Alphanumeric subtype codes are uppercased (e.g. 7a → 7A, 3a → 3A).
Immunoglobulin abbreviations: IgA, IgD, IgE, IgG, IgM, IgY.
Word-level eponym substitutions from the eponyms argument (default: [disease_eponyms]).
Phrase-level regex substitutions from the patterns argument (default: [disease_cap_patterns]), applied longest-first and overriding any conflicting eponym substitutions.

Known limitations

Unrecognized proper nouns remain lowercase. Add missing eponyms to a custom eponyms vector, or submit a PR to extend [disease_eponyms].
Context-sensitive capitalization (e.g. SHORT as an acronym vs short as an adjective) cannot be resolved by word-level eponyms. Use patterns with a phrase-level regex:
```
parse_omim_name(
    "SHORT SYNDROME; SHORTSYN",
    patterns = c("short syndrome" = "SHORT syndrome")
)
#> [1] "SHORT syndrome; SHORTSYN"
```
Context-specific word substitutions (e.g. WITH → associated with) cannot be inferred and require manual post-processing.
Qualifiers outside the forcing list may not trigger rearrangement. The list covers the most common OMIM qualifier types; edge cases exist (submit an issue to extend it).