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Unified Medical Language System (UMLS)

UMLS Vocabularies

OMIM (Online Mendelian Inheritance in Man) - Metathesaurus Representation


This page lists UMLS Metathesaurus data elements and traces them back to the specific source data that populates them.

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Atoms
Attributes
Definitions
Relationships
Mappings

VSAB: OMIM2023_02_05

Summary of Changes

No changes were made to the OMIM source format. In the Metathesaurus, relationships (RQ/entry_term_of) were added between PTs and their ETs.

Source Provided Files:

XML records are formatted to Metathesaurus specifications.

Identifiers:

Identifiers are assigned as follows:
  • CODE:
    • TTY = ACR, ET, ETAL, PHENO, PHENO_ET, PT: <Mim-entry_mimNumber>
    • TTY = PTAV: <Mim-entry_mimNumber>.<Mim-allelic-variant_number> (e.g. "606158.0015")
    • TTY = HT, PTCS: an MTHU# assigned during Metathesaurus source processing
  • SAUI: not applicable
  • SCUI: not applicable
  • SDUI: same as CODE

Atoms (MRCONSO):


Note:Entries with <Mim-entry_mimType> value of "2" (caret) are not included in Metathesaurus source processing. This value indicates that an entry no longer exists because it was removed from the database or moved to another entry as indicated.
Term Type Origin
ACR CODE: <Mim-entry_mimNumber>

STRING:
value of tag = <Mim-entry_title>
Information after semicolon is parsed to create ACR atoms

value of tag = <Mim-entry_included_E>
Information after semicolon is parsed to create ACR atoms
The pattern ", INCLUDED" is removed from the string

value of tag = <Mim-entry_aliases_E>
Information after semicolon is parsed to create ACR atoms

SDUI: <Mim-entry_mimNumber>
ET CODE: <Mim-entry_mimNumber>

STRING:
value of tag = <Mim-entry_included_E>
Information before the first semicolon is used to create ET atoms
The pattern ", INCLUDED" is removed from the string

SDUI: <Mim-entry_mimNumber>
ETAL CODE: <Mim-entry_mimNumber>

STRING:
value of tag = <Mim-entry_aliases_E>
Information before the first semicolon is used to create an ETAL atom
The pattern ", INCLUDED" is removed from the string

SDUI: <Mim-entry_mimNumber>
HT CODE: An MTHU# assigned during Metathesaurus source processing

STRING:
value of tag = <Mim-index-term_key>
Values are excluded from Metathesaurus source processing if they meet any of the following criteria:
  • The string is mixed-case/lower-case. These values have not yet been reviewed by OMIM
  • Have an edit date where the year is before 1996
  • Do not have a "MIM-entry_synopsisEditHistory"
value of tag = <Mim-index-term_terms_E>
If the value is contained within square brackets, the entry is considered a subheading and TTY = "HT" is assigned; otherwise it is considered a leaf node and TTY= "PTCS" is assigned

SDUI: An MTHU# assigned during Metathesaurus source processing
PHENO CODE: <Mim-entry_mimNumber>

STRING:
value of tag = <Mim-allelic-variant_name>
Parenthetical frequency information such as "1 family" or "1 patient" may be removed from the atom name and is included as an attribute on the relationship to the preferred form. See ATN = "QUALIFIER"

SDUI: <Mim-entry_mimNumber>
PHENO_ET CODE: <Mim-entry_mimNumber>

STRING:
value of tag = <Mim-allelic-variant_aliases_E>
The pattern ", INCLUDED" is removed from the string
Parenthetical frequency information such as "1 family" or "1 patient" may be removed from the atom name and is included as an attribute on the relationship to the preferred form. See ATN = "QUALIFIER"

SDUI: <Mim-entry_mimNumber>
PT CODE: <Mim-entry_mimNumber>

STRING:
value of tag = <Mim-entry_title>
Information before the first semicolon is used to create PT atoms

SDUI: <Mim-entry_mimNumber>
PTAV CODE: <Mim-entry_mimNumber>.<Mim-allelic-variant_number>

STRING:
value of tag <Mim-allelic-variant_mutation><Mim_text_text>

SDUI: <Mim-entry_mimNumber>.<Mim-allelic-variant_number>
PTCS CODE: An MTHU# assigned during Metathesaurus source processing

STRING:
value of tag = <Mim-index-term_terms_E>
If the value is contained within square brackets, the entry is considered a subheading and TTY = "HT" is assigned; otherwise it is considered a leaf node and TTY= "PTCS" is assigned

Parenthetical frequency information such as "In some patients" or "rare" may be removed from the atom name and is included as an attribute on the relationship to the preferred form. See ATN = "QUALIFIER"
SDUI: An MTHU# assigned during Metathesaurus source processing

Attributes (MRSAT):

Attribute Name Origin
GENELOCUS tag = <Mim-entry_locus>
Comma-separated values are parsed to create one or more attributes
GENESYMBOL tag = <Mim-entry_symbol>
Comma-separated values are parsed to create one or more attributes
MIMTYPE tag = <Mim-entry_mimType>
MIMTYPEMEANING Textual description of the mimType, extracted from OMIM documentation
MIMTYPEVALUE <Mim-entry_mimType value>
MOVED_FROM Extracted from tag = <MIM-entry_title> where the value contains the pattern "MOVED TO"
The "MOVED_FROM" attribute is created for the current entry, the ATV is the obsolete <Mim-entry_mimNumber>. No atom is created for the obsolete entry.
QUALIFIER Parenthetical information indicating frequency, stripped from the PTCS, PHENO, or PHENO_ET string in the original source data. Examples include "In some patients," "rare," or "1 family." STYPE = RUI.
SOS Strings in the "MISCELLANEOUS" and "MOLECULAR BASIS" branches of the Clinical Synopsis (PTCS tree). STYPE = AUI.

Definitions (MRDEF):

No definitions are included in the OMIM data.

Relationships (MRREL):

REL RELA
Inverse RELA		 ORIGIN
PAR
CHD
 (no rela) Hierarchy representing the clinical synopses.

All atoms with TTY = HT or PTCS participate in the hierarchy.
RO has_inheritance_type
inheritance_type_of 		Connects PTCS atom treed under "INHERITANCE" to PT atom
RO has_manifestation
manifestation_of 		Connects PTCS atom not treed under inheritance to PT atom
RO phenotype_of
has_phenotype 		Connects PTAV to PHENO or PHENO_ET
RQ alias_of
has_alias 		Connects ETAL atom to PT atom
RQ allelic_variant_of
has_allelic_variant 		Connects PTAV atom to its PT atom
RQ entry_term_of
has_entry_term 		Connects PT atom to its ET atoms
SY expanded_form
has_expanded_form 		Connects ACR atom to ET, ETAL or PT atom

Mappings (MRMAP):

No mappings to external sources are processed from OMIM data.