Skip Navigation Bar

Unified Medical Language System® (UMLS®)

2015AB UMLS OMIM Source Information

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




Skip to: Atoms, Attributes, Definitions, Relationships, Mappings

VSAB: 2015_03_18

Summary of Changes

Significant changes have been made to OMIM source processing.

As a result of the changes, the following data elements have been added or deprecated:

New TTY:
ETAL: Entry term alias
PHENO: Phenotype
PHENO_ET: Phenotype entry term

Deprecated TTY:
ETAV: Entry term allelic variant
SYN: Designated alias

New REL/RELA
RQ|allelic_variant_of
RO|has_phenotype

Deprecated REL/RELA
RO|allelic_variant_of
RO|related_to

Source Provided Files:

XML records are formatted to Metathesaurus specifications.

The DTD is available here:
http://www.ncbi.nlm.nih.gov/dtd/NCBI_Mim.mod.dtd

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):

(return to top)

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>

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

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

SDUI: An MTHU# assigned during Metathesaurus source processing

Attributes (MRSAT):

(return to top)
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.

Definitions (MRDEF):

(return to top)

No definitions are included in the OMIM data.


Relationships (MRREL):

(return to top)
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.
RQ
allelic_variant_of
has_allelic_variant
Connects PTAV atom to its PT atom
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
RQ alias_of
has_alias
Connects ETAL atom to PT atom
RO phenotype_of
has_phenotype
Connects PTAV to PHENO or PHENO_ET
SY expanded_form
has_expanded_form
Connects ACR atom to ET, ETAL or PT atom

Mappings (MRMAP):

(return to top)

No mappings to external sources are processed from OMIM data.